Science.gov

Sample records for allowable time step

  1. Development of a Real-Time PCR for a Sensitive One-Step Coprodiagnosis Allowing both the Identification of Carnivore Feces and the Detection of Toxocara spp. and Echinococcus multilocularis

    PubMed Central

    Umhang, Gérald; Poulle, Marie-Lazarine; Millon, Laurence

    2016-01-01

    Studying the environmental occurrence of parasites of concern for humans and animals based on coprosamples is an expanding field of work in epidemiology and the ecology of health. Detecting and quantifying Toxocara spp. and Echinococcus multilocularis, two predominant zoonotic helminths circulating in European carnivores, in feces may help to better target measures for prevention. A rapid, sensitive, and one-step quantitative PCR (qPCR) allowing detection of E. multilocularis and Toxocara spp. was developed in the present study, combined with a host fecal test based on the identification of three carnivores (red fox, dog, and cat) involved in the life cycles of these parasites. A total of 68 coprosamples were collected from identified specimens from Vulpes vulpes, Canis lupus familiaris, Canis lupus, Felis silvestris catus, Meles meles, Martes foina, and Martes martes. With DNA coprosamples, real-time PCR was performed in duplex with a qPCR inhibitor control specifically designed for this study. All the coprosample host identifications were confirmed by qPCR combined with sequencing, and parasites were detected and confirmed (E. multilocularis in red foxes and Toxocara cati in cats; 16% of samples presented inhibition). By combining parasite detection and quantification, the host fecal test, and a new qPCR inhibitor control, we created a technique with a high sensitivity that may considerably improve environmental studies of pathogens. PMID:26969697

  2. Development of a Real-Time PCR for a Sensitive One-Step Coprodiagnosis Allowing both the Identification of Carnivore Feces and the Detection of Toxocara spp. and Echinococcus multilocularis.

    PubMed

    Knapp, Jenny; Umhang, Gérald; Poulle, Marie-Lazarine; Millon, Laurence

    2016-05-15

    Studying the environmental occurrence of parasites of concern for humans and animals based on coprosamples is an expanding field of work in epidemiology and the ecology of health. Detecting and quantifying Toxocara spp. and Echinococcus multilocularis, two predominant zoonotic helminths circulating in European carnivores, in feces may help to better target measures for prevention. A rapid, sensitive, and one-step quantitative PCR (qPCR) allowing detection of E. multilocularis and Toxocara spp. was developed in the present study, combined with a host fecal test based on the identification of three carnivores (red fox, dog, and cat) involved in the life cycles of these parasites. A total of 68 coprosamples were collected from identified specimens from Vulpes vulpes, Canis lupus familiaris, Canis lupus, Felis silvestris catus, Meles meles, Martes foina, and Martes martes With DNA coprosamples, real-time PCR was performed in duplex with a qPCR inhibitor control specifically designed for this study. All the coprosample host identifications were confirmed by qPCR combined with sequencing, and parasites were detected and confirmed (E. multilocularis in red foxes and Toxocara cati in cats; 16% of samples presented inhibition). By combining parasite detection and quantification, the host fecal test, and a new qPCR inhibitor control, we created a technique with a high sensitivity that may considerably improve environmental studies of pathogens. PMID:26969697

  3. Optimal time step for incompressible SPH

    NASA Astrophysics Data System (ADS)

    Violeau, Damien; Leroy, Agnès

    2015-05-01

    A classical incompressible algorithm for Smoothed Particle Hydrodynamics (ISPH) is analyzed in terms of critical time step for numerical stability. For this purpose, a theoretical linear stability analysis is conducted for unbounded homogeneous flows, leading to an analytical formula for the maximum CFL (Courant-Friedrichs-Lewy) number as a function of the Fourier number. This gives the maximum time step as a function of the fluid viscosity, the flow velocity scale and the SPH discretization size (kernel standard deviation). Importantly, the maximum CFL number at large Reynolds number appears twice smaller than with the traditional Weakly Compressible (WCSPH) approach. As a consequence, the optimal time step for ISPH is only five times larger than with WCSPH. The theory agrees very well with numerical data for two usual kernels in a 2-D periodic flow. On the other hand, numerical experiments in a plane Poiseuille flow show that the theory overestimates the maximum allowed time step for small Reynolds numbers.

  4. Extrapolated implicit-explicit time stepping.

    SciTech Connect

    Constantinescu, E. M.; Sandu, A.; Mathematics and Computer Science; Virginia Polytechnic Inst. and State Univ.

    2010-01-01

    This paper constructs extrapolated implicit-explicit time stepping methods that allow one to efficiently solve problems with both stiff and nonstiff components. The proposed methods are based on Euler steps and can provide very high order discretizations of ODEs, index-1 DAEs, and PDEs in the method-of-lines framework. Implicit-explicit schemes based on extrapolation are simple to construct, easy to implement, and straightforward to parallelize. This work establishes the existence of perturbed asymptotic expansions of global errors, explains the convergence orders of these methods, and studies their linear stability properties. Numerical results with stiff ODE, DAE, and PDE test problems confirm the theoretical findings and illustrate the potential of these methods to solve multiphysics multiscale problems.

  5. Adaptive time stepping in biomolecular dynamics.

    PubMed

    Franklin, J; Doniach, S

    2005-09-22

    We present an adaptive time stepping scheme based on the extrapolative method of Barth and Schlick [LN, J. Chem. Phys. 109, 1633 (1998)] to numerically integrate the Langevin equation with a molecular-dynamics potential. This approach allows us to use (on average) a time step for the strong nonbonded force integration corresponding to half the period of the fastest bond oscillation, without compromising the slow degrees of freedom in the problem. We show with simple examples how the dynamic step size stabilizes integration operators, and discuss some of the limitations of such stability. The method introduced uses a slightly more accurate inner integrator than LN to accommodate the larger steps. The adaptive time step approach reproduces temporal features of the bovine pancreatic trypsin inhibitor (BPTI) test system (similar to the one used in the original introduction of LN) compared to short-time integrators, but with energies that are shifted with respect to both LN, and traditional stochastic versions of Verlet. Although the introduction of longer steps has the effect of systematically heating the bonded components of the potential, the temporal fluctuations of the slow degrees of freedom are reproduced accurately. The purpose of this paper is to display a mechanism by which the resonance traditionally associated with using time steps corresponding to half the period of oscillations in molecular dynamics can be avoided. This has theoretical utility in terms of designing numerical integration schemes--the key point is that by factoring a propagator so that time steps are not constant one can recover stability with an overall (average) time step at a resonance frequency. There are, of course, limitations to this approach associated with the complicated, nonlinear nature of the molecular-dynamics (MD) potential (i.e., it is not as straightforward as the linear test problem we use to motivate the method). While the basic notion remains in the full Newtonian problem

  6. 40 CFR 265.113 - Closure; time allowed for closure.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... to human health and the environment, including compliance with all applicable interim status... the site; and (2) He has taken and will continue to take all steps to prevent threats -to human health... Regional Administrator may allow an owner or operator to receive non-hazardous wastes in a landfill,...

  7. 40 CFR 265.113 - Closure; time allowed for closure.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... to human health and the environment, including compliance with all applicable interim status... the site; and (2) He has taken and will continue to take all steps to prevent threats -to human health... Regional Administrator may allow an owner or operator to receive non-hazardous wastes in a landfill,...

  8. 40 CFR 264.113 - Closure; time allowed for closure.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... health and the environment, including compliance with all applicable permit requirements. (b) The owner... (2) He has taken and will continue to take all steps to prevent threats to human health and the... Administrator may allow an owner or operator to receive only non-hazardous wastes in a landfill, land...

  9. 40 CFR 264.113 - Closure; time allowed for closure.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... health and the environment, including compliance with all applicable permit requirements. (b) The owner... (2) He has taken and will continue to take all steps to prevent threats to human health and the... Administrator may allow an owner or operator to receive only non-hazardous wastes in a landfill, land...

  10. Progress Report on Alloy 617 Time Dependent Allowables

    SciTech Connect

    Wright, Julie Knibloe

    2015-06-01

    Time dependent allowable stresses are required in the ASME Boiler and Pressure Vessel Code for design of components in the temperature range where time dependent deformation (i.e., creep) is expected to become significant. There are time dependent allowable stresses in Section IID of the Code for use in the non-nuclear construction codes, however, there are additional criteria that must be considered in developing time dependent allowables for nuclear components. These criteria are specified in Section III NH. St is defined as the lesser of three quantities: 100% of the average stress required to obtain a total (elastic, plastic, primary and secondary creep) strain of 1%; 67% of the minimum stress to cause rupture; and 80% of the minimum stress to cause the initiation of tertiary creep. The values are reported for a range of temperatures and for time increments up to 100,000 hours. These values are determined from uniaxial creep tests, which involve the elevated temperature application of a constant load which is relatively small, resulting in deformation over a long time period prior to rupture. The stress which is the minimum resulting from these criteria is the time dependent allowable stress St. In this report data from a large number of creep and creep-rupture tests on Alloy 617 are analyzed using the ASME Section III NH criteria. Data which are used in the analysis are from the ongoing DOE sponsored high temperature materials program, form Korea Atomic Energy Institute through the Generation IV VHTR Materials Program and historical data from previous HTR research and vendor data generated in developing the alloy. It is found that the tertiary creep criterion determines St at highest temperatures, while the stress to cause 1% total strain controls at low temperatures. The ASME Section III Working Group on Allowable Stress Criteria has recommended that the uncertainties associated with determining the onset of tertiary creep and the lack of significant

  11. A Stochastic, Resonance-Free Multiple Time-Step Algorithm for Polarizable Models That Permits Very Large Time Steps.

    PubMed

    Margul, Daniel T; Tuckerman, Mark E

    2016-05-10

    the polarizable AMOEBA water model. As was seen with fixed-charge models, we are able to obtain large time steps exceeding 100 fs, allowing calculations to be performed 10 to 20 times faster than standard thermostated molecular dynamics. PMID:27054809

  12. Time to pause before the next step

    SciTech Connect

    Siemon, R.E.

    1998-12-31

    Many scientists, who have staunchly supported ITER for years, are coming to realize it is time to further rethink fusion energy`s development strategy. Specifically, as was suggested by Grant Logan and Dale Meade, and in keeping with the restructuring of 1996, a theme of better, cheaper, faster fusion would serve the program more effectively than ``demonstrating controlled ignition...and integrated testing of the high-heat-flux and nuclear components required to utilize fusion energy...`` which are the important ingredients of ITER`s objectives. The author has personally shifted his view for a mixture of technical and political reasons. On the technical side, he senses that through advanced tokamak research, spherical tokamak research, and advanced stellarator work, scientists are coming to a new understanding that might make a burning-plasma device significantly smaller and less expensive. Thus waiting for a few years, even ten years, seems prudent. Scientifically, there is fascinating physics to be learned through studies of burning plasma on a tokamak. And clearly if one wishes to study burning plasma physics in a sustained plasma, there is no other configuration with an adequate database on which to proceed. But what is the urgency of moving towards an ITER-like step focused on burning plasma? Some of the arguments put forward and the counter arguments are discussed here.

  13. Adaptive time steps in trajectory surface hopping simulations

    NASA Astrophysics Data System (ADS)

    Spörkel, Lasse; Thiel, Walter

    2016-05-01

    Trajectory surface hopping (TSH) simulations are often performed in combination with active-space multi-reference configuration interaction (MRCI) treatments. Technical problems may arise in such simulations if active and inactive orbitals strongly mix and switch in some particular regions. We propose to use adaptive time steps when such regions are encountered in TSH simulations. For this purpose, we present a computational protocol that is easy to implement and increases the computational effort only in the critical regions. We test this procedure through TSH simulations of a GFP chromophore model (OHBI) and a light-driven rotary molecular motor (F-NAIBP) on semiempirical MRCI potential energy surfaces, by comparing the results from simulations with adaptive time steps to analogous ones with constant time steps. For both test molecules, the number of successful trajectories without technical failures rises significantly, from 53% to 95% for OHBI and from 25% to 96% for F-NAIBP. The computed excited-state lifetime remains essentially the same for OHBI and increases somewhat for F-NAIBP, and there is almost no change in the computed quantum efficiency for internal rotation in F-NAIBP. We recommend the general use of adaptive time steps in TSH simulations with active-space CI methods because this will help to avoid technical problems, increase the overall efficiency and robustness of the simulations, and allow for a more complete sampling.

  14. Multiple time step integrators in ab initio molecular dynamics

    SciTech Connect

    Luehr, Nathan; Martínez, Todd J.; Markland, Thomas E.

    2014-02-28

    Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy.

  15. Assessment Data at Your Fingertips: Advances Allow for Timely Reporting

    ERIC Educational Resources Information Center

    Bolch, Matt

    2009-01-01

    The ever-increasing standards of No Child Left Behind regulations and various state assessments have put more pressure on teachers and administrators to monitor the learning process. Fortunately, the advent of technology is allowing teachers to test more often to prepare students for high-stakes tests and for districts to understand results for…

  16. Collocation and Galerkin Time-Stepping Methods

    NASA Technical Reports Server (NTRS)

    Huynh, H. T.

    2011-01-01

    We study the numerical solutions of ordinary differential equations by one-step methods where the solution at tn is known and that at t(sub n+1) is to be calculated. The approaches employed are collocation, continuous Galerkin (CG) and discontinuous Galerkin (DG). Relations among these three approaches are established. A quadrature formula using s evaluation points is employed for the Galerkin formulations. We show that with such a quadrature, the CG method is identical to the collocation method using quadrature points as collocation points. Furthermore, if the quadrature formula is the right Radau one (including t(sub n+1)), then the DG and CG methods also become identical, and they reduce to the Radau IIA collocation method. In addition, we present a generalization of DG that yields a method identical to CG and collocation with arbitrary collocation points. Thus, the collocation, CG, and generalized DG methods are equivalent, and the latter two methods can be formulated using the differential instead of integral equation. Finally, all schemes discussed can be cast as s-stage implicit Runge-Kutta methods.

  17. Time scaling relations for step bunches from models with step-step attractions (B1-type models)

    NASA Astrophysics Data System (ADS)

    Krasteva, A.; Popova, H.; Akutsu, N.; Tonchev, V.

    2016-03-01

    The step bunching instability is studied in three models of step motion defined in terms of ordinary differential equations (ODE). The source of instability in these models is step-step attraction, it is opposed by step-step repulsion and the developing surface patterns reflect the balance between the two. The first model, TE2, is a generalization of the seminal model of Tersoff et al. (1995). The second one, LW2, is obtained from the model of Liu and Weeks (1998) using the repulsions term to construct the attractions one with retained possibility to change the parameters in the two independently. The third model, MM2, is a minimal one constructed ad hoc and in this article it plays a central role. New scheme for scaling the ODE in vicinal studies is applied towards deciphering the pre-factors in the time-scaling relations. In all these models the patterned surface is self-similar - only one length scale is necessary to describe its evolution (hence B1-type). The bunches form finite angles with the terraces. Integrating numerically the equations for step motion and changing systematically the parameters we obtain the overall dependence of time-scaling exponent β on the power of step-step attractions p as β = 1/(3+p) for MM2 and hypothesize based on restricted set of data that it is β = 1/(5+p) for LW2 and TE2.

  18. Multiple-time-stepping generalized hybrid Monte Carlo methods

    SciTech Connect

    Escribano, Bruno; Akhmatskaya, Elena; Reich, Sebastian; Azpiroz, Jon M.

    2015-01-01

    Performance of the generalized shadow hybrid Monte Carlo (GSHMC) method [1], which proved to be superior in sampling efficiency over its predecessors [2–4], molecular dynamics and hybrid Monte Carlo, can be further improved by combining it with multi-time-stepping (MTS) and mollification of slow forces. We demonstrate that the comparatively simple modifications of the method not only lead to better performance of GSHMC itself but also allow for beating the best performed methods, which use the similar force splitting schemes. In addition we show that the same ideas can be successfully applied to the conventional generalized hybrid Monte Carlo method (GHMC). The resulting methods, MTS-GHMC and MTS-GSHMC, provide accurate reproduction of thermodynamic and dynamical properties, exact temperature control during simulation and computational robustness and efficiency. MTS-GHMC uses a generalized momentum update to achieve weak stochastic stabilization to the molecular dynamics (MD) integrator. MTS-GSHMC adds the use of a shadow (modified) Hamiltonian to filter the MD trajectories in the HMC scheme. We introduce a new shadow Hamiltonian formulation adapted to force-splitting methods. The use of such Hamiltonians improves the acceptance rate of trajectories and has a strong impact on the sampling efficiency of the method. Both methods were implemented in the open-source MD package ProtoMol and were tested on a water and a protein systems. Results were compared to those obtained using a Langevin Molly (LM) method [5] on the same systems. The test results demonstrate the superiority of the new methods over LM in terms of stability, accuracy and sampling efficiency. This suggests that putting the MTS approach in the framework of hybrid Monte Carlo and using the natural stochasticity offered by the generalized hybrid Monte Carlo lead to improving stability of MTS and allow for achieving larger step sizes in the simulation of complex systems.

  19. IMPROVEMENTS TO THE TIME STEPPING ALGORITHM OF RELAP5-3D

    SciTech Connect

    Cumberland, R.; Mesina, G.

    2009-01-01

    The RELAP5-3D time step method is used to perform thermo-hydraulic and neutronic simulations of nuclear reactors and other devices. It discretizes time and space by numerically solving several differential equations. Previously, time step size was controlled by halving or doubling the size of a previous time step. This process caused the code to run slower than it potentially could. In this research project, the RELAP5-3D time step method was modifi ed to allow a new method of changing time steps to improve execution speed and to control error. The new RELAP5-3D time step method being studied involves making the time step proportional to the material courant limit (MCL), while insuring that the time step does not increase by more than a factor of two between advancements. As before, if a step fails or mass error is excessive, the time step is cut in half. To examine performance of the new method, a measure of run time and a measure of error were plotted against a changing MCL proportionality constant (m) in seven test cases. The removal of the upper time step limit produced a small increase in error, but a large decrease in execution time. The best value of m was found to be 0.9. The new algorithm is capable of producing a signifi cant increase in execution speed, with a relatively small increase in mass error. The improvements made are now under consideration for inclusion as a special option in the RELAP5-3D production code.

  20. Short‐term time step convergence in a climate model

    PubMed Central

    Rasch, Philip J.; Taylor, Mark A.; Jablonowski, Christiane

    2015-01-01

    Abstract This paper evaluates the numerical convergence of very short (1 h) simulations carried out with a spectral‐element (SE) configuration of the Community Atmosphere Model version 5 (CAM5). While the horizontal grid spacing is fixed at approximately 110 km, the process‐coupling time step is varied between 1800 and 1 s to reveal the convergence rate with respect to the temporal resolution. Special attention is paid to the behavior of the parameterized subgrid‐scale physics. First, a dynamical core test with reduced dynamics time steps is presented. The results demonstrate that the experimental setup is able to correctly assess the convergence rate of the discrete solutions to the adiabatic equations of atmospheric motion. Second, results from full‐physics CAM5 simulations with reduced physics and dynamics time steps are discussed. It is shown that the convergence rate is 0.4—considerably slower than the expected rate of 1.0. Sensitivity experiments indicate that, among the various subgrid‐scale physical parameterizations, the stratiform cloud schemes are associated with the largest time‐stepping errors, and are the primary cause of slow time step convergence. While the details of our findings are model specific, the general test procedure is applicable to any atmospheric general circulation model. The need for more accurate numerical treatments of physical parameterizations, especially the representation of stratiform clouds, is likely common in many models. The suggested test technique can help quantify the time‐stepping errors and identify the related model sensitivities.

  1. 40 CFR 97.41 - Timing requirements for NOX allowance allocations.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 21 2014-07-01 2014-07-01 false Timing requirements for NOX allowance... PROGRAMS (CONTINUED) FEDERAL NOX BUDGET TRADING PROGRAM AND CAIR NOX AND SO2 TRADING PROGRAMS NOX Allowance Allocations § 97.41 Timing requirements for NOX allowance allocations. (a) The NOX allowance...

  2. 40 CFR 97.41 - Timing requirements for NOX allowance allocations.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 22 2013-07-01 2013-07-01 false Timing requirements for NOX allowance... PROGRAMS (CONTINUED) FEDERAL NOX BUDGET TRADING PROGRAM AND CAIR NOX AND SO2 TRADING PROGRAMS NOX Allowance Allocations § 97.41 Timing requirements for NOX allowance allocations. (a) The NOX allowance...

  3. 40 CFR 97.41 - Timing requirements for NOX allowance allocations.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 22 2012-07-01 2012-07-01 false Timing requirements for NOX allowance... PROGRAMS (CONTINUED) FEDERAL NOX BUDGET TRADING PROGRAM AND CAIR NOX AND SO2 TRADING PROGRAMS NOX Allowance Allocations § 97.41 Timing requirements for NOX allowance allocations. (a) The NOX allowance...

  4. 40 CFR 97.41 - Timing requirements for NOX allowance allocations.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Timing requirements for NOX allowance... PROGRAMS (CONTINUED) FEDERAL NOX BUDGET TRADING PROGRAM AND CAIR NOX AND SO2 TRADING PROGRAMS NOX Allowance Allocations § 97.41 Timing requirements for NOX allowance allocations. (a) The NOX allowance...

  5. Dynamical multiple-time stepping methods for overcoming resonance instabilities.

    PubMed

    Chin, Siu A

    2004-01-01

    Current molecular dynamics simulations of biomolecules using multiple time steps to update the slowly changing force are hampered by instabilities beginning at time steps near the half period of the fastest vibrating mode. These "resonance" instabilities have became a critical barrier preventing the long time simulation of biomolecular dynamics. Attempts to tame these instabilities by altering the slowly changing force and efforts to damp them out by Langevin dynamics do not address the fundamental cause of these instabilities. In this work, we trace the instability to the nonanalytic character of the underlying spectrum and show that a correct splitting of the Hamiltonian, which renders the spectrum analytic, restores stability. The resulting Hamiltonian dictates that in addition to updating the momentum due to the slowly changing force, one must also update the position with a modified mass. Thus multiple-time stepping must be done dynamically.

  6. Multiple-step model-experiment matching allows precise definition of dynamical leg parameters in human running.

    PubMed

    Ludwig, C; Grimmer, S; Seyfarth, A; Maus, H-M

    2012-09-21

    The spring-loaded inverted pendulum (SLIP) model is a well established model for describing bouncy gaits like human running. The notion of spring-like leg behavior has led many researchers to compute the corresponding parameters, predominantly stiffness, in various experimental setups and in various ways. However, different methods yield different results, making the comparison between studies difficult. Further, a model simulation with experimentally obtained leg parameters typically results in comparatively large differences between model and experimental center of mass trajectories. Here, we pursue the opposite approach which is calculating model parameters that allow reproduction of an experimental sequence of steps. In addition, to capture energy fluctuations, an extension of the SLIP (ESLIP) is required and presented. The excellent match of the models with the experiment validates the description of human running by the SLIP with the obtained parameters which we hence call dynamical leg parameters.

  7. Short‐term time step convergence in a climate model

    PubMed Central

    Rasch, Philip J.; Taylor, Mark A.; Jablonowski, Christiane

    2015-01-01

    Abstract This paper evaluates the numerical convergence of very short (1 h) simulations carried out with a spectral‐element (SE) configuration of the Community Atmosphere Model version 5 (CAM5). While the horizontal grid spacing is fixed at approximately 110 km, the process‐coupling time step is varied between 1800 and 1 s to reveal the convergence rate with respect to the temporal resolution. Special attention is paid to the behavior of the parameterized subgrid‐scale physics. First, a dynamical core test with reduced dynamics time steps is presented. The results demonstrate that the experimental setup is able to correctly assess the convergence rate of the discrete solutions to the adiabatic equations of atmospheric motion. Second, results from full‐physics CAM5 simulations with reduced physics and dynamics time steps are discussed. It is shown that the convergence rate is 0.4—considerably slower than the expected rate of 1.0. Sensitivity experiments indicate that, among the various subgrid‐scale physical parameterizations, the stratiform cloud schemes are associated with the largest time‐stepping errors, and are the primary cause of slow time step convergence. While the details of our findings are model specific, the general test procedure is applicable to any atmospheric general circulation model. The need for more accurate numerical treatments of physical parameterizations, especially the representation of stratiform clouds, is likely common in many models. The suggested test technique can help quantify the time‐stepping errors and identify the related model sensitivities. PMID:27660669

  8. 40 CFR 96.41 - Timing requirements for NOX allowance allocations.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 21 2014-07-01 2014-07-01 false Timing requirements for NOX allowance... PROGRAMS (CONTINUED) NOX BUDGET TRADING PROGRAM AND CAIR NOX AND SO2 TRADING PROGRAMS FOR STATE IMPLEMENTATION PLANS NOX Allowance Allocations § 96.41 Timing requirements for NOX allowance allocations. (a)...

  9. 40 CFR 96.41 - Timing requirements for NOX allowance allocations.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 22 2012-07-01 2012-07-01 false Timing requirements for NOX allowance... PROGRAMS (CONTINUED) NOX BUDGET TRADING PROGRAM AND CAIR NOX AND SO2 TRADING PROGRAMS FOR STATE IMPLEMENTATION PLANS NOX Allowance Allocations § 96.41 Timing requirements for NOX allowance allocations. (a)...

  10. 40 CFR 96.41 - Timing requirements for NOX allowance allocations.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 21 2011-07-01 2011-07-01 false Timing requirements for NOX allowance... PROGRAMS (CONTINUED) NOX BUDGET TRADING PROGRAM AND CAIR NOX AND SO2 TRADING PROGRAMS FOR STATE IMPLEMENTATION PLANS NOX Allowance Allocations § 96.41 Timing requirements for NOX allowance allocations. (a)...

  11. 40 CFR 96.41 - Timing requirements for NOX allowance allocations.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 22 2013-07-01 2013-07-01 false Timing requirements for NOX allowance... PROGRAMS (CONTINUED) NOX BUDGET TRADING PROGRAM AND CAIR NOX AND SO 2 TRADING PROGRAMS FOR STATE IMPLEMENTATION PLANS NOX Allowance Allocations § 96.41 Timing requirements for NOX allowance allocations. (a)...

  12. 40 CFR 96.41 - Timing requirements for NOX allowance allocations.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Timing requirements for NOX allowance... PROGRAMS (CONTINUED) NOX BUDGET TRADING PROGRAM AND CAIR NOX AND SO2 TRADING PROGRAMS FOR STATE IMPLEMENTATION PLANS NOX Allowance Allocations § 96.41 Timing requirements for NOX allowance allocations. (a)...

  13. Accuracy of Pedometer Steps and Time for Youth with Disabilities

    ERIC Educational Resources Information Center

    Beets, Michael W.; Combs, Cindy; Pitetti, Kenneth H.; Morgan, Melinda; Bryan, Rebecca R.; Foley, John T.

    2007-01-01

    The purpose of the study was to examine the accuracy of pedometer steps and activity time (Walk4Life, WL) for youth with developmental disabilities. Eighteen youth (11 girls, 7 boys) 4-14 years completed six 80-meter self-paced walking trials while wearing a pedometer at five waist locations (front right, front left, back right, back left, middle…

  14. Modified Chebyshev pseudospectral method with O(N exp -1) time step restriction

    NASA Technical Reports Server (NTRS)

    Kosloff, Dan; Tal-Ezer, Hillel

    1989-01-01

    The extreme eigenvalues of the Chebyshev pseudospectral differentiation operator are O(N exp 2) where N is the number of grid points. As a result of this, the allowable time step in an explicit time marching algorithm is O(N exp -2) which, in many cases, is much below the time step dictated by the physics of the partial differential equation. A new set of interpolating points is introduced such that the eigenvalues of the differentiation operator are O(N) and the allowable time step is O(N exp -1). The properties of the new algorithm are similar to those of the Fourier method. The new algorithm also provides a highly accurate solution for non-periodic boundary value problems.

  15. Additional efficient computation of branched nerve equations: adaptive time step and ideal voltage clamp.

    PubMed

    Borg-Graham, L J

    2000-01-01

    Various improvements are described for the simulation of biophysically and anatomically detailed compartmental models of single neurons and networks of neurons. These include adaptive time-step integration and a reordering of the circuit matrix to allow ideal voltage clamp of arbitrary nodes. We demonstrate how the adaptive time-step method can give equivalent accuracy as a fixed time-step method for typical current clamp simulation protocols, with about a 2.5 reduction in runtime. The ideal voltage clamp method is shown to be more stable than the nonideal case, in particular when used with the adaptive time-step method. Simulation results are presented using the Surf-Hippo Neuron Simulation System, a public domain object-oriented simulator written in Lisp. PMID:10809013

  16. On the Time Step Error of the DSMC

    NASA Astrophysics Data System (ADS)

    Hokazono, Tomokuni; Kobayashi, Seijiro; Ohsawa, Tomoki; Ohwada, Taku

    2003-05-01

    The time step truncation error of the DSMC is examined numerically. Contrary to the claim of [S.V. Bogomolov, U.S.S.R. Comput. Math. Math. Phys., Vol. 28, 79 (1988)] and in agreement with that of [T. Ohwada, J. Compt. Phys., Vol. 139, 1 (1998)], it is demonstrated that the error of the conventional DSMC per time step Δt is not O(Δt3) but O(Δt2). Further, it is shown that the error of the DSMC is reduced to O(Δt3) by applying Strang's splitting for the partial differential equations to the Boltzmann equation. The error resulting from the boundary condition, which is not studied in the abovementioned theoretical studies, is also discussed.

  17. 40 CFR 96.341 - Timing requirements for CAIR NOX Ozone Season allowance allocations.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 22 2012-07-01 2012-07-01 false Timing requirements for CAIR NOX Ozone... PROGRAMS FOR STATE IMPLEMENTATION PLANS CAIR NOX Ozone Season Allowance Allocations § 96.341 Timing requirements for CAIR NOX Ozone Season allowance allocations. (a) By October 31, 2006, the permitting...

  18. 40 CFR 96.341 - Timing requirements for CAIR NOX Ozone Season allowance allocations.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Timing requirements for CAIR NOX Ozone... PROGRAMS FOR STATE IMPLEMENTATION PLANS CAIR NOX Ozone Season Allowance Allocations § 96.341 Timing requirements for CAIR NOX Ozone Season allowance allocations. (a) By October 31, 2006, the permitting...

  19. 40 CFR 97.341 - Timing requirements for CAIR NOX Ozone Season allowance allocations.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 22 2013-07-01 2013-07-01 false Timing requirements for CAIR NOX Ozone... TRADING PROGRAMS CAIR NOX Ozone Season Allowance Allocations § 97.341 Timing requirements for CAIR NOX Ozone Season allowance allocations. (a) The Administrator will determine by order the CAIR NOX...

  20. 40 CFR 97.511 - Timing requirements for TR NOX Ozone Season allowance allocations.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 22 2012-07-01 2012-07-01 false Timing requirements for TR NOX Ozone... TRADING PROGRAMS TR NOX Ozone Season Trading Program § 97.511 Timing requirements for TR NOX Ozone Season allowance allocations. (a) Existing units. (1) TR NOX Ozone Season allowances are allocated, for the...

  1. 40 CFR 97.341 - Timing requirements for CAIR NOX Ozone Season allowance allocations.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 22 2012-07-01 2012-07-01 false Timing requirements for CAIR NOX Ozone... TRADING PROGRAMS CAIR NOX Ozone Season Allowance Allocations § 97.341 Timing requirements for CAIR NOX Ozone Season allowance allocations. (a) The Administrator will determine by order the CAIR NOX...

  2. 40 CFR 97.341 - Timing requirements for CAIR NOX Ozone Season allowance allocations.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 21 2011-07-01 2011-07-01 false Timing requirements for CAIR NOX Ozone... TRADING PROGRAMS CAIR NOX Ozone Season Allowance Allocations § 97.341 Timing requirements for CAIR NOX Ozone Season allowance allocations. (a) The Administrator will determine by order the CAIR NOX...

  3. 40 CFR 97.341 - Timing requirements for CAIR NOX Ozone Season allowance allocations.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Timing requirements for CAIR NOX Ozone... TRADING PROGRAMS CAIR NOX Ozone Season Allowance Allocations § 97.341 Timing requirements for CAIR NOX Ozone Season allowance allocations. (a) The Administrator will determine by order the CAIR NOX...

  4. 40 CFR 96.341 - Timing requirements for CAIR NOX Ozone Season allowance allocations.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 21 2011-07-01 2011-07-01 false Timing requirements for CAIR NOX Ozone... PROGRAMS FOR STATE IMPLEMENTATION PLANS CAIR NOX Ozone Season Allowance Allocations § 96.341 Timing requirements for CAIR NOX Ozone Season allowance allocations. (a) By October 31, 2006, the permitting...

  5. 40 CFR 97.341 - Timing requirements for CAIR NOX Ozone Season allowance allocations.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 21 2014-07-01 2014-07-01 false Timing requirements for CAIR NOX Ozone... TRADING PROGRAMS CAIR NOX Ozone Season Allowance Allocations § 97.341 Timing requirements for CAIR NOX Ozone Season allowance allocations. (a) The Administrator will determine by order the CAIR NOX...

  6. 40 CFR 96.341 - Timing requirements for CAIR NOX Ozone Season allowance allocations.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 21 2014-07-01 2014-07-01 false Timing requirements for CAIR NOX Ozone... PROGRAMS FOR STATE IMPLEMENTATION PLANS CAIR NOX Ozone Season Allowance Allocations § 96.341 Timing requirements for CAIR NOX Ozone Season allowance allocations. (a) By October 31, 2006, the permitting...

  7. 40 CFR 96.341 - Timing requirements for CAIR NOX Ozone Season allowance allocations.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 22 2013-07-01 2013-07-01 false Timing requirements for CAIR NOX Ozone... PROGRAMS FOR STATE IMPLEMENTATION PLANS CAIR NOX Ozone Season Allowance Allocations § 96.341 Timing requirements for CAIR NOX Ozone Season allowance allocations. (a) By October 31, 2006, the permitting...

  8. 40 CFR 97.511 - Timing requirements for TR NOX Ozone Season allowance allocations.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 21 2014-07-01 2014-07-01 false Timing requirements for TR NOX Ozone... TRADING PROGRAMS TR NOX Ozone Season Trading Program § 97.511 Timing requirements for TR NOX Ozone Season allowance allocations. (a) Existing units. (1) TR NOX Ozone Season allowances are allocated, for the...

  9. 40 CFR 97.511 - Timing requirements for TR NOX Ozone Season allowance allocations.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 22 2013-07-01 2013-07-01 false Timing requirements for TR NOX Ozone... TRADING PROGRAMS TR NOX Ozone Season Trading Program § 97.511 Timing requirements for TR NOX Ozone Season allowance allocations. (a) Existing units. (1) TR NOX Ozone Season allowances are allocated, for the...

  10. 40 CFR 97.141 - Timing requirements for CAIR NOX allowance allocations.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 22 2012-07-01 2012-07-01 false Timing requirements for CAIR NOX... (CONTINUED) AIR PROGRAMS (CONTINUED) FEDERAL NOX BUDGET TRADING PROGRAM AND CAIR NOX AND SO2 TRADING PROGRAMS CAIR NOX Allowance Allocations § 97.141 Timing requirements for CAIR NOX allowance allocations. (a)...

  11. 40 CFR 97.141 - Timing requirements for CAIR NOX allowance allocations.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 22 2013-07-01 2013-07-01 false Timing requirements for CAIR NOX... (CONTINUED) AIR PROGRAMS (CONTINUED) FEDERAL NOX BUDGET TRADING PROGRAM AND CAIR NOX AND SO2 TRADING PROGRAMS CAIR NOX Allowance Allocations § 97.141 Timing requirements for CAIR NOX allowance allocations. (a)...

  12. 40 CFR 97.141 - Timing requirements for CAIR NOX allowance allocations.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 21 2014-07-01 2014-07-01 false Timing requirements for CAIR NOX... (CONTINUED) AIR PROGRAMS (CONTINUED) FEDERAL NOX BUDGET TRADING PROGRAM AND CAIR NOX AND SO2 TRADING PROGRAMS CAIR NOX Allowance Allocations § 97.141 Timing requirements for CAIR NOX allowance allocations. (a)...

  13. 40 CFR 97.141 - Timing requirements for CAIR NOX allowance allocations.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Timing requirements for CAIR NOX... (CONTINUED) AIR PROGRAMS (CONTINUED) FEDERAL NOX BUDGET TRADING PROGRAM AND CAIR NOX AND SO2 TRADING PROGRAMS CAIR NOX Allowance Allocations § 97.141 Timing requirements for CAIR NOX allowance allocations. (a)...

  14. 40 CFR 97.141 - Timing requirements for CAIR NOX allowance allocations.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 21 2011-07-01 2011-07-01 false Timing requirements for CAIR NOX... (CONTINUED) AIR PROGRAMS (CONTINUED) FEDERAL NOX BUDGET TRADING PROGRAM AND CAIR NOX AND SO2 TRADING PROGRAMS CAIR NOX Allowance Allocations § 97.141 Timing requirements for CAIR NOX allowance allocations. (a)...

  15. 36 CFR 1120.33 - Time allowed for initial action on requests.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 36 Parks, Forests, and Public Property 3 2010-07-01 2010-07-01 false Time allowed for initial... § 1120.33 Time allowed for initial action on requests. (a) Except as otherwise provided in this section... initial request, or during the period for consideration of an appeal, the requestor shall be deemed...

  16. A method for improving time-stepping numerics

    NASA Astrophysics Data System (ADS)

    Williams, P. D.

    2012-04-01

    In contemporary numerical simulations of the atmosphere, evidence suggests that time-stepping errors may be a significant component of total model error, on both weather and climate time-scales. This presentation will review the available evidence, and will then suggest a simple but effective method for substantially improving the time-stepping numerics at no extra computational expense. The most common time-stepping method is the leapfrog scheme combined with the Robert-Asselin (RA) filter. This method is used in the following atmospheric models (and many more): ECHAM, MAECHAM, MM5, CAM, MESO-NH, HIRLAM, KMCM, LIMA, SPEEDY, IGCM, PUMA, COSMO, FSU-GSM, FSU-NRSM, NCEP-GFS, NCEP-RSM, NSEAM, NOGAPS, RAMS, and CCSR/NIES-AGCM. Although the RA filter controls the time-splitting instability in these models, it also introduces non-physical damping and reduces the accuracy. This presentation proposes a simple modification to the RA filter. The modification has become known as the RAW filter (Williams 2011). When used in conjunction with the leapfrog scheme, the RAW filter eliminates the non-physical damping and increases the amplitude accuracy by two orders, yielding third-order accuracy. (The phase accuracy remains second-order.) The RAW filter can easily be incorporated into existing models, typically via the insertion of just a single line of code. Better simulations are obtained at no extra computational expense. Results will be shown from recent implementations of the RAW filter in various atmospheric models, including SPEEDY and COSMO. For example, in SPEEDY, the skill of weather forecasts is found to be significantly improved. In particular, in tropical surface pressure predictions, five-day forecasts made using the RAW filter have approximately the same skill as four-day forecasts made using the RA filter (Amezcua, Kalnay & Williams 2011). These improvements are encouraging for the use of the RAW filter in other models.

  17. Accurate Monotonicity - Preserving Schemes With Runge-Kutta Time Stepping

    NASA Technical Reports Server (NTRS)

    Suresh, A.; Huynh, H. T.

    1997-01-01

    A new class of high-order monotonicity-preserving schemes for the numerical solution of conservation laws is presented. The interface value in these schemes is obtained by limiting a higher-order polynominal reconstruction. The limiting is designed to preserve accuracy near extrema and to work well with Runge-Kutta time stepping. Computational efficiency is enhanced by a simple test that determines whether the limiting procedure is needed. For linear advection in one dimension, these schemes are shown as well as the Euler equations also confirm their high accuracy, good shock resolution, and computational efficiency.

  18. 30 CFR 203.66 - What happens if BSEE does not act in the time allowed?

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... allowed? 203.66 Section 203.66 Mineral Resources BUREAU OF SAFETY AND ENVIRONMENTAL ENFORCEMENT... Sulfur General § 203.66 What happens if BSEE does not act in the time allowed? If we do not act within the timeframes established under § 203.65, you get royalty relief according to the following table....

  19. 30 CFR 203.66 - What happens if MMS does not act in the time allowed?

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Expansion Projects § 203.66 What happens if MMS does not act in the time allowed? If we do not act within.... (b) An expansion project You get a royalty suspension for the first year of production Abide...

  20. Enabling fast, stable and accurate peridynamic computations using multi-time-step integration

    DOE PAGES

    Lindsay, P.; Parks, M. L.; Prakash, A.

    2016-04-13

    Peridynamics is a nonlocal extension of classical continuum mechanics that is well-suited for solving problems with discontinuities such as cracks. This paper extends the peridynamic formulation to decompose a problem domain into a number of smaller overlapping subdomains and to enable the use of different time steps in different subdomains. This approach allows regions of interest to be isolated and solved at a small time step for increased accuracy while the rest of the problem domain can be solved at a larger time step for greater computational efficiency. Lastly, performance of the proposed method in terms of stability, accuracy, andmore » computational cost is examined and several numerical examples are presented to corroborate the findings.« less

  1. 40 CFR 96.141 - Timing requirements for CAIR NOX allowance allocations.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 22 2012-07-01 2012-07-01 false Timing requirements for CAIR NOX... (CONTINUED) AIR PROGRAMS (CONTINUED) NOX BUDGET TRADING PROGRAM AND CAIR NOX AND SO2 TRADING PROGRAMS FOR STATE IMPLEMENTATION PLANS CAIR NOX Allowance Allocations § 96.141 Timing requirements for CAIR...

  2. 40 CFR 96.141 - Timing requirements for CAIR NOX allowance allocations.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 21 2011-07-01 2011-07-01 false Timing requirements for CAIR NOX... (CONTINUED) AIR PROGRAMS (CONTINUED) NOX BUDGET TRADING PROGRAM AND CAIR NOX AND SO2 TRADING PROGRAMS FOR STATE IMPLEMENTATION PLANS CAIR NOX Allowance Allocations § 96.141 Timing requirements for CAIR...

  3. 40 CFR 96.141 - Timing requirements for CAIR NOX allowance allocations.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 40 Protection of Environment 22 2013-07-01 2013-07-01 false Timing requirements for CAIR NOX... (CONTINUED) AIR PROGRAMS (CONTINUED) NOX BUDGET TRADING PROGRAM AND CAIR NOX AND SO 2 TRADING PROGRAMS FOR STATE IMPLEMENTATION PLANS CAIR NOX Allowance Allocations § 96.141 Timing requirements for CAIR...

  4. 40 CFR 96.141 - Timing requirements for CAIR NOX allowance allocations.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 20 2010-07-01 2010-07-01 false Timing requirements for CAIR NOX... (CONTINUED) AIR PROGRAMS (CONTINUED) NOX BUDGET TRADING PROGRAM AND CAIR NOX AND SO2 TRADING PROGRAMS FOR STATE IMPLEMENTATION PLANS CAIR NOX Allowance Allocations § 96.141 Timing requirements for CAIR...

  5. 40 CFR 96.141 - Timing requirements for CAIR NOX allowance allocations.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 21 2014-07-01 2014-07-01 false Timing requirements for CAIR NOX... (CONTINUED) AIR PROGRAMS (CONTINUED) NOX BUDGET TRADING PROGRAM AND CAIR NOX AND SO2 TRADING PROGRAMS FOR STATE IMPLEMENTATION PLANS CAIR NOX Allowance Allocations § 96.141 Timing requirements for CAIR...

  6. Viral DNA Packaging: One Step at a Time

    NASA Astrophysics Data System (ADS)

    Bustamante, Carlos; Moffitt, Jeffrey R.

    During its life-cycle the bacteriophage φ29 actively packages its dsDNA genome into a proteinacious capsid, compressing its genome to near crystalline densities against large electrostatic, elastic, and entropic forces. This remarkable process is accomplished by a nano-scale, molecular DNA pump - a complex assembly of three protein and nucleic acid rings which utilizes the free energy released in ATP hydrolysis to perform the mechanical work necessary to overcome these large energetic barriers. We have developed a single molecule optical tweezers assay which has allowed us to probe the detailed mechanism of this packaging motor. By following the rate of packaging of a single bacteriophage as the capsid is filled with genome and as a function of optically applied load, we find that the compression of the genome results in the build-up of an internal force, on the order of ˜ 55 pN, due to the compressed genome. The ability to work against such large forces makes the packaging motor one of the strongest known molecular motors. By titrating the concentration of ATP, ADP, and inorganic phosphate at different opposing load, we are able to determine features of the mechanochemistry of this motor - the coupling between the mechanical and chemical cycles. We find that force is generated not upon binding of ATP, but rather upon release of hydrolysis products. Finally, by improving the resolution of the optical tweezers assay, we are able to observe the discrete increments of DNA encapsidated each cycle of the packaging motor. We find that DNA is packaged in 10-bp increments preceded by the binding of multiple ATPs. The application of large external forces slows the packaging rate of the motor, revealing that the 10-bp steps are actually composed of four 2.5-bp steps which occur in rapid succession. These data show that the individual subunits of the pentameric ring-ATPase at the core of the packaging motor are highly coordinated, with the binding of ATP and the

  7. 40 CFR 97.41 - Timing requirements for NOX allowance allocations.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 21 2011-07-01 2011-07-01 false Timing requirements for NOX allowance allocations. 97.41 Section 97.41 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) FEDERAL NOX BUDGET TRADING PROGRAM AND CAIR NOX AND SO2 TRADING PROGRAMS NOX...

  8. 47 CFR 3.41 - Amount of time allowed before initial settlements.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... ADMINISTRATION OF ACCOUNTING AUTHORITIES IN MARITIME AND MARITIME MOBILE-SATELLITE RADIO SERVICES Settlement Operations § 3.41 Amount of time allowed before initial settlements. An accounting authority must begin... operations is cause for suspension or cancellation of an accounting authority certification....

  9. The USMLE Step 2 CS: Time for a change.

    PubMed

    Alvin, Matthew D

    2016-08-01

    The United States Medical Licensing Examination (USMLE(®)) Steps are a series of mandatory licensing assessments for all allopathic (MD degree) medical students in their transition from student to intern to resident physician. Steps 1, 2 Clinical Knowledge (CK), and 3 are daylong multiple-choice exams that quantify a medical student's basic science and clinical knowledge as well as their application of that knowledge using a three-digit score. In doing so, these Steps provide a standardized assessment that residency programs use to differentiate applicants and evaluate their competitiveness. Step 2 Clinical Skills (CS), the only other Step exam and the second component of Step 2, was created in 2004 to test clinical reasoning and patient-centered skills. As a Pass/Fail exam without a numerical scoring component, Step 2 CS provides minimal differentiation among applicants for residency programs. In this personal view article, it is argued that the current Step 2 CS exam should be eliminated for US medical students and propose an alternative consistent with the mission and purpose of the exam that imposes less of a burden on medical students.

  10. Watching Proteins Direct Crystal Growth One Step at a Time

    SciTech Connect

    2009-01-01

    Researchers at Berkeley Labs Molecular Foundry use an atomic force microscope to record this movie of a peptide being adsorbed to a crystal surface while two successive crystal steps interact, then progress beyond the peptide. The peptide temporarily slows the step before transferring up to the next atomic layer. The lattice pattern on the surface corresponds to the molecular structure of the underlying crystal.

  11. Thermodynamics and kinetics of large-time-step molecular dynamics.

    PubMed

    Rao, Francesco; Spichty, Martin

    2012-02-15

    Molecular dynamics (MD) simulations provide essential information about the thermodynamics and kinetics of proteins. Technological advances in both hardware and algorithms have seen this method accessing timescales that used to be unreachable only few years ago. The quest to simulate slow, biologically relevant macromolecular conformational changes, is still open. Here, we present an approximate approach to increase the speed of MD simulations by a factor of ∼4.5. This is achieved by using a large integration time step of 7 fs, in combination with frozen covalent bonds and look-up tables for nonbonded interactions of the solvent. Extensive atomistic MD simulations for a flexible peptide in water show that the approach reproduces the peptide's equilibrium conformational changes, preserving the essential properties of both thermodynamics and kinetics. Comparison of this approximate method with state-of-the-art implicit solvation simulations indicates that the former provides a better description of the underlying free-energy surface. Finally, simulations of a 33-residue peptide show that these fast MD settings are readily applicable to investigate biologically relevant systems.

  12. Wooden hutch space allowance influences male Holstein calf health, performance, daily lying time, and respiratory immunity.

    PubMed

    Calvo-Lorenzo, M S; Hulbert, L E; Fowler, A L; Louie, A; Gershwin, L J; Pinkerton, K E; Ballou, M A; Klasing, K C; Mitloehner, F M

    2016-06-01

    Dairy calves in the western United States are commonly raised individually in wooden hutches with a space allowance of 1.23m(2)/calf. Recent legislative initiatives in California and across the United States were passed regarding concern over space allowance for farm animals. The objective of this study was to determine if rearing male Holstein calves in wooden hutches modified to increase space allowance would influence measures of performance, lying time per day, health, and respiratory immunocompetence. At 4d of age, 60 calves were randomly assigned to 1 of 3housing treatments: (1) conventional housing (CONV; 1.23m(2)/calf), (2) 1.5 × CONV (MOD; 1.85m(2)/calf), or (3) 3 × CONV (MAX; 3.71m(2)/calf). Intakes of milk and solid feed were recorded daily and body weight was measured at 0, 3, 6, 10, and 12 wk of age. For the first 3 wk of the trial, calves were scored daily for fecal consistency, hydration, and hide cleanliness. In addition, calves were scored for respiratory health (i.e., nasal and eye discharge, ear position) until 7 wk of age. The total lying duration per day was recorded using data loggers at 3, 6, and 10 wk of age. Eight clinically healthy calves from each treatment were sensitized with subcutaneous ovalbumin (OVA) and then challenged with aerosolized OVA to assess calf respiratory immunity at 11 wk of age. Bronchoalveolar lavage fluid (BALF) was collected 4d after the OVA challenge and analyzed for leukocyte differentials and OVA-specific IgG, IgG1, IgA, and IgE. Calf average daily gain and body weight were positively associated with space allowance at approximately 3 wk before weaning and throughout postweaning, respectively. A greater space allowance decreased lying time after 46d. Space allowance did not influence fecal consistency, but there was a tendency for MAX calves to take 1d longer to recover from loose feces than MOD calves. The MAX calves had the fewest (%) observations with feces on their body compared with CONV or MOD. At 3 wk of

  13. Optimized particle-mesh Ewald/multiple-time step integration for molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Batcho, Paul F.; Case, David A.; Schlick, Tamar

    2001-09-01

    We develop an efficient multiple time step (MTS) force splitting scheme for biological applications in the AMBER program in the context of the particle-mesh Ewald (PME) algorithm. Our method applies a symmetric Trotter factorization of the Liouville operator based on the position-Verlet scheme to Newtonian and Langevin dynamics. Following a brief review of the MTS and PME algorithms, we discuss performance speedup and the force balancing involved to maximize accuracy, maintain long-time stability, and accelerate computational times. Compared to prior MTS efforts in the context of the AMBER program, advances are possible by optimizing PME parameters for MTS applications and by using the position-Verlet, rather than velocity-Verlet, scheme for the inner loop. Moreover, ideas from the Langevin/MTS algorithm LN are applied to Newtonian formulations here. The algorithm's performance is optimized and tested on water, solvated DNA, and solvated protein systems. We find CPU speedup ratios of over 3 for Newtonian formulations when compared to a 1 fs single-step Verlet algorithm using outer time steps of 6 fs in a three-class splitting scheme; accurate conservation of energies is demonstrated over simulations of length several hundred ps. With modest Langevin forces, we obtain stable trajectories for outer time steps up to 12 fs and corresponding speedup ratios approaching 5. We end by suggesting that modified Ewald formulations, using tailored alternatives to the Gaussian screening functions for the Coulombic terms, may allow larger time steps and thus further speedups for both Newtonian and Langevin protocols; such developments are reported separately.

  14. Spot Variation Fluorescence Correlation Spectroscopy Allows for Superresolution Chronoscopy of Confinement Times in Membranes

    PubMed Central

    Ruprecht, Verena; Wieser, Stefan; Marguet, Didier; Schütz, Gerhard J.

    2011-01-01

    Resolving the dynamical interplay of proteins and lipids in the live-cell plasma membrane represents a central goal in current cell biology. Superresolution concepts have introduced a means of capturing spatial heterogeneity at a nanoscopic length scale. Similar concepts for detecting dynamical transitions (superresolution chronoscopy) are still lacking. Here, we show that recently introduced spot-variation fluorescence correlation spectroscopy allows for sensing transient confinement times of membrane constituents at dramatically improved resolution. Using standard diffraction-limited optics, spot-variation fluorescence correlation spectroscopy captures signatures of single retardation events far below the transit time of the tracer through the focal spot. We provide an analytical description of special cases of transient binding of a tracer to pointlike traps, or association of a tracer with nanodomains. The influence of trap mobility and the underlying binding kinetics are quantified. Experimental approaches are suggested that allow for gaining quantitative mechanistic insights into the interaction processes of membrane constituents. PMID:21641330

  15. Error correction in short time steps during the application of quantum gates

    NASA Astrophysics Data System (ADS)

    de Castro, L. A.; Napolitano, R. d. J.

    2016-04-01

    We propose a modification of the standard quantum error-correction method to enable the correction of errors that occur due to the interaction with a noisy environment during quantum gates without modifying the codification used for memory qubits. Using a perturbation treatment of the noise that allows us to separate it from the ideal evolution of the quantum gate, we demonstrate that in certain cases it is necessary to divide the logical operation in short time steps intercalated by correction procedures. A prescription of how these gates can be constructed is provided, as well as a proof that, even for the cases when the division of the quantum gate in short time steps is not necessary, this method may be advantageous for reducing the total duration of the computation.

  16. Automatic multirate methods for ordinary differential equations. [Adaptive time steps

    SciTech Connect

    Gear, C.W.

    1980-01-01

    A study is made of the application of integration methods in which different step sizes are used for different members of a system of equations. Such methods can result in savings if the cost of derivative evaluation is high or if a system is sparse; however, the estimation and control of errors is very difficult and can lead to high overheads. Three approaches are discussed, and it is shown that the least intuitive is the most promising. 2 figures.

  17. Two-step phase separation of a polymer mixture. II. Time evolution of structure factor

    NASA Astrophysics Data System (ADS)

    Hayashi, Masaki; Jinnai, Hiroshi; Hashimoto, Takeji

    2000-04-01

    Nonlinear time evolution of phase-separating structures in the two-step phase separation process was investigated for a deuterated polybutadiene-polyisoprene mixture by using a time-resolved light scattering technique. The mixture studied has a lower critical solution temperature type phase diagram with a spinodal temperature of 36 °C. The first-step phase separation via spinodal decomposition (SD) was conducted by a temperature jump (T-jump) from 23 °C to 42 °C, and to the late stage of the SD for varying time periods, t0, in order to develop phase-separated domains with varying characteristic size Λm,1. This phase separation was followed by the second-step T-jump to a higher temperature of 70 °C so that each phase-separated domain is again quenched into thermodynamically unstable region. Nonlinear time evolution processes of phase-separating structures after the second-step SD were explored as a function of size of the initial structures Λm,1. We found the following intriguing effects of the initial structures on further evolution of phase-separating structure via the second-step SD: (1) When Λm,1≫Λm,0 (characteristic length of composition fluctuations developed in the early stage SD after quenching the system from a single-phase state to 70 °C), small domains were evolved within the initial domains (defined as large domains) developed during the first-step SD process, while (2) when Λm,1⩽Λm,0, the small domains were not developed, but only the large domains grew at a growth rate larger than that at 42 °C. In the former case (1), we succeeded in separating the scattering due to the small domains and that due to large domains from the observed scattering profile. The separation allows us to investigate a coupling of the time evolution of the large and small domains and nonlinear pathways for the system to achieve a new equilibrium structure after the second-step SD process.

  18. The prevalence of upright non-stepping time in comparison to stepping time in 11-13 year old school children across seasons.

    PubMed

    McCrorie, P Rw; Duncan, E; Granat, M H; Stansfield, B W

    2012-11-01

    Evidence suggests that behaviours such as standing are beneficial for our health. Unfortunately, little is known of the prevalence of this state, its importance in relation to time spent stepping or variation across seasons. The aim of this study was to quantify, in young adolescents, the prevalence and seasonal changes in time spent upright and not stepping (UNSt(time)) as well as time spent upright and stepping (USt(time)), and their contribution to overall upright time (U(time)). Thirty-three adolescents (12.2 ± 0.3 y) wore the activPAL activity monitor during four school days on two occasions: November/December (winter) and May/June (summer). UNSt(time) contributed 60% of daily U(time) at winter (Mean = 196 min) and 53% at summer (Mean = 171 min); a significant seasonal effect, p < 0.001. USt(time) was significantly greater in summer compared to winter (153 min versus 131 min, p < 0.001). The effects in UNSt(time) could be explained through significant seasonal differences during the school hours (09:00-16:00), whereas the effects in USt(time) could be explained through significant seasonal differences in the evening period (16:00-22:00). Adolescents spent a greater amount of time upright and not stepping than they did stepping, in both winter and summer. The observed seasonal effects for both UNSt(time) and USt(time) provide important information for behaviour change intervention programs.

  19. Variable time-stepping in the pathwise numerical solution of the chemical Langevin equation.

    PubMed

    Ilie, Silvana

    2012-12-21

    Stochastic modeling is essential for an accurate description of the biochemical network dynamics at the level of a single cell. Biochemically reacting systems often evolve on multiple time-scales, thus their stochastic mathematical models manifest stiffness. Stochastic models which, in addition, are stiff and computationally very challenging, therefore the need for developing effective and accurate numerical methods for approximating their solution. An important stochastic model of well-stirred biochemical systems is the chemical Langevin Equation. The chemical Langevin equation is a system of stochastic differential equation with multidimensional non-commutative noise. This model is valid in the regime of large molecular populations, far from the thermodynamic limit. In this paper, we propose a variable time-stepping strategy for the numerical solution of a general chemical Langevin equation, which applies for any level of randomness in the system. Our variable stepsize method allows arbitrary values of the time-step. Numerical results on several models arising in applications show significant improvement in accuracy and efficiency of the proposed adaptive scheme over the existing methods, the strategies based on halving/doubling of the stepsize and the fixed step-size ones.

  20. Risk-based evaluation of Allowed Outage Times (AOTs) considering risk of shutdown

    SciTech Connect

    Mankamo, T.; Kim, I.S.; Samanta, P.K.

    1992-12-31

    When safety systems fail during power operation, Technical Specifications (TS) usually limit the repair within Allowed Outage Time (AOT). If the repair cannot be completed within the AOT, or no AOT is allowed, the plant is required to be shut down for the repair. However, if the capability to remove decay heat is degraded, shutting down the plant with the need to operate the affected decay-heat removal systems may impose a substantial risk compared to continued power operation over a usual repair time. Thus, defining a proper AOT in such situations can be considered as a risk-comparison between the repair in frill power state with a temporarily increased level of risk, and the altemative of shutting down the plant for the repair in zero power state with a specific associated risk. The methodology of the risk-comparison approach, with a due consideration of the shutdown risk, has been further developed and applied to the AOT considerations of residual heat removal and standby service water systems of a boiling water reactor (BWR) plant. Based on the completed work, several improvements to the TS requirements for the systems studied can be suggested.

  1. Risk-based evaluation of Allowed Outage Times (AOTs) considering risk of shutdown

    SciTech Connect

    Mankamo, T. ); Kim, I.S.; Samanta, P.K. )

    1992-01-01

    When safety systems fail during power operation, Technical Specifications (TS) usually limit the repair within Allowed Outage Time (AOT). If the repair cannot be completed within the AOT, or no AOT is allowed, the plant is required to be shut down for the repair. However, if the capability to remove decay heat is degraded, shutting down the plant with the need to operate the affected decay-heat removal systems may impose a substantial risk compared to continued power operation over a usual repair time. Thus, defining a proper AOT in such situations can be considered as a risk-comparison between the repair in frill power state with a temporarily increased level of risk, and the altemative of shutting down the plant for the repair in zero power state with a specific associated risk. The methodology of the risk-comparison approach, with a due consideration of the shutdown risk, has been further developed and applied to the AOT considerations of residual heat removal and standby service water systems of a boiling water reactor (BWR) plant. Based on the completed work, several improvements to the TS requirements for the systems studied can be suggested.

  2. Magnet tracking allows assessment of regional gastrointestinal transit times in children

    PubMed Central

    Hedsund, Caroline; Joensson, Iben Moeller; Gregersen, Tine; Fynne, Lotte; Schlageter, Vincent; Krogh, Klaus

    2013-01-01

    Background Data on small intestinal transit time in healthy children are lacking, and normal values for gastric emptying and colonic transit time are sparse. Conventional methods, including radiopaque markers, scintigraphy, and PillCam™ involve radiation or require the child to swallow a large pill. The minimally invasive, radiation-free Motility Tracking System-1 (MTS-1) has been introduced for description of gastrointestinal motility in adults. The aim of the study was to evaluate the MTS-1 for assessment of gastrointestinal transit times and motility patterns in healthy children. Methods Twenty-one healthy children (nine girls), median age 10 (range 7–12) years were included. For evaluation with MTS-1, a small magnetic pill was ingested and tracked through the gastrointestinal tract by a matrix of 16 magnetic sensors placed behind a nonmagnetic bed. The children were investigated for 8 hours after swallowing the magnetic pill and again for 4 hours the following morning. After leaving the unit, each child came back after every bowel movement to determine if the pill had been expelled. Results Nineteen children could swallow the pill. Characteristic contraction patterns were identified for the stomach (three per minute), small intestine (9–11 per minute), and colon (4–5 per minute). Median total gastrointestinal transit time was 37.7 (range 9.5–95.8) hours, median gastric emptying time was 37 (range 2–142) minutes, median small intestinal transit time was 302 (range 164 to >454) minutes, and median colorectal transit time was 38.1 (range 5.6–90.0) hours. Conclusion MTS-1 allows minimally invasive evaluation of gastrointestinal motility in children. Use of the method is, however, restricted by the nonambulatory setup. PMID:24399881

  3. One step at a time: endoplasmic reticulum-associated degradation

    PubMed Central

    Vembar, Shruthi S.; Brodsky, Jeffrey L.

    2009-01-01

    Protein folding in the endoplasmic reticulum (ER) is monitored by ER quality control (ERQC) mechanisms. Proteins that pass ERQC criteria traffic to their final destinations through the secretory pathway, whereas non-native and unassembled subunits of multimeric proteins are degraded by the ER-associated degradation (ERAD) pathway. During ERAD, molecular chaperones and associated factors recognize and target substrates for retrotranslocation to the cytoplasm, where they are degraded by the ubiquitin–proteasome machinery. The discovery of diseases that are associated with ERAD substrates highlights the importance of this pathway. Here, we summarize our current understanding of each step during ERAD, with emphasis on the factors that catalyse distinct activities. PMID:19002207

  4. Its Time to Step into Science at Medgar Evers College

    PubMed Central

    Carroll, Margaret A.; Skeete, Dereck; Catapane, Edward J.

    2015-01-01

    Over the next decade, demand and job opportunities in science and engineering (S&E) are expected to grow. With so many S&E “baby-boomers” retiring, questions arise as to whether America will be able to attract enough young people into Science, Technology, Engineering and Mathematics (STEM) to maintain a S&E workforce that keeps up with what is becoming a more globally technologically and scientifically advancing society. Furthermore, considering recent projections of a nation more racially and ethnically diverse by mid-century, will America’s future STEM workforce reflect the diversity projected for our growing U.S. population? In 2006, the authors received an award from the National Science Foundation (NSF) to direct a new initiative titled “STEP into Science.” Funded under the Science, Technology, Engineering and Mathematics Talent Expansion Program (STEP) of the NSF Division of Undergraduate Education, the main goal of the project is to increase the number of STEM majors that graduate with baccalaureate degree, specifically B.S. degrees in Biology or Environmental Science. The program has had great success implementing the use of “peer recruiters” to attract more high school, transfer, and non-science college students into STEM majors and places emphasis on the role of undergraduate research experiences as a successful strategy to increase the quality and retention of science majors through their baccalaureate degree. Since the inception of the program, total STEM enrollment has more than doubled and the number of majors actively engaged in research has risen 38% with a concurrent increase in student research presentations at scientific conference, and the number of students receiving external research internships and travel awards to attend national conferences. The number of STEM graduates (both A.S. and B.S.) has also increased and the program anticipates that these and future STEP into Science graduates will continue on to Masters and Doctoral

  5. Are elderly pedestrians allowed enough time at pedestrian crossings in Cape Town, South Africa?

    PubMed

    Amosun, S L; Burgess, T; Groeneveldt, L; Hodgson, T

    2007-01-01

    A descriptive, cross-sectional analytical study was conducted to determine whether the recommended walking speed of 1.2 ms(-1) would allow elderly pedestrians to safely clear pedestrian crossings in Cape Town, South Africa. Male and female volunteers (n = 47), aged 65-93 years and resident in four homes for older persons, were recruited. Pedestrian clearance intervals at 40 traffic lights within 5-km radius of the selected homes were measured. The mean walking speed required at these traffic lights was 0.86 +/- 0.32 ms(1). The maximal walking speed over 12 m was measured without carrying any load and when carrying a predetermined weight of an average shopping bag. Participants' emotions associated with pedestrian road safety were also assessed through an interview. The mean maximal unloaded and loaded walking speeds were 1.36 +/- 0.31 ms(-1) (0.73-2.03 ms(-1)), and 1.36 +/- 0.33 ms(-1) (0.58-2.12 ms(-1)), respectively. Over 30% of the participants walked slower than the recommended walking speed of 1.2 ms(-1). Participants felt that traffic lights did not allow for sufficient time to cross roads (51.1%) and reported emotions of apprehension (44.7%), anxiety (17.0%), and fear (10.6%) when crossing. A review of traffic planning and public policy is recommended to ensure older pedestrians safely clear pedestrian crossings.

  6. Allowing time to consolidate knowledge gained through random practice facilitates later novel motor sequence acquisition.

    PubMed

    Kim, Taewon; Rhee, Joohyun; Wright, David L

    2016-01-01

    Two experiments were conducted to examine the efficacy of random (RP) and blocked practice (BP) for enhancing later motor learning. Each experiment involved practicing three unique seven key serial reaction time (SRT) tasks in either a blocked or random format followed by practice of a novel SRT task either 2-min (Experiment 1) or 24-h (Experiment 2) later. While the expected benefit of RP for retention was present in both experiments, in Experiment 1 there was no advantage from prior RP for new learning. Experiment 2 explored the possibility that increasing the interval, from 2-min to 24-h, between BP or RP and practice of the novel motor task might allow consolidation of sequence knowledge acquired during BP or RP which in turn might facilitate new learning. As a result of the additional time between training bouts RP facilitated the rate at which the novel motor task was acquired. Interestingly, when this additional time was provided, both BP and RP supported (a) a performance saving for the first trial with the novel task, and (b) an offline improvement in performance across a 24-h interval not present when only the novel motor task was practiced. The latter benefits for new learning may have resulted from exposure to prior physical practice per se. or practice variability. These data are discussed with respect to (a) future learning benefits from prior experience training with greater CI, and (b) the importance of memory consolidation for motor learning. PMID:26686835

  7. Time-Gated Optical Projection Tomography Allows Visualization of Adult Zebrafish Internal Structures

    PubMed Central

    Foglia, Efrem Alessandro; Pistocchi, Anna; D'Andrea, Cosimo; Valentini, Gianluca; Cubeddu, Rinaldo; De Silvestri, Sandro; Cerullo, Giulio; Cotelli, Franco

    2012-01-01

    Optical imaging through biological samples is compromised by tissue scattering and currently various approaches aim to overcome this limitation. In this paper we demonstrate that an all optical technique, based on non-linear upconversion of infrared ultrashort laser pulses and on multiple view acquisition, allows the reduction of scattering effects in tomographic imaging. This technique, namely Time-Gated Optical Projection Tomography (TGOPT), is used to reconstruct three dimensionally the internal structure of adult zebrafish without staining or clearing agents. This method extends the use of Optical Projection Tomography to optically diffusive samples yielding reconstructions with reduced artifacts, increased contrast and improved resolution with respect to those obtained with non-gated techniques. The paper shows that TGOPT is particularly suited for imaging the skeletal system and nervous structures of adult zebrafish. PMID:23185643

  8. A LC-MS method allowing the analysis of HMX and RDX present at the picogram level in natural aqueous samples without a concentration step.

    PubMed

    Vigneau, Olivier; Machuron-Mandard, Xavier

    2009-03-15

    The introduction of chloroform into the nebulising gas of a LC/MS electrospray interface (ESI), in a perfectly controlled way, leads to the formation of intense adducts ([M+Cl](-)) when a mobile phase containing HMX (1,3,5,7-tetranitro-1,3,5,7-tetrazacyclooctane or octogen) and RDX (1,3,5-trintro-1,3,5-triazacyclohexane or hexogen) is eluted. This LC/MS method allows the direct analysis of aqueous samples containing HMX and RDX at the pictogram level without a concentration step. The method is used to determine HMX and RDX concentrations in ground water samples from a military site.

  9. Empirical versus time stepping with embedded error control for density-driven flow in porous media

    NASA Astrophysics Data System (ADS)

    Younes, Anis; Ackerer, Philippe

    2010-08-01

    Modeling density-driven flow in porous media may require very long computational time due to the nonlinear coupling between flow and transport equations. Time stepping schemes are often used to adapt the time step size in order to reduce the computational cost of the simulation. In this work, the empirical time stepping scheme which adapts the time step size according to the performance of the iterative nonlinear solver is compared to an adaptive time stepping scheme where the time step length is controlled by the temporal truncation error. Results of the simulations of the Elder problem show that (1) the empirical time stepping scheme can lead to inaccurate results even with a small convergence criterion, (2) accurate results are obtained when the time step size selection is based on the truncation error control, (3) a non iterative scheme with proper time step management can be faster and leads to more accurate solution than the standard iterative procedure with the empirical time stepping and (4) the temporal truncation error can have a significant effect on the results and can be considered as one of the reasons for the differences observed in the Elder numerical results.

  10. Effect of Two-step Time-restricted Feeding on the Fattening Traits in Geese.

    PubMed

    Lui, Zhen-Jia; Chu, Hung-Hsin; Wu, Yun-Chu; Yang, Shyi-Kuen

    2014-06-01

    The present study was conducted to determine whether the two-step time-restricted feeding improves the fattening traits of one-step time-restricted feeding in geese. Thirty-six 8-wk-old geese were allotted into one of three groups. Group R1 (the 1-step restricted feeding group) was allowed access to feed for 2 h in the morning from 8 wk to 14 wk of age. Group R2 (the 2-step restricted feeding group) was treated as Group R1, but was additionally fed for 2 h in the afternoon from 12 wk to 14 wk of age. Group C (the control group) was fed ad libitum from 8 wk to 14 wk of age. Feed intake and body weight (BW) were recorded daily and weekly, respectively. At 14 wk of age, the blood samples were collected to determine the fasting plasma levels of glucose, triacylglycerols and uric acid before sacrifice. The results showed that daily feed intake (DFI) was lower, feed efficiency (FE) was higher in both Groups R1 and R2 than in Group C, and daily gain (DG) in Group R2 was higher than in Group R1 during the whole experimental period (p<0.05). Group R1 exhibited lower abdominal and visceral fat weights in carcass than did Group C (p<0.05), and Group R2 was in intermediate. The fasting plasma glucose levels in Group C were higher, and triacylglycerol levels in Group R1 were higher, compared with the other groups (p<0.05). It is concluded that time-restricted feeding in the fattening period not only increases FE but reduces DFI, and the additional meal during the late fattening period improves the DG without the expense of FE in geese.

  11. Continuous online monitoring of ionic dialysance allows modification of delivered hemodialysis treatment time.

    PubMed

    Chesterton, Lindsay J; Priestman, William S; Lambie, Stewart H; Fielding, Catherine A; Taal, Maarten W; Fluck, Richard J; McIntyre, Christopher W

    2006-10-01

    Considerable intrinsic intrapatient variability influences the actual delivery of Kt/V. The aim of this study is to examine the feasibility of using continuous online assessment of ionic dialysance measurements (Kt/V(ID)) to allow dialysis sessions to be altered on an individual basis. Ten well-established chronic hemodialysis (HD) patients without significant residual renal function were studied (mean age 65+/-4.3 [38-81] years, mean length of time on dialysis 66+/-18 [14-189] months). These patients had all been receiving thrice-weekly 4-hr dialysis using Integra dialysis monitors. Dialysis monitors were equipped with Diascan modules permitting measurement of Kt/V(ID). Predicted treatment time required to achieve a Kt/V(ID) > or = 1.1 (equivalent to a urea-based method of 1.2) was calculated from the delivered Kt/V(ID) at 60 and 120 min. Treatment time was reprogrammed at 2 hr (ensuring all planned ultrafiltration would be accommodated into the new modified session duration). Owing to practical issues, and to avoid excessively short dialysis times, these changes were censored at no more than+/-10% of the usual 240-min treatment time (210-265 min). Data were collected from a total of 50 dialysis sessions. Almost all sessions (47/50) required modification of the standard treatment time: 13/50 sessions were lengthened and 34/50 shortened (mean length of session 232.2+/-2.5 [210-265] min). A Kt/V(ID) of > or = 1.1 was achieved in 39/50 sessions. The difference in mean urea-based Kt/V poststudy (1.3+/-0.05 [1.1-1.6]) and mean achieved Kt/V(ID) (1.16+/-0.02 [0.7-1.37]) was significant (p = 0.002). The use of individualized variable dialysis treatment time using online ionic dialysance measurements of Kt/V(ID) appears both practicable and effective at ensuring consistently delivered adequate dialysis.

  12. Terahertz time domain spectroscopy allows contactless monitoring of grapevine water status

    PubMed Central

    Santesteban, Luis G.; Palacios, Inés; Miranda, Carlos; Iriarte, Juan C.; Royo, José B.; Gonzalo, Ramón

    2015-01-01

    Agriculture is the sector with the greatest water consumption, since food production is frequently based on crop irrigation. Proper irrigation management requires reliable information on plant water status, but all the plant-based methods to determine it suffer from several inconveniences, mainly caused by the necessity of destructive sampling or of alteration of the plant organ due to contact installation. The aim of this work is to test if terahertz (THz) time domain reflectance measurements made on the grapevine trunk allows contactless monitoring of plant status. The experiments were performed on a potted 14-years-old plant, using a general purpose THz emitter receiver head. Trunk THz time-domain reflection signal proved to be very sensitive to changes in plant water availability, as its pattern follows the trend of soil water content and trunk growth variations. Therefore, it could be used to contactless monitor plant water status. Apart from that, THz reflection signal was observed to respond to light conditions which, according to a specifically designed girdling experiment, was caused by changes in the phloem. This latter results opens a promising field of research for contactless monitoring of phloem activity. PMID:26082791

  13. Terahertz time domain spectroscopy allows contactless monitoring of grapevine water status.

    PubMed

    Santesteban, Luis G; Palacios, Inés; Miranda, Carlos; Iriarte, Juan C; Royo, José B; Gonzalo, Ramón

    2015-01-01

    Agriculture is the sector with the greatest water consumption, since food production is frequently based on crop irrigation. Proper irrigation management requires reliable information on plant water status, but all the plant-based methods to determine it suffer from several inconveniences, mainly caused by the necessity of destructive sampling or of alteration of the plant organ due to contact installation. The aim of this work is to test if terahertz (THz) time domain reflectance measurements made on the grapevine trunk allows contactless monitoring of plant status. The experiments were performed on a potted 14-years-old plant, using a general purpose THz emitter receiver head. Trunk THz time-domain reflection signal proved to be very sensitive to changes in plant water availability, as its pattern follows the trend of soil water content and trunk growth variations. Therefore, it could be used to contactless monitor plant water status. Apart from that, THz reflection signal was observed to respond to light conditions which, according to a specifically designed girdling experiment, was caused by changes in the phloem. This latter results opens a promising field of research for contactless monitoring of phloem activity. PMID:26082791

  14. Timing of adiposity rebound: a step toward preventing obesity.

    PubMed

    Boonpleng, Wannaporn; Park, Chang Gi; Gallo, Agatha M

    2012-01-01

    Adiposity rebound (AR) is used as an indicator to predict obesity in adults. Previous studies about AR in the U.S. were based on local data; therefore, the generalizability of study results is limited. The purpose of this study was to identify the timing of AR for U.S. children using a national survey data set, the National Health and Nutrition Examination Survey (NHANES). Combined data of NHANES 1999-2008 were used to estimate the national level of this critical period for U.S. children developing obesity. Data of 8813 children 2 to 10 years of age were analyzed. Mean body mass index was estimated using the survey sample analysis method. Visual inspection method was employed to examine the timing of AR. Gender and race/ethnicity differences in AR were identified at an early age. AR occurred earlier in girls and in Non-Hispanic African-American children than in Non-Hispanic Caucasian children. Differences in timing for AR by gender and race/ethnicity should be considered in planning early and timely intervention efforts to prevent childhood obesity.

  15. Fluorescently labeled adrenomedullin allows real-time monitoring of adrenomedullin receptor trafficking in living cells.

    PubMed

    Schönauer, Ria; Kaiser, Anette; Holze, Cathleen; Babilon, Stefanie; Köbberling, Johannes; Riedl, Bernd; Beck-Sickinger, Annette G

    2015-12-01

    The human adrenomedullin (ADM) is a 52 amino acid peptide hormone belonging to the calcitonin family of peptides, which plays a major role in the development and regulation of cardiovascular and lymphatic systems. For potential use in clinical applications, we aimed to investigate the fate of the peptide ligand after binding and activation of the adrenomedullin receptor (AM1), a heterodimer consisting of the calcitonin receptor-like receptor (CLR), a G protein-coupled receptor, associated with the receptor activity-modifying protein 2 (RAMP2). Full length and N-terminally shortened ADM peptides were synthesized using Fmoc/tBu solid phase peptide synthesis and site-specifically labeled with the fluorophore carboxytetramethylrhodamine (Tam) either by amide bond formation or copper(I)-catalyzed azide alkyne cycloaddition. For the first time, Tam-labeled ligands allowed the observation of co-internalization of the whole ligand-receptor complex in living cells co-transfected with fluorescent fusion proteins of CLR and RAMP2. Application of a fluorescent probe to track lysosomal compartments revealed that ADM together with the CLR/RAMP2-complex is routed to the degradative pathway. Moreover, we found that the N-terminus of ADM is not a crucial component of the peptide sequence in terms of AM1 internalization behavior. PMID:26767744

  16. Time-step limits for a Monte Carlo Compton-scattering method

    SciTech Connect

    Densmore, Jeffery D; Warsa, James S; Lowrie, Robert B

    2009-01-01

    We perform a stability analysis of a Monte Carlo method for simulating the Compton scattering of photons by free electron in high energy density applications and develop time-step limits that avoid unstable and oscillatory solutions. Implementing this Monte Carlo technique in multi physics problems typically requires evaluating the material temperature at its beginning-of-time-step value, which can lead to this undesirable behavior. With a set of numerical examples, we demonstrate the efficacy of our time-step limits.

  17. Finite element/finite volume approaches with adaptive time stepping strategies for transient thermal problems

    NASA Technical Reports Server (NTRS)

    Mohan, Ram V.; Tamma, Kumar K.

    1993-01-01

    An adaptive time stepping strategy for transient thermal analysis of engineering systems is described which computes the time step based on the local truncation error with a good global error control and obtains optimal time steps to be used during the analysis. Combined mesh partitionings involving FEM/FVM meshes based on physical situations to obtain numerically improved physical representations are also proposed. Numerical test cases are described and comparative pros and cons are identified for practical situations.

  18. Formulation of an explicit-multiple-time-step time integration method for use in a global primitive equation grid model

    NASA Technical Reports Server (NTRS)

    Chao, W. C.

    1982-01-01

    With appropriate modifications, a recently proposed explicit-multiple-time-step scheme (EMTSS) is incorporated into the UCLA model. In this scheme, the linearized terms in the governing equations that generate the gravity waves are split into different vertical modes. Each mode is integrated with an optimal time step, and at periodic intervals these modes are recombined. The other terms are integrated with a time step dictated by the CFL condition for low-frequency waves. This large time step requires a special modification of the advective terms in the polar region to maintain stability. Test runs for 72 h show that EMTSS is a stable, efficient and accurate scheme.

  19. A new approach for determining the time step when propagating with the Lanczos algorithm

    NASA Astrophysics Data System (ADS)

    Mohankumar, N.; Carrington, Tucker

    2010-11-01

    A new criterion for choosing the time step used when numerically solving time-dependent Schroedinger equation with the Lanczos method is presented. Following Saad, Stewart and Leyk, an explicit expression for the time step is obtained from the remainder of the Chebyshev series of the matrix exponential.

  20. Large time-step stability of explicit one-dimensional advection schemes

    NASA Technical Reports Server (NTRS)

    Leonard, B. P.

    1993-01-01

    There is a wide-spread belief that most explicit one-dimensional advection schemes need to satisfy the so-called 'CFL condition' - that the Courant number, c = udelta(t)/delta(x), must be less than or equal to one, for stability in the von Neumann sense. This puts severe limitations on the time-step in high-speed, fine-grid calculations and is an impetus for the development of implicit schemes, which often require less restrictive time-step conditions for stability, but are more expensive per time-step. However, it turns out that, at least in one dimension, if explicit schemes are formulated in a consistent flux-based conservative finite-volume form, von Neumann stability analysis does not place any restriction on the allowable Courant number. Any explicit scheme that is stable for c is less than 1, with a complex amplitude ratio, G(c), can be easily extended to arbitrarily large c. The complex amplitude ratio is then given by exp(- (Iota)(Nu)(Theta)) G(delta(c)), where N is the integer part of c, and delta(c) = c - N (less than 1); this is clearly stable. The CFL condition is, in fact, not a stability condition at all, but, rather, a 'range restriction' on the 'pieces' in a piece-wise polynomial interpolation. When a global view is taken of the interpolation, the need for a CFL condition evaporates. A number of well-known explicit advection schemes are considered and thus extended to large delta(t). The analysis also includes a simple interpretation of (large delta(t)) total-variation-diminishing (TVD) constraints.

  1. Convergence Acceleration for Multistage Time-Stepping Schemes

    NASA Technical Reports Server (NTRS)

    Swanson, R. C.; Turkel, Eli L.; Rossow, C-C; Vasta, V. N.

    2006-01-01

    The convergence of a Runge-Kutta (RK) scheme with multigrid is accelerated by preconditioning with a fully implicit operator. With the extended stability of the Runge-Kutta scheme, CFL numbers as high as 1000 could be used. The implicit preconditioner addresses the stiffness in the discrete equations associated with stretched meshes. Numerical dissipation operators (based on the Roe scheme, a matrix formulation, and the CUSP scheme) as well as the number of RK stages are considered in evaluating the RK/implicit scheme. Both the numerical and computational efficiency of the scheme with the different dissipation operators are discussed. The RK/implicit scheme is used to solve the two-dimensional (2-D) and three-dimensional (3-D) compressible, Reynolds-averaged Navier-Stokes equations. In two dimensions, turbulent flows over an airfoil at subsonic and transonic conditions are computed. The effects of mesh cell aspect ratio on convergence are investigated for Reynolds numbers between 5.7 x 10(exp 6) and 100.0 x 10(exp 6). Results are also obtained for a transonic wing flow. For both 2-D and 3-D problems, the computational time of a well-tuned standard RK scheme is reduced at least a factor of four.

  2. An adaptive time-stepping strategy for solving the phase field crystal model

    SciTech Connect

    Zhang, Zhengru; Ma, Yuan; Qiao, Zhonghua

    2013-09-15

    In this work, we will propose an adaptive time step method for simulating the dynamics of the phase field crystal (PFC) model. The numerical simulation of the PFC model needs long time to reach steady state, and then large time-stepping method is necessary. Unconditionally energy stable schemes are used to solve the PFC model. The time steps are adaptively determined based on the time derivative of the corresponding energy. It is found that the use of the proposed time step adaptivity cannot only resolve the steady state solution, but also the dynamical development of the solution efficiently and accurately. The numerical experiments demonstrate that the CPU time is significantly saved for long time simulations.

  3. 40 CFR 35.2025 - Allowance and advance of allowance.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... advance of allowance. (a) Allowance. Step 2+3 and Step 3 grant agreements will include an allowance for facilities planning and design of the project and Step 7 agreements will include an allowance for facility... would receive under paragraph (a) of this section. (5) In the event a Step 2+3, Step 3 or Step 7...

  4. 40 CFR 97.611 - Timing requirements for TR SO2 Group 1 allowance allocations.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... new unit set-aside after promulgation of each notice of data availability required in paragraph (b)(1... Group 1 allowances to the new unit set-aside for such control period; or (B) If the State has a SIP... each year thereafter, as provided in a notice of data availability issued by the...

  5. 40 CFR 97.611 - Timing requirements for TR SO2 Group 1 allowance allocations.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... new unit set-aside after promulgation of each notice of data availability required in paragraph (b)(1... Group 1 allowances to the new unit set-aside for such control period; or (B) If the State has a SIP... each year thereafter, as provided in a notice of data availability issued by the...

  6. 40 CFR 97.611 - Timing requirements for TR SO2 Group 1 allowance allocations.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... new unit set-aside after promulgation of each notice of data availability required in paragraph (b)(1... Group 1 allowances to the new unit set-aside for such control period; or (B) If the State has a SIP... each year thereafter, as provided in a notice of data availability issued by the...

  7. Consistency of internal fluxes in a hydrological model running at multiple time steps

    NASA Astrophysics Data System (ADS)

    Ficchi, Andrea; Perrin, Charles; Andréassian, Vazken

    2016-04-01

    Improving hydrological models remains a difficult task and many ways can be explored, among which one can find the improvement of spatial representation, the search for more robust parametrization, the better formulation of some processes or the modification of model structures by trial-and-error procedure. Several past works indicate that model parameters and structure can be dependent on the modelling time step, and there is thus some rationale in investigating how a model behaves across various modelling time steps, to find solutions for improvements. Here we analyse the impact of data time step on the consistency of the internal fluxes of a rainfall-runoff model run at various time steps, by using a large data set of 240 catchments. To this end, fine time step hydro-climatic information at sub-hourly resolution is used as input of a parsimonious rainfall-runoff model (GR) that is run at eight different model time steps (from 6 minutes to one day). The initial structure of the tested model (i.e. the baseline) corresponds to the daily model GR4J (Perrin et al., 2003), adapted to be run at variable sub-daily time steps. The modelled fluxes considered are interception, actual evapotranspiration and intercatchment groundwater flows. Observations of these fluxes are not available, but the comparison of modelled fluxes at multiple time steps gives additional information for model identification. The joint analysis of flow simulation performance and consistency of internal fluxes at different time steps provides guidance to the identification of the model components that should be improved. Our analysis indicates that the baseline model structure is to be modified at sub-daily time steps to warrant the consistency and realism of the modelled fluxes. For the baseline model improvement, particular attention is devoted to the interception model component, whose output flux showed the strongest sensitivity to modelling time step. The dependency of the optimal model

  8. Automatic Time Stepping with Global Error Control for Groundwater Flow Models

    SciTech Connect

    Tang, Guoping

    2008-09-01

    An automatic time stepping with global error control is proposed for the time integration of the diffusion equation to simulate groundwater flow in confined aquifers. The scheme is based on an a posteriori error estimate for the discontinuous Galerkin (dG) finite element methods. A stability factor is involved in the error estimate and it is used to adapt the time step and control the global temporal error for the backward difference method. The stability factor can be estimated by solving a dual problem. The stability factor is not sensitive to the accuracy of the dual solution and the overhead computational cost can be minimized by solving the dual problem using large time steps. Numerical experiments are conducted to show the application and the performance of the automatic time stepping scheme. Implementation of the scheme can lead to improvement in accuracy and efficiency for groundwater flow models.

  9. Entosis allows timely elimination of the luminal epithelial barrier for embryo implantation.

    PubMed

    Li, Yingju; Sun, Xiaofei; Dey, Sudhansu K

    2015-04-21

    During implantation, uterine luminal epithelial (LE) cells first interact with the blastocyst trophectoderm. Within 30 hr after the initiation of attachment, LE cells surrounding the blastocyst in the implantation chamber (crypt) disappear, allowing trophoblast cells to make direct physical contact with the underneath stroma for successful implantation. The mechanism for the extraction of LE cells was thought to be mediated by apoptosis. Here, we show that LE cells in direct contact with the blastocyst are endocytosed by trophoblast cells by adopting the nonapoptotic cell-in-cell invasion process (entosis) in the absence of caspase 3 activation. Our in vivo observations were reinforced by the results of co-culture experiments with primary uterine epithelial cells with trophoblast stem cells or blastocysts showing internalization of epithelial cells by trophoblasts. We have identified entosis as a mechanism to remove LE cells by trophoblast cells in implantation, conferring a role for entosis in an important physiological process. PMID:25865893

  10. Simple and versatile modifications allowing time gated spectral acquisition, imaging and lifetime profiling on conventional wide-field microscopes

    NASA Astrophysics Data System (ADS)

    Pal, Robert; Beeby, Andrew

    2014-09-01

    An inverted microscope has been adapted to allow time-gated imaging and spectroscopy to be carried out on samples containing responsive lanthanide probes. The adaptation employs readily available components, including a pulsed light source, time-gated camera, spectrometer and photon counting detector, allowing imaging, emission spectroscopy and lifetime measurements. Each component is controlled by a suite of software written in LabVIEW and is powered via conventional USB ports.

  11. Real-time quantum trajectories for classically allowed dynamics in strong laser fields

    NASA Astrophysics Data System (ADS)

    Plimak, L. I.; Ivanov, Misha Yu.

    2015-10-01

    Both the physical picture of the dynamics of atoms and molecules in intense infrared fields and its theoretical description use the concept of electron trajectories. Here, we address a key question which arises in this context: Are distinctly quantum features of these trajectories, such as the complex-valued coordinates, physically relevant in the classically allowed region of phase space, and what is their origin? First, we argue that solutions of classical equations of motion can account for quantum effects. To this end, we construct an exact solution to the classical Hamilton-Jacobi equation which accounts for dynamics of the wave packet, and show that this solution is physically correct in the limit ?. Second, we show that imaginary components of classical trajectories are directly linked to the finite size of the initial wave packet in momentum space. This way, if the electronic wave packet produced by optical tunnelling in strong infrared fields is localised both in coordinate and momentum, its motion after tunnelling ipso facto cannot be described with purely classical trajectories - in contrast to popular models in the literature.

  12. Robust discretizations versus increase of the time step for the Lorenz system

    NASA Astrophysics Data System (ADS)

    Letellier, Christophe; Mendes, Eduardo M. A. M.

    2005-03-01

    When continuous systems are discretized, their solutions depend on the time step chosen a priori. Such solutions are not necessarily spurious in the sense that they can still correspond to a solution of the differential equations but with a displacement in the parameter space. Consequently, it is of great interest to obtain discrete equations which are robust even when the discretization time step is large. In this paper, different discretizations of the Lorenz system are discussed versus the values of the discretization time step. It is shown that the sets of difference equations proposed are more robust versus increases of the time step than conventional discretizations built with standard schemes such as the forward Euler, backward Euler, or centered finite difference schemes. The nonstandard schemes used here are Mickens' scheme and Monaco and Normand-Cyrot's scheme.

  13. Time Gating of Chloroplast Autofluorescence Allows Clearer Fluorescence Imaging In Planta.

    PubMed

    Kodama, Yutaka

    2016-01-01

    Chloroplast, an organelle facilitating photosynthesis, exhibits strong autofluorescence, which is an undesired background signal that restricts imaging experiments with exogenous fluorophore in plants. In this study, the autofluorescence was characterized in planta under confocal laser microscopy, and it was found that the time-gated imaging technique completely eliminates the autofluorescence. As a demonstration of the technique, a clearer signal of fluorescent protein-tagged phototropin, a blue-light photoreceptor localized at the chloroplast periphery, was visualized in planta. PMID:27027881

  14. Time Gating of Chloroplast Autofluorescence Allows Clearer Fluorescence Imaging In Planta

    PubMed Central

    Kodama, Yutaka

    2016-01-01

    Chloroplast, an organelle facilitating photosynthesis, exhibits strong autofluorescence, which is an undesired background signal that restricts imaging experiments with exogenous fluorophore in plants. In this study, the autofluorescence was characterized in planta under confocal laser microscopy, and it was found that the time-gated imaging technique completely eliminates the autofluorescence. As a demonstration of the technique, a clearer signal of fluorescent protein-tagged phototropin, a blue-light photoreceptor localized at the chloroplast periphery, was visualized in planta. PMID:27027881

  15. Cherenkov Video Imaging Allows for the First Visualization of Radiation Therapy in Real Time

    SciTech Connect

    Jarvis, Lesley A.; Zhang, Rongxiao; Gladstone, David J.; Jiang, Shudong; Hitchcock, Whitney; Friedman, Oscar D.; Glaser, Adam K.; Jermyn, Michael; Pogue, Brian W.

    2014-07-01

    Purpose: To determine whether Cherenkov light imaging can visualize radiation therapy in real time during breast radiation therapy. Methods and Materials: An intensified charge-coupled device (CCD) camera was synchronized to the 3.25-μs radiation pulses of the clinical linear accelerator with the intensifier set × 100. Cherenkov images were acquired continuously (2.8 frames/s) during fractionated whole breast irradiation with each frame an accumulation of 100 radiation pulses (approximately 5 monitor units). Results: The first patient images ever created are used to illustrate that Cherenkov emission can be visualized as a video during conditions typical for breast radiation therapy, even with complex treatment plans, mixed energies, and modulated treatment fields. Images were generated correlating to the superficial dose received by the patient and potentially the location of the resulting skin reactions. Major blood vessels are visible in the image, providing the potential to use these as biological landmarks for improved geometric accuracy. The potential for this system to detect radiation therapy misadministrations, which can result from hardware malfunction or patient positioning setup errors during individual fractions, is shown. Conclusions: Cherenkoscopy is a unique method for visualizing surface dose resulting in real-time quality control. We propose that this system could detect radiation therapy errors in everyday clinical practice at a time when these errors can be corrected to result in improved safety and quality of radiation therapy.

  16. An Adaptive Fourier Filter for Relaxing Time Stepping Constraints for Explicit Solvers

    SciTech Connect

    Gelb, Anne; Archibald, Richard K

    2015-01-01

    Filtering is necessary to stabilize piecewise smooth solutions. The resulting diffusion stabilizes the method, but may fail to resolve the solution near discontinuities. Moreover, high order filtering still requires cost prohibitive time stepping. This paper introduces an adaptive filter that controls spurious modes of the solution, but is not unnecessarily diffusive. Consequently we are able to stabilize the solution with larger time steps, but also take advantage of the accuracy of a high order filter.

  17. Numerical time-step restrictions as a result of capillary waves

    NASA Astrophysics Data System (ADS)

    Denner, Fabian; van Wachem, Berend G. M.

    2015-03-01

    The propagation of capillary waves on material interfaces between two fluids imposes a strict constraint on the numerical time-step applied to solve the equations governing this problem and is directly associated with the stability of interfacial flow simulations. The explicit implementation of surface tension is the generally accepted reason for the restrictions on the temporal resolution caused by capillary waves. In this article, a fully-coupled numerical framework with an implicit treatment of surface tension is proposed and applied, demonstrating that the capillary time-step constraint is in fact a constraint imposed by the temporal sampling of capillary waves, irrespective of the type of implementation. The presented results show that the capillary time-step constraint can be exceeded by several orders of magnitude, with the explicit as well as the implicit treatment of surface tension, if capillary waves are absent. Furthermore, a revised capillary time-step constraint is derived by studying the temporal resolution of capillary waves based on numerical stability and signal processing theory, including the Doppler shift caused by an underlying fluid motion. The revised capillary time-step constraint assures a robust, aliasing-free result, as demonstrated by representative numerical experiments, and is in the static case less restrictive than previously proposed time-step limits associated with capillary waves.

  18. Database Integration: An Intial Step Towards the Deep-Time Data Infrastructure

    NASA Astrophysics Data System (ADS)

    Kolankowski, S. M.; Fox, P. A.; Ma, X.

    2015-12-01

    As our knowledge of Earth's geologic history grows, we require more robust methods of sharing immense amounts of data. Various databases across numerous disciplines have been widely utilized to offer extensive information on very specific pieces of both Earth's history and its current state, ie. fossil record, rock composition, proteins, etc. In order to gain a deeper understanding of our planet's past we must combine the resources present in our online communities. These databases could be a powerful force in identifying previously unseen correlations if used in tandem rather than as separate entities. Creating a unifying site that provides links to these databases will aid in our ability as a collaborative scientific community to utilize our findings on a larger scale. The Deep-Time Data Infrastructure is currently underway as part of a larger effort to accomplish this goal. DTDI works not to build a new database, but to integrate existing resources. This research is the beginning step in the DTDI program. To create this infrastructure, all current geologic and related databases had to be identified and their schema recorded. Using variables from their combined records, we are able to determine the best way to integrate them using common factors. The Deep-Time Data Infrastructure will allow geoscientists to bridge gaps in data and further our understanding of our planet's history.

  19. Modeling solute transport in distribution networks with variable demand and time step sizes.

    SciTech Connect

    Peyton, Chad E.; Bilisoly, Roger Lee; Buchberger, Steven G.; McKenna, Sean Andrew; Yarrington, Lane

    2004-06-01

    The effect of variable demands at short time scales on the transport of a solute through a water distribution network has not previously been studied. We simulate flow and transport in a small water distribution network using EPANET to explore the effect of variable demand on solute transport across a range of hydraulic time step scales from 1 minute to 2 hours. We show that variable demands at short time scales can have the following effects: smoothing of a pulse of tracer injected into a distribution network and increasing the variability of both the transport pathway and transport timing through the network. Variable demands are simulated for these different time step sizes using a previously developed Poisson rectangular pulse (PRP) demand generator that considers demand at a node to be a combination of exponentially distributed arrival times with log-normally distributed intensities and durations. Solute is introduced at a tank and at three different network nodes and concentrations are modeled through the system using the Lagrangian transport scheme within EPANET. The transport equations within EPANET assume perfect mixing of the solute within a parcel of water and therefore physical dispersion cannot occur. However, variation in demands along the solute transport path contribute to both removal and distortion of the injected pulse. The model performance measures examined are the distribution of the Reynolds number, the variation in the center of mass of the solute across time, and the transport path and timing of the solute through the network. Variation in all three performance measures is greatest at the shortest time step sizes. As the scale of the time step increases, the variability in these performance measures decreases. The largest time steps produce results that are inconsistent with the results produced by the smaller time steps.

  20. Overcoming the Barrier on Time Step Size in Multiscale Molecular Dynamics Simulation of Molecular Liquids.

    PubMed

    Omelyan, Igor P; Kovalenko, Andriy

    2012-01-10

    We propose and validate a new multiscale technique, the extrapolative isokinetic Nóse-Hoover chain orientational (EINO) motion multiple time step algorithm for rigid interaction site models of molecular liquids. It nontrivially combines the multiple time step decomposition operator method with a specific extrapolation of intermolecular interactions, complemented by an extended isokinetic Nosé-Hoover chain approach in the presence of translational and orientational degrees of freedom. The EINO algorithm obviates the limitations on time step size in molecular dynamics simulations. While the best existing multistep algorithms can advance from a 5 fs single step to a maximum 100 fs outer step, we show on the basis of molecular dynamics simulations of the TIP4P water that our EINO technique overcomes this barrier. Specifically, we have achieved giant time steps on the order of 500 fs up to 5 ps, which now become available in the study of equilibrium and conformational properties of molecular liquids without a loss of stability and accuracy.

  1. The energy expenditure of stair climbing one step and two steps at a time: estimations from measures of heart rate.

    PubMed

    Halsey, Lewis G; Watkins, David A R; Duggan, Brendan M

    2012-01-01

    Stairway climbing provides a ubiquitous and inconspicuous method of burning calories. While typically two strategies are employed for climbing stairs, climbing one stair step per stride or two steps per stride, research to date has not clarified if there are any differences in energy expenditure between them. Fourteen participants took part in two stair climbing trials whereby measures of heart rate were used to estimate energy expenditure during stairway ascent at speeds chosen by the participants. The relationship between rate of oxygen consumption ([Formula: see text]) and heart rate was calibrated for each participant using an inclined treadmill. The trials involved climbing up and down a 14.05 m high stairway, either ascending one step per stride or ascending two stair steps per stride. Single-step climbing used 8.5±0.1 kcal min(-1), whereas double step climbing used 9.2±0.1 kcal min(-1). These estimations are similar to equivalent measures in all previous studies, which have all directly measured [Formula: see text] The present study findings indicate that (1) treadmill-calibrated heart rate recordings can be used as a valid alternative to respirometry to ascertain rate of energy expenditure during stair climbing; (2) two step climbing invokes a higher rate of energy expenditure; however, one step climbing is energetically more expensive in total over the entirety of a stairway. Therefore to expend the maximum number of calories when climbing a set of stairs the single-step strategy is better. PMID:23251455

  2. Role of step size and max dwell time in anatomy based inverse optimization for prostate implants.

    PubMed

    Manikandan, Arjunan; Sarkar, Biplab; Rajendran, Vivek Thirupathur; King, Paul R; Sresty, N V Madhusudhana; Holla, Ragavendra; Kotur, Sachin; Nadendla, Sujatha

    2013-07-01

    In high dose rate (HDR) brachytherapy, the source dwell times and dwell positions are vital parameters in achieving a desirable implant dose distribution. Inverse treatment planning requires an optimal choice of these parameters to achieve the desired target coverage with the lowest achievable dose to the organs at risk (OAR). This study was designed to evaluate the optimum source step size and maximum source dwell time for prostate brachytherapy implants using an Ir-192 source. In total, one hundred inverse treatment plans were generated for the four patients included in this study. Twenty-five treatment plans were created for each patient by varying the step size and maximum source dwell time during anatomy-based, inverse-planned optimization. Other relevant treatment planning parameters were kept constant, including the dose constraints and source dwell positions. Each plan was evaluated for target coverage, urethral and rectal dose sparing, treatment time, relative target dose homogeneity, and nonuniformity ratio. The plans with 0.5 cm step size were seen to have clinically acceptable tumor coverage, minimal normal structure doses, and minimum treatment time as compared with the other step sizes. The target coverage for this step size is 87% of the prescription dose, while the urethral and maximum rectal doses were 107.3 and 68.7%, respectively. No appreciable difference in plan quality was observed with variation in maximum source dwell time. The step size plays a significant role in plan optimization for prostate implants. Our study supports use of a 0.5 cm step size for prostate implants.

  3. A three dimensional multigrid multiblock multistage time stepping scheme for the Navier-Stokes equations

    NASA Technical Reports Server (NTRS)

    Elmiligui, Alaa; Cannizzaro, Frank; Melson, N. D.

    1991-01-01

    A general multiblock method for the solution of the three-dimensional, unsteady, compressible, thin-layer Navier-Stokes equations has been developed. The convective and pressure terms are spatially discretized using Roe's flux differencing technique while the viscous terms are centrally differenced. An explicit Runge-Kutta method is used to advance the solution in time. Local time stepping, adaptive implicit residual smoothing, and the Full Approximation Storage (FAS) multigrid scheme are added to the explicit time stepping scheme to accelerate convergence to steady state. Results for three-dimensional test cases are presented and discussed.

  4. Thermal fatigue: The impact of the length of time step on the amount of stress cycles

    NASA Astrophysics Data System (ADS)

    Beran, Pavel

    2013-10-01

    One of the degradation processes in stones and other building materials is caused by cyclic thermal stress. For the determination of the amount and amplitude of the thermal stress cycles may be used numerical simulation. The length of time step during simulation of thermal cycles significantly affected the magnitude and the amount of cycles because the intensity of global solar radiation may vary during the time. The dependence of temperature and stress response of the damaged stone block on the length of time step is described in this paper.

  5. Efficient multiple time step method for use with Ewald and particle mesh Ewald for large biomolecular systems

    NASA Astrophysics Data System (ADS)

    Zhou, Ruhong; Harder, Edward; Xu, Huafeng; Berne, B. J.

    2001-08-01

    The particle-particle particle-mesh (P3M) method for calculating long-range electrostatic forces in molecular simulations is modified and combined with the reversible reference system propagator algorithm (RESPA) for treating the multiple time scale problems in the molecular dynamics of complex systems with multiple time scales and long-range forces. The resulting particle-particle particle-mesh Ewald RESPA (P3ME/RESPA) method provides a fast and accurate representation of the long-range electrostatic interactions for biomolecular systems such as protein solutions. The method presented here uses a different breakup of the electrostatic forces than was used by other authors when they combined the Particle Mesh Ewald method with RESPA. The usual breakup is inefficient because it treats the reciprocal space forces in an outer loop even though they contain a part that changes rapidly in time. This does not allow use of a large time step for the outer loop. Here, we capture the short-range contributions in the reciprocal space forces and include them in the inner loop, thereby allowing for larger outer loop time steps and thus for a much more efficient RESPA implementation. The new approach has been applied to both regular Ewald and P3ME. The timings of Ewald/RESPA and P3ME/RESPA are compared in detail with the previous approach for protein water solutions as a function of number of atoms in the system, and significant speedups are reported.

  6. Time Step Rescaling Recovers Continuous-Time Dynamical Properties for Discrete-Time Langevin Integration of Nonequilibrium Systems

    PubMed Central

    2015-01-01

    When simulating molecular systems using deterministic equations of motion (e.g., Newtonian dynamics), such equations are generally numerically integrated according to a well-developed set of algorithms that share commonly agreed-upon desirable properties. However, for stochastic equations of motion (e.g., Langevin dynamics), there is still broad disagreement over which integration algorithms are most appropriate. While multiple desiderata have been proposed throughout the literature, consensus on which criteria are important is absent, and no published integration scheme satisfies all desiderata simultaneously. Additional nontrivial complications stem from simulating systems driven out of equilibrium using existing stochastic integration schemes in conjunction with recently developed nonequilibrium fluctuation theorems. Here, we examine a family of discrete time integration schemes for Langevin dynamics, assessing how each member satisfies a variety of desiderata that have been enumerated in prior efforts to construct suitable Langevin integrators. We show that the incorporation of a novel time step rescaling in the deterministic updates of position and velocity can correct a number of dynamical defects in these integrators. Finally, we identify a particular splitting (related to the velocity Verlet discretization) that has essentially universally appropriate properties for the simulation of Langevin dynamics for molecular systems in equilibrium, nonequilibrium, and path sampling contexts. PMID:24555448

  7. Multi time-step wavefront reconstruction for tomographic adaptive-optics systems.

    PubMed

    Ono, Yoshito H; Akiyama, Masayuki; Oya, Shin; Lardiére, Olivier; Andersen, David R; Correia, Carlos; Jackson, Kate; Bradley, Colin

    2016-04-01

    In tomographic adaptive-optics (AO) systems, errors due to tomographic wavefront reconstruction limit the performance and angular size of the scientific field of view (FoV), where AO correction is effective. We propose a multi time-step tomographic wavefront reconstruction method to reduce the tomographic error by using measurements from both the current and previous time steps simultaneously. We further outline the method to feed the reconstructor with both wind speed and direction of each turbulence layer. An end-to-end numerical simulation, assuming a multi-object AO (MOAO) system on a 30 m aperture telescope, shows that the multi time-step reconstruction increases the Strehl ratio (SR) over a scientific FoV of 10 arc min in diameter by a factor of 1.5-1.8 when compared to the classical tomographic reconstructor, depending on the guide star asterism and with perfect knowledge of wind speeds and directions. We also evaluate the multi time-step reconstruction method and the wind estimation method on the RAVEN demonstrator under laboratory setting conditions. The wind speeds and directions at multiple atmospheric layers are measured successfully in the laboratory experiment by our wind estimation method with errors below 2  ms-1. With these wind estimates, the multi time-step reconstructor increases the SR value by a factor of 1.2-1.5, which is consistent with a prediction from the end-to-end numerical simulation. PMID:27140785

  8. Time-step limits for a Monte Carlo Compton-scattering method

    SciTech Connect

    Densmore, Jeffery D; Warsa, James S; Lowrie, Robert B

    2008-01-01

    Compton scattering is an important aspect of radiative transfer in high energy density applications. In this process, the frequency and direction of a photon are altered by colliding with a free electron. The change in frequency of a scattered photon results in an energy exchange between the photon and target electron and energy coupling between radiation and matter. Canfield, Howard, and Liang have presented a Monte Carlo method for simulating Compton scattering that models the photon-electron collision kinematics exactly. However, implementing their technique in multiphysics problems that include the effects of radiation-matter energy coupling typically requires evaluating the material temperature at its beginning-of-time-step value. This explicit evaluation can lead to unstable and oscillatory solutions. In this paper, we perform a stability analysis of this Monte Carlo method and present time-step limits that avoid instabilities and nonphysical oscillations by considering a spatially independent, purely scattering radiative-transfer problem. Examining a simplified problem is justified because it isolates the effects of Compton scattering, and existing Monte Carlo techniques can robustly model other physics (such as absorption, emission, sources, and photon streaming). Our analysis begins by simplifying the equations that are solved via Monte Carlo within each time step using the Fokker-Planck approximation. Next, we linearize these approximate equations about an equilibrium solution such that the resulting linearized equations describe perturbations about this equilibrium. We then solve these linearized equations over a time step and determine the corresponding eigenvalues, quantities that can predict the behavior of solutions generated by a Monte Carlo simulation as a function of time-step size and other physical parameters. With these results, we develop our time-step limits. This approach is similar to our recent investigation of time discretizations for the

  9. Exponential time-differencing with embedded Runge–Kutta adaptive step control

    SciTech Connect

    Whalen, P.; Brio, M.; Moloney, J.V.

    2015-01-01

    We have presented the first embedded Runge–Kutta exponential time-differencing (RKETD) methods of fourth order with third order embedding and fifth order with third order embedding for non-Rosenbrock type nonlinear systems. A procedure for constructing RKETD methods that accounts for both order conditions and stability is outlined. In our stability analysis, the fast time scale is represented by a full linear operator in contrast to particular scalar cases considered before. An effective time-stepping strategy based on reducing both ETD function evaluations and rejected steps is described. Comparisons of performance with adaptive-stepping integrating factor (IF) are carried out on a set of canonical partial differential equations: the shock-fronts of Burgers equation, interacting KdV solitons, KS controlled chaos, and critical collapse of two-dimensional NLS.

  10. Boosting the accuracy and speed of quantum Monte Carlo: Size consistency and time step

    NASA Astrophysics Data System (ADS)

    Zen, Andrea; Sorella, Sandro; Gillan, Michael J.; Michaelides, Angelos; Alfè, Dario

    2016-06-01

    Diffusion Monte Carlo (DMC) simulations for fermions are becoming the standard for providing high-quality reference data in systems that are too large to be investigated via quantum chemical approaches. DMC with the fixed-node approximation relies on modifications of the Green's function to avoid singularities near the nodal surface of the trial wave function. Here we show that these modifications affect the DMC energies in a way that is not size consistent, resulting in large time-step errors. Building on the modifications of Umrigar et al. and DePasquale et al. we propose a simple Green's function modification that restores size consistency to large values of the time step, which substantially reduces time-step errors. This algorithm also yields remarkable speedups of up to two orders of magnitude in the calculation of molecule-molecule binding energies and crystal cohesive energies, thus extending the horizons of what is possible with DMC.

  11. Effects of Academic Ability, Time Allowed for Study, and Teacher Directedness on Achievement in a High School Science Course (ISIS).

    ERIC Educational Resources Information Center

    Burkman, Ernest; And Others

    1981-01-01

    The simultaneous effects of two instructional variables of degree of teacher direction (student- versus teacher-directed) and time allowed for study and the student variable of general ability are described for student achievement (N=912) in three life-science instructional modules. (Author)

  12. Piloted simulator study of allowable time delay in pitch flight control system of a transport airplane with negative static stability

    NASA Technical Reports Server (NTRS)

    Grantham, William D.; Smith, Paul M.; Person, Lee H., Jr.; Meyer, Robert T.; Tingas, Stephen A.

    1987-01-01

    A piloted simulation study was conducted to determine the permissible time delay in the flight control system of a 10-percent statically unstable transport airplane during cruise flight conditions. The math model used for the simulation was a derivative Lockheed L-1011 wide-body jet transport. Data were collected and analyzed from a total of 137 cruising flights in both calm- and turbulent-air conditions. Results of this piloted simulation study verify previous findings that show present military specifications for allowable control-system time delay may be too stringent when applied to transport-size airplanes. Also, the degree of handling-qualities degradation due to time delay is shown to be strongly dependent on the source of the time delay in an advanced flight control system. Maximum allowable time delay for each source of time delay in the control system, in addition to a less stringent overall maximum level of time delay, should be considered for large aircraft. Preliminary results also suggest that adverse effects of control-system time delay may be at least partially offset by variations in control gearing. It is recommended that the data base include different airplane baselines, control systems, and piloting tasks with many pilots participating, so that a reasonable set of limits for control-system time delay can be established to replace the military specification limits currently being used.

  13. Steps and Time to Process Clinical Trials at the Cancer Therapy Evaluation Program

    PubMed Central

    Dilts, David M.; Sandler, Alan B.; Cheng, Steven K.; Crites, Joshua S.; Ferranti, Lori B.; Wu, Amy Y.; Finnigan, Shanda; Friedman, Steven; Mooney, Margaret; Abrams, Jeffrey

    2009-01-01

    Purpose To examine the processes and document the calendar time required for the National Cancer Institute's Cancer Therapy Evaluation Program (CTEP) and Central Institutional Review Board (CIRB) to evaluate and approve phase III clinical trials. Methods Process steps were documented by (1) interviewing CTEP and CIRB staff regarding the steps required to activate a trial from initial concept submission to trial activation by a cooperative group, (2) reviewing standard operating procedures, and (3) inspecting trial records and documents for selected trials to identify any additional steps. Calendar time was collected from initial concept submission to activation using retrospective data from the CTEP Protocol and Information Office. Results At least 296 distinct processes are required for phase III trial activation: at least 239 working steps, 52 major decision points, 20 processing loops, and 11 stopping points. Of the 195 trials activated during the January 1, 2000, to December 31, 2007, study period, a sample of 167 (85.6%) was used for gathering timing data. Median calendar days from initial formal concept submission to CTEP to trial activation by a cooperative group was 602 days (interquartile range, 454 to 861 days). This time has not significantly changed over the past 8 years. There is a high variation in the time required to activate a clinical trial. Conclusion Because of their complexity, the overall development time for phase III clinical trials is lengthy, process laden, and highly variable. To streamline the process, a solution must be sought that includes all parties involved in developing trials. PMID:19255315

  14. Time-step Considerations in Particle Simulation Algorithms for Coulomb Collisions in Plasmas

    SciTech Connect

    Cohen, B I; Dimits, A; Friedman, A; Caflisch, R

    2009-10-29

    The accuracy of first-order Euler and higher-order time-integration algorithms for grid-based Langevin equations collision models in a specific relaxation test problem is assessed. We show that statistical noise errors can overshadow time-step errors and argue that statistical noise errors can be conflated with time-step effects. Using a higher-order integration scheme may not achieve any benefit in accuracy for examples of practical interest. We also investigate the collisional relaxation of an initial electron-ion relative drift and the collisional relaxation to a resistive steady-state in which a quasi-steady current is driven by a constant applied electric field, as functions of the time step used to resolve the collision processes using binary and grid-based, test-particle Langevin equations models. We compare results from two grid-based Langevin equations collision algorithms to results from a binary collision algorithm for modeling electronion collisions. Some guidance is provided regarding how large a time step can be used compared to the inverse of the characteristic collision frequency for specific relaxation processes.

  15. A step in time: Changes in standard-frequency and time-signal broadcasts, 1 January 1972

    NASA Technical Reports Server (NTRS)

    Chi, A. R.; Fosque, H. S.

    1973-01-01

    An improved coordinated universal time (UTC) system has been adopted by the International Radio Consultative Committee. It was implemented internationally by the standard-frequency and time-broadcast stations on 1 Jan. 1972. The new UTC system eliminates the frequency offset of 300 parts in 10 to the 10th power between the old UTC and atomic time, thus making the broadcast time interval (the UTC second) constant and defined by the resonant frequency of cesium atoms. The new time scale is kept in synchronism with the rotation of the Earth within plus or minus 0.7 s by step-time adjustments of exactly 1 s, when needed. A time code has been added to the disseminated time signals to permit universal time to be obtained from the broadcasts to the nearest 0.1 s for users requiring such precision. The texts of the International Radio Consultative Committee recommendation and report to implement the new UTC system are given. The coding formats used by various standard time broadcast services to transmit the difference between the universal time (UT1) and the UTC are also given. For users' convenience, worldwide primary VLF and HF transmissions stations, frequencies, and schedules of time emissions are also included. Actual time-step adjustments made by various stations on 1 Jan. 1972, are provided for future reference.

  16. The large discretization step method for time-dependent partial differential equations

    NASA Technical Reports Server (NTRS)

    Haras, Zigo; Taasan, Shlomo

    1995-01-01

    A new method for the acceleration of linear and nonlinear time dependent calculations is presented. It is based on the Large Discretization Step (LDS) approximation, defined in this work, which employs an extended system of low accuracy schemes to approximate a high accuracy discrete approximation to a time dependent differential operator. Error bounds on such approximations are derived. These approximations are efficiently implemented in the LDS methods for linear and nonlinear hyperbolic equations, presented here. In these algorithms the high and low accuracy schemes are interpreted as the same discretization of a time dependent operator on fine and coarse grids, respectively. Thus, a system of correction terms and corresponding equations are derived and solved on the coarse grid to yield the fine grid accuracy. These terms are initialized by visiting the fine grid once in many coarse grid time steps. The resulting methods are very general, simple to implement and may be used to accelerate many existing time marching schemes.

  17. Double loop control strategy with different time steps based on human characteristics.

    PubMed

    Gu, Gwang Min; Lee, Jinoh; Kim, Jung

    2012-01-01

    This paper proposes a cooperative control strategy in consideration of the force sensitivity of human. The strategy consists of two loops: one is the intention estimation loop whose sampling time can be variable in order to investigate the effect of the sampling time; the other is the position control loop with fixed time step. A high sampling rate is not necessary for the intention estimation loop due to the bandwidth of the mechanoreceptors in humans. In addition, the force sensor implemented in the robot is sensitive to the noise induced from the sensor itself and tremor of the human. Multiple experiments were performed with the experimental protocol using various time steps of the intention estimation loop to find the suitable sampling times in physical human robot interaction. The task involves pull-and-push movement with a two-degree-of-freedom robot, and the norm of the interaction force was obtained for each experiment as the measure of the cooperative control performance.

  18. Simulating diffusion processes in discontinuous media: A numerical scheme with constant time steps

    SciTech Connect

    Lejay, Antoine; Pichot, Geraldine

    2012-08-30

    In this article, we propose new Monte Carlo techniques for moving a diffusive particle in a discontinuous media. In this framework, we characterize the stochastic process that governs the positions of the particle. The key tool is the reduction of the process to a Skew Brownian motion (SBM). In a zone where the coefficients are locally constant on each side of the discontinuity, the new position of the particle after a constant time step is sampled from the exact distribution of the SBM process at the considered time. To do so, we propose two different but equivalent algorithms: a two-steps simulation with a stop at the discontinuity and a one-step direct simulation of the SBM dynamic. Some benchmark tests illustrate their effectiveness.

  19. Displacement in the parameter space versus spurious solution of discretization with large time step

    NASA Astrophysics Data System (ADS)

    Mendes, Eduardo; Letellier, Christophe

    2004-01-01

    In order to investigate a possible correspondence between differential and difference equations, it is important to possess discretization of ordinary differential equations. It is well known that when differential equations are discretized, the solution thus obtained depends on the time step used. In the majority of cases, such a solution is considered spurious when it does not resemble the expected solution of the differential equation. This often happens when the time step taken into consideration is too large. In this work, we show that, even for quite large time steps, some solutions which do not correspond to the expected ones are still topologically equivalent to solutions of the original continuous system if a displacement in the parameter space is considered. To reduce such a displacement, a judicious choice of the discretization scheme should be made. To this end, a recent discretization scheme, based on the Lie expansion of the original differential equations, proposed by Monaco and Normand-Cyrot will be analysed. Such a scheme will be shown to be sufficient for providing an adequate discretization for quite large time steps compared to the pseudo-period of the underlying dynamics.

  20. Making Progress in Mental Health Policy in Conservative Times: One Step at a Time

    PubMed Central

    Goldman, Howard H.

    2006-01-01

    Progress in mental health services has been made incrementally in a sequence of policy steps. In recent years, in spite of political conservatism, progressive changes have advanced new principles of service delivery. Reports from the surgeon general and the President's New Freedom Commission on Mental Health advanced these principles, including recovery and evidence-based practices. Both of these high-level reports were influenced by the findings of the Schizophrenia Patient Outcomes Research Team (PORT). The Schizophrenia PORT established the effectiveness of mental health treatments and supports, which provided a scientific foundation for the optimistic focus on recovery and its expectation of improved outcomes for individuals with severe mental disorders. The PORT study also established the gap between treatment recommendations and actual services. Concern about this gap has motivated efforts to transform services by implementing evidence-based practices. Advances in broad mental health and social policy, coupled with continued advances in science, have the potential to improve the care of individuals who experience severe mental disorders, such as schizophrenia. PMID:16436626

  1. Time-stepping stability of continuous and discontinuous finite-element methods for 3-D wave propagation

    NASA Astrophysics Data System (ADS)

    Mulder, W. A.; Zhebel, E.; Minisini, S.

    2014-02-01

    We analyse the time-stepping stability for the 3-D acoustic wave equation, discretized on tetrahedral meshes. Two types of methods are considered: mass-lumped continuous finite elements and the symmetric interior-penalty discontinuous Galerkin method. Combining the spatial discretization with the leap-frog time-stepping scheme, which is second-order accurate and conditionally stable, leads to a fully explicit scheme. We provide estimates of its stability limit for simple cases, namely, the reference element with Neumann boundary conditions, its distorted version of arbitrary shape, the unit cube that can be partitioned into six tetrahedra with periodic boundary conditions and its distortions. The Courant-Friedrichs-Lewy stability limit contains an element diameter for which we considered different options. The one based on the sum of the eigenvalues of the spatial operator for the first-degree mass-lumped element gives the best results. It resembles the diameter of the inscribed sphere but is slightly easier to compute. The stability estimates show that the mass-lumped continuous and the discontinuous Galerkin finite elements of degree 2 have comparable stability conditions, whereas the mass-lumped elements of degree one and three allow for larger time steps.

  2. A Multiple Time Stepping Algorithm for Efficient Multiscale Modeling of Platelets Flowing in Blood Plasma

    PubMed Central

    Zhang, Peng; Zhang, Na; Deng, Yuefan; Bluestein, Danny

    2015-01-01

    We developed a multiple time-stepping (MTS) algorithm for multiscale modeling of the dynamics of platelets flowing in viscous blood plasma. This MTS algorithm improves considerably the computational efficiency without significant loss of accuracy. This study of the dynamic properties of flowing platelets employs a combination of the dissipative particle dynamics (DPD) and the coarse-grained molecular dynamics (CGMD) methods to describe the dynamic microstructures of deformable platelets in response to extracellular flow-induced stresses. The disparate spatial scales between the two methods are handled by a hybrid force field interface. However, the disparity in temporal scales between the DPD and CGMD that requires time stepping at microseconds and nanoseconds respectively, represents a computational challenge that may become prohibitive. Classical MTS algorithms manage to improve computing efficiency by multi-stepping within DPD or CGMD for up to one order of magnitude of scale differential. In order to handle 3–4 orders of magnitude disparity in the temporal scales between DPD and CGMD, we introduce a new MTS scheme hybridizing DPD and CGMD by utilizing four different time stepping sizes. We advance the fluid system at the largest time step, the fluid-platelet interface at a middle timestep size, and the nonbonded and bonded potentials of the platelet structural system at two smallest timestep sizes. Additionally, we introduce parameters to study the relationship of accuracy versus computational complexities. The numerical experiments demonstrated 3000x reduction in computing time over standard MTS methods for solving the multiscale model. This MTS algorithm establishes a computationally feasible approach for solving a particle-based system at multiple scales for performing efficient multiscale simulations. PMID:25641983

  3. An implicit time-stepping scheme for rigid body dynamics with Coulomb friction

    SciTech Connect

    STEWART,DAVID; TRINKLE,JEFFREY C.

    2000-02-15

    In this paper a new time-stepping method for simulating systems of rigid bodies is given. Unlike methods which take an instantaneous point of view, the method is based on impulse-momentum equations, and so does not need to explicitly resolve impulsive forces. On the other hand, the method is distinct from previous impulsive methods in that it does not require explicit collision checking and it can handle simultaneous impacts. Numerical results are given for one planar and one three-dimensional example, which demonstrate the practicality of the method, and its convergence as the step size becomes small.

  4. Dual-Time Stepping Method for Solar Wind Model in Spherical Coordinates

    NASA Astrophysics Data System (ADS)

    Feng, X. S.

    2014-12-01

    In this paper, an implicit dual-time stepping scheme based on the finite volume method in spherical coordinates with a six-component grid system is developed to model the steady state solar wind ambient. The base numerical scheme is established by splitting the magnetohydrodynamics equations into a fluid part and a magnetic part, and a finite volume method is used for the fluid part and the constrained-transport method that can maintain the divergence-free constraint on the magnetic field is used for the magnetic induction part. By adding a pseudo-time derivative to the magnetohydrodynamics equations for solar wind plasma, the governing equations are solved implicitly at each physical time step by advancing in pseudo time. As validation, solar wind ambient for Carrington rotations for CR 1915 (solar minimum), CR 1930 (rising phase), CR 1965 (solar maximum) and CR 2030 (declining phase) have been studied. Numerical tests with different Courant factors show its capability of producing structured solar wind, and that the physical time step can be enlarged to be one hundred times that of the original one. Of importance, our numerical results have demonstrated overall good agreements with observations.

  5. Stance time variability during stair stepping before and after total knee arthroplasty: A pilot study.

    PubMed

    Smith, Jessica W; Marcus, Robin L; Tracy, Brian L; Foreman, K Bo; Christensen, Jesse C; LaStayo, Paul C

    2016-02-01

    The main objectives of this pilot study were to: (1) investigate stance time variability (STV) during stair stepping in older adults with osteoarthritis (OA) before and after total knee arthroplasty (TKA), and compare to an age- and sex-matched group of healthy controls with native knees and (2) evaluate the relationship between quadriceps strength and STV during stair stepping before and after TKA. A prospective, observational, pilot study was carried out on 13 individuals (15% male, mean age 62.71±6.84years) before and after TKA using an instrumented stairway, patient-reported outcomes, timed stair stepping test, and quadriceps strength measures. At 6-months post-operatively, STV during stair descent was significantly greater in the TKA-GROUP compared to the CONTROL-GROUP, but was not significantly different at 12-months compared to controls. There were no significant differences in STV for stair ascent between the pre- and post-operative visits, or compared to controls. There was a trend toward significance for the relationship between quadriceps strength and STV during stair ascent (P=0.059) and descent (P=0.073). Variability during stair stepping may provide an important, short-term rehabilitation target for individuals following TKA and may represent another parameter to predict declines in functional mobility.

  6. High-Order Implicit-Explicit Multi-Block Time-stepping Method for Hyperbolic PDEs

    NASA Technical Reports Server (NTRS)

    Nielsen, Tanner B.; Carpenter, Mark H.; Fisher, Travis C.; Frankel, Steven H.

    2014-01-01

    This work seeks to explore and improve the current time-stepping schemes used in computational fluid dynamics (CFD) in order to reduce overall computational time. A high-order scheme has been developed using a combination of implicit and explicit (IMEX) time-stepping Runge-Kutta (RK) schemes which increases numerical stability with respect to the time step size, resulting in decreased computational time. The IMEX scheme alone does not yield the desired increase in numerical stability, but when used in conjunction with an overlapping partitioned (multi-block) domain significant increase in stability is observed. To show this, the Overlapping-Partition IMEX (OP IMEX) scheme is applied to both one-dimensional (1D) and two-dimensional (2D) problems, the nonlinear viscous Burger's equation and 2D advection equation, respectively. The method uses two different summation by parts (SBP) derivative approximations, second-order and fourth-order accurate. The Dirichlet boundary conditions are imposed using the Simultaneous Approximation Term (SAT) penalty method. The 6-stage additive Runge-Kutta IMEX time integration schemes are fourth-order accurate in time. An increase in numerical stability 65 times greater than the fully explicit scheme is demonstrated to be achievable with the OP IMEX method applied to 1D Burger's equation. Results from the 2D, purely convective, advection equation show stability increases on the order of 10 times the explicit scheme using the OP IMEX method. Also, the domain partitioning method in this work shows potential for breaking the computational domain into manageable sizes such that implicit solutions for full three-dimensional CFD simulations can be computed using direct solving methods rather than the standard iterative methods currently used.

  7. On large time step TVD scheme for hyperbolic conservation laws and its efficiency evaluation

    NASA Astrophysics Data System (ADS)

    Qian, ZhanSen; Lee, Chun-Hian

    2012-08-01

    A large time step (LTS) TVD scheme originally proposed by Harten is modified and further developed in the present paper and applied to Euler equations in multidimensional problems. By firstly revealing the drawbacks of Harten's original LTS TVD scheme, and reasoning the occurrence of the spurious oscillations, a modified formulation of its characteristic transformation is proposed and a high resolution, strongly robust LTS TVD scheme is formulated. The modified scheme is proven to be capable of taking larger number of time steps than the original one. Following the modified strategy, the LTS TVD schemes for Yee's upwind TVD scheme and Yee-Roe-Davis's symmetric TVD scheme are constructed. The family of the LTS schemes is then extended to multidimensional by time splitting procedure, and the associated boundary condition treatment suitable for the LTS scheme is also imposed. The numerical experiments on Sod's shock tube problem, inviscid flows over NACA0012 airfoil and ONERA M6 wing are performed to validate the developed schemes. Computational efficiencies for the respective schemes under different CFL numbers are also evaluated and compared. The results reveal that the improvement is sizable as compared to the respective single time step schemes, especially for the CFL number ranging from 1.0 to 4.0.

  8. Daily Time Step Refinement of Optimized Flood Control Rule Curves for a Global Warming Scenario

    NASA Astrophysics Data System (ADS)

    Lee, S.; Fitzgerald, C.; Hamlet, A. F.; Burges, S. J.

    2009-12-01

    Pacific Northwest temperatures have warmed by 0.8 °C since 1920 and are predicted to further increase in the 21st century. Simulated streamflow timing shifts associated with climate change have been found in past research to degrade water resources system performance in the Columbia River Basin when using existing system operating policies. To adapt to these hydrologic changes, optimized flood control operating rule curves were developed in a previous study using a hybrid optimization-simulation approach which rebalanced flood control and reservoir refill at a monthly time step. For the climate change scenario, use of the optimized flood control curves restored reservoir refill capability without increasing flood risk. Here we extend the earlier studies using a detailed daily time step simulation model applied over a somewhat smaller portion of the domain (encompassing Libby, Duncan, and Corra Linn dams, and Kootenai Lake) to evaluate and refine the optimized flood control curves derived from monthly time step analysis. Moving from a monthly to daily analysis, we found that the timing of flood control evacuation needed adjustment to avoid unintended outcomes affecting Kootenai Lake. We refined the flood rule curves derived from monthly analysis by creating a more gradual evacuation schedule, but kept the timing and magnitude of maximum evacuation the same as in the monthly analysis. After these refinements, the performance at monthly time scales reported in our previous study proved robust at daily time scales. Due to a decrease in July storage deficits, additional benefits such as more revenue from hydropower generation and more July and August outflow for fish augmentation were observed when the optimized flood control curves were used for the climate change scenario.

  9. Implementation of variable time step stochastic dynamics for electronically inelastic gas-surface collisions

    NASA Technical Reports Server (NTRS)

    Garrett, Bruce C.; Swaminathan, P. K.; Murthy, C. S.; Redmon, Michael J.

    1987-01-01

    A variable time step algorithm has been implemented for solving the stochastic equations of motion for gas-surface collisions. It has been tested for a simple model of electronically inelastic collisions with an insulator surface in which the phonon manifold acts as a heat bath and electronic states are localized. In addition to reproducing the accurate nuclear dynamics of the surface atoms, numerical calculations have shown the algorithm to yield accurate ensemble averages of physical observables such as electronic transition probabilities and total energy loss of the gas atom to the surface. This new algorithm offers a gain in efficieny of up to an order of magnitude compared to fixed time step integration.

  10. Schwarz type domain decomposition and subcycling multi-time step approach for solving Richards equation

    NASA Astrophysics Data System (ADS)

    Kuraz, Michal

    2016-06-01

    Modelling the transport processes in a vadose zone, e.g. modelling contaminant transport or the effect of the soil water regime on changes in soil structure and composition, plays an important role in predicting the reactions of soil biotopes to anthropogenic activity. Water flow is governed by the quasilinear Richards equation. The paper concerns the implementation of a multi-time-step approach for solving a nonlinear Richards equation. When modelling porous media flow with a Richards equation, due to a possible convection dominance and a convergence of a nonlinear solver, a stable finite element approximation requires accurate temporal and spatial integration. The method presented here enables adaptive domain decomposition algorithm together with a multi-time-step treatment of actively changing subdomains.

  11. Explicit large time-step schemes for the shallow water equations

    NASA Technical Reports Server (NTRS)

    Turkel, E.; Zwas, G.

    1979-01-01

    Modifications to explicit finite difference schemes for solving the shallow water equations for meteorological applications by increasing the time step for the fast gravity waves are analyzed. Terms associated with the gravity waves in the shallow water equations are treated on a coarser grid than those associated with the slow Rossby waves, which contain much more of the available energy and must be treated with higher accuracy, enabling a several-fold increase in time step without degrading the accuracy of the solution. The method is presented in Cartesian and spherical coordinates for a rotating earth, using generalized leapfrog, frozen coefficient, and Fourier filtering finite difference schemes. Computational results verify the numerical stability of the approach.

  12. Accuracy of Pedometer Steps and Time for Youth with Intellectual Disabilities during Dynamic Movements

    ERIC Educational Resources Information Center

    Pitetti, Kenneth H.; Beets, Michael W.; Flaming, Judy

    2009-01-01

    Pedometer accuracy for steps and activity time during dynamic movement for youth with intellectual disabilities (ID) were examined. Twenty-four youth with ID (13 girls, 13.1 [plus or minus] 3.2 yrs; 11 boys, 14.7 [plus or minus] 2.7 yrs) were videotaped during adapted physical education class while wearing a Walk4Life 2505 pedometer in five…

  13. Multiple Time-Step Dual-Hamiltonian Hybrid Molecular Dynamics — Monte Carlo Canonical Propagation Algorithm

    PubMed Central

    Weare, Jonathan; Dinner, Aaron R.; Roux, Benoît

    2016-01-01

    A multiple time-step integrator based on a dual Hamiltonian and a hybrid method combining molecular dynamics (MD) and Monte Carlo (MC) is proposed to sample systems in the canonical ensemble. The Dual Hamiltonian Multiple Time-Step (DHMTS) algorithm is based on two similar Hamiltonians: a computationally expensive one that serves as a reference and a computationally inexpensive one to which the workload is shifted. The central assumption is that the difference between the two Hamiltonians is slowly varying. Earlier work has shown that such dual Hamiltonian multiple time-step schemes effectively precondition nonlinear differential equations for dynamics by reformulating them into a recursive root finding problem that can be solved by propagating a correction term through an internal loop, analogous to RESPA. Of special interest in the present context, a hybrid MD-MC version of the DHMTS algorithm is introduced to enforce detailed balance via a Metropolis acceptance criterion and ensure consistency with the Boltzmann distribution. The Metropolis criterion suppresses the discretization errors normally associated with the propagation according to the computationally inexpensive Hamiltonian, treating the discretization error as an external work. Illustrative tests are carried out to demonstrate the effectiveness of the method. PMID:26918826

  14. Real-Time, Single-Step Bioassay Using Nanoplasmonic Resonator With Ultra-High Sensitivity

    NASA Technical Reports Server (NTRS)

    Zhang, Xiang (Inventor); Ellman, Jonathan A. (Inventor); Chen, Fanqing Frank (Inventor); Su, Kai-Hang (Inventor); Wei, Qi-Huo (Inventor); Sun, Cheng (Inventor)

    2014-01-01

    A nanoplasmonic resonator (NPR) comprising a metallic nanodisk with alternating shielding layer(s), having a tagged biomolecule conjugated or tethered to the surface of the nanoplasmonic resonator for highly sensitive measurement of enzymatic activity. NPRs enhance Raman signals in a highly reproducible manner, enabling fast detection of protease and enzyme activity, such as Prostate Specific Antigen (paPSA), in real-time, at picomolar sensitivity levels. Experiments on extracellular fluid (ECF) from paPSA-positive cells demonstrate specific detection in a complex bio-fluid background in real-time single-step detection in very small sample volumes.

  15. Real-time, single-step bioassay using nanoplasmonic resonator with ultra-high sensitivity

    DOEpatents

    Zhang, Xiang; Ellman, Jonathan A; Chen, Fanqing Frank; Su, Kai-Hang; Wei, Qi-Huo; Sun, Cheng

    2014-04-01

    A nanoplasmonic resonator (NPR) comprising a metallic nanodisk with alternating shielding layer(s), having a tagged biomolecule conjugated or tethered to the surface of the nanoplasmonic resonator for highly sensitive measurement of enzymatic activity. NPRs enhance Raman signals in a highly reproducible manner, enabling fast detection of protease and enzyme activity, such as Prostate Specific Antigen (paPSA), in real-time, at picomolar sensitivity levels. Experiments on extracellular fluid (ECF) from paPSA-positive cells demonstrate specific detection in a complex bio-fluid background in real-time single-step detection in very small sample volumes.

  16. Extension of a spectral time-stepping domain decomposition method for dispersive and dissipative wave propagation.

    PubMed

    Botts, Jonathan; Savioja, Lauri

    2015-04-01

    For time-domain modeling based on the acoustic wave equation, spectral methods have recently demonstrated promise. This letter presents an extension of a spectral domain decomposition approach, previously used to solve the lossless linear wave equation, which accommodates frequency-dependent atmospheric attenuation and assignment of arbitrary dispersion relations. Frequency-dependence is straightforward to assign when time-stepping is done in the spectral domain, so combined losses from molecular relaxation, thermal conductivity, and viscosity can be approximated with little extra computation or storage. A mode update free from numerical dispersion is derived, and the model is confirmed with a numerical experiment.

  17. Single-step propagators for calculation of time evolution in quantum systems with arbitrary interactions

    NASA Astrophysics Data System (ADS)

    Gonoskov, Ivan; Marklund, Mattias

    2016-05-01

    We propose and develop a general method of numerical calculation of the wave function time evolution in a quantum system which is described by Hamiltonian of an arbitrary dimensionality and with arbitrary interactions. For this, we obtain a general n-order single-step propagator in closed-form, which could be used for the numerical solving of the problem with any prescribed accuracy. We demonstrate the applicability of the proposed approach by considering a quantum problem with non-separable time-dependent Hamiltonian: the propagation of an electron in focused electromagnetic field with vortex electric field component.

  18. A novel adaptive time stepping variant of the Boris–Buneman integrator for the simulation of particle accelerators with space charge

    SciTech Connect

    Toggweiler, Matthias; Adelmann, Andreas; Arbenz, Peter; Yang, Jianjun

    2014-09-15

    We show that adaptive time stepping in particle accelerator simulation is an enhancement for certain problems. The new algorithm has been implemented in the OPAL (Object Oriented Parallel Accelerator Library) framework. The idea is to adjust the frequency of costly self-field calculations, which are needed to model Coulomb interaction (space charge) effects. In analogy to a Kepler orbit simulation that requires a higher time step resolution at the close encounter, we propose to choose the time step based on the magnitude of the space charge forces. Inspired by geometric integration techniques, our algorithm chooses the time step proportional to a function of the current phase space state instead of calculating a local error estimate like a conventional adaptive procedure. Building on recent work, a more profound argument is given on how exactly the time step should be chosen. An intermediate algorithm, initially built to allow a clearer analysis by introducing separate time steps for external field and self-field integration, turned out to be useful by its own, for a large class of problems.

  19. A shorter time step for eco-friendly reservoir operation does not always produce better water availability and ecosystem benefits

    NASA Astrophysics Data System (ADS)

    Yu, Chunxue; Yin, Xin'an; Yang, Zhifeng; Cai, Yanpeng; Sun, Tao

    2016-09-01

    The time step used in the operation of eco-friendly reservoirs has decreased from monthly to daily, and even sub-daily. The shorter time step is considered a better choice for satisfying downstream environmental requirements because it more closely resembles the natural flow regime. However, little consideration has been given to the influence of different time steps on the ability to simultaneously meet human and environmental flow requirements. To analyze this influence, we used an optimization model to explore the relationships among the time step, environmental flow (e-flow) requirements, and human water needs for a wide range of time steps and e-flow scenarios. We used the degree of hydrologic alteration to evaluate the regime's ability to satisfy the e-flow requirements of riverine ecosystems, and used water supply reliability to evaluate the ability to satisfy human needs. We then applied the model to a case study of China's Tanghe Reservoir. We found four efficient time steps (2, 3, 4, and 5 days), with a remarkably high water supply reliability (around 80%) and a low alteration of the flow regime (<35%). Our analysis of the hydrologic alteration revealed the smallest alteration at time steps ranging from 1 to 7 days. However, longer time steps led to higher water supply reliability to meet human needs under several e-flow scenarios. Our results show that adjusting the time step is a simple way to improve reservoir operation performance to balance human and e-flow needs.

  20. Oscillation-Driven Spike-Timing Dependent Plasticity Allows Multiple Overlapping Pattern Recognition in Inhibitory Interneuron Networks.

    PubMed

    Garrido, Jesús A; Luque, Niceto R; Tolu, Silvia; D'Angelo, Egidio

    2016-08-01

    The majority of operations carried out by the brain require learning complex signal patterns for future recognition, retrieval and reuse. Although learning is thought to depend on multiple forms of long-term synaptic plasticity, the way this latter contributes to pattern recognition is still poorly understood. Here, we have used a simple model of afferent excitatory neurons and interneurons with lateral inhibition, reproducing a network topology found in many brain areas from the cerebellum to cortical columns. When endowed with spike-timing dependent plasticity (STDP) at the excitatory input synapses and at the inhibitory interneuron-interneuron synapses, the interneurons rapidly learned complex input patterns. Interestingly, induction of plasticity required that the network be entrained into theta-frequency band oscillations, setting the internal phase-reference required to drive STDP. Inhibitory plasticity effectively distributed multiple patterns among available interneurons, thus allowing the simultaneous detection of multiple overlapping patterns. The addition of plasticity in intrinsic excitability made the system more robust allowing self-adjustment and rescaling in response to a broad range of input patterns. The combination of plasticity in lateral inhibitory connections and homeostatic mechanisms in the inhibitory interneurons optimized mutual information (MI) transfer. The storage of multiple complex patterns in plastic interneuron networks could be critical for the generation of sparse representations of information in excitatory neuron populations falling under their control. PMID:27079422

  1. Sensitivity of The High-resolution Wam Model With Respect To Time Step

    NASA Astrophysics Data System (ADS)

    Kasemets, K.; Soomere, T.

    The northern part of the Baltic Proper and its subbasins (Bothnian Sea, the Gulf of Finland, Moonsund) serve as a challenge for wave modellers. In difference from the southern and the eastern parts of the Baltic Sea, their coasts are highly irregular and contain many peculiarities with the characteristic horizontal scale of the order of a few kilometres. For example, the northern coast of the Gulf of Finland is extremely ragged and contains a huge number of small islands. Its southern coast is more or less regular but has up to 50m high cliff that is frequently covered by high forests. The area also contains numerous banks that have water depth a couple of meters and that may essentially modify wave properties near the banks owing to topographical effects. This feature suggests that a high-resolution wave model should be applied for the region in question, with a horizontal resolution of an order of 1 km or even less. According to the Courant-Friedrich-Lewy criterion, the integration time step for such models must be of the order of a few tens of seconds. A high-resolution WAM model turns out to be fairly sensitive with respect to the particular choice of the time step. In our experiments, a medium-resolution model for the whole Baltic Sea was used, with the horizontal resolution 3 miles (3' along latitudes and 6' along longitudes) and the angular resolution 12 directions. The model was run with steady wind blowing 20 m/s from different directions and with two time steps (1 and 3 minutes). For most of the wind directions, the rms. difference of significant wave heights calculated with differ- ent time steps did not exceed 10 cm and typically was of the order of a few per cents. The difference arose within a few tens of minutes and generally did not increase in further computations. However, in the case of the north wind, the difference increased nearly monotonously and reached 25-35 cm (10-15%) within three hours of integra- tion whereas mean of significant wave

  2. BIOMAP A Daily Time Step, Mechanistic Model for the Study of Ecosystem Dynamics

    NASA Astrophysics Data System (ADS)

    Wells, J. R.; Neilson, R. P.; Drapek, R. J.; Pitts, B. S.

    2010-12-01

    BIOMAP simulates competition between two Plant Functional Types (PFT) at any given point in the conterminous U.S. using a time series of daily temperature (mean, minimum, maximum), precipitation, humidity, light and nutrients, with PFT-specific rooting within a multi-layer soil. The model employs a 2-layer canopy biophysics, Farquhar photosynthesis, the Beer-Lambert Law for light attenuation and a mechanistic soil hydrology. In essence, BIOMAP is a re-built version of the biogeochemistry model, BIOME-BGC, into the form of the MAPSS biogeography model. Specific enhancements are: 1) the 2-layer canopy biophysics of Dolman (1993); 2) the unique MAPSS-based hydrology, which incorporates canopy evaporation, snow dynamics, infiltration and saturated and unsaturated percolation with ‘fast’ flow and base flow and a ‘tunable aquifer’ capacity, a metaphor of D’Arcy’s Law; and, 3) a unique MAPSS-based stomatal conductance algorithm, which simultaneously incorporates vapor pressure and soil water potential constraints, based on physiological information and many other improvements. Over small domains the PFTs can be parameterized as individual species to investigate fundamental vs. potential niche theory; while, at more coarse scales the PFTs can be rendered as more general functional groups. Since all of the model processes are intrinsically leaf to plot scale (physiology to PFT competition), it essentially has no ‘intrinsic’ scale and can be implemented on a grid of any size, taking on the characteristics defined by the homogeneous climate of each grid cell. Currently, the model is implemented on the VEMAP 1/2 degree, daily grid over the conterminous U.S. Although both the thermal and water-limited ecotones are dynamic, following climate variability, the PFT distributions remain fixed. Thus, the model is currently being fitted with a ‘reproduction niche’ to allow full dynamic operation as a Dynamic General Vegetation Model (DGVM). While global simulations

  3. Application times for the single-step/double-mix technique for impression materials in clinical practice.

    PubMed

    Rupp, Frank; Saker, Odie; Axmann, Detlef; Geis-Gerstorfer, Jurgen; Engel, Eva

    2011-01-01

    Hydrophilicity of unset impression materials underlies changes occurring during working time. Hence, the clinical application time when impression materials contact oral tissues after mixing may play a critical role in successful impressions. The aim of this study was to analyze the clinical time course of impression taking applying the single-step/double-mix technique. Application times of 86 impressions, comprising 265 prepared teeth and 46 implants, taken by 14 different clinicians at a university dental clinic were analyzed. The mean time from loading the impression tray until its final position in the patient's mouth (total application time) was 51.2 seconds; confidence intervals were 46.9 (lower limit) and 55.5 (upper limit). The number of registered teeth and implants did not influence the duration of impression taking. Related to wettability data, several polyvinyl siloxane impression materials show decreased hydrophilicity with respect to estimated application times. The authors suggest considering clinically relevant application times for impression taking in future in vitro studies on physicochemical characteristics of impression materials.

  4. Imaginary Time Step Method to Solve the Dirac Equation with Nonlocal Potential

    SciTech Connect

    Zhang Ying; Liang Haozhao; Meng Jie

    2009-08-26

    The imaginary time step (ITS) method is applied to solve the Dirac equation with nonlocal potentials in coordinate space. Taking the nucleus {sup 12}C as an example, even with nonlocal potentials, the direct ITS evolution for the Dirac equation still meets the disaster of the Dirac sea. However, following the recipe in our former investigation, the disaster can be avoided by the ITS evolution for the corresponding Schroedinger-like equation without localization, which gives the convergent results exactly the same with those obtained iteratively by the shooting method with localized effective potentials.

  5. Multiple time step molecular dynamics in the optimized isokinetic ensemble steered with the molecular theory of solvation: Accelerating with advanced extrapolation of effective solvation forces

    SciTech Connect

    Omelyan, Igor E-mail: omelyan@icmp.lviv.ua; Kovalenko, Andriy

    2013-12-28

    steered by effective solvation forces allows huge outer time steps up to tens of picoseconds without affecting the equilibrium and conformational properties, and thus provides a 100- to 500-fold effective speedup in comparison to conventional MD with explicit solvent. With the statistical-mechanical 3D-RISM-KH account for effective solvation forces, the method provides efficient sampling of biomolecular processes with slow and/or rare solvation events such as conformational transitions of hydrated alanine dipeptide with the mean life times ranging from 30 ps up to 10 ns for “flip-flop” conformations, and is particularly beneficial for biomolecular systems with exchange and localization of solvent and ions, ligand binding, and molecular recognition.

  6. Multiple time step molecular dynamics in the optimized isokinetic ensemble steered with the molecular theory of solvation: Accelerating with advanced extrapolation of effective solvation forces

    NASA Astrophysics Data System (ADS)

    Omelyan, Igor; Kovalenko, Andriy

    2013-12-01

    steered by effective solvation forces allows huge outer time steps up to tens of picoseconds without affecting the equilibrium and conformational properties, and thus provides a 100- to 500-fold effective speedup in comparison to conventional MD with explicit solvent. With the statistical-mechanical 3D-RISM-KH account for effective solvation forces, the method provides efficient sampling of biomolecular processes with slow and/or rare solvation events such as conformational transitions of hydrated alanine dipeptide with the mean life times ranging from 30 ps up to 10 ns for "flip-flop" conformations, and is particularly beneficial for biomolecular systems with exchange and localization of solvent and ions, ligand binding, and molecular recognition.

  7. A simple method for improving the time-stepping accuracy in atmosphere and ocean models

    NASA Astrophysics Data System (ADS)

    Williams, P. D.

    2012-12-01

    In contemporary numerical simulations of the atmosphere and ocean, evidence suggests that time-stepping errors may be a significant component of total model error, on both weather and climate time-scales. This presentation will review the available evidence, and will then suggest a simple but effective method for substantially improving the time-stepping numerics at no extra computational expense. A common time-stepping method in atmosphere and ocean models is the leapfrog scheme combined with the Robert-Asselin (RA) filter. This method is used in the following models (and many more): ECHAM, MAECHAM, MM5, CAM, MESO-NH, HIRLAM, KMCM, LIMA, SPEEDY, IGCM, PUMA, COSMO, FSU-GSM, FSU-NRSM, NCEP-GFS, NCEP-RSM, NSEAM, NOGAPS, RAMS, and CCSR/NIES-AGCM. Although the RA filter controls the time-splitting instability, it also introduces non-physical damping and reduces the accuracy. This presentation proposes a simple modification to the RA filter, which has become known as the RAW filter (Williams 2009, 2011). When used in conjunction with the leapfrog scheme, the RAW filter eliminates the non-physical damping and increases the amplitude accuracy by two orders, yielding third-order accuracy. (The phase accuracy remains second-order.) The RAW filter can easily be incorporated into existing models, typically via the insertion of just a single line of code. Better simulations are obtained at no extra computational expense. Results will be shown from recent implementations of the RAW filter in various models, including SPEEDY and COSMO. For example, in SPEEDY, the skill of weather forecasts is found to be significantly improved. In particular, in tropical surface pressure predictions, five-day forecasts made using the RAW filter have approximately the same skill as four-day forecasts made using the RA filter (Amezcua, Kalnay & Williams 2011). These improvements are encouraging for the use of the RAW filter in other atmosphere and ocean models. References PD Williams (2009) A

  8. One-Step Direct Aeroacoustic Simulation Using Space-Time Conservation Element and Solution Element Method

    NASA Astrophysics Data System (ADS)

    Ho, C. Y.; Leung, R. C. K.; Zhou, K.; Lam, G. C. Y.; Jiang, Z.

    2011-09-01

    One-step direct aeroacoustic simulation (DAS) has received attention from aerospace and mechanical high-pressure fluid-moving system manufacturers for quite some time. They aim to simulate the unsteady flow and acoustic field in the duct simultaneously in order to investigate the aeroacoustic generation mechanisms. Because of the large length and energy scale disparities between the acoustic far field and the aerodynamic near field, highly accurate and high-resolution simulation scheme is required. This involves the use of high order compact finite difference and time advancement schemes in simulation. However, in this situation, large buffer zones are always needed to suppress the spurious numerical waves emanating from computational boundaries. This further increases the computational resources to yield accurate results. On the other hand, for such problem as supersonic jet noise, the numerical scheme should be able to resolve both strong shock waves and weak acoustic waves simultaneously. Usually numerical aeroa-coustic scheme that is good for low Mach number flow is not able to give satisfactory simulation results for shock wave. Therefore, the aeroacoustic research community has been looking for a more efficient one-step DAS scheme that has the comparable accuracy to the finite-difference approach with smaller buffer regions, yet is able to give accurate solutions from subsonic to supersonic flows. The conservation element and solution element (CE/SE) scheme is one of the possible schemes satisfying the above requirements. This paper aims to report the development of a CE/SE scheme for one-step DAS and illustrate its robustness and effectiveness with two selected benchmark problems.

  9. Block Time Step Storage Scheme for Astrophysical N-body Simulations

    NASA Astrophysics Data System (ADS)

    Cai, Maxwell Xu; Meiron, Yohai; Kouwenhoven, M. B. N.; Assmann, Paulina; Spurzem, Rainer

    2015-08-01

    Astrophysical research in recent decades has made significant progress thanks to the availability of various N-body simulation techniques. With the rapid development of high-performance computing technologies, modern simulations have been able to use the computing power of massively parallel clusters with more than 105 GPU cores. While unprecedented accuracy and dynamical scales have been achieved, the enormous amount of data being generated continuously poses great challenges for the subsequent procedures of data analysis and archiving. In this paper, we propose an adaptive storage scheme for simulation data, inspired by the block time step (BTS) integration scheme found in a number of direct N-body integrators available nowadays, as an urgent response to these challenges. The proposed scheme, namely, the BTS storage scheme, works by minimizing the data redundancy by assigning individual output frequencies to the data as required by the researcher. As demonstrated by benchmarks, the proposed scheme is applicable to a wide variety of simulations. Despite the main focus of developing a solution for direct N-body simulation data, the methodology is transferable for grid-based or tree-based simulations where hierarchical time stepping is used.

  10. Detection of Zika virus by SYBR green one-step real-time RT-PCR.

    PubMed

    Xu, Ming-Yue; Liu, Si-Qing; Deng, Cheng-Lin; Zhang, Qiu-Yan; Zhang, Bo

    2016-10-01

    The ongoing Zika virus (ZIKV) outbreak has rapidly spread to new areas of Americas, which were the first transmissions outside its traditional endemic areas in Africa and Asia. Due to the link with newborn defects and neurological disorder, numerous infected cases throughout the world and various mosquito vectors, the virus has been considered to be an international public health emergency. In the present study, we developed a SYBR Green based one-step real-time RT-PCR assay for rapid detection of ZIKV. Our results revealed that the real-time assay is highly specific and sensitive in detection of ZIKV in cell samples. Importantly, the replication of ZIKV at different time points in infected cells could be rapidly monitored by the real-time RT-PCR assay. Specifically, the real-time RT-PCR showed acceptable performance in measurement of infectious ZIKV RNA. This assay could detect ZIKV at a titer as low as 1PFU/mL. The real-time RT-PCR assay could be a useful tool for further virology surveillance and diagnosis of ZIKV. PMID:27444120

  11. Detection of Zika virus by SYBR green one-step real-time RT-PCR.

    PubMed

    Xu, Ming-Yue; Liu, Si-Qing; Deng, Cheng-Lin; Zhang, Qiu-Yan; Zhang, Bo

    2016-10-01

    The ongoing Zika virus (ZIKV) outbreak has rapidly spread to new areas of Americas, which were the first transmissions outside its traditional endemic areas in Africa and Asia. Due to the link with newborn defects and neurological disorder, numerous infected cases throughout the world and various mosquito vectors, the virus has been considered to be an international public health emergency. In the present study, we developed a SYBR Green based one-step real-time RT-PCR assay for rapid detection of ZIKV. Our results revealed that the real-time assay is highly specific and sensitive in detection of ZIKV in cell samples. Importantly, the replication of ZIKV at different time points in infected cells could be rapidly monitored by the real-time RT-PCR assay. Specifically, the real-time RT-PCR showed acceptable performance in measurement of infectious ZIKV RNA. This assay could detect ZIKV at a titer as low as 1PFU/mL. The real-time RT-PCR assay could be a useful tool for further virology surveillance and diagnosis of ZIKV.

  12. Critical time step for a bilinear laminated composite Mindlin shell element.

    SciTech Connect

    Hammerand, Daniel Carl

    2004-06-01

    The critical time step needed for explicit time integration of laminated shell finite element models is presented. Each layer is restricted to be orthotropic when viewed from a properly oriented material coordinate system. Mindlin shell theory is used in determining the laminated response that includes the effects of transverse shear. The effects of the membrane-bending coupling matrix from the laminate material model are included. Such a coupling matrix arises even in the case of non-symmetric lay-ups of differing isotropic layers. Single point integration is assumed to be used in determining a uniform strain response from the element. Using a technique based upon one from the literature, reduced eigenvalue problems are established to determine the remaining non-zero frequencies. It is shown that the eigenvalue problem arising from the inplane normal and shear stresses is decoupled from that arising from the transverse shear stresses. A verification example is presented where the exact and approximate results are compared.

  13. An Efficient Time-Stepping Scheme for Ab Initio Molecular Dynamics Simulations

    NASA Astrophysics Data System (ADS)

    Tsuchida, Eiji

    2016-08-01

    In ab initio molecular dynamics simulations of real-world problems, the simple Verlet method is still widely used for integrating the equations of motion, while more efficient algorithms are routinely used in classical molecular dynamics. We show that if the Verlet method is used in conjunction with pre- and postprocessing, the accuracy of the time integration is significantly improved with only a small computational overhead. We also propose several extensions of the algorithm required for use in ab initio molecular dynamics. The validity of the processed Verlet method is demonstrated in several examples including ab initio molecular dynamics simulations of liquid water. The structural properties obtained from the processed Verlet method are found to be sufficiently accurate even for large time steps close to the stability limit. This approach results in a 2× performance gain over the standard Verlet method for a given accuracy. We also show how to generate a canonical ensemble within this approach.

  14. Aid for health in times of political unrest in Mali: does donors' way of intervening allow protecting people's health?

    PubMed

    Paul, Elisabeth; Samaké, Salif; Berthé, Issa; Huijts, Ini; Balique, Hubert; Dujardin, Bruno

    2014-12-01

    Mali has long been a leader in francophone Africa in developing systems aimed at improving aid effectiveness, especially in the health sector. But following the invasion of the Northern regions of the country by terrorist groups and a coup in March 2012, donors suspended official development assistance, except for support to NGOs and humanitarian assistance. They resumed aid after transfer of power to a civil government, but this was not done in a harmonized framework. This article describes and analyses how donors in the health sector reacted to the political unrest in Mali. It shows that despite its long sector-wide approach experience and international agreements to respect aid effectiveness principles, donors have not been able to intervene in view of safeguarding the investments of co-operation in the past decade, and of protecting the health system's functioning. They reacted to the political unrest on a bilateral basis, stopped working with their ministerial partners, interrupted support to the health system which was still expected to serve populations' needs and took months before organizing alternative and only partial solutions to resume aid to the health sector. The Malian example leads to a worrying conclusion: while protecting the health system's achievements and functioning for the population should be a priority, and while harmonizing donors' interventions seems the most appropriate way for that purpose, donors' management practices do not allow for reacting adequately in times of unrest. The article concludes by a number of recommendations.

  15. Multi-rate time stepping schemes for hydro-geomechanical model for subsurface methane hydrate reservoirs

    NASA Astrophysics Data System (ADS)

    Gupta, Shubhangi; Wohlmuth, Barbara; Helmig, Rainer

    2016-05-01

    We present an extrapolation-based semi-implicit multi-rate time stepping (MRT) scheme and a compound-fast MRT scheme for a naturally partitioned, multi-time-scale hydro-geomechanical hydrate reservoir model. We evaluate the performance of the two MRT methods compared to an iteratively coupled solution scheme and discuss their advantages and disadvantages. The performance of the two MRT methods is evaluated in terms of speed-up and accuracy by comparison to an iteratively coupled solution scheme. We observe that the extrapolation-based semi-implicit method gives a higher speed-up but is strongly dependent on the relative time scales of the latent (slow) and active (fast) components. On the other hand, the compound-fast method is more robust and less sensitive to the relative time scales, but gives lower speed up as compared to the semi-implicit method, especially when the relative time scales of the active and latent components are comparable.

  16. Time-Accurate Local Time Stepping and High-Order Time CESE Methods for Multi-Dimensional Flows Using Unstructured Meshes

    NASA Technical Reports Server (NTRS)

    Chang, Chau-Lyan; Venkatachari, Balaji Shankar; Cheng, Gary

    2013-01-01

    With the wide availability of affordable multiple-core parallel supercomputers, next generation numerical simulations of flow physics are being focused on unsteady computations for problems involving multiple time scales and multiple physics. These simulations require higher solution accuracy than most algorithms and computational fluid dynamics codes currently available. This paper focuses on the developmental effort for high-fidelity multi-dimensional, unstructured-mesh flow solvers using the space-time conservation element, solution element (CESE) framework. Two approaches have been investigated in this research in order to provide high-accuracy, cross-cutting numerical simulations for a variety of flow regimes: 1) time-accurate local time stepping and 2) highorder CESE method. The first approach utilizes consistent numerical formulations in the space-time flux integration to preserve temporal conservation across the cells with different marching time steps. Such approach relieves the stringent time step constraint associated with the smallest time step in the computational domain while preserving temporal accuracy for all the cells. For flows involving multiple scales, both numerical accuracy and efficiency can be significantly enhanced. The second approach extends the current CESE solver to higher-order accuracy. Unlike other existing explicit high-order methods for unstructured meshes, the CESE framework maintains a CFL condition of one for arbitrarily high-order formulations while retaining the same compact stencil as its second-order counterpart. For large-scale unsteady computations, this feature substantially enhances numerical efficiency. Numerical formulations and validations using benchmark problems are discussed in this paper along with realistic examples.

  17. A One-Step, Real-Time PCR Assay for Rapid Detection of Rhinovirus

    PubMed Central

    Do, Duc H.; Laus, Stella; Leber, Amy; Marcon, Mario J.; Jordan, Jeanne A.; Martin, Judith M.; Wadowsky, Robert M.

    2010-01-01

    One-step, real-time PCR assays for rhinovirus have been developed for a limited number of PCR amplification platforms and chemistries, and some exhibit cross-reactivity with genetically similar enteroviruses. We developed a one-step, real-time PCR assay for rhinovirus by using a sequence detection system (Applied Biosystems; Foster City, CA). The primers were designed to amplify a 120-base target in the noncoding region of picornavirus RNA, and a TaqMan (Applied Biosystems) degenerate probe was designed for the specific detection of rhinovirus amplicons. The PCR assay had no cross-reactivity with a panel of 76 nontarget nucleic acids, which included RNAs from 43 enterovirus strains. Excellent lower limits of detection relative to viral culture were observed for the PCR assay by using 38 of 40 rhinovirus reference strains representing different serotypes, which could reproducibly detect rhinovirus serotype 2 in viral transport medium containing 10 to 10,000 TCID50 (50% tissue culture infectious dose endpoint) units/ml of the virus. However, for rhinovirus serotypes 59 and 69, the PCR assay was less sensitive than culture. Testing of 48 clinical specimens from children with cold-like illnesses for rhinovirus by the PCR and culture assays yielded detection rates of 16.7% and 6.3%, respectively. For a batch of 10 specimens, the entire assay was completed in 4.5 hours. This real-time PCR assay enables detection of many rhinovirus serotypes with the Applied Biosystems reagent-instrument platform. PMID:19948820

  18. The two-step shape and timing of the last deglaciation in Antarctica

    SciTech Connect

    Jouzel, J.; Petit, J.R. |; Duclos, Y.

    1995-04-01

    The two-step character of the last deglaciation is well recognized in Western Europe, in Greenland and in the North Atlantic. For example, in Greenland, a gradual temperature decrease started at the Boelling (B) around 14.5 ky BP, spanned through the Alleroed (A) and was followed by the cold Younger Dryas (YD) event which terminated abruptly around 11.5 ky BP. Recent results suggest that this BA/YD sequence may have extended throughout all the Northern Hemisphere but the evidence of a late transition cooling is still poor for the Southern Hemisphere. Here we present a detailed isotopic record analyzed in a new ice core drilled at Dome B in East Antarctica that fully demonstrates the existence of an Antarctic cold reversal (ACR). These results suggest that the two-step shape of the last deglaciation has a worldwide character but they also point to noticeable interhemispheric differences. Thus. the coldest part of the ACR. which shows a temperature drop about three times weaker than that recorded during the YD in Greenland, may have preceded the YD. Antarctica did not experienced abrupt changes and the two warming periods started there before they started in Greenland. The links between Southern and Northern Hemisphere climates throughout this period are discussed in the light of additional information derived from the Antarctic dust record. 87 refs., 5 figs.

  19. [Photodissociation of Acetylene and Acetone using Step-Scan Time-Resolved FTIR Emission Spectroscopy

    NASA Technical Reports Server (NTRS)

    McLaren, Ian A.; Wrobel, Jacek D.

    1997-01-01

    The photodissociation of acetylene and acetone was investigated as a function of added quenching gas pressures using step-scan time-resolved FTIR emission spectroscopy. Its main components consist of Bruker IFS88, step-scan Fourier Transform Infrared (FTIR) spectrometer coupled to a flow cell equipped with Welsh collection optics. Vibrationally excited C2H radicals were produced from the photodissociation of acetylene in the unfocused experiments. The infrared (IR) emission from these excited C2H radicals was investigated as a function of added argon pressure. Argon quenching rate constants for all C2H emission bands are of the order of 10(exp -13)cc/molecule.sec. Quenching of these radicals by acetylene is efficient, with a rate constant in the range of 10(exp -11) cc/molecule.sec. The relative intensity of the different C2H emission bands did not change with the increasing argon or acetylene pressure. However, the overall IR emission intensity decreased, for example, by more than 50% when the argon partial pressure was raised from 0.2 to 2 Torr at fixed precursor pressure of 160mTorr. These observations provide evidence for the formation of a metastable C2H2 species, which are collisionally quenched by argon or acetylene. Problems encountered in the course of the experimental work are also described.

  20. Incorporating system latency associated with real-time target tracking radiotherapy in the dose prediction step

    NASA Astrophysics Data System (ADS)

    Roland, Teboh; Mavroidis, Panayiotis; Shi, Chengyu; Papanikolaou, Nikos

    2010-05-01

    System latency introduces geometric errors in the course of real-time target tracking radiotherapy. This effect can be minimized, for example by the use of predictive filters, but cannot be completely avoided. In this work, we present a convolution technique that can incorporate the effect as part of the treatment planning process. The method can be applied independently or in conjunction with the predictive filters to compensate for residual latency effects. The implementation was performed on TrackBeam (Initia Ltd, Israel), a prototype real-time target tracking system assembled and evaluated at our Cancer Institute. For the experimental system settings examined, a Gaussian distribution attributable to the TrackBeam latency was derived with σ = 3.7 mm. The TrackBeam latency, expressed as an average response time, was deduced to be 172 ms. Phantom investigations were further performed to verify the convolution technique. In addition, patient studies involving 4DCT volumes of previously treated lung cancer patients were performed to incorporate the latency effect in the dose prediction step. This also enabled us to effectively quantify the dosimetric and radiobiological impact of the TrackBeam and other higher latency effects on the clinical outcome of a real-time target tracking delivery.

  1. Electric and hybrid electric vehicle study utilizing a time-stepping simulation

    NASA Technical Reports Server (NTRS)

    Schreiber, Jeffrey G.; Shaltens, Richard K.; Beremand, Donald G.

    1992-01-01

    The applicability of NASA's advanced power technologies to electric and hybrid vehicles was assessed using a time-stepping computer simulation to model electric and hybrid vehicles operating over the Federal Urban Driving Schedule (FUDS). Both the energy and power demands of the FUDS were taken into account and vehicle economy, range, and performance were addressed simultaneously. Results indicate that a hybrid electric vehicle (HEV) configured with a flywheel buffer energy storage device and a free-piston Stirling convertor fulfills the emissions, fuel economy, range, and performance requirements that would make it acceptable to the consumer. It is noted that an assessment to determine which of the candidate technologies are suited for the HEV application has yet to be made. A proper assessment should take into account the fuel economy and range, along with the driveability and total emissions produced.

  2. Detection and Correction of Step Discontinuities in Kepler Flux Time Series

    NASA Technical Reports Server (NTRS)

    Kolodziejczak, J. J.; Morris, R. L.

    2011-01-01

    PDC 8.0 includes an implementation of a new algorithm to detect and correct step discontinuities appearing in roughly one of every 20 stellar light curves during a given quarter. The majority of such discontinuities are believed to result from high-energy particles (either cosmic or solar in origin) striking the photometer and causing permanent local changes (typically -0.5%) in quantum efficiency, though a partial exponential recovery is often observed [1]. Since these features, dubbed sudden pixel sensitivity dropouts (SPSDs), are uncorrelated across targets they cannot be properly accounted for by the current detrending algorithm. PDC detrending is based on the assumption that features in flux time series are due either to intrinsic stellar phenomena or to systematic errors and that systematics will exhibit measurable correlations across targets. SPSD events violate these assumptions and their successful removal not only rectifies the flux values of affected targets, but demonstrably improves the overall performance of PDC detrending [1].

  3. Comparison of Fixed and Variable Time Step Trajectory Integration Methods for Cislunar Trajectories

    NASA Technical Reports Server (NTRS)

    Weeks, ichael W.; Thrasher, Stephen W.

    2007-01-01

    Due to the nonlinear nature of the Earth-Moon-Sun three-body problem and non-spherical gravity, CEV cislunar targeting algorithms will require many propagations in their search for a desired trajectory. For on-board targeting especially, the algorithm must have a simple, fast, and accurate propagator to calculate a trajectory with reasonable computation time, and still be robust enough to remain stable in the various flight regimes that the CEV will experience. This paper compares Cowell s method with a fourth-order Runge- Kutta integrator (RK4), Encke s method with a fourth-order Runge-Kutta- Nystr m integrator (RKN4), and a method known as Multi-Conic. Additionally, the study includes the Bond-Gottlieb 14-element method (BG14) and extends the investigation of Encke-Nystrom methods to integrators of higher order and with variable step size.

  4. Effect of the processing steps on compositions of table olive since harvesting time to pasteurization.

    PubMed

    Nikzad, Nasim; Sahari, Mohammad A; Vanak, Zahra Piravi; Safafar, Hamed; Boland-nazar, Seyed A

    2013-08-01

    Weight, oil, fatty acids, tocopherol, polyphenol, and sterol properties of 5 olive cultivars (Zard, Fishomi, Ascolana, Amigdalolia, and Conservalia) during crude, lye treatment, washing, fermentation, and pasteurization steps were studied. Results showed: oil percent was higher and lower in Ascolana (crude step) and in Fishomi (pasteurization step), respectively; during processing steps, in all cultivars, oleic, palmitic, linoleic, and stearic acids were higher; the highest changes in saturated and unsaturated fatty acids were in fermentation step; the highest and the lowest ratios of ω3 / ω6 were in Ascolana (washing step) and in Zard (pasteurization step), respectively; the highest and the lowest tocopherol were in Amigdalolia and Fishomi, respectively, and major damage occurred in lye step; the highest and the lowest polyphenols were in Ascolana (crude step) and in Zard and Ascolana (pasteurization step), respectively; the major damage among cultivars occurred during lye step, in which the polyphenol reduced to 1/10 of first content; sterol did not undergo changes during steps. Reviewing of olive patents shows that many compositions of fruits such as oil quality, fatty acids, quantity and its fraction can be changed by alteration in cultivar and process.

  5. Induction of an LH surge and ovulation by buserelin (as Receptal) allows breeding of weaned sows with a single fixed-time insemination.

    PubMed

    Driancourt, M A; Cox, P; Rubion, S; Harnois-Milon, G; Kemp, B; Soede, N M

    2013-09-01

    The aim of this study was to demonstrate successful breeding of sows with a single fixed-time insemination following ovulation induction by buserelin, a GnRH analogue. In a first step, the optimal dose of buserelin (6, 10, or 16 μg) injected at 77 hours after weaning was determined in weaned sows (N = 15, 11, and 12, respectively) using its ability to induce an LH surge of similar magnitude as in control sows (N = 15) and induce ovulation. In 29/38 treated sows (76%), ovulation was induced and synchronized between 32 and 44 hours after injection, and the proportion of females ovulating during this time window was similar between groups at 73%, 73%, and 83% (6, 10, or 16 μg, respectively). Interestingly, whereas ovulation of 100% multiparous sows was induced and synchronized in the 32 to 44 hours posttreatment time window, successful induction was achieved in a lower proportion of primiparous sows (50%, 50%, and 67% following 6, 10, or 16 μg, respectively), the dose effect being nonsignificant. The magnitude of the LH surge was similar between control and treated sows, irrespective of the buserelin dose injected. Neither ovulation rate nor the number of good embryos on Day 5 postovulation differed between groups. Interestingly, the frequency of follicular cysts at slaughter was significantly affected by treatment (P < 0.05), being minimal and maximal in sows treated with 10 or 6 μg buserelin, respectively. In a second step, 419 sows from commercial herds in Spain, Germany, and France were randomly allocated to a control or treated group. The control sows were inseminated twice 12 ± 4 hours apart once estrus was detected. Treated sows received 10 μg buserelin at 86 ± 3 hours after weaning and were inseminated once 30 to 33 hours later. Farrowing rate of treated sows (87%, 166/192) was similar to that of control sows (84.5%, 169/200). Litter size was also similar between treated and control sows (13.6 ± 3.8 vs. 13.7 ± 3.2). In multiparous sows, neither

  6. Influence of simulation time-step (temporal-scale) on optimal parameter estimation and runoff prediction performance in hydrological modeling

    NASA Astrophysics Data System (ADS)

    Loizu, Javier; Álvarez-Mozos, Jesús; Casalí, Javier; Goñi, Mikel

    2015-04-01

    Nowadays, most hydrological catchment models are designed to allow their use for streamflow simulation at different time-scales. While this permits models to be applied for broader purposes, it can also be a source of error in hydrological processes simulation at catchment scale. Those errors seem not to affect significantly simple conceptual models, but this flexibility may lead to large behavior errors in physically based models. Equations used in processes such as those related to soil moisture time-variation are usually representative at certain time-scales but they may not characterize properly water transfer in soil layers at larger scales. This effect is especially relevant as we move from detailed hourly scale to daily time-step, which are common time scales used at catchment streamflow simulation for different research and management practices purposes. This study aims to provide an objective methodology to identify the degree of similarity of optimal parameter values when hydrological catchment model calibration is developed at different time-scales. Thus, providing information for an informed discussion of physical parameter significance on hydrological models. In this research, we analyze the influence of time scale simulation on: 1) the optimal values of six highly sensitive parameters of the TOPLATS model and 2) the streamflow simulation efficiency, while optimization is carried out at different time scales. TOPLATS (TOPMODEL-based Land-Atmosphere Transfer Scheme) has been applied on its lumped version on three catchments of varying size located in northern Spain. The model has its basis on shallow groundwater gradients (related to local topography) that set up spatial patterns of soil moisture and are assumed to control infiltration and runoff during storm events and evaporation and drainage in between storm events. The model calculates the saturated portion of the catchment at each time step based on Topographical Index (TI) intervals. Surface

  7. Silver nanoparticle enhanced immunoassays: one step real time kinetic assay for insulin in serum.

    PubMed

    Lochner, Nina; Lobmaier, Christina; Wirth, Michael; Leitner, Alfred; Pittner, Fritz; Gabor, Franz

    2003-11-01

    Silver nanoparticle enhanced fluorescence is introduced as an alternative method to surface plasmon resonance techniques for real time monitoring of biorecognitive interactions or immunoassays. This method relies on the phenomenon that an electromagnetic near field is generated upon illumination on the surface of silver nanoparticles. The interaction of this field with nearby fluorophores results in fluorescence enhancement. Thus, fluorophores in the bulk solution can be discriminated from surface bound fluorophores. Anti-insulin-antibodies were immobilized on the surface of silver colloids in the following order: A ready to use microplate was prepared by bottom up coating with layers of aminosilane, silver nanoparticles, Fc-recognizing F(ab)(2)-fragments and anti-insulin-antibodies. At equilibrium conditions fluorescein-labeled insulin could only be detected in the presence of the colloid; the detection limit was 250 nM, and a fourfold increase in fluorescence was observed upon real time monitoring. The competitive assay of labeled and unlabeled insulin revealed a working range of 10-200 nM insulin in serum. The rapid single step immunoassay is easy to perform even in microplate format, its sensitivity is comparable to ELISA techniques, and offers broad application for real time monitoring of molecular recognitive processes.

  8. Security: Step by Step

    ERIC Educational Resources Information Center

    Svetcov, Eric

    2005-01-01

    This article provides a list of the essential steps to keeping a school's or district's network safe and sound. It describes how to establish a security architecture and approach that will continually evolve as the threat environment changes over time. The article discusses the methodology for implementing this approach and then discusses the…

  9. Time-resolved step-scan Fourier transform infrared spectroscopy reveals differences between early and late M intermediates of bacteriorhodopsin.

    PubMed

    Rödig, C; Chizhov, I; Weidlich, O; Siebert, F

    1999-05-01

    In this report, from time-resolved step-scan Fourier transform infrared investigations from 15 ns to 160 ms, we provide evidence for the subsequent rise of three different M states that differ in their structures. The first state rises with approximately 3 microseconds to only a small percentage. Its structure as judged from amide I/II bands differs in small but well-defined aspects from the L state. The next M state, which appears in approximately 40 microseconds, has almost all of the characteristics of the "late" M state, i.e., it differs considerably from the first one. Here, the L left arrow over right arrow M equilibrium is shifted toward M, although some percentage of L still persists. In the last M state (rise time approximately 130 microseconds), the equilibrium is shifted toward full deprotonation of the Schiff base, and only small additional structural changes take place. In addition to these results obtained for unbuffered conditions or at pH 7, experiments performed at lower and higher pH are presented. These results are discussed in terms of the molecular changes postulated to occur in the M intermediate to allow the shift of the L/M equilibrium toward M and possibly to regulate the change of the accessibility of the Schiff base necessary for effective proton pumping. PMID:10233083

  10. Time-resolved step-scan Fourier transform infrared spectroscopy reveals differences between early and late M intermediates of bacteriorhodopsin.

    PubMed Central

    Rödig, C; Chizhov, I; Weidlich, O; Siebert, F

    1999-01-01

    In this report, from time-resolved step-scan Fourier transform infrared investigations from 15 ns to 160 ms, we provide evidence for the subsequent rise of three different M states that differ in their structures. The first state rises with approximately 3 microseconds to only a small percentage. Its structure as judged from amide I/II bands differs in small but well-defined aspects from the L state. The next M state, which appears in approximately 40 microseconds, has almost all of the characteristics of the "late" M state, i.e., it differs considerably from the first one. Here, the L left arrow over right arrow M equilibrium is shifted toward M, although some percentage of L still persists. In the last M state (rise time approximately 130 microseconds), the equilibrium is shifted toward full deprotonation of the Schiff base, and only small additional structural changes take place. In addition to these results obtained for unbuffered conditions or at pH 7, experiments performed at lower and higher pH are presented. These results are discussed in terms of the molecular changes postulated to occur in the M intermediate to allow the shift of the L/M equilibrium toward M and possibly to regulate the change of the accessibility of the Schiff base necessary for effective proton pumping. PMID:10233083

  11. Electric and magnetic losses modeled by a stable hybrid with explicit-implicit time-stepping for Maxwell's equations

    SciTech Connect

    Halleroed, Tomas Rylander, Thomas

    2008-04-20

    A stable hybridization of the finite-element method (FEM) and the finite-difference time-domain (FDTD) scheme for Maxwell's equations with electric and magnetic losses is presented for two-dimensional problems. The hybrid method combines the flexibility of the FEM with the efficiency of the FDTD scheme and it is based directly on Ampere's and Faraday's law. The electric and magnetic losses can be treated implicitly by the FEM on an unstructured mesh, which allows for local mesh refinement in order to resolve rapid variations in the material parameters and/or the electromagnetic field. It is also feasible to handle larger homogeneous regions with losses by the explicit FDTD scheme connected to an implicitly time-stepped and lossy FEM region. The hybrid method shows second-order convergence for smooth scatterers. The bistatic radar cross section (RCS) for a circular metal cylinder with a lossy coating converges to the analytical solution and an accuracy of 2% is achieved for about 20 points per wavelength. The monostatic RCS for an airfoil that features sharp corners yields a lower order of convergence and it is found to agree well with what can be expected for singular fields at the sharp corners. A careful convergence study with resolutions from 20 to 140 points per wavelength provides accurate extrapolated results for this non-trivial test case, which makes it possible to use as a reference problem for scattering codes that model both electric and magnetic losses.

  12. Outward Bound to the Galaxies--One Step at a Time

    ERIC Educational Resources Information Center

    Ward, R. Bruce; Miller-Friedmann, Jaimie; Sienkiewicz, Frank; Antonucci, Paul

    2012-01-01

    Less than a century ago, astronomers began to unlock the cosmic distances within and beyond the Milky Way. Understanding the size and scale of the universe is a continuing, step-by-step process that began with the remarkably accurate measurement of the distance to the Moon made by early Greeks. In part, the authors have ITEAMS (Innovative…

  13. A user-defined data type for the storage of time series data allowing efficient similarity screening.

    PubMed

    Sorokin, Anatoly; Selkov, Gene; Goryanin, Igor

    2012-07-16

    The volume of the experimentally measured time series data is rapidly growing, while storage solutions offering better data types than simple arrays of numbers or opaque blobs for keeping series data are sorely lacking. A number of indexing methods have been proposed to provide efficient access to time series data, but none has so far been integrated into a tried-and-proven database system. To explore the possibility of such integration, we have developed a data type for time series storage in PostgreSQL, an object-relational database system, and equipped it with an access method based on SAX (Symbolic Aggregate approXimation). This new data type has been successfully tested in a database supporting a large-scale plant gene expression experiment, and it was additionally tested on a very large set of simulated time series data.

  14. One step at a time: how to toilet train children with learning disabilities.

    PubMed

    Rogers, June

    Toilet training children with learning disabilities can present challenges and requires careful assessmentand management. This article examines strategies for toilet training using a five step approach bladder and bowel control.

  15. A fast, robust, and simple implicit method for adaptive time-stepping on adaptive mesh-refinement grids

    NASA Astrophysics Data System (ADS)

    Commerçon, B.; Debout, V.; Teyssier, R.

    2014-03-01

    Context. Implicit solvers present strong limitations when used on supercomputing facilities and in particular for adaptive mesh-refinement codes. Aims: We present a new method for implicit adaptive time-stepping on adaptive mesh-refinement grids. We implement it in the radiation-hydrodynamics solver we designed for the RAMSES code for astrophysical purposes and, more particularly, for protostellar collapse. Methods: We briefly recall the radiation-hydrodynamics equations and the adaptive time-stepping methodology used for hydrodynamical solvers. We then introduce the different types of boundary conditions (Dirichlet, Neumann, and Robin) that are used at the interface between levels and present our implementation of the new method in the RAMSES code. The method is tested against classical diffusion and radiation-hydrodynamics tests, after which we present an application for protostellar collapse. Results: We show that using Dirichlet boundary conditions at level interfaces is a good compromise between robustness and accuracy and that it can be used in structure formation calculations. The gain in computational time over our former unique time step method ranges from factors of 5 to 50 depending on the level of adaptive time-stepping and on the problem. We successfully compare the old and new methods for protostellar collapse calculations that involve highly non linear physics. Conclusions: We have developed a simple but robust method for adaptive time-stepping of implicit scheme on adaptive mesh-refinement grids. It can be applied to a wide variety of physical problems that involve diffusion processes.

  16. Non-iterative adaptive time-stepping scheme with temporal truncation error control for simulating variable-density flow

    NASA Astrophysics Data System (ADS)

    Hirthe, Eugenia M.; Graf, Thomas

    2012-12-01

    The automatic non-iterative second-order time-stepping scheme based on the temporal truncation error proposed by Kavetski et al. [Kavetski D, Binning P, Sloan SW. Non-iterative time-stepping schemes with adaptive truncation error control for the solution of Richards equation. Water Resour Res 2002;38(10):1211, http://dx.doi.org/10.1029/2001WR000720.] is implemented into the code of the HydroGeoSphere model. This time-stepping scheme is applied for the first time to the low-Rayleigh-number thermal Elder problem of free convection in porous media [van Reeuwijk M, Mathias SA, Simmons CT, Ward JD. Insights from a pseudospectral approach to the Elder problem. Water Resour Res 2009;45:W04416, http://dx.doi.org/10.1029/2008WR007421.], and to the solutal [Shikaze SG, Sudicky EA, Schwartz FW. Density-dependent solute transport in discretely-fractured geological media: is prediction possible? J Contam Hydrol 1998;34:273-91] problem of free convection in fractured-porous media. Numerical simulations demonstrate that the proposed scheme efficiently limits the temporal truncation error to a user-defined tolerance by controlling the time-step size. The non-iterative second-order time-stepping scheme can be applied to (i) thermal and solutal variable-density flow problems, (ii) linear and non-linear density functions, and (iii) problems including porous and fractured-porous media.

  17. Generalized shot noise model for time-reversal in multiple-scattering media allowing for arbitrary inputs and windowing

    PubMed Central

    Haworth, Kevin J.; Fowlkes, J. Brian; Carson, Paul L.; Kripfgans, Oliver D.

    2009-01-01

    A theoretical shot noise model to describe the output of a time-reversal experiment in a multiple-scattering medium is developed. This (non-wave equation based) model describes the following process. An arbitrary waveform is transmitted through a high-order multiple-scattering environment and recorded. The recorded signal is arbitrarily windowed and then time-reversed. The processed signal is retransmitted into the environment and the resulting signal recorded. The temporal and spatial signal and noise of this process is predicted statistically. It is found that the time when the noise is largest depends on the arbitrary windowing and this noise peak can occur at times outside the main lobe. To determine further trends, a common set of parameters is applied to the general result. It is seen that as the duration of the input function increases, the signal-to-noise ratio (SNR) decreases (independent of signal bandwidth). It is also seen that longer persisting impulse responses result in increased main lobe amplitudes and SNR. Assumptions underpinning the generalized shot noise model are compared to an experimental realization of a multiple-scattering medium (a time-reversal chaotic cavity). Results from the model are compared to random number numerical simulation. PMID:19425655

  18. The Influence of Time Spent in Outdoor Play on Daily and Aerobic Step Count in Costa Rican Children

    ERIC Educational Resources Information Center

    Morera Castro, Maria del Rocio

    2011-01-01

    The purpose of this study is to examine the influence of time spent in outdoor play (i.e., on weekday and weekend days) on daily (i.e., average step count) and aerobic step count (i.e., average moderate to vigorous physical activity [MVPA] during the weekdays and weekend days) in fifth grade Costa Rican children. It was hypothesized that: (a)…

  19. Kinetic Analysis of Parallel-Consecutive First-Order Reactions with a Reversible Step: Concentration-Time Integrals Method

    ERIC Educational Resources Information Center

    Mucientes, A. E.; de la Pena, M. A.

    2009-01-01

    The concentration-time integrals method has been used to solve kinetic equations of parallel-consecutive first-order reactions with a reversible step. This method involves the determination of the area under the curve for the concentration of a given species against time. Computer techniques are used to integrate experimental curves and the method…

  20. Single particle optical extinction and scattering allows real time quantitative characterization of drug payload and degradation of polymeric nanoparticles

    NASA Astrophysics Data System (ADS)

    Potenza, M. A. C.; Sanvito, T.; Argentiere, S.; Cella, C.; Paroli, B.; Lenardi, C.; Milani, P.

    2015-12-01

    The behavior of nanoparticles in biological systems is determined by their dimensions, size distribution, shape, surface chemistry, density, drug loading and stability; the characterization of these parameters in realistic conditions and the possibility to follow their evolution in vitro and in vivo are, in most of the cases, far from the capabilities of the standard characterization technologies. Optical techniques such as dynamic light scattering (DLS) are, in principle, well suited for in line characterization of nanoparticle, however their fail in characterizing the evolution of nanoparticle in solution where change in particle dimension and density is present. Here we present an in-line optical technique based on single particle extinction and scattering (SPES) overcoming the limitations typical of DLS and allowing for the efficient characterization of nanoparticle polydispersity, index of refraction and degradation dynamics in solution. Using SPES, we characterized the evolution of PLGA nanoparticles with different structures and drug payloads in solution and we compared the results with DLS. Our results suggest that SPES could be used as a process analytical technology for pharmaceutical nanoparticle production.

  1. A Step Response Based Mixed-Signal BIST Approach for Continuous-time Linear Circuits

    NASA Technical Reports Server (NTRS)

    Walker, Alvernon; Lala, P. K.

    2001-01-01

    A new Mixed-Signal Built-in self-test approach that is based upon the step response of a reconfigurable (or multifunction) analog block is presented in this paper. The technique requires the overlapping step response of the Circuit Under Test (CUT) for two circuit configurations. Each configuration can be realized by changing the topology of the CUT or by sampling two CUT nodes with differing step responses. The technique can effectively detect both soft and hard faults and does not require an analog-to-digital converter (ADC) and/or digital-to-analog converter(DAC). It also does not require any precision voltage sources or comparators. This approach does not require any additional analog circuits to realize the test signal generator and sample circuits. The paper is concluded with the application of the proposed approach to a circuit found in the work of Epstein et al and two ITC 97 analog benchmark circuits.

  2. Using a scale selective tendency filter and forward-backward time stepping to calculate consistent semi-Lagrangian trajectories

    NASA Astrophysics Data System (ADS)

    Alerskans, Emy; Kaas, Eigil

    2016-04-01

    In semi-Lagrangian models used for climate and NWP the trajectories are normally/often determined kinematically. Here we propose a new method for calculating trajectories in a more dynamically consistent way by pre-integrating the governing equations in a pseudo-Lagrangian manner using a short time step. Only non-advective adiabatic terms are included in this calculation, i.e., the Coriolis and pressure gradient force plus gravity in the momentum equations, and the divergence term in the continuity equation. This integration is performed with a forward-backward time step. Optionally, the tendencies are filtered with a local space filter, which reduces the phase speed of short wave gravity and sound waves. The filter relaxes the time step limitation related to high frequency oscillations without compromising locality of the solution. The filter can be considered as an alternative to less local or global semi-implicit solvers. Once trajectories are estimated over a complete long advective time step the full set of governing equations is stepped forward using these trajectories in combination with a flux form semi-Lagrangian formulation of the equations. The methodology is designed to improve consistency and scalability on massively parallel systems, although here it has only been verified that the technique produces realistic results in a shallow water model and a 2D model based on the full Euler equations.

  3. The effect of selection of time steps and average assumptions on the continuous simulation of rainwater harvesting strategies.

    PubMed

    Coombes, P J; Barry, M E

    2007-01-01

    The use of domestic rainwater tanks with back up from mains water supplies in urban areas can produce considerable reductions in mains water demands and stormwater runoff. It is commonplace to analyse the performance of rainwater tanks using continuous simulation with daily time steps and average water use assumptions. This paper compares this simplistic analysis to more detailed analysis that employs 6 minute time steps and climate dependent water demand. The use of daily time steps produced considerable under-estimation of annual rainwater yields that were dependent on tank size, rain depth, seasonal distribution of rainfall, water demand and tank configuration. It is shown that analysis of the performance of rainwater tanks is critically dependent on detailed inputs.

  4. Transient Crack Growth Behavior Under Cycle/Time-Dependent Step Loading for Pb-Containing and Pb-Free Solders

    NASA Astrophysics Data System (ADS)

    Fakpan, Kittichai; Otsuka, Yuichi; Miyashita, Yukio; Mutoh, Yoshiharu; Nagata, Kohsoku

    2013-12-01

    In the present study, fatigue crack growth tests of Pb-containing [Sn-37Pb (wt.%)] and Pb-free [Sn-3.0Ag-0.5Cu (wt.%)] solders were performed under cycle/time-dependent step loading at a constant J-integral range (Δ J). The C * parameter was also estimated for discussing time-dependent crack growth behavior. The experimental results indicated that acceleration of the crack growth rate at the beginning of the second loading step was induced when the C * value for the first loading step was high, regardless of time- or cycle-dependent crack growth and for both Sn-37Pb and Sn-3.0Ag-0.5Cu solders. The length of the acceleration region of the crack growth rate for both solders was in good agreement with the creep damage zone size estimated by the creep zone model proposed by Riedel and Rice.

  5. Optical monitor for real time thickness change measurements via lateral-translation induced phase-stepping interferometry

    DOEpatents

    Rushford, Michael C.

    2002-01-01

    An optical monitoring instrument monitors etch depth and etch rate for controlling a wet-etching process. The instrument provides means for viewing through the back side of a thick optic onto a nearly index-matched interface. Optical baffling and the application of a photoresist mask minimize spurious reflections to allow for monitoring with extremely weak signals. A Wollaston prism enables linear translation for phase stepping.

  6. When the Time Comes for the Community College President to Step Aside: Daunting Realities of Leading

    ERIC Educational Resources Information Center

    Maslin-Ostrowski, Patricia; Floyd, Deborah L.

    2012-01-01

    This interview study examined seven community college presidents' experiences of facing a sudden and unplanned stepping aside (e.g., unexpectedly needing to resign or termination) in order to understand the meaning of the transition experience for leaders. It provides an up-close view of presidents' perspectives on leaving the college. Despite the…

  7. Changing Step or Marking Time? Teacher Education Reforms for the Learning and Skills Sector in England

    ERIC Educational Resources Information Center

    Thompson, Ron; Robinson, Denise

    2008-01-01

    The unprecedented degree of attention given to the learning and skills sector in England by successive New Labour governments has led to a significant increase in what is expected of the teaching workforce. To help meet these expectations, a "step change" in the quality of initial teacher training for the sector is promised, alongside provisions…

  8. 41 CFR 302-2.110 - Are there time factors that we must consider for allowing an employee to complete all aspects of...

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 41 Public Contracts and Property Management 4 2010-07-01 2010-07-01 false Are there time factors... 302-2.110 Public Contracts and Property Management Federal Travel Regulation System RELOCATION ALLOWANCES INTRODUCTION 2-EMPLOYEES ELIGIBILITY REQUIREMENTS Agency Responsibilities Time Limits §...

  9. 41 CFR 302-2.110 - Are there time factors that we must consider for allowing an employee to complete all aspects of...

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 41 Public Contracts and Property Management 4 2011-07-01 2011-07-01 false Are there time factors... 302-2.110 Public Contracts and Property Management Federal Travel Regulation System RELOCATION ALLOWANCES INTRODUCTION 2-EMPLOYEES ELIGIBILITY REQUIREMENTS Agency Responsibilities Time Limits §...

  10. 41 CFR 302-2.110 - Are there time factors that we must consider for allowing an employee to complete all aspects of...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 41 Public Contracts and Property Management 4 2013-07-01 2012-07-01 true Are there time factors... 302-2.110 Public Contracts and Property Management Federal Travel Regulation System RELOCATION ALLOWANCES INTRODUCTION 2-EMPLOYEES ELIGIBILITY REQUIREMENTS Agency Responsibilities Time Limits §...

  11. 41 CFR 302-2.110 - Are there time factors that we must consider for allowing an employee to complete all aspects of...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 41 Public Contracts and Property Management 4 2012-07-01 2012-07-01 false Are there time factors... 302-2.110 Public Contracts and Property Management Federal Travel Regulation System RELOCATION ALLOWANCES INTRODUCTION 2-EMPLOYEES ELIGIBILITY REQUIREMENTS Agency Responsibilities Time Limits §...

  12. 41 CFR 302-2.110 - Are there time factors that we must consider for allowing an employee to complete all aspects of...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 41 Public Contracts and Property Management 4 2014-07-01 2014-07-01 false Are there time factors... 302-2.110 Public Contracts and Property Management Federal Travel Regulation System RELOCATION ALLOWANCES INTRODUCTION 2-EMPLOYEES ELIGIBILITY REQUIREMENTS Agency Responsibilities Time Limits §...

  13. The effect of timing electrical stimulation to robotic-assisted stepping on neuromuscular activity and associated kinematics.

    PubMed

    Askari, Sina; Chao, TeKang; de Leon, Ray D; Won, Deborah S

    2013-01-01

    Results of previous studies raise the question of how timing neuromuscular functional electrical stimulation (FES) to limb movements during stepping might alter neuromuscular control differently than patterned stimulation alone. We have developed a prototype FES system for a rodent model of spinal cord injury (SCI) that times FES to robotic treadmill training (RTT). In this study, one group of rats (n = 6) was trained with our FES+RTT system and received stimulation of the ankle flexor (tibialis anterior [TA]) muscle timed according to robot-controlled hind-limb position (FES+RTT group); a second group (n = 5) received a similarly patterned stimulation, randomly timed with respect to the rats' hind-limb movements, while they were in their cages (randomly timed stimulation [RS] group). After 4 wk of training, we tested treadmill stepping ability and compared kinematic measures of hind-limb movement and electromyography (EMG) activity in the TA. The FES+RTT group stepped faster and exhibited TA EMG profiles that better matched the applied stimulation profile during training than the RS group. The shape of the EMG profile was assessed by "gamma," a measure that quantified the concentration of EMG activity during the early swing phase of the gait cycle. This gamma measure was 112% higher for the FES+RTT group than for the RS group. The FES+RTT group exhibited burst-to-step latencies that were 41% shorter and correspondingly exhibited a greater tendency to perform ankle flexion movements during stepping than the RS group, as measured by the percentage of time the hind limb was either dragging or in withdrawal. The results from this study support the hypothesis that locomotor training consisting of FES timed to hind-limb movement improves the activation of hind-limb muscle more so than RS alone. Our rodent FES+RTT system can serve as a tool to help further develop this combined therapy to target appropriate neurophysiological changes for locomotor control.

  14. Adaptice-step time integration package for stiff, nonstiff and multi-rate systems of ordinary differential equations (ODEs)

    SciTech Connect

    2014-06-01

    ARKode is part of a software family called SUNDIALS: SUite of Nonlinear and Differential/ALgebraic equation Solvers [1]. The ARKode solver library provides an adaptive-step time integration package for stiff, nonstiff and multi-rate systems of ordinary differential equations (ODEs) using Runge Kutta methods [2].

  15. Operational flood control of a low-lying delta system using large time step Model Predictive Control

    NASA Astrophysics Data System (ADS)

    Tian, Xin; van Overloop, Peter-Jules; Negenborn, Rudy R.; van de Giesen, Nick

    2015-01-01

    The safety of low-lying deltas is threatened not only by riverine flooding but by storm-induced coastal flooding as well. For the purpose of flood control, these deltas are mostly protected in a man-made environment, where dikes, dams and other adjustable infrastructures, such as gates, barriers and pumps are widely constructed. Instead of always reinforcing and heightening these structures, it is worth considering making the most of the existing infrastructure to reduce the damage and manage the delta in an operational and overall way. In this study, an advanced real-time control approach, Model Predictive Control, is proposed to operate these structures in the Dutch delta system (the Rhine-Meuse delta). The application covers non-linearity in the dynamic behavior of the water system and the structures. To deal with the non-linearity, a linearization scheme is applied which directly uses the gate height instead of the structure flow as the control variable. Given the fact that MPC needs to compute control actions in real-time, we address issues regarding computational time. A new large time step scheme is proposed in order to save computation time, in which different control variables can have different control time steps. Simulation experiments demonstrate that Model Predictive Control with the large time step setting is able to control a delta system better and much more efficiently than the conventional operational schemes.

  16. Efficient multiple-time-step integrators with distance-based force splitting for particle-mesh-Ewald molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Qian, Xiaoliang; Schlick, Tamar

    2002-04-01

    We develop an efficient multiple-time-step force splitting scheme for particle-mesh-Ewald molecular dynamics simulations. Our method exploits smooth switch functions effectively to regulate direct and reciprocal space terms for the electrostatic interactions. The reciprocal term with the near field contributions removed is assigned to the slow class; the van der Waals and regulated particle-mesh-Ewald direct-space terms, each associated with a tailored switch function, are assigned to the medium class. All other bonded terms are assigned to the fast class. This versatile protocol yields good stability and accuracy for Newtonian algorithms, with temperature and pressure coupling, as well as for Langevin dynamics. Since the van der Waals interactions need not be cut at short distances to achieve moderate speedup, this integrator represents an enhancement of our prior multiple-time-step implementation for microcanonical ensembles. Our work also tests more rigorously the stability of such splitting schemes, in combination with switching methodology. Performance of the algorithms is optimized and tested on liquid water, solvated DNA, and solvated protein systems over 400 ps or longer simulations. With a 6 fs outer time step, we find computational speedup ratios of over 6.5 for Newtonian dynamics, compared with 0.5 fs single-time-step simulations. With modest Langevin damping, an outer time step of up to 16 fs can be used with a speedup ratio of 7.5. Theoretical analyses in our appendices produce guidelines for choosing the Langevin damping constant and show the close relationship among the leapfrog Verlet, velocity Verlet, and position Verlet variants.

  17. Ancient numerical daemons of conceptual hydrological modeling: 2. Impact of time stepping schemes on model analysis and prediction

    NASA Astrophysics Data System (ADS)

    Kavetski, Dmitri; Clark, Martyn P.

    2010-10-01

    Despite the widespread use of conceptual hydrological models in environmental research and operations, they remain frequently implemented using numerically unreliable methods. This paper considers the impact of the time stepping scheme on model analysis (sensitivity analysis, parameter optimization, and Markov chain Monte Carlo-based uncertainty estimation) and prediction. It builds on the companion paper (Clark and Kavetski, 2010), which focused on numerical accuracy, fidelity, and computational efficiency. Empirical and theoretical analysis of eight distinct time stepping schemes for six different hydrological models in 13 diverse basins demonstrates several critical conclusions. (1) Unreliable time stepping schemes, in particular, fixed-step explicit methods, suffer from troublesome numerical artifacts that severely deform the objective function of the model. These deformations are not rare isolated instances but can arise in any model structure, in any catchment, and under common hydroclimatic conditions. (2) Sensitivity analysis can be severely contaminated by numerical errors, often to the extent that it becomes dominated by the sensitivity of truncation errors rather than the model equations. (3) Robust time stepping schemes generally produce "better behaved" objective functions, free of spurious local optima, and with sufficient numerical continuity to permit parameter optimization using efficient quasi Newton methods. When implemented within a multistart framework, modern Newton-type optimizers are robust even when started far from the optima and provide valuable diagnostic insights not directly available from evolutionary global optimizers. (4) Unreliable time stepping schemes lead to inconsistent and biased inferences of the model parameters and internal states. (5) Even when interactions between hydrological parameters and numerical errors provide "the right result for the wrong reason" and the calibrated model performance appears adequate, unreliable

  18. One step at a time: action mechanism of Sushi 1 antimicrobial peptide and derived molecules.

    PubMed

    Leptihn, Sebastian; Guo, Lin; Frecer, Vladimir; Ho, Bow; Ding, Jeak Ling; Wohland, Thorsten

    2010-01-01

    Antimicrobial peptides (AMPs) are a crucial part of the innate immune system of eukaryotes and present a possible alternative to common antibiotics. It is therefore of great importance to understand their modes of action. Using a single-molecule approach in combination with high resolution imaging and bio-functional assays we were able to determine the different steps occurring during the action of the α-helical AMP Sushi 1 during bacterial lysis in spatial and temporal resolution in a biologically relevant context. Furthermore, we comment on the use of Sushi 1 as a template for new peptides to learn more about structure-function relationship of AMPs.

  19. An accurate treatment of diffuse reflection boundary conditions for a stochastic particle Fokker-Planck algorithm with large time steps

    NASA Astrophysics Data System (ADS)

    Önskog, Thomas; Zhang, Jun

    2015-12-01

    In this paper, we present a stochastic particle algorithm for the simulation of flows of wall-confined gases with diffuse reflection boundary conditions. Based on the theoretical observation that the change in location of the particles consists of a deterministic part and a Wiener process if the time scale is much larger than the relaxation time, a new estimate for the first hitting time at the boundary is obtained. This estimate facilitates the construction of an algorithm with large time steps for wall-confined flows. Numerical simulations verify that the proposed algorithm reproduces the correct boundary behaviour.

  20. Novel algorithm for real-time onset detection of surface electromyography in step-tracking wrist movements.

    PubMed

    Kuroda, Yoshihiro; Nisky, Ilana; Uranishi, Yuki; Imura, Masataka; Okamura, Allison M; Oshiro, Osamu

    2013-01-01

    We present a novel algorithm for real-time detection of the onset of surface electromyography signal in step-tracking wrist movements. The method identifies abrupt increase of the quasi-tension signal calculated from sEMG resulting from the step-by-step recruitment of activated motor units. We assessed the performance of our proposed algorithm using both simulated and real sEMG signals, and compared with two existing detection methods. Evaluation with simulated sEMG showed that the detection accuracy of our method is robust to different signal-to-noise ratios, and that it outperforms the existing methods in terms of bias when the noise is large (low SNR). Evaluation with real sEMG analysis also indicated better detection performance compared to existing methods. PMID:24110123

  1. Ultra-fast consensus of discrete-time multi-agent systems with multi-step predictive output feedback

    NASA Astrophysics Data System (ADS)

    Zhang, Wenle; Liu, Jianchang

    2016-04-01

    This article addresses the ultra-fast consensus problem of high-order discrete-time multi-agent systems based on a unified consensus framework. A novel multi-step predictive output mechanism is proposed under a directed communication topology containing a spanning tree. By predicting the outputs of a network several steps ahead and adding this information into the consensus protocol, it is shown that the asymptotic convergence factor is improved by a power of q + 1 compared to the routine consensus. The difficult problem of selecting the optimal control gain is solved well by introducing a variable called convergence step. In addition, the ultra-fast formation achievement is studied on the basis of this new consensus protocol. Finally, the ultra-fast consensus with respect to a reference model and robust consensus is discussed. Some simulations are performed to illustrate the effectiveness of the theoretical results.

  2. DOUBLE-STEP MULTIPLEX REAL TIME PCR WITH MELTING CURVE ANALYSIS FOR DETECTION AND DIFFERENTIATION OF MYCOBACTERIA IN SPUTUM.

    PubMed

    Kasa, Sawinee; Faksri, Kiatichai; Kaewkes, Wanlop; Lulitanond, Viraphong; Namwat, Wises

    2015-01-01

    Mycobacterium tuberculosis (M. tb) is a causative agent of tuberculosis, a worldwide public health problem. In recent years, the incidence of human mycobacterial infection due to species other than M. tb has increased. However, the lack of specific, rapid, and inexpensive methods for identification of mycobacterial species remains a pressing problem. A diagnostic test was developed for mycobacterial strain differentiation utilizing a double-step multiplex real time PCR together with melting curve analysis for identifying and distinguishing among M. tb, M. bovis BCG, other members of M. tb. complex, M. avium, and non-tuberculosis mycobacteria. The assay was tested using 167 clinical sputum samples in comparison with acid-fast staining and culturing. Using only the first step (step A) the assay achieved sensitivity and specificity of 81% and 95%, respectively. The detection limit was equivalent to 50 genome copies.

  3. DOUBLE-STEP MULTIPLEX REAL TIME PCR WITH MELTING CURVE ANALYSIS FOR DETECTION AND DIFFERENTIATION OF MYCOBACTERIA IN SPUTUM.

    PubMed

    Kasa, Sawinee; Faksri, Kiatichai; Kaewkes, Wanlop; Lulitanond, Viraphong; Namwat, Wises

    2015-01-01

    Mycobacterium tuberculosis (M. tb) is a causative agent of tuberculosis, a worldwide public health problem. In recent years, the incidence of human mycobacterial infection due to species other than M. tb has increased. However, the lack of specific, rapid, and inexpensive methods for identification of mycobacterial species remains a pressing problem. A diagnostic test was developed for mycobacterial strain differentiation utilizing a double-step multiplex real time PCR together with melting curve analysis for identifying and distinguishing among M. tb, M. bovis BCG, other members of M. tb. complex, M. avium, and non-tuberculosis mycobacteria. The assay was tested using 167 clinical sputum samples in comparison with acid-fast staining and culturing. Using only the first step (step A) the assay achieved sensitivity and specificity of 81% and 95%, respectively. The detection limit was equivalent to 50 genome copies. PMID:26513906

  4. Modeling Stepped Leaders Using a Time Dependent Multi-dipole Model and High-speed Video Data

    NASA Astrophysics Data System (ADS)

    Karunarathne, S.; Marshall, T.; Stolzenburg, M.; Warner, T. A.; Orville, R. E.

    2012-12-01

    In summer of 2011, we collected lightning data with 10 stations of electric field change meters (bandwidth of 0.16 Hz - 2.6 MHz) on and around NASA/Kennedy Space Center (KSC) covering nearly 70 km × 100 km area. We also had a high-speed video (HSV) camera recording 50,000 images per second collocated with one of the electric field change meters. In this presentation we describe our use of these data to model the electric field change caused by stepped leaders. Stepped leaders of a cloud to ground lightning flash typically create the initial path for the first return stroke (RS). Most of the time, stepped leaders have multiple complex branches, and one of these branches will create the ground connection for the RS to start. HSV data acquired with a short focal length lens at ranges of 5-25 km from the flash are useful for obtaining the 2-D location of these multiple branches developing at the same time. Using HSV data along with data from the KSC Lightning Detection and Ranging (LDAR2) system and the Cloud to Ground Lightning Surveillance System (CGLSS), the 3D path of a leader may be estimated. Once the path of a stepped leader is obtained, the time dependent multi-dipole model [ Lu, Winn,and Sonnenfeld, JGR 2011] can be used to match the electric field change at various sensor locations. Based on this model, we will present the time-dependent charge distribution along a leader channel and the total charge transfer during the stepped leader phase.

  5. Issues in measure-preserving three dimensional flow integrators: Self-adjointness, reversibility, and non-uniform time stepping

    SciTech Connect

    Finn, John M.

    2015-03-01

    Properties of integration schemes for solenoidal fields in three dimensions are studied, with a focus on integrating magnetic field lines in a plasma using adaptive time stepping. It is shown that implicit midpoint (IM) and a scheme we call three-dimensional leapfrog (LF) can do a good job (in the sense of preserving KAM tori) of integrating fields that are reversible, or (for LF) have a 'special divergence-free' property. We review the notion of a self-adjoint scheme, showing that such schemes are at least second order accurate and can always be formed by composing an arbitrary scheme with its adjoint. We also review the concept of reversibility, showing that a reversible but not exactly volume-preserving scheme can lead to a fractal invariant measure in a chaotic region, although this property may not often be observable. We also show numerical results indicating that the IM and LF schemes can fail to preserve KAM tori when the reversibility property (and the SDF property for LF) of the field is broken. We discuss extensions to measure preserving flows, the integration of magnetic field lines in a plasma and the integration of rays for several plasma waves. The main new result of this paper relates to non-uniform time stepping for volume-preserving flows. We investigate two potential schemes, both based on the general method of Ref. [11], in which the flow is integrated in split time steps, each Hamiltonian in two dimensions. The first scheme is an extension of the method of extended phase space, a well-proven method of symplectic integration with non-uniform time steps. This method is found not to work, and an explanation is given. The second method investigated is a method based on transformation to canonical variables for the two split-step Hamiltonian systems. This method, which is related to the method of non-canonical generating functions of Ref. [35], appears to work very well.

  6. Simultaneous Effects of Allowed Time, Teaching Method, Ability, and Student Assessment of Treatment on Achievement in a High School Biology Course (ISIS).

    ERIC Educational Resources Information Center

    Burkman, Ernest; And Others

    1982-01-01

    Examined effects of teaching method (self-directed, group-directed, teacher-directed), academic ability, student assessment of treatment, and allowed time on achievement in three Individualized Science Instructional System (ISIS) biology minicourses. Results, among others, indicated that individualized instruction favored high-ability students and…

  7. Identification of the coupling step in Na(+)-translocating NADH:quinone oxidoreductase from real-time kinetics of electron transfer.

    PubMed

    Belevich, Nikolai P; Bertsova, Yulia V; Verkhovskaya, Marina L; Baykov, Alexander A; Bogachev, Alexander V

    2016-02-01

    Bacterial Na(+)-translocating NADH:quinone oxidoreductase (Na(+)-NQR) uses a unique set of prosthetic redox groups-two covalently bound FMN residues, a [2Fe-2S] cluster, FAD, riboflavin and a Cys4[Fe] center-to catalyze electron transfer from NADH to ubiquinone in a reaction coupled with Na(+) translocation across the membrane. Here we used an ultra-fast microfluidic stopped-flow instrument to determine rate constants and the difference spectra for the six consecutive reaction steps of Vibrio harveyi Na(+)-NQR reduction by NADH. The instrument, with a dead time of 0.25 ms and optical path length of 1 cm allowed collection of visible spectra in 50-μs intervals. By comparing the spectra of reaction steps with the spectra of known redox transitions of individual enzyme cofactors, we were able to identify the chemical nature of most intermediates and the sequence of electron transfer events. A previously unknown spectral transition was detected and assigned to the Cys4[Fe] center reduction. Electron transfer from the [2Fe-2S] cluster to the Cys4[Fe] center and all subsequent steps were markedly accelerated when Na(+) concentration was increased from 20 μM to 25 mM, suggesting coupling of the former step with tight Na(+) binding to or occlusion by the enzyme. An alternating access mechanism was proposed to explain electron transfer between subunits NqrF and NqrC. According to the proposed mechanism, the Cys4[Fe] center is alternatively exposed to either side of the membrane, allowing the [2Fe-2S] cluster of NqrF and the FMN residue of NqrC to alternatively approach the Cys4[Fe] center from different sides of the membrane. PMID:26655930

  8. "I Have to Rest All the Time Because You Are Not Allowed to Play": Exploring Children's Perceptions of Autonomy during Sleep-Time in Long Day Care Services

    ERIC Educational Resources Information Center

    Nothard, Michaela; Irvine, Susan; Theobald, Maryanne; Staton, Sally; Pattinson, Cassandra; Thorpe, Karen

    2015-01-01

    Daytime sleep is a significant part of the daily routine for children attending early childhood education and care (ECEC) services in Australia and many other countries. The practice of sleep-time can account for a substantial portion of the day in ECEC and often involves a mandated sleep/rest period for all children, including older…

  9. PHOEBE - step by step manual

    NASA Astrophysics Data System (ADS)

    Zasche, P.

    2016-03-01

    An easy step-by-step manual of PHOEBE is presented. It should serve as a starting point for the first time users of PHOEBE analyzing the eclipsing binary light curve. It is demonstrated on one particular detached system also with the downloadable data and the whole procedure is described easily till the final trustworthy fit is being reached.

  10. A high-order adaptive time-stepping TVD solver for Boussinesq modeling of breaking waves and coastal inundation

    NASA Astrophysics Data System (ADS)

    Shi, Fengyan; Kirby, James T.; Harris, Jeffrey C.; Geiman, Joseph D.; Grilli, Stephan T.

    We present a high-order adaptive time-stepping TVD solver for the fully nonlinear Boussinesq model of Chen (2006), extended to include moving reference level as in Kennedy et al. (2001). The equations are reorganized in order to facilitate high-order Runge-Kutta time-stepping and a TVD type scheme with a Riemann solver. Wave breaking is modeled by locally switching to the nonlinear shallow water equations when the Froude number exceeds a certain threshold. The moving shoreline boundary condition is implemented using the wetting-drying algorithm with the adjusted wave speed of the Riemann solver. The code is parallelized using the Message Passing Interface (MPI) with non-blocking communication. Model validations show good performance in modeling wave shoaling, breaking, wave runup and wave-averaged nearshore circulation.

  11. Convergence of a class of semi-implicit time-stepping schemes for nonsmooth rigid multibody dynamics.

    SciTech Connect

    Gavrea, B. I.; Anitescu, M.; Potra, F. A.; Mathematics and Computer Science; Univ. of Pennsylvania; Univ. of Maryland

    2008-01-01

    In this work we present a framework for the convergence analysis in a measure differential inclusion sense of a class of time-stepping schemes for multibody dynamics with contacts, joints, and friction. This class of methods solves one linear complementarity problem per step and contains the semi-implicit Euler method, as well as trapezoidal-like methods for which second-order convergence was recently proved under certain conditions. By using the concept of a reduced friction cone, the analysis includes, for the first time, a convergence result for the case that includes joints. An unexpected intermediary result is that we are able to define a discrete velocity function of bounded variation, although the natural discrete velocity function produced by our algorithm may have unbounded variation.

  12. Finite-difference modeling with variable grid-size and adaptive time-step in porous media

    NASA Astrophysics Data System (ADS)

    Liu, Xinxin; Yin, Xingyao; Wu, Guochen

    2014-04-01

    Forward modeling of elastic wave propagation in porous media has great importance for understanding and interpreting the influences of rock properties on characteristics of seismic wavefield. However, the finite-difference forward-modeling method is usually implemented with global spatial grid-size and time-step; it consumes large amounts of computational cost when small-scaled oil/gas-bearing structures or large velocity-contrast exist underground. To overcome this handicap, combined with variable grid-size and time-step, this paper developed a staggered-grid finite-difference scheme for elastic wave modeling in porous media. Variable finite-difference coefficients and wavefield interpolation were used to realize the transition of wave propagation between regions of different grid-size. The accuracy and efficiency of the algorithm were shown by numerical examples. The proposed method is advanced with low computational cost in elastic wave simulation for heterogeneous oil/gas reservoirs.

  13. Adaptive discrete-time controller design with neural network for hypersonic flight vehicle via back-stepping

    NASA Astrophysics Data System (ADS)

    Xu, Bin; Sun, Fuchun; Yang, Chenguang; Gao, Daoxiang; Ren, Jianxin

    2011-09-01

    In this article, the adaptive neural controller in discrete time is investigated for the longitudinal dynamics of a generic hypersonic flight vehicle. The dynamics are decomposed into the altitude subsystem and the velocity subsystem. The altitude subsystem is transformed into the strict-feedback form from which the discrete-time model is derived by the first-order Taylor expansion. The virtual control is designed with nominal feedback and neural network (NN) approximation via back-stepping. Meanwhile, one adaptive NN controller is designed for the velocity subsystem. To avoid the circular construction problem in the practical control, the design of coefficients adopts the upper bound instead of the nominal value. Under the proposed controller, the semiglobal uniform ultimate boundedness stability is guaranteed. The square and step responses are presented in the simulation studies to show the effectiveness of the proposed control approach.

  14. Adaptive statistic tracking control based on two-step neural networks with time delays.

    PubMed

    Yi, Yang; Guo, Lei; Wang, Hong

    2009-03-01

    This paper presents a new type of control framework for dynamical stochastic systems, called statistic tracking control (STC). The system considered is general and non-Gaussian and the tracking objective is the statistical information of a given target probability density function (pdf), rather than a deterministic signal. The control aims at making the statistical information of the output pdfs to follow those of a target pdf. For such a control framework, a variable structure adaptive tracking control strategy is first established using two-step neural network models. Following the B-spline neural network approximation to the integrated performance function, the concerned problem is transferred into the tracking of given weights. The dynamic neural network (DNN) is employed to identify the unknown nonlinear dynamics between the control input and the weights related to the integrated function. To achieve the required control objective, an adaptive controller based on the proposed DNN is developed so as to track a reference trajectory. Stability analysis for both the identification and tracking errors is developed via the use of Lyapunov stability criterion. Simulations are given to demonstrate the efficiency of the proposed approach. PMID:19179249

  15. High resolution frequency to time domain transformations applied to the stepped carrier MRIS measurements

    NASA Technical Reports Server (NTRS)

    Ardalan, Sasan H.

    1992-01-01

    Two narrow-band radar systems are developed for high resolution target range estimation in inhomogeneous media. They are reformulations of two presently existing systems such that high resolution target range estimates may be achieved despite the use of narrow bandwidth radar pulses. A double sideband suppressed carrier radar technique originally derived in 1962, and later abandoned due to its inability to accurately measure target range in the presence of an interfering reflection, is rederived to incorporate the presence of an interfering reflection. The new derivation shows that the interfering reflection causes a period perturbation in the measured phase response. A high resolution spectral estimation technique is used to extract the period of this perturbation leading to accurate target range estimates independent of the signal-to-interference ratio. A non-linear optimal signal processing algorithm is derived for a frequency-stepped continuous wave radar system. The resolution enhancement offered by optimal signal processing of the data over the conventional Fourier Transform technique is clearly demonstrated using measured radar data. A method for modeling plane wave propagation in inhomogeneous media based on transmission line theory is derived and studied. Several simulation results including measurement of non-uniform electron plasma densities that develop near the heat tiles of a space re-entry vehicle are presented which verify the validity of the model.

  16. Spectral (600-1050 nm) time exposures (99.6 μs) of a lightning stepped leader

    NASA Astrophysics Data System (ADS)

    Warner, Tom A.; Orville, Richard E.; Marshall, J. L.; Huggins, Kyle

    2011-06-01

    A cloud-to-ground lightning stepped leader has been recorded with a slitless spectrograph at a recording rate of 10,000 images per second at a distance of 0.6 km. Five sequential images of the leader spectra were recorded with an exposure (integration) time of 99.6 μs each over a spectral range from 600 to 1050 nm. These are the first stepped leader spectra covering the range 600 to 1050 nm. The last three spectra, obtained immediately before the return stroke, were analyzed at an altitude of between 108 and 122 m above a struck vehicle. The spectral emissions in the near infrared are dominated by neutral nitrogen and oxygen emissions, and Hα, with only a few emission lines from singly ionized nitrogen. A singly ionized nitrogen line at 661.1 nm is present in the first analyzed image, but not in the two subsequent images at the same height, which suggests a cooling of the channel. The emissions are integrated over a 99.6 μs exposure time and therefore show no evidence of stepping. The ensuing negative return stroke was detected by the National Lightning Detection Network and had an estimated peak current of -15.2 kA. One subsequent stroke was outside the field of view of the spectrograph. The flash occurred on 11 September 2009 near New Underwood, South Dakota, and the exact location of the first stroke is known because it struck a car traveling on Interstate 90. The stepped leader two-dimensional speed increased in the last four steps from 1.53 × 105 to 2.42 × 105 m/s with an average of 2.03 × 105 m/s.

  17. Discrete step model of helix-coil kinetics: Distribution of fluctuation times

    NASA Astrophysics Data System (ADS)

    Poland, Douglas

    1996-07-01

    A method is outlined for the computer simulation of the cooperative kinetics required to construct the distribution function for time intervals between fluctuations in conformational states in macromolecules. Using the helix-coil transition in polyamino acids as an example, we develop a Monte Carlo cellular automata approximation of the kinetics of this system in discrete time. This approximation is tested against a number of exact solutions for homopolymers and is then used to calculate moments of the distribution function for the time intervals between switches in conformational state at a given site (e.g., given a switch from coil to helix at zero time, how long will it take before the state switches back). The maximum-entropy method is used to construct the very broad distribution function from the moments. In heteropolymers the diffusion of helix-coil boundaries is reduced, helix being more localized on strong helix-forming residues. We investigate the effect of a specific sequence of amino acid residues on conformational fluctuations by using the known σ and s values for the naturally occurring amino acids to simulate the kinetics of helix formation (limiting the range of cooperativity to the α-helix) in sperm whale myoglobin, giving the time evolution to the equilibrium probability profile in this system.

  18. Parallel machine scheduling with step-deteriorating jobs and setup times by a hybrid discrete cuckoo search algorithm

    NASA Astrophysics Data System (ADS)

    Guo, Peng; Cheng, Wenming; Wang, Yi

    2015-11-01

    This article considers the parallel machine scheduling problem with step-deteriorating jobs and sequence-dependent setup times. The objective is to minimize the total tardiness by determining the allocation and sequence of jobs on identical parallel machines. In this problem, the processing time of each job is a step function dependent upon its starting time. An individual extended time is penalized when the starting time of a job is later than a specific deterioration date. The possibility of deterioration of a job makes the parallel machine scheduling problem more challenging than ordinary ones. A mixed integer programming model for the optimal solution is derived. Due to its NP-hard nature, a hybrid discrete cuckoo search algorithm is proposed to solve this problem. In order to generate a good initial swarm, a modified Biskup-Hermann-Gupta (BHG) heuristic called MBHG is incorporated into the population initialization. Several discrete operators are proposed in the random walk of Lévy flights and the crossover search. Moreover, a local search procedure based on variable neighbourhood descent is integrated into the algorithm as a hybrid strategy in order to improve the quality of elite solutions. Computational experiments are executed on two sets of randomly generated test instances. The results show that the proposed hybrid algorithm can yield better solutions in comparison with the commercial solver CPLEX® with a one hour time limit, the discrete cuckoo search algorithm and the existing variable neighbourhood search algorithm.

  19. 40 CFR 35.2025 - Allowance and advance of allowance.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... facilities planning and design of the project and Step 7 agreements will include an allowance for facility... grant applicants for facilities planning and project design. (2) The State may request that the right...

  20. 40 CFR 35.2025 - Allowance and advance of allowance.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... facilities planning and design of the project and Step 7 agreements will include an allowance for facility... grant applicants for facilities planning and project design. (2) The State may request that the right...

  1. 40 CFR 35.2025 - Allowance and advance of allowance.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... facilities planning and design of the project and Step 7 agreements will include an allowance for facility... grant applicants for facilities planning and project design. (2) The State may request that the right...

  2. 40 CFR 35.2025 - Allowance and advance of allowance.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... facilities planning and design of the project and Step 7 agreements will include an allowance for facility... grant applicants for facilities planning and project design. (2) The State may request that the right...

  3. Leap Frog and Time Step Sub-Cycle Scheme for Coupled Neutronics and Thermal-Hydraulic Codes

    SciTech Connect

    Lu, S.

    2002-07-01

    As the result of the advancing TCP/IP based inter-process communication technology, more and more legacy thermal-hydraulic codes have been coupled with neutronics codes to provide best-estimate capabilities for reactivity related reactor transient analysis. Most of the coupling schemes are based on closely coupled serial or parallel approaches. Therefore, the execution of the coupled codes usually requires significant CPU time, when a complicated system is analyzed. Leap Frog scheme has been used to reduce the run time. The extent of the decoupling is usually determined based on a trial and error process for a specific analysis. It is the intent of this paper to develop a set of general criteria, which can be used to invoke the automatic Leap Frog algorithm. The algorithm will not only provide the run time reduction but also preserve the accuracy. The criteria will also serve as the base of an automatic time step sub-cycle scheme when a sudden reactivity change is introduced and the thermal-hydraulic code is marching with a relatively large time step. (authors)

  4. Paper Laser: a step towards a time scale generation from an ensemble of optical clocks

    NASA Astrophysics Data System (ADS)

    Ortiz, C. A.; de Carlos, E.; Lopez, J. M.

    2016-06-01

    In this paper a simple and innovative technique to combine n optical frequencies with the aim to produce a virtual laser with superior metrological characteristics is introduced. The algorithms to combine a number of clocks to produce a virtual clock, which is also referred as paper clock, are well known. An example of this is the statistical generation of the UTC time scale by the Bureau International des Poids et Mesures (BIPM) using a recursive algorithm (ALGOS). A similar algorithm to combine n optical frequencies, all of them with same nominal value, to produce a “paper laser” whose frequency is known through its difference with respect to the optical frequencies of the ensemble is proposed here. As a demonstration of this, three optical frequencies stabilized to the D2 Cs-133 line, all of them with similar frequency stability were experimentally combined. A paper laser has been produced during hours whose frequency stability is about 3-1/2 times with respect to the original optical frequencies. This technique can be applied to combine ultra-stable optical frequencies to produce a paper laser that can be materialized by correcting one of the real optical frequencies of the ensemble. The robustness and stability of a paper laser is very attractive to produce a time scale from its operation.

  5. Accelerometer data requirements for reliable estimation of habitual physical activity and sedentary time of children during the early years - a worked example following a stepped approach.

    PubMed

    Bingham, Daniel D; Costa, Silvia; Clemes, Stacy A; Routen, Ash C; Moore, Helen J; Barber, Sally E

    2016-10-01

    This study presents a worked example of a stepped process to reliably estimate the habitual physical activity and sedentary time of a sample of young children. A total of 299 children (2.9 ± 0.6 years) were recruited. Outcome variables were daily minutes of total physical activity, sedentary time, moderate to vigorous physical activity and proportional values of each variable. In total, 282 (94%) provided 3 h of accelerometer data on ≥1 day and were included in a 6-step process: Step-1: determine minimum wear-time; Step-2: process 7-day-data; Step-3: determine the inclusion of a weekend day; Step-4: examine day-to-day variability; Step-5: calculate single day intraclass correlation (ICC) (2,1); Step-6: calculate number of days required to reach reliability. Following the process the results were, Step-1: 6 h was estimated as minimum wear-time of a standard day. Step-2: 98 (32%) children had ≥6 h wear on 7 days. Step-3: no differences were found between weekdays and weekend days (P ≥ 0.05). Step-4: no differences were found between day-to-day variability (P ≥ 0.05). Step-5: single day ICC's (2,1) ranged from 0.48 (total physical activity and sedentary time) to 0.53 (proportion of moderate to vigorous physical activity). Step-6: to reach reliability (ICC = 0.7), 3 days were required for all outcomes. In conclusion following a 7 day wear protocol, ≥6 h on any 3 days was found to have acceptable reliability. The stepped-process offers researchers a method to derive sample-specific wear-time criterion.

  6. Issues in measure-preserving three dimensional flow integrators: Self-adjointness, reversibility, and non-uniform time stepping

    DOE PAGES

    Finn, John M.

    2015-03-01

    Properties of integration schemes for solenoidal fields in three dimensions are studied, with a focus on integrating magnetic field lines in a plasma using adaptive time stepping. It is shown that implicit midpoint (IM) and a scheme we call three-dimensional leapfrog (LF) can do a good job (in the sense of preserving KAM tori) of integrating fields that are reversible, or (for LF) have a 'special divergence-free' property. We review the notion of a self-adjoint scheme, showing that such schemes are at least second order accurate and can always be formed by composing an arbitrary scheme with its adjoint. Wemore » also review the concept of reversibility, showing that a reversible but not exactly volume-preserving scheme can lead to a fractal invariant measure in a chaotic region, although this property may not often be observable. We also show numerical results indicating that the IM and LF schemes can fail to preserve KAM tori when the reversibility property (and the SDF property for LF) of the field is broken. We discuss extensions to measure preserving flows, the integration of magnetic field lines in a plasma and the integration of rays for several plasma waves. The main new result of this paper relates to non-uniform time stepping for volume-preserving flows. We investigate two potential schemes, both based on the general method of Ref. [11], in which the flow is integrated in split time steps, each Hamiltonian in two dimensions. The first scheme is an extension of the method of extended phase space, a well-proven method of symplectic integration with non-uniform time steps. This method is found not to work, and an explanation is given. The second method investigated is a method based on transformation to canonical variables for the two split-step Hamiltonian systems. This method, which is related to the method of non-canonical generating functions of Ref. [35], appears to work very well.« less

  7. Issues in measure-preserving three dimensional flow integrators: Self-adjointness, reversibility, and non-uniform time stepping

    SciTech Connect

    Finn, John M.

    2015-03-15

    Properties of integration schemes for solenoidal fields in three dimensions are studied, with a focus on integrating magnetic field lines in a plasma using adaptive time stepping. It is shown that implicit midpoint (IM) and a scheme we call three-dimensional leapfrog (LF) can do a good job (in the sense of preserving KAM tori) of integrating fields that are reversible, or (for LF) have a “special divergence-free” (SDF) property. We review the notion of a self-adjoint scheme, showing that such schemes are at least second order accurate and can always be formed by composing an arbitrary scheme with its adjoint. We also review the concept of reversibility, showing that a reversible but not exactly volume-preserving scheme can lead to a fractal invariant measure in a chaotic region, although this property may not often be observable. We also show numerical results indicating that the IM and LF schemes can fail to preserve KAM tori when the reversibility property (and the SDF property for LF) of the field is broken. We discuss extensions to measure preserving flows, the integration of magnetic field lines in a plasma and the integration of rays for several plasma waves. The main new result of this paper relates to non-uniform time stepping for volume-preserving flows. We investigate two potential schemes, both based on the general method of Feng and Shang [Numer. Math. 71, 451 (1995)], in which the flow is integrated in split time steps, each Hamiltonian in two dimensions. The first scheme is an extension of the method of extended phase space, a well-proven method of symplectic integration with non-uniform time steps. This method is found not to work, and an explanation is given. The second method investigated is a method based on transformation to canonical variables for the two split-step Hamiltonian systems. This method, which is related to the method of non-canonical generating functions of Richardson and Finn [Plasma Phys. Controlled Fusion 54, 014004 (2012

  8. Steps Toward Real-Time Atmospheric Phase Fluctuation Correction for a High Resolution Radar System

    NASA Astrophysics Data System (ADS)

    Denn, Grant R.; Geldzahler, Barry; Birr, Rick; Brown, Robert; Hoblitzell, Richard; Grant, Kevin; Miller, Michael; Woods, Gary; Archuleta, Arby; Ciminera, Michael; Cornish, Timothy; davarian, faramaz; kocz, jonathan; lee, dennis; Morabito, David Dominic; Soriano, Melissa; Tsao, Philip; Vilnrotter, Victor; Jakeman-Flores, Hali; Ott, melanie; Thomes, W. Joe; Soloff, Jason; NASA Kennedy Space Center, Jet Propulsion Laboratory, NASA Goddard Space Flight Center, NASA Johnson Space Flight Center, Metropolitan State University of Denver

    2016-01-01

    NASA is pursuing a demonstration of coherent uplink arraying at 7.145-7.190 GHz (X-band) and 30-31 GHz (Ka-band) using three 12m diameter COTS antennas separated by 60m at the Kennedy Space Center in Florida, with the goal of a high-power, high-resolution radar array that employs real-time correction for tropospheric phase fluctuation. The major uses for this array will be (a) observations of Near Earth Objects, (b) detection and tracking of orbital debris, (c) high power emergency uplink capability for spacecraft, and (d) radio science experiments.

  9. One-step Real-time Food Quality Analysis by Simultaneous DSC-FTIR Microspectroscopy.

    PubMed

    Lin, Shan-Yang; Lin, Chih-Cheng

    2016-01-01

    This review discusses an analytical technique that combines differential scanning calorimetry and Fourier-transform infrared (DSC-FTIR) microspectroscopy, which simulates the accelerated stability test and detects decomposition products simultaneously in real time. We show that the DSC-FTIR technique is a fast, simple and powerful analytical tool with applications in food sciences. This technique has been applied successfully to the simultaneous investigation of: encapsulated squid oil stability; the dehydration and intramolecular condensation of sweetener (aspartame); the dehydration, rehydration and solidification of trehalose; and online monitoring of the Maillard reaction for glucose (Glc)/asparagine (Asn) in the solid state. This technique delivers rapid and appropriate interpretations with food science applications.

  10. Steps Towards an Operational Service Using Near Real-Time Altimeter Data

    NASA Astrophysics Data System (ADS)

    Ash, E. R.

    2006-07-01

    Thanks largely to modern computing power, numerical forecasts of w inds and waves over the oceans ar e ev er improving, offering greater accuracy and finer resolution in time and sp ace. Howev er, it is recognized that met-ocean models still have difficulty in accurately forecasting sever e w eather conditions, conditions that cause the most damag e and difficulty in mar itime operations. Ther efore a key requir emen t is to provid e improved information on sever e conditions. No individual measur emen t or prediction system is perfect. Offshore buoys provide a continuous long-ter m record of wind and wave conditions, but only at a limited numb er of sites. Satellite data offer all-weath er global cov erage, but with relatively infrequen t samp ling. Forecasts rely on imperf ect numerical schemes and the ab ility to manage a vast quantity of input data. Therefore the best system is one that integr ates information from all available sources, taking advantage of the benef its that each can offer. We report on an initiative supported by the European Space Agen cy (ESA) which investig ated how satellite data could be used to enhan ce systems to provide Near Real Time mon itor ing of met-ocean conditions.

  11. A High-Order Adaptive Time-Stepping TVD Solver for BOUSSINESQ Modeling of Breaking Waves and Coastal Inundation

    NASA Astrophysics Data System (ADS)

    Shi, F.; Kirby, J. T.; Tehranirad, B.

    2010-12-01

    Recent progress in the development of Boussinesq-type wave models using TVD-MUSCL schemes have shown robust performance of the shock-capturing method in simulating breaking waves and coastal inundation (Tonelli and Petti, 2009, Roeber et al., 2010, Shiach and Mingham, 2009, Erduran et al., 2005, and others). Shock-capturing schemes make the treatment of wave breaking straightforward without an artificial viscosity adopted in some breaking wave models such as in Kennedy et al. (2000). The schemes are also able to capture the sharp wave front occurring in the swash zone. A high-order temporal scheme usually requires uniform time-stepping, decreasing model efficiency in applications to breaking waves and inundation where super-critical fluid conditions limit the time step associated with the CFL-criterion. In this presentation, we describe the use of a higher order, adaptive time-stepping algorithm using the Runge-Kutta method in a fully nonlinear Boussinesq wave model. Higher-order numerical schemes in both space and time were applied in order to avoid contamination of the physical dispersive terms in Boussinesq equations resulting from truncation errors in the lower-order (second-order) approximation. The spatial derivatives are discritized using a combination of finite-volume and finite-difference methods. A fourth-order MUSCL reconstruction technique is used in the Riemann solver. The model code is parallelized for the MPI computational environment. We illustrate the model's application to the problems of wave runup and coastal inundation in the context of a standard suite of benchmark tests.

  12. In the time of significant generational diversity - surgical leadership must step up!

    PubMed

    Money, Samuel R; O'Donnell, Mark E; Gray, Richard J

    2014-02-01

    The diverse attitudes and motivations of surgeons and surgical trainees within different age groups present an important challenge for surgical leaders and educators. These challenges to surgical leadership are not unique, and other industries have likewise needed to grapple with how best to manage these various age groups. The authors will herein explore management and leadership for surgeons in a time of age diversity, define generational variations within "Baby-Boomer", "Generation X" and "Generation Y" populations, and identify work ethos concepts amongst these three groups. The surgical community must understand and embrace these concepts in order to continue to attract a stellar pool of applicants from medical school. By not accepting the changing attitudes and motivations of young trainees and medical students, we may disenfranchise a high percentage of potential future surgeons. Surgical training programs will fill, but will they contain the highest quality trainees?

  13. Modelling of Thermal Advective Reactive Flow in Hydrothermal Mineral Systems Using an Implicit Time-stepped Finite Element Method.

    NASA Astrophysics Data System (ADS)

    Hornby, P. G.

    2005-12-01

    Understanding chemical and thermal processes taking place in hydrothermal mineral deposition systems could well be a key to unlocking new mineral reserves through improved targeting of exploration efforts. To aid in this understanding it is very helpful to be able to model such processes with sufficient fidelity to test process hypotheses. To gain understanding, it is often sufficient to obtain semi-quantitative results that model the broad aspects of the complex set of thermal and chemical effects taking place in hydrothermal systems. For example, it is often sufficient to gain an understanding of where thermal, geometric and chemical factors converge to precipitate gold (say) without being perfectly precise about how much gold is precipitated. The traditional approach is to use incompressible Darcy flow together with the Boussinesq approximation. From the flow field, the heat equation is used to advect-conduct the heat. The flow field is also used to transport solutes by solving an advection-dispersion-diffusion equation. The reactions in the fluid and between fluid and rock act as source terms for these advection-dispersion equations. Many existing modelling systems that are used for simulating such systems use explicit time marching schemes and finite differences. The disadvantage of this approach is the need to work on rectilinear grids and the number of time steps required by the Courant condition in the solute transport step. The second factor can be particularly significant if the chemical system is complex, requiring (at a minimum) an equilibrium calculation at each grid point at each time step. In the approach we describe, we use finite elements rather than finite differences, and the pressure, heat and advection-dispersion equations are solved implicitly. The general idea is to put unconditional numerical stability of the time integration first, and let accuracy assume a secondary role. It is in this sense that the method is semi-quantiative. However

  14. Detection of Listeria monocytogenes in ready-to-eat food by Step One real-time polymerase chain reaction.

    PubMed

    Pochop, Jaroslav; Kačániová, Miroslava; Hleba, Lukáš; Lopasovský, L'ubomír; Bobková, Alica; Zeleňáková, Lucia; Stričík, Michal

    2012-01-01

    The aim of this study was to follow contamination of ready-to-eat food with Listeria monocytogenes by using the Step One real time polymerase chain reaction (PCR). We used the PrepSEQ Rapid Spin Sample Preparation Kit for isolation of DNA and MicroSEQ® Listeria monocytogenes Detection Kit for the real-time PCR performance. In 30 samples of ready-to-eat milk and meat products without incubation we detected strains of Listeria monocytogenes in five samples (swabs). Internal positive control (IPC) was positive in all samples. Our results indicated that the real-time PCR assay developed in this study could sensitively detect Listeria monocytogenes in ready-to-eat food without incubation.

  15. Elastic wave finite-difference simulation using discontinuous curvilinear grid with non-uniform time step: two-dimensional case

    NASA Astrophysics Data System (ADS)

    Li, Hong; Zhang, Wei; Zhang, Zhenguo; Chen, Xiaofei

    2015-07-01

    A discontinuous grid finite-difference (FD) method with non-uniform time step Runge-Kutta scheme on curvilinear collocated-grid is developed for seismic wave simulation. We introduce two transition zones: a spatial transition zone and a temporal transition zone, to exchange wavefield across the spatial and temporal discontinuous interfaces. A Gaussian filter is applied to suppress artificial numerical noise caused by down-sampling the wavefield from the finer grid to the coarser grid. We adapt the non-uniform time step Runge-Kutta scheme to a discontinuous grid FD method for further increasing the computational efficiency without losing the accuracy of time marching through the whole simulation region. When the topography is included in the modelling, we carry out the discontinuous grid method on a curvilinear collocated-grid to obtain a sufficiently accurate free-surface boundary condition implementation. Numerical tests show that the proposed method can sufficiently accurately simulate the seismic wave propagation on such grids and significantly reduce the computational resources consumption with respect to regular grids.

  16. Changing Safety Culture, One Step at a Time: The Value of the DOE-VPP Program at PNNL

    SciTech Connect

    Wright, Patrick A.; Isern, Nancy G.

    2005-02-01

    The primary value of the Pacific Northwest National Laboratory (PNNL) Voluntary Protection Program (VPP) is the ongoing partnership between management and staff committed to change Laboratory safety culture one step at a time. VPP enables PNNL's safety and health program to transcend a top-down, by-the-book approach to safety, and it also raises grassroots safety consciousness by promoting a commitment to safety and health 24 hours a day, 7 days a week. PNNL VPP is a dynamic, evolving program that fosters innovative approaches to continuous improvement in safety and health performance at the Laboratory.

  17. Time-dependent rheological behavior of natural polysaccharide xanthan gum solutions in interrupted shear and step-incremental/reductional shear flow fields

    NASA Astrophysics Data System (ADS)

    Lee, Ji-Seok; Song, Ki-Won

    2015-11-01

    The objective of the present study is to systematically elucidate the time-dependent rheological behavior of concentrated xanthan gum systems in complicated step-shear flow fields. Using a strain-controlled rheometer (ARES), step-shear flow behaviors of a concentrated xanthan gum model solution have been experimentally investigated in interrupted shear flow fields with a various combination of different shear rates, shearing times and rest times, and step-incremental and step-reductional shear flow fields with various shearing times. The main findings obtained from this study are summarized as follows. (i) In interrupted shear flow fields, the shear stress is sharply increased until reaching the maximum stress at an initial stage of shearing times, and then a stress decay towards a steady state is observed as the shearing time is increased in both start-up shear flow fields. The shear stress is suddenly decreased immediately after the imposed shear rate is stopped, and then slowly decayed during the period of a rest time. (ii) As an increase in rest time, the difference in the maximum stress values between the two start-up shear flow fields is decreased whereas the shearing time exerts a slight influence on this behavior. (iii) In step-incremental shear flow fields, after passing through the maximum stress, structural destruction causes a stress decay behavior towards a steady state as an increase in shearing time in each step shear flow region. The time needed to reach the maximum stress value is shortened as an increase in step-increased shear rate. (iv) In step-reductional shear flow fields, after passing through the minimum stress, structural recovery induces a stress growth behavior towards an equilibrium state as an increase in shearing time in each step shear flow region. The time needed to reach the minimum stress value is lengthened as a decrease in step-decreased shear rate.

  18. Review of Real-Time Simulator and the Steps Involved for Implementation of a Model from MATLAB/SIMULINK to Real-Time

    NASA Astrophysics Data System (ADS)

    Mikkili, Suresh; Panda, Anup Kumar; Prattipati, Jayanthi

    2014-07-01

    Nowadays the researchers want to develop their model in real-time environment. Simulation tools have been widely used for the design and improvement of electrical systems since the mid twentieth century. The evolution of simulation tools has progressed in step with the evolution of computing technologies. In recent years, computing technologies have improved dramatically in performance and become widely available at a steadily decreasing cost. Consequently, simulation tools have also seen dramatic performance gains and steady cost decreases. Researchers and engineers now have the access to affordable, high performance simulation tools that were previously too cost prohibitive, except for the largest manufacturers. This work has introduced a specific class of digital simulator known as a real-time simulator by answering the questions "what is real-time simulation", "why is it needed" and "how it works". The latest trend in real-time simulation consists of exporting simulation models to FPGA. In this article, the Steps involved for implementation of a model from MATLAB to REAL-TIME are provided in detail.

  19. A quantitative method for evaluating numerical simulation accuracy of time-transient Lamb wave propagation with its applications to selecting appropriate element size and time step.

    PubMed

    Wan, Xiang; Xu, Guanghua; Zhang, Qing; Tse, Peter W; Tan, Haihui

    2016-01-01

    Lamb wave technique has been widely used in non-destructive evaluation (NDE) and structural health monitoring (SHM). However, due to the multi-mode characteristics and dispersive nature, Lamb wave propagation behavior is much more complex than that of bulk waves. Numerous numerical simulations on Lamb wave propagation have been conducted to study its physical principles. However, few quantitative studies on evaluating the accuracy of these numerical simulations were reported. In this paper, a method based on cross correlation analysis for quantitatively evaluating the simulation accuracy of time-transient Lamb waves propagation is proposed. Two kinds of error, affecting the position and shape accuracies are firstly identified. Consequently, two quantitative indices, i.e., the GVE (group velocity error) and MACCC (maximum absolute value of cross correlation coefficient) derived from cross correlation analysis between a simulated signal and a reference waveform, are proposed to assess the position and shape errors of the simulated signal. In this way, the simulation accuracy on the position and shape is quantitatively evaluated. In order to apply this proposed method to select appropriate element size and time step, a specialized 2D-FEM program combined with the proposed method is developed. Then, the proper element size considering different element types and time step considering different time integration schemes are selected. These results proved that the proposed method is feasible and effective, and can be used as an efficient tool for quantitatively evaluating and verifying the simulation accuracy of time-transient Lamb wave propagation. PMID:26315506

  20. Length and time for development of laminar flow in tubes following a step increase of volume flux

    NASA Astrophysics Data System (ADS)

    Chaudhury, Rafeed A.; Herrmann, Marcus; Frakes, David H.; Adrian, Ronald J.

    2015-01-01

    Laminar flows starting up from rest in round tubes are relevant to numerous industrial and biomedical applications. The two most common types are flows driven by an abruptly imposed constant pressure gradient or by an abruptly imposed constant volume flux. Analytical solutions are available for transient, fully developed flows, wherein streamwise development over the entrance length is absent (Szymanski in J de Mathématiques Pures et Appliquées 11:67-107, 1932; Andersson and Tiseth in Chem Eng Commun 112(1):121-133, 1992, respectively). They represent the transient responses of flows in tubes that are very long compared with the entrance length, a condition that is seldom satisfied in biomedical tube networks. This study establishes the entrance (development) length and development time of starting laminar flow in a round tube of finite length driven by a piston pump that produces a step change from zero flow to a constant volume flux for Reynolds numbers between 500 and 3,000. The flows are examined experimentally, using stereographic particle image velocimetry and computationally using computational fluid dynamics, and are then compared with the known analytical solutions for fully developed flow conditions in infinitely long tubes. Results show that step function volume flux start-up flows reach steady state and fully developed flow five times more quickly than those driven by a step function pressure gradient, a 500 % change when compared with existing estimates. Based on these results, we present new, simple guidelines for achieving experimental flows that are fully developed in space and time in realistic (finite) tube geometries. To a first approximation, the time to achieve steady spatially developing flow is nearly equal to the time needed to achieve steady, fully developed flow. Conversely, the entrance length needed to achieve fully developed transient flow is approximately equal to the length needed to achieve fully developed steady flow. Beyond this

  1. Response time of a normal-metal/superconductor hybrid system under a step-like pulse bias

    NASA Astrophysics Data System (ADS)

    Xing, Yanxia; Sun, Qing-Feng; Wang, Jian

    2007-03-01

    The response of a quantum dot coupled with one normal lead and a superconductor lead driven by a step-like pulse bias VL is studied using the nonequilibrium Green’s function method. In the linear pulse bias regime, the responses of the upward and downward biases are symmetric. In this regime, the turn-on time and turn-off time are much slower than those of the normal system due to the Andreev reflection. On the other hand, for the large pulse bias VL , the instantaneous current exhibits oscillatory behaviors with the frequency ℏΩ=qVL . The turn-on/off times are in (or shorter than) the scale of 1/VL , so they are faster for the larger bias VL . In addition, the responses for the upward and downward biases are asymmetric at large VL . The turn-on time is larger than the turn-off time, but the relaxation time depends only on the coupling strength Γ and it is much smaller than the turn-on/off times for the large bias VL . [The turn-on/off time describes how fast a device can turn on/off a current, which is also named rise/fall time in M. Plihal , Phys. Rev. B 61, R13341 (2000), while the relaxation time was referred to how fast the device can go to a new steady state after a bias is abruptly switched on. It is also named saturation time in A. Schiller and S. Hershfield, Phys. Rev. B 62, R16271 (2000).

  2. Restricting daily time at pasture at low and high pasture allowance: effects on pasture intake and behavioral adaptation of lactating dairy cows.

    PubMed

    Pérez-Ramírez, E; Peyraud, J L; Delagarde, R

    2009-07-01

    In pasture-based dairy systems, daily time at pasture is restricted during several periods of the year. The aim of this experiment was to evaluate the effect of restricting time at pasture on milk yield, pasture dry matter (DM) intake, and grazing behavior of dairy cows according to pasture allowance (PA), which partly defines pasture availability. The experiment was carried out in spring on strip-grazed perennial ryegrass pastures. The 6 treatments consisted of 3 durations of daily time at pasture [U: unrestricted day and night grazing (22 h at pasture); R9: 1 grazing session restricted to 9 h between the 2 milkings; R5: 2 grazing sessions of 2.75 h after each milking) compared at low and high PA (13 and 24 kg of DM/d per cow >5 cm, respectively). Eighteen mid-lactation Holstein dairy cows were used according to a 6 x 4 incomplete Latin square design replicated 3 times with four 14-d periods. Pasture DM intake was measured by the ytterbium-fecal index method and grazing behavior from portable devices. On average, restricting time at pasture from U to R (mean of R5 + R9) decreased pasture intake by 2.9 kg of DM, milk yield by 1.3 kg, and milk protein concentration by 0.11%, and increased milk fat concentration by 0.20%. Pasture intake and milk yield did not differ significantly between R9 and R5. The reduction of pasture intake and milk yield with decreasing time at pasture was greater at high compared with low PA. Grazing times were 536, 414, and 305 min, representing proportions of time spent grazing of 0.40, 0.77, and 0.93 for treatments U, R9, and R5, respectively. The reduction of grazing time with decreasing time at pasture was greater at high compared with low PA. Pasture intake rate greatly increased with decreasing time at pasture, but mainly on R5 (29.8, 31.6, and 42.1 g of DM/min for U, R9, and R5, respectively). The effect of time at pasture on pasture intake rate was unaffected by PA. In conclusion, the effect of restriction of time at pasture on

  3. Compact Two-step Laser Time-of-Flight Mass Spectrometer for in Situ Analyses of Aromatic Organics on Planetary Missions

    NASA Technical Reports Server (NTRS)

    Getty, Stephanie; Brickerhoff, William; Cornish, Timothy; Ecelberger, Scott; Floyd, Melissa

    2012-01-01

    RATIONALE A miniature time-of-flight mass spectrometer has been adapted to demonstrate two-step laser desorption-ionization (LOI) in a compact instrument package for enhanced organics detection. Two-step LDI decouples the desorption and ionization processes, relative to traditional laser ionization-desorption, in order to produce low-fragmentation conditions for complex organic analytes. Tuning UV ionization laser energy allowed control ofthe degree of fragmentation, which may enable better identification of constituent species. METHODS A reflectron time-of-flight mass spectrometer prototype measuring 20 cm in length was adapted to a two-laser configuration, with IR (1064 nm) desorption followed by UV (266 nm) postionization. A relatively low ion extraction voltage of 5 kV was applied at the sample inlet. Instrument capabilities and performance were demonstrated with analysis of a model polycyclic aromatic hydrocarbon, representing a class of compounds important to the fields of Earth and planetary science. RESULTS L2MS analysis of a model PAH standard, pyrene, has been demonstrated, including parent mass identification and the onset o(tunable fragmentation as a function of ionizing laser energy. Mass resolution m/llm = 380 at full width at half-maximum was achieved which is notable for gas-phase ionization of desorbed neutrals in a highly-compact mass analyzer. CONCLUSIONS Achieving two-step laser mass spectrometry (L2MS) in a highly-miniature instrument enables a powerful approach to the detection and characterization of aromatic organics in remote terrestrial and planetary applications. Tunable detection of parent and fragment ions with high mass resolution, diagnostic of molecular structure, is possible on such a compact L2MS instrument. Selectivity of L2MS against low-mass inorganic salt interferences is a key advantage when working with unprocessed, natural samples, and a mechanism for the observed selectivity is presented.

  4. The STEP model: Characterizing simultaneous time effects on practice for flight simulator performance among middle-aged and older pilots.

    PubMed

    Kennedy, Quinn; Taylor, Joy; Noda, Art; Yesavage, Jerome; Lazzeroni, Laura C

    2015-09-01

    Understanding the possible effects of the number of practice sessions (practice) and time between practice sessions (interval) among middle-aged and older adults in real-world tasks has important implications for skill maintenance. Prior training and cognitive ability may impact practice and interval effects on real-world tasks. In this study, we took advantage of existing practice data from 5 simulated flights among 263 middle-aged and older pilots with varying levels of flight expertise (defined by U.S. Federal Aviation Administration proficiency ratings). We developed a new Simultaneous Time Effects on Practice (STEP) model: (a) to model the simultaneous effects of practice and interval on performance of the 5 flights, and (b) to examine the effects of selected covariates (i.e., age, flight expertise, and 3 composite measures of cognitive ability). The STEP model demonstrated consistent positive practice effects, negative interval effects, and predicted covariate effects. Age negatively moderated the beneficial effects of practice. Additionally, cognitive processing speed and intraindividual variability (IIV) in processing speed moderated the benefits of practice and/or the negative influence of interval for particular flight performance measures. Expertise did not interact with practice or interval. Results indicated that practice and interval effects occur in simulated flight tasks. However, processing speed and IIV may influence these effects, even among high-functioning adults. Results have implications for the design and assessment of training interventions targeted at middle-aged and older adults for complex real-world tasks. PMID:26280383

  5. The STEP model: Characterizing simultaneous time effects on practice for flight simulator performance among middle-aged and older pilots.

    PubMed

    Kennedy, Quinn; Taylor, Joy; Noda, Art; Yesavage, Jerome; Lazzeroni, Laura C

    2015-09-01

    Understanding the possible effects of the number of practice sessions (practice) and time between practice sessions (interval) among middle-aged and older adults in real-world tasks has important implications for skill maintenance. Prior training and cognitive ability may impact practice and interval effects on real-world tasks. In this study, we took advantage of existing practice data from 5 simulated flights among 263 middle-aged and older pilots with varying levels of flight expertise (defined by U.S. Federal Aviation Administration proficiency ratings). We developed a new Simultaneous Time Effects on Practice (STEP) model: (a) to model the simultaneous effects of practice and interval on performance of the 5 flights, and (b) to examine the effects of selected covariates (i.e., age, flight expertise, and 3 composite measures of cognitive ability). The STEP model demonstrated consistent positive practice effects, negative interval effects, and predicted covariate effects. Age negatively moderated the beneficial effects of practice. Additionally, cognitive processing speed and intraindividual variability (IIV) in processing speed moderated the benefits of practice and/or the negative influence of interval for particular flight performance measures. Expertise did not interact with practice or interval. Results indicated that practice and interval effects occur in simulated flight tasks. However, processing speed and IIV may influence these effects, even among high-functioning adults. Results have implications for the design and assessment of training interventions targeted at middle-aged and older adults for complex real-world tasks.

  6. The STEP model: Characterizing simultaneous time effects on practice for flight simulator performance among middle-aged and older pilots

    PubMed Central

    Kennedy, Quinn; Taylor, Joy; Noda, Art; Yesavage, Jerome; Lazzeroni, Laura C.

    2015-01-01

    Understanding the possible effects of the number of practice sessions (practice) and time between practice sessions (interval) among middle-aged and older adults in real world tasks has important implications for skill maintenance. Prior training and cognitive ability may impact practice and interval effects on real world tasks. In this study, we took advantage of existing practice data from five simulated flights among 263 middle-aged and older pilots with varying levels of flight expertise (defined by FAA proficiency ratings). We developed a new STEP (Simultaneous Time Effects on Practice) model to: (1) model the simultaneous effects of practice and interval on performance of the five flights, and (2) examine the effects of selected covariates (age, flight expertise, and three composite measures of cognitive ability). The STEP model demonstrated consistent positive practice effects, negative interval effects, and predicted covariate effects. Age negatively moderated the beneficial effects of practice. Additionally, cognitive processing speed and intra-individual variability (IIV) in processing speed moderated the benefits of practice and/or the negative influence of interval for particular flight performance measures. Expertise did not interact with either practice or interval. Results indicate that practice and interval effects occur in simulated flight tasks. However, processing speed and IIV may influence these effects, even among high functioning adults. Results have implications for the design and assessment of training interventions targeted at middle-aged and older adults for complex real world tasks. PMID:26280383

  7. Simultaneous effects of allowed time, teaching method, ability, and student assessment of treatment on achievement in a high school biology course (ISIS)

    NASA Astrophysics Data System (ADS)

    Burkman, Ernest; Brezin, Michael; Griffin, Patrick

    The simultaneous effects of teaching method (self-directed, group directed, and teacher directed), allowed time for study, and two student variables (academic ability and assessment of treatment implementation) are described for student achievement in a high school biology course (ISIS). The variable student assessment of treatment implementation was viewed as a particularly important variable for two reasons: (1) in research by Stayrook, Corno, and Winne (1978) it has accounted for as much variance in achievement as the assigned treatment; and (2) it provides a means for controlling the range of implementation of teaching methods. A between-student analysis resulted in a description of effects complicated by interactions among all the variables. While the interactions were particularly strong in the student-directed method, it may generally be concluded that as time allowed for study decreased, students who perceived the treatment as being well implemented tended to have higher achievement. Also, it was found that the main effect of ability was quite strong. The results confirmed the importance of student assessment of treatment implementation as a descriptive variable. Additionally, the results suggest a qualification in the conclusion of Cronbach and Snow (1971) that individualized instruction tends to favor high-ability students; that conclusion may need to be modified to situations in which students fully perceive their autonomy.

  8. High-order time-stepping for nonlinear PDEs through rapid estimation of block Gaussian quadrature nodes

    NASA Astrophysics Data System (ADS)

    Lambers, James V.

    2016-06-01

    The stiffness of systems of ODEs that arise from spatial discretization of PDEs causes difficulties for both explicit and implicit time-stepping methods. Krylov Subspace Spectral (KSS) methods present a balance between the efficiency of explicit methods and the stability of implicit methods by computing each Fourier coefficient from an individualized approximation of the solution operator of the PDE. While KSS methods are explicit methods that exhibit a high order of accuracy and stability similar to that of implicit methods, their efficiency needs to be improved. Here, a detailed asymptotic study is performed in order to rapidly estimate all nodes, thus drastically reducing computational expense without sacrificing accuracy. Extension to PDEs on a disk, through expansions built on Legendre polynomials, is also discussed. Exponential propagation iterative (EPI) methods provide an efficient approach to the solution of large stiff nonlinear systems of ODE, compared to standard integrators. However, the bulk of the computational effort in these methods is due to products of matrix functions and vectors, which can become very costly at high resolution due to an increase in the number of Krylov projection steps needed to maintain accuracy. In this talk, it is proposed to modify EPI methods by using KSS methods, instead of standard Krylov projection methods, to compute products of matrix functions and vectors. Numerical experiments demonstrate that this modification causes the number of Krylov projection steps to become bounded independently of the grid size, thus dramatically improving efficiency and scalability. It is also demonstrated that the convergence of Krylov projection can be significantly accelerated, without noticeable loss of accuracy, through filtering techniques, thus improving performance and scalability even further.

  9. An FPGA-based frequency response analyzer for multisine and stepped sine measurements on stationary and time-varying impedance

    NASA Astrophysics Data System (ADS)

    Sanchez, B.; Fernandez, X.; Reig, S.; Bragos, R.

    2014-01-01

    We report the development of a field programmable gate array (FPGA) based frequency response analyzer (FRA) for impedance frequency response function (FRF) measurements using periodic excitations, i.e. sine waves and multisines. The stepped sine measurement uses two dedicated hardware-built digital embedded multiplier blocks to extract the phase and quadrature components of the output signal. The multisine FRF measurements compute the fast Fourier transform (FFT) of the input/output signals. In this paper, we describe its design, implementation and performance evaluation, performing electrical impedance spectroscopy (EIS) measurements on phantoms. The stepped sine accuracy is 1.21% at 1 kΩ (1%), the precision is 35 mΩ and the total harmonic distortion plus noise (THD+N) is -120 dB. As for the multisine impedance FRF measurements, the magnitude and phase precision are, respectively, 0.23 Ω at 48.828 kHz and 0.021 deg at 8.087 MHz when measuring a resistor 505 Ω (1%). The magnitude accuracy is 0.55% at 8.087 MHz while the phase accuracy is 0.17 deg at 6.54 MHz. In all, the stepped sine signal-to-noise ratio (SNR) is 84 dB and 65 dB at frequencies below and above 1 MHz respectively. The SNR for the multisine FRF measurements is above 65 dB (30 kHz-10 MHz). The FRA bandwidth is 610.4 mHz-12.5 MHz and the maximum FRF measurement rate exciting with multisines starting at 30 kHz is 200 spectra s-1. Based on its technical specifications and versatility, the FRA presented can be used in many applications, e.g. for getting insight quickly into the instantaneous impedance FRF of the time-varying impedance under test.

  10. Biological nitrogen removal in a step-feed CAST with real-time control treating municipal wastewater.

    PubMed

    Juan, Ma; Chengyao, Peng; Li, Wang; Shuying, Wang; Yang, Liu; Ningping, Ma; Xia, Yu; Yongzhen, Peng

    2010-01-01

    The performance of a 18 L step-feed cyclic activated sludge technology (CAST) combined with real-time control treating real municipal wastewater was evaluated. The operation strategies employed pH and oxidation reduction potential (ORP) as on-line control parameters, which can control the durations of oxic and anoxic phases flexibly. The obtained results showed that the studied process had achieved advanced and enhanced nitrogen removal by several phases of consecutive oxic/anoxic periods. Total nitrogen in effluent was lower than 2 mg/L and the average TN removal efficiency was higher than 98%, while only requiring small amount of external carbon source. Unexpected characteristic points in pH and ORP profiles denoting the depletion of nitrate were also observed during the last anoxic phase. Denitrification rate was found to be more dependent on the system temperature compared to nitrification rate. Moreover, a stable and efficient phosphorus removal rate above 90% was achieved by using step-feed strategy which enabled the influent carbon source to be fully used and the favourable condition for phosphorus releasing to be created during the anoxic phases.

  11. Third-order-accurate numerical methods for efficient, large time-step solutions of mixed linear and nonlinear problems

    SciTech Connect

    Cobb, J.W.

    1995-02-01

    There is an increasing need for more accurate numerical methods for large-scale nonlinear magneto-fluid turbulence calculations. These methods should not only increase the current state of the art in terms of accuracy, but should also continue to optimize other desired properties such as simplicity, minimized computation, minimized memory requirements, and robust stability. This includes the ability to stably solve stiff problems with long time-steps. This work discusses a general methodology for deriving higher-order numerical methods. It also discusses how the selection of various choices can affect the desired properties. The explicit discussion focuses on third-order Runge-Kutta methods, including general solutions and five examples. The study investigates the linear numerical analysis of these methods, including their accuracy, general stability, and stiff stability. Additional appendices discuss linear multistep methods, discuss directions for further work, and exhibit numerical analysis results for some other commonly used lower-order methods.

  12. Space-time block code based MIMO encoding for large core step index plastic optical fiber transmission systems.

    PubMed

    Raptis, Nikos; Grivas, Evangelos; Pikasis, Evangelos; Syvridis, Dimitris

    2011-05-23

    The performance of Space-Time Block Codes combined with Discrete MultiTone modulation applied in a Large Core Step-Index POF link is examined theoretically. A comparative study is performed considering several schemes that employ multiple transmitters/receivers and a fiber span of 100 m. The performance enhancement of the higher diversity order configurations is revealed by application of a Margin Adaptive Bit Loading technique that employs Chow's algorithm. Simulations results of the above schemes, in terms of Bit Error Rate as a function of the received Signal to Noise Ratio, are provided. An improvement of more than 6 dB for the required electrical SNR is observed for a 3 × 1 configuration, in order to achieve a 10(-3) BER value, as compared to a conventional Single Input Single output scheme.

  13. Volume and enthalpy changes in the early steps of bacteriorhodopsin photocycle studied by time-resolved photoacoustics.

    PubMed Central

    Zhang, D; Mauzerall, D

    1996-01-01

    We have studied the photoinduced volume changes, energetics, and kinetics in the early steps of the bacteriorhodopsin (BR) photocycle with pulsed, time-resolved photoacoustics. Our data show that there are two volume changes. The fast volume change ( < or = 200 ns) is an expansion (2.5 +/- 0.3 A3/molecule) and is observed exclusively in the purple membrane (PM), vanishing in the 3-[(3-cholamidopropyl)-dimethylammonio] -1-propane-sulfonate-sulfonate-solubilized BR sample; the slow change (approximately 1 micros) is a volume contraction (-3.7 +/- 0.3 A3/molecule). The fast expansion is assigned to the restructuring of the aggregated BR in the PM, and the 1-micros contraction to the change in hydrogen bonding of water at Asp 212 (Kandori et al. 1995. J. Am. Chem. Soc. 117:2118-2119). The formation of the K intermediate releases most of the absorbed energy as heat, with delta Hk = -36 +/- 8 kJ/mol. The activation energy of the K --> L step is 49 +/- 6 kJ/mol, but the enthalpy change is small, -4 +/- 10 kJ/mol. On the time scale we studied, the primary photochemical kinetics, enthalpy, and volume changes are not affected by substituting the solvent D2O for H2O. Comparing data on monomeric and aggregated BR, we conclude that the functional unit for the photocycle is the BR monomer, because both the kinetics (rate constant and activation energy) and the enthalpy changes are independent of its aggregation state. PMID:8804620

  14. A novel enterovirus and parechovirus multiplex one-step real-time PCR-validation and clinical experience.

    PubMed

    Nielsen, Alex Christian Yde; Böttiger, Blenda; Midgley, Sofie Elisabeth; Nielsen, Lars Peter

    2013-11-01

    As the number of new enteroviruses and human parechoviruses seems ever growing, the necessity for updated diagnostics is relevant. We have updated an enterovirus assay and combined it with a previously published assay for human parechovirus resulting in a multiplex one-step RT-PCR assay. The multiplex assay was validated by analysing the sensitivity and specificity of the assay compared to the respective monoplex assays, and a good concordance was found. Furthermore, the enterovirus assay was able to detect 42 reference strains from all 4 species, and an additional 9 genotypes during panel testing and routine usage. During 15 months of routine use, from October 2008 to December 2009, we received and analysed 2187 samples (stool samples, cerebrospinal fluids, blood samples, respiratory samples and autopsy samples) were tested, from 1546 patients and detected enteroviruses and parechoviruses in 171 (8%) and 66 (3%) of the samples, respectively. 180 of the positive samples could be genotyped by PCR and sequencing and the most common genotypes found were human parechovirus type 3, echovirus 9, enterovirus 71, Coxsackievirus A16, and echovirus 25. During 2009 in Denmark, both enterovirus and human parechovirus type 3 had a similar seasonal pattern with a peak during the summer and autumn. Human parechovirus type 3 was almost invariably found in children less than 4 months of age. In conclusion, a multiplex assay was developed allowing simultaneous detection of 2 viruses, which can cause similar clinical symptoms.

  15. Development of one-step real-time PCR assay for titrating trivalent live attenuated influenza vaccines.

    PubMed

    Zang, Yang; Du, Dongchuan; Ge, Peng; Xu, Yongqing; Liu, Xintao; Zhang, Yan; Su, Weiheng; Kiseleva, Irina; Rudenko, Larisa; Xu, Fei; Kong, Wei; Jiang, Chunlai

    2014-01-01

    Traditionally, infectivity of a trivalent live attenuated influenza vaccines (LAIVs) is titrated by determining the 50% egg infectious dose assay (EID50) or plaque forming units (PFU), which requires specific monoclonal antibodies to neutralize 2 strains while estimating the titer of the non-neutralized strain. Compared to this time-consuming, laborious, subjective and variable process, reverse transcription-quantitative real-time PCR (RT-qPCR) technology has advantages of rapidity, sensitivity, reproducibility and reduced contamination, thus has been applied widely for detecting pathogens and measuring viral titers. In this study, the critical harvest time was determined to be 18 h post-infection (hpi) for type A influenza and 12 hpi for type B influenza, but no significant difference between titers at 12 hpi and 18 hpi for the type B strain was observed. In conclusion, trivalent LAIVs can be titrated simultaneously within 24 h by this one-step RT-qPCR assay, which yielded titers comparable to those obtained by the traditional EID50 assay. Therefore, the RT-qPCR assay may be used as a highly specific, sensitive, precise and rapid alternative to the EID50 assay for titering LAIVs.

  16. Development of a One-Step Immunocapture Real-Time RT-PCR Assay for Detection of Tobacco Mosaic Virus in Soil

    PubMed Central

    Yang, Jin-Guang; Wang, Feng-Long; Chen, De-Xin; Shen, Li-Li; Qian, Yu-Mei; Liang, Zhi-Yong; Zhou, Wen-Chang; Yan, Tai-He

    2012-01-01

    Tobacco mosaic virus (TMV) causes significant losses in many economically important crops. Contaminated soils may play roles as reservoirs and sources of transmission for TMV. In this study we report the development of an immunocapture real-time RT-PCR (IC-real-time RT-PCR) assay for direct detection of TMV in soils without RNA isolation. A series of TMV infected leaf sap dilutions of 1:101, 1:102, 1:103, 1:104, 1:105 and 1:106 (w/v, g/mL) were added to one gram of soil. The reactivity of DAS-ELISA and conventional RT-PCR was in the range of 1:102 and 1:103 dilution in TMV-infested soils, respectively. Meanwhile, the detection limit of IC-real-time RT-PCR sensitivity was up to 1:106 dilution. However, in plant sap infected by TMV, both IC-real-time RT-PCR and real-time RT-PCR were up to 1:106 dilution, DAS-ELISA could detect at least 1:103 dilution. IC-real-time RT-PCR method can use either plant sample extracts or cultivated soils, and show higher sensitivity than RT-PCR and DAS-ELISA for detection of TMV in soils. Therefore, the proposed IC-real-time RT-PCR assay provides an alternative for quick and very sensitive detection of TMV in soils, with the advantage of not requiring a concentration or RNA purification steps while still allowing detection of TMV for disease control. PMID:23211755

  17. Modifications of the chemical profile of hosts after parasitism allow parasitoid females to assess the time elapsed since the first attack.

    PubMed

    Lebreton, Sebastien; Christidès, Jean-Philippe; Bagnères, Anne-Geneviève; Chevrier, Claude; Darrouzet, Eric

    2010-05-01

    In solitary parasitoids, only one adult can emerge from a given host. In some of these species, when several eggs are laid on the same host, supernumerary individuals are eliminated by lethal larval fights. In the solitary parasitoid Anisopteromalus calandrae, the probability of a second larva winning the fight depends on the time elapsed since the first oviposition. The older the first egg is at the moment a second egg is laid, the less chance the second egg has of winning the competition. As a consequence, females of this species lay their eggs preferentially on recently parasitized hosts rather than on hosts parasitized by an egg about to hatch. Anisopteromalus calandrae females parasitize bruchid larvae located in cowpea seeds. In a series of choice test experiments using an artificial seed system, we demonstrated that the cue that allows parasitoid females to differentiate between hosts parasitized for different lengths of time comes from the host and not from the artificial seed or the previously laid egg. This cue is perceived at short range, indicating that the chemicals involved are probably partly volatile. Interestingly, although parasitism stops host development, cuticular profiles continue to evolve, but in a different way from those of unparasitized hosts. This difference in the host's cuticular profile after parasitism, therefore, probably underlies the parasitoid female's discrimination.

  18. Determination of breath isoprene allows the identification of the expiratory fraction of the propofol breath signal during real-time propofol breath monitoring.

    PubMed

    Hornuss, Cyrill; Dolch, Michael E; Janitza, Silke; Souza, Kimberly; Praun, Siegfried; Apfel, Christian C; Schelling, Gustav

    2013-10-01

    Real-time measurement of propofol in the breath may be used for routine clinical monitoring. However, this requires unequivocal identification of the expiratory phase of the respiratory propofol signal as only expiratory propofol reflects propofol blood concentrations. Determination of CO2 breath concentrations is the current gold standard for the identification of expiratory gas but usually requires additional equipment. Human breath also contains isoprene, a volatile organic compound with low inspiratory breath concentration and an expiratory concentration plateau. We investigated whether breath isoprene could be used similarly to CO2 to identify the expiratory fraction of the propofol breath signal. We investigated real-time breath data obtained from 40 study subjects during routine anesthesia. Propofol, isoprene, and CO2 breath concentrations were determined by a combined ion molecule reaction/electron impact mass spectrometry system. The expiratory propofol signal was identified according to breath CO2 and isoprene concentrations and presented as median of intervals of 30 s duration. Bland-Altman analysis was applied to detect differences (bias) in the expiratory propofol signal extracted by the two identification methods. We investigated propofol signals in a total of 3,590 observation intervals of 30 s duration in the 40 study subjects. In 51.4 % of the intervals (1,844/3,590) both methods extracted the same results for expiratory propofol signal. Overall bias between the two data extraction methods was -0.12 ppb. The lower and the upper limits of the 95 % CI were -0.69 and 0.45 ppb. Determination of isoprene breath concentrations allows the identification of the expiratory propofol signal during real-time breath monitoring.

  19. Using a two-step matrix solution to reduce the run time in KULL's magnetic diffusion package

    SciTech Connect

    Brunner, T A; Kolev, T V

    2010-12-17

    Recently a Resistive Magnetohydrodynamics (MHD) package has been added to the KULL code. In order to be compatible with the underlying hydrodynamics algorithm, a new sub-zonal magnetics discretization was developed that supports arbitrary polygonal and polyhedral zones. This flexibility comes at the cost of many more unknowns per zone - approximately ten times more for a hexahedral mesh. We can eliminate some (or all, depending on the dimensionality) of the extra unknowns from the global matrix during assembly by using a Schur complement approach. This trades expensive global work for cache-friendly local work, while still allowing solution for the full system. Significant improvements in the solution time are observed for several test problems.

  20. Automatic classification of minelike targets buried underground using time-frequency signatures extracted by a stepped-frequency radar

    NASA Astrophysics Data System (ADS)

    Strifors, Hans C.; Gustafsson, Anders; Abrahamson, Steffan; Gaunaurd, Guillermo C.

    2001-10-01

    Ultra-wideband radar systems are feasible for extracting signature infor-ma-tion use-ful for target recognition purposes. An ultra-wideband radar system emits either an extremely short pulse, impulse, or a frequency modulated signal. The frequency content of the emitted signals is designed to match the size and kind of typical targets and environments. We investigate the backscattered echoes from selected targets that are extracted by a stepped-frequency continuous wave (SFCW) radar system playing the role of ground penetrating radar (GPR). The targets are metal and non-metal objects buried in dry sand. The SFCW radar transmits 55 different frequencies from 300 to 3,000 MHz in steps of 50 MHz. The duration of each frequency is about 100 ´s, which means that each transmitted waveform has an extremely narrow band. The in-phase (I) sampled signals and quadrature-phase (Q) sampled signals give information of both the amplitude and phase of the signal returned from the target. As a result a complex-valued line spectrum of the target is obtained that can be used for synthesizing real-valued repetitive waveforms, using the inverse Fourier transform. We analyze synthe-sized back-scat-tered echoes from each target in the joint time-frequency domain us-ing a pseudo-Wigner distribution (PWD). A classification method that we developed previously using the fuzzy C-means clustering technique is then used to reduce the number and kind of fea-tures in the derived target signatures. Using a template for each member of the class the classifier decides the membership of a given target based on best fit of the templates measured by a cost function. We also address the problem of how to select suitable waveforms for the templates used by the classification algorithm.

  1. Two-Step Self-Assembly of Liposome-Multidomain Peptide Nanofiber Hydrogel for Time-Controlled Release

    PubMed Central

    2015-01-01

    Progress in self-assembly and supramolecular chemistry has been directed toward obtaining macromolecular assemblies with higher degrees of complexity, simulating the highly structured environment in natural systems. One approach to this type of complexity are multistep, multicomponent, self-assembling systems that allow approaches comparable to traditional multistep synthetic organic chemistry; however, only a few examples of this approach have appeared in the literature. Our previous work demonstrated nanofibrous mimics of the extracellular matrix. Here we demonstrate the ability to create a unique hydrogel, developed by stepwise self-assembly of multidomain peptide fibers and liposomes. The two-component system allows for controlled release of bioactive factors at multiple time points. The individual components of the self-assembled gel and the composite hydrogel were characterized by TEM, SEM, and rheometry, demonstrating that peptide nanofibers and lipid vesicles both retain their structural integrity in the composite gel. The rheological robustness of the hydrogel is shown to be largely unaffected by the presence of liposomes. Release studies from the composite gels loaded with different growth factors EGF, MCP-1, and PlGF-1 showed delay and prolongation of release by liposomes entrapped in the hydrogel compared to more rapid release from the hydrogel alone. This bimodal release system may have utility in systems where timed cascades of biological signals may be valuable, such as in tissue regeneration. PMID:25308335

  2. Milk production of Friesian cows subjected to high daytime temperatures when allowed food either ad lib or at night-time only.

    PubMed

    Richards, J I

    1985-08-01

    Four lactating Friesian cows housed in climate chambers were exposed to the following sequential treatments: I, a four-week period when they were allowed constant access to an ad lib supply of a complete diet and water in a thermoneutral environment (ambient temperature (Ta) 14 to 20 degrees C and relative humidity (r.h.) 50 to 75%); II, a five-week period during which they were exposed to Ta 38.5 degrees C/r.h. 85% for 61/2 h during daytime and Ta 14 to 20 degrees C/r.h. 50 to 75% for the remainder of each day with constant access to ad lib complete diet and water; III, a four-week period under the same environment as treatment II but with access to food restricted to between 19.00 and 07.00; IV; a four-week period under the environment and feeding regime described for treatment II. The voluntary food intake (VFI) of cows subjected to II was not depressed as a result of high daytime temperature despite the fact that they exhibited daytime clinical features indicative of heat stress; this was because of a 27.8% compensatory increase in night-time feeding. Nevertheless there was an accompanying significant increase in the rate of lactation decline of 8.7% per month greater than that normally expected under the thermoneutral conditions (I). Subsequent restriction of food access to night-time (III) resulted in a significant reduction in mean VFI of 7.5%; however, the rate of lactation decline was drastically reduced to a value not dissimilar to the natural decline of 3.97% per month observed under thermoneutral conditions (I).

  3. Identification of Dobrava, Hantaan, Seoul, and Puumala viruses by one-step real-time RT-PCR.

    PubMed

    Aitichou, Mohamed; Saleh, Sharron S; McElroy, Anita K; Schmaljohn, C; Ibrahim, M Sofi

    2005-03-01

    We developed four assays for specifically identifying Dobrava (DOB), Hantaan (HTN), Puumala (PUU), and Seoul (SEO) viruses. The assays are based on the real-time one-step reverse transcriptase polymerase chain reaction (RT-PCR) with the small segment used as the target sequence. The detection limits of DOB, HTN, PUU, and SEO assays were 25, 25, 25, and 12.5 plaque-forming units, respectively. The assays were evaluated in blinded experiments, each with 100 samples that contained Andes, Black Creek Canal, Crimean-Congo hemorrhagic fever, Rift Valley fever and Sin Nombre viruses in addition to DOB, HTN, PUU and SEO viruses. The sensitivity levels of the DOB, HTN, PUU, and SEO assays were 98%, 96%, 92% and 94%, respectively. The specificity of DOB, HTN and SEO assays was 100% and the specificity of the PUU assay was 98%. Because of the high levels of sensitivity, specificity, and reproducibility, we believe that these assays can be useful for diagnosing and differentiating these four Old-World hantaviruses.

  4. A two-step real-time PCR assay for quantitation and genotyping of human parvovirus 4.

    PubMed

    Väisänen, E; Lahtinen, A; Eis-Hübinger, A M; Lappalainen, M; Hedman, K; Söderlund-Venermo, M

    2014-01-01

    Human parvovirus 4 (PARV4) of the family Parvoviridae was discovered in a plasma sample of a patient with an undiagnosed acute infection in 2005. Currently, three PARV4 genotypes have been identified, however, with an unknown clinical significance. Interestingly, these genotypes seem to differ in epidemiology. In Northern Europe, USA and Asia, genotypes 1 and 2 have been found to occur mainly in persons with a history of injecting drug use or other parenteral exposure. In contrast, genotype 3 appears to be endemic in sub-Saharan Africa, where it infects children and adults without such risk behaviour. In this study, a novel straightforward and cost-efficient molecular assay for both quantitation and genotyping of PARV4 DNA was developed. The two-step method first applies a single-probe pan-PARV4 qPCR for screening and quantitation of this relatively rare virus, and subsequently, only the positive samples undergo a real-time PCR-based multi-probe genotyping. The new qPCR-GT method is highly sensitive and specific regardless of the genotype, and thus being suitable for studying the clinical impact and occurrence of the different PARV4 genotypes.

  5. Research Designs for Intervention Research with Small Samples II: Stepped Wedge and Interrupted Time-Series Designs.

    PubMed

    Fok, Carlotta Ching Ting; Henry, David; Allen, James

    2015-10-01

    The stepped wedge design (SWD) and the interrupted time-series design (ITSD) are two alternative research designs that maximize efficiency and statistical power with small samples when contrasted to the operating characteristics of conventional randomized controlled trials (RCT). This paper provides an overview and introduction to previous work with these designs and compares and contrasts them with the dynamic wait-list design (DWLD) and the regression point displacement design (RPDD), which were presented in a previous article (Wyman, Henry, Knoblauch, and Brown, Prevention Science. 2015) in this special section. The SWD and the DWLD are similar in that both are intervention implementation roll-out designs. We discuss similarities and differences between the SWD and DWLD in their historical origin and application, along with differences in the statistical modeling of each design. Next, we describe the main design characteristics of the ITSD, along with some of its strengths and limitations. We provide a critical comparative review of strengths and weaknesses in application of the ITSD, SWD, DWLD, and RPDD as small sample alternatives to application of the RCT, concluding with a discussion of the types of contextual factors that influence selection of an optimal research design by prevention researchers working with small samples.

  6. Real-time multi-step-ahead water level forecasting by recurrent neural networks for urban flood control

    NASA Astrophysics Data System (ADS)

    Chang, Fi-John; Chen, Pin-An; Lu, Ying-Ray; Huang, Eric; Chang, Kai-Yao

    2014-09-01

    Urban flood control is a crucial task, which commonly faces fast rising peak flows resulting from urbanization. To mitigate future flood damages, it is imperative to construct an on-line accurate model to forecast inundation levels during flood periods. The Yu-Cheng Pumping Station located in Taipei City of Taiwan is selected as the study area. Firstly, historical hydrologic data are fully explored by statistical techniques to identify the time span of rainfall affecting the rise of the water level in the floodwater storage pond (FSP) at the pumping station. Secondly, effective factors (rainfall stations) that significantly affect the FSP water level are extracted by the Gamma test (GT). Thirdly, one static artificial neural network (ANN) (backpropagation neural network-BPNN) and two dynamic ANNs (Elman neural network-Elman NN; nonlinear autoregressive network with exogenous inputs-NARX network) are used to construct multi-step-ahead FSP water level forecast models through two scenarios, in which scenario I adopts rainfall and FSP water level data as model inputs while scenario II adopts only rainfall data as model inputs. The results demonstrate that the GT can efficiently identify the effective rainfall stations as important inputs to the three ANNs; the recurrent connections from the output layer (NARX network) impose more effects on the output than those of the hidden layer (Elman NN) do; and the NARX network performs the best in real-time forecasting. The NARX network produces coefficients of efficiency within 0.9-0.7 (scenario I) and 0.7-0.5 (scenario II) in the testing stages for 10-60-min-ahead forecasts accordingly. This study suggests that the proposed NARX models can be valuable and beneficial to the government authority for urban flood control.

  7. Step by Step

    ERIC Educational Resources Information Center

    Ruder, Robert

    2008-01-01

    Sometimes a principal just has to get out of the office. A walk around the building might provide an escape from the pace of a hectic day, a chance to clear the head and perhaps allow a new perspective on a seemingly monumental school-related challenge to emerge. Wherever the principal walks, he or she is able to identify things that need…

  8. Spectrum of Slip Processes on the Subduction Interface in a Continuum Framework Resolved by Rate-and State Dependent Friction and Adaptive Time Stepping

    NASA Astrophysics Data System (ADS)

    Herrendoerfer, R.; van Dinther, Y.; Gerya, T.

    2015-12-01

    To explore the relationships between subduction dynamics and the megathrust earthquake potential, we have recently developed a numerical model that bridges the gap between processes on geodynamic and earthquake cycle time scales. In a self-consistent, continuum-based framework including a visco-elasto-plastic constitutive relationship, cycles of megathrust earthquake-like ruptures were simulated through a purely slip rate-dependent friction, albeit with very low slip rates (van Dinther et al., JGR, 2013). In addition to much faster earthquakes, a range of aseismic slip processes operate at different time scales in nature. These aseismic processes likely accommodate a considerable amount of the plate convergence and are thus relevant in order to estimate the long-term seismic coupling and related hazard in subduction zones. To simulate and resolve this wide spectrum of slip processes, we innovatively implemented rate-and state dependent friction (RSF) and an adaptive time-stepping into our continuum framework. The RSF formulation, in contrast to our previous friction formulation, takes the dependency of frictional strength on a state variable into account. It thereby allows for continuous plastic yielding inside rate-weakening regions, which leads to aseismic slip. In contrast to the conventional RSF formulation, we relate slip velocities to strain rates and use an invariant formulation. Thus we do not require the a priori definition of infinitely thin, planar faults in a homogeneous elastic medium. With this new implementation of RSF, we succeed to produce consistent cycles of frictional instabilities. By changing the frictional parameter a, b, and the characteristic slip distance, we observe a transition from stable sliding to stick-slip behaviour. This transition is in general agreement with predictions from theoretical estimates of the nucleation size, thereby to first order validating our implementation. By incorporating adaptive time-stepping based on a

  9. Photo-activated ionic gelation of alginate hydrogel: real-time rheological monitoring of the two-step crosslinking mechanism.

    PubMed

    Higham, Alina K; Bonino, Christopher A; Raghavan, Srinivasa R; Khan, Saad A

    2014-07-21

    We examine the gelation of alginate undergoing ionic crosslinking upon ultraviolet (UV) irradiation using in situ dynamic rheology. Hydrogels are formed by combining alginate with calcium carbonate (CaCO3) particles and a photoacid generator (PAG). The PAG is photolyzed upon UV irradiation, resulting in the release of free calcium ions for ionic crosslinking. The viscous and elastic moduli during gelation are monitored as a function of the UV irradiation intensity, exposure time, alginate concentration, and the ratio between alginate and calcium carbonate. Gel time decreases as irradiation intensity increases because a larger concentration of PAG is photolyzed. Interestingly, dark curing, the continuing growth of microstructure in the absence of UV light, is observed. In some instances, the sample transitions from a solution to a gel during the dark curing phase. Additionally, when exposed to constant UV irradiation after the dark curing phase, samples reach the same plateau modulus as samples exposed to constant UV without dark curing, implying that dark curing does not affect the gelation mechanism. We believe the presence of dark curing is the result of the acidic environment persisting within the sample, allowing CaCO3 to dissociate, thereby releasing free Ca(2+) ions capable of binding with the available appropriate ionic blocks of the polymer chains. The growth of microstructure is then detected if the activation barrier has been crossed to release sufficient calcium ions. In this regard, we calculate a value of 30 J that represents the activation energy required to initiate gelation.

  10. Photo-activated ionic gelation of alginate hydrogel: real-time rheological monitoring of the two-step crosslinking mechanism.

    PubMed

    Higham, Alina K; Bonino, Christopher A; Raghavan, Srinivasa R; Khan, Saad A

    2014-07-21

    We examine the gelation of alginate undergoing ionic crosslinking upon ultraviolet (UV) irradiation using in situ dynamic rheology. Hydrogels are formed by combining alginate with calcium carbonate (CaCO3) particles and a photoacid generator (PAG). The PAG is photolyzed upon UV irradiation, resulting in the release of free calcium ions for ionic crosslinking. The viscous and elastic moduli during gelation are monitored as a function of the UV irradiation intensity, exposure time, alginate concentration, and the ratio between alginate and calcium carbonate. Gel time decreases as irradiation intensity increases because a larger concentration of PAG is photolyzed. Interestingly, dark curing, the continuing growth of microstructure in the absence of UV light, is observed. In some instances, the sample transitions from a solution to a gel during the dark curing phase. Additionally, when exposed to constant UV irradiation after the dark curing phase, samples reach the same plateau modulus as samples exposed to constant UV without dark curing, implying that dark curing does not affect the gelation mechanism. We believe the presence of dark curing is the result of the acidic environment persisting within the sample, allowing CaCO3 to dissociate, thereby releasing free Ca(2+) ions capable of binding with the available appropriate ionic blocks of the polymer chains. The growth of microstructure is then detected if the activation barrier has been crossed to release sufficient calcium ions. In this regard, we calculate a value of 30 J that represents the activation energy required to initiate gelation. PMID:24894636

  11. Stepping motor controller

    DOEpatents

    Bourret, S.C.; Swansen, J.E.

    1982-07-02

    A stepping motor is microprocessor controlled by digital circuitry which monitors the output of a shaft encoder adjustably secured to the stepping motor and generates a subsequent stepping pulse only after the preceding step has occurred and a fixed delay has expired. The fixed delay is variable on a real-time basis to provide for smooth and controlled deceleration.

  12. Stepping motor controller

    DOEpatents

    Bourret, Steven C.; Swansen, James E.

    1984-01-01

    A stepping motor is microprocessingly controlled by digital circuitry which monitors the output of a shaft encoder adjustably secured to the stepping motor and generates a subsequent stepping pulse only after the preceding step has occurred and a fixed delay has expired. The fixed delay is variable on a real-time basis to provide for smooth and controlled deceleration.

  13. Using RFID and accelerometer-embedded tracers to measure probabilities of bed load transport, step lengths, and rest times in a mountain stream

    NASA Astrophysics Data System (ADS)

    Olinde, Lindsay; Johnson, Joel P. L.

    2015-09-01

    We present new measurements of bed load tracer transport in a mountain stream over several snowmelt seasons. Cumulative displacements were measured using passive tracers, which consisted of gravel and cobbles embedded with radio frequency identification tags. The timing of bed load motion during 11 transporting events was quantified with active tracers, i.e., accelerometer-embedded cobbles. Probabilities of cobble transport increased with discharge above a threshold, and exhibited slight to moderate hysteresis during snowmelt hydrographs. Dividing cumulative displacements by the number of movements recorded by each active tracer constrained average step lengths. Average step lengths increased with discharge, and distributions of average step lengths and cumulative displacements were thin tailed. Distributions of rest times followed heavy-tailed power law scaling. Rest time scaling varied somewhat with discharge and with the degree to which tracers were incorporated into the streambed. The combination of thin-tailed displacement distributions and heavy-tailed rest time distributions predict superdiffusive dispersion.

  14. Next Step for STEP

    SciTech Connect

    Wood, Claire; Bremner, Brenda

    2013-08-09

    The Siletz Tribal Energy Program (STEP), housed in the Tribe’s Planning Department, will hire a data entry coordinator to collect, enter, analyze and store all the current and future energy efficiency and renewable energy data pertaining to administrative structures the tribe owns and operates and for homes in which tribal members live. The proposed data entry coordinator will conduct an energy options analysis in collaboration with the rest of the Siletz Tribal Energy Program and Planning Department staff. An energy options analysis will result in a thorough understanding of tribal energy resources and consumption, if energy efficiency and conservation measures being implemented are having the desired effect, analysis of tribal energy loads (current and future energy consumption), and evaluation of local and commercial energy supply options. A literature search will also be conducted. In order to educate additional tribal members about renewable energy, we will send four tribal members to be trained to install and maintain solar panels, solar hot water heaters, wind turbines and/or micro-hydro.

  15. Stepped nozzle

    DOEpatents

    Sutton, George P.

    1998-01-01

    An insert which allows a supersonic nozzle of a rocket propulsion system to operate at two or more different nozzle area ratios. This provides an improved vehicle flight performance or increased payload. The insert has significant advantages over existing devices for increasing nozzle area ratios. The insert is temporarily fastened by a simple retaining mechanism to the aft end of the diverging segment of the nozzle and provides for a multi-step variation of nozzle area ratio. When mounted in place, the insert provides the nozzle with a low nozzle area ratio. During flight, the retaining mechanism is released and the insert ejected thereby providing a high nozzle area ratio in the diverging nozzle segment.

  16. Stepped nozzle

    DOEpatents

    Sutton, G.P.

    1998-07-14

    An insert is described which allows a supersonic nozzle of a rocket propulsion system to operate at two or more different nozzle area ratios. This provides an improved vehicle flight performance or increased payload. The insert has significant advantages over existing devices for increasing nozzle area ratios. The insert is temporarily fastened by a simple retaining mechanism to the aft end of the diverging segment of the nozzle and provides for a multi-step variation of nozzle area ratio. When mounted in place, the insert provides the nozzle with a low nozzle area ratio. During flight, the retaining mechanism is released and the insert ejected thereby providing a high nozzle area ratio in the diverging nozzle segment. 5 figs.

  17. Time-stepping techniques to enable the simulation of bursting behavior in a physiologically realistic computational islet.

    PubMed

    Khuvis, Samuel; Gobbert, Matthias K; Peercy, Bradford E

    2015-05-01

    Physiologically realistic simulations of computational islets of beta cells require the long-time solution of several thousands of coupled ordinary differential equations (ODEs), resulting from the combination of several ODEs in each cell and realistic numbers of several hundreds of cells in an islet. For a reliable and accurate solution of complex nonlinear models up to the desired final times on the scale of several bursting periods, an appropriate ODE solver designed for stiff problems is eventually a necessity, since other solvers may not be able to handle the problem or are exceedingly inefficient. But stiff solvers are potentially significantly harder to use, since their algorithms require at least an approximation of the Jacobian matrix. For sophisticated models, systems of several complex ODEs in each cell, it is practically unworkable to differentiate these intricate nonlinear systems analytically and to manually program the resulting Jacobian matrix in computer code. This paper demonstrates that automatic differentiation can be used to obtain code for the Jacobian directly from code for the ODE system, which allows a full accounting for the sophisticated model equations. This technique is also feasible in source-code languages Fortran and C, and the conclusions apply to a wide range of systems of coupled, nonlinear reaction equations. However, when we combine an appropriately supplied Jacobian with slightly modified memory management in the ODE solver, simulations on the realistic scale of one thousand cells in the islet become possible that are several orders of magnitude faster than the original solver in the software Matlab, a language that is particularly user friendly for programming complicated model equations. We use the efficient simulator to analyze electrical bursting and show non-monotonic average burst period between fast and slow cells for increasing coupling strengths. We also find that interestingly, the arrangement of the connected fast

  18. Time-stepping techniques to enable the simulation of bursting behavior in a physiologically realistic computational islet.

    PubMed

    Khuvis, Samuel; Gobbert, Matthias K; Peercy, Bradford E

    2015-05-01

    Physiologically realistic simulations of computational islets of beta cells require the long-time solution of several thousands of coupled ordinary differential equations (ODEs), resulting from the combination of several ODEs in each cell and realistic numbers of several hundreds of cells in an islet. For a reliable and accurate solution of complex nonlinear models up to the desired final times on the scale of several bursting periods, an appropriate ODE solver designed for stiff problems is eventually a necessity, since other solvers may not be able to handle the problem or are exceedingly inefficient. But stiff solvers are potentially significantly harder to use, since their algorithms require at least an approximation of the Jacobian matrix. For sophisticated models, systems of several complex ODEs in each cell, it is practically unworkable to differentiate these intricate nonlinear systems analytically and to manually program the resulting Jacobian matrix in computer code. This paper demonstrates that automatic differentiation can be used to obtain code for the Jacobian directly from code for the ODE system, which allows a full accounting for the sophisticated model equations. This technique is also feasible in source-code languages Fortran and C, and the conclusions apply to a wide range of systems of coupled, nonlinear reaction equations. However, when we combine an appropriately supplied Jacobian with slightly modified memory management in the ODE solver, simulations on the realistic scale of one thousand cells in the islet become possible that are several orders of magnitude faster than the original solver in the software Matlab, a language that is particularly user friendly for programming complicated model equations. We use the efficient simulator to analyze electrical bursting and show non-monotonic average burst period between fast and slow cells for increasing coupling strengths. We also find that interestingly, the arrangement of the connected fast

  19. Simplified Two-Time Step Method for Calculating Combustion and Emission Rates of Jet-A and Methane Fuel With and Without Water Injection

    NASA Technical Reports Server (NTRS)

    Molnar, Melissa; Marek, C. John

    2005-01-01

    A simplified kinetic scheme for Jet-A, and methane fuels with water injection was developed to be used in numerical combustion codes, such as the National Combustor Code (NCC) or even simple FORTRAN codes. The two time step method is either an initial time averaged value (step one) or an instantaneous value (step two). The switch is based on the water concentration in moles/cc of 1x10(exp -20). The results presented here results in a correlation that gives the chemical kinetic time as two separate functions. This two time step method is used as opposed to a one step time averaged method previously developed to determine the chemical kinetic time with increased accuracy. The first time averaged step is used at the initial times for smaller water concentrations. This gives the average chemical kinetic time as a function of initial overall fuel air ratio, initial water to fuel mass ratio, temperature, and pressure. The second instantaneous step, to be used with higher water concentrations, gives the chemical kinetic time as a function of instantaneous fuel and water mole concentration, pressure and temperature (T4). The simple correlations would then be compared to the turbulent mixing times to determine the limiting rates of the reaction. The NASA Glenn GLSENS kinetics code calculates the reaction rates and rate constants for each species in a kinetic scheme for finite kinetic rates. These reaction rates are used to calculate the necessary chemical kinetic times. Chemical kinetic time equations for fuel, carbon monoxide and NOx are obtained for Jet-A fuel and methane with and without water injection to water mass loadings of 2/1 water to fuel. A similar correlation was also developed using data from NASA's Chemical Equilibrium Applications (CEA) code to determine the equilibrium concentrations of carbon monoxide and nitrogen oxide as functions of overall equivalence ratio, water to fuel mass ratio, pressure and temperature (T3). The temperature of the gas entering

  20. New Reduced Two-Time Step Method for Calculating Combustion and Emission Rates of Jet-A and Methane Fuel With and Without Water Injection

    NASA Technical Reports Server (NTRS)

    Molnar, Melissa; Marek, C. John

    2004-01-01

    A simplified kinetic scheme for Jet-A, and methane fuels with water injection was developed to be used in numerical combustion codes, such as the National Combustor Code (NCC) or even simple FORTRAN codes that are being developed at Glenn. The two time step method is either an initial time averaged value (step one) or an instantaneous value (step two). The switch is based on the water concentration in moles/cc of 1x10(exp -20). The results presented here results in a correlation that gives the chemical kinetic time as two separate functions. This two step method is used as opposed to a one step time averaged method previously developed to determine the chemical kinetic time with increased accuracy. The first time averaged step is used at the initial times for smaller water concentrations. This gives the average chemical kinetic time as a function of initial overall fuel air ratio, initial water to fuel mass ratio, temperature, and pressure. The second instantaneous step, to be used with higher water concentrations, gives the chemical kinetic time as a function of instantaneous fuel and water mole concentration, pressure and temperature (T4). The simple correlations would then be compared to the turbulent mixing times to determine the limiting properties of the reaction. The NASA Glenn GLSENS kinetics code calculates the reaction rates and rate constants for each species in a kinetic scheme for finite kinetic rates. These reaction rates were then used to calculate the necessary chemical kinetic times. Chemical kinetic time equations for fuel, carbon monoxide and NOx were obtained for Jet-A fuel and methane with and without water injection to water mass loadings of 2/1 water to fuel. A similar correlation was also developed using data from NASA's Chemical Equilibrium Applications (CEA) code to determine the equilibrium concentrations of carbon monoxide and nitrogen oxide as functions of overall equivalence ratio, water to fuel mass ratio, pressure and temperature (T3

  1. ChromAlign: A two-step algorithmic procedure for time alignment of three-dimensional LC-MS chromatographic surfaces.

    PubMed

    Sadygov, Rovshan G; Maroto, Fernando Martin; Hühmer, Andreas F R

    2006-12-15

    We present an algorithmic approach to align three-dimensional chromatographic surfaces of LC-MS data of complex mixture samples. The approach consists of two steps. In the first step, we prealign chromatographic profiles: two-dimensional projections of chromatographic surfaces. This is accomplished by correlation analysis using fast Fourier transforms. In this step, a temporal offset that maximizes the overlap and dot product between two chromatographic profiles is determined. In the second step, the algorithm generates correlation matrix elements between full mass scans of the reference and sample chromatographic surfaces. The temporal offset from the first step indicates a range of the mass scans that are possibly correlated, then the correlation matrix is calculated only for these mass scans. The correlation matrix carries information on highly correlated scans, but it does not itself determine the scan or time alignment. Alignment is determined as a path in the correlation matrix that maximizes the sum of the correlation matrix elements. The computational complexity of the optimal path generation problem is reduced by the use of dynamic programming. The program produces time-aligned surfaces. The use of the temporal offset from the first step in the second step reduces the computation time for generating the correlation matrix and speeds up the process. The algorithm has been implemented in a program, ChromAlign, developed in C++ language for the .NET2 environment in WINDOWS XP. In this work, we demonstrate the applications of ChromAlign to alignment of LC-MS surfaces of several datasets: a mixture of known proteins, samples from digests of surface proteins of T-cells, and samples prepared from digests of cerebrospinal fluid. ChromAlign accurately aligns the LC-MS surfaces we studied. In these examples, we discuss various aspects of the alignment by ChromAlign, such as constant time axis shifts and warping of chromatographic surfaces.

  2. Novel One-Tube-One-Step Real-Time Methodology for Rapid Transcriptomic Biomarker Detection: Signal Amplification by Ternary Initiation Complexes.

    PubMed

    Fujita, Hiroto; Kataoka, Yuka; Tobita, Seiji; Kuwahara, Masayasu; Sugimoto, Naoki

    2016-07-19

    We have developed a novel RNA detection method, termed signal amplification by ternary initiation complexes (SATIC), in which an analyte sample is simply mixed with the relevant reagents and allowed to stand for a short time under isothermal conditions (37 °C). The advantage of the technique is that there is no requirement for (i) heat annealing, (ii) thermal cycling during the reaction, (iii) a reverse transcription step, or (iv) enzymatic or mechanical fragmentation of the target RNA. SATIC involves the formation of a ternary initiation complex between the target RNA, a circular DNA template, and a DNA primer, followed by rolling circle amplification (RCA) to generate multiple copies of G-quadruplex (G4) on a long DNA strand like beads on a string. The G4s can be specifically fluorescence-stained with N(3)-hydroxyethyl thioflavin T (ThT-HE), which emits weakly with single- and double-stranded RNA/DNA but strongly with parallel G4s. An improved dual SATIC system, which involves the formation of two different ternary initiation complexes in the RCA process, exhibited a wide quantitative detection range of 1-5000 pM. Furthermore, this enabled visual observation-based RNA detection, which is more rapid and convenient than conventional isothermal methods, such as reverse transcription-loop-mediated isothermal amplification, signal mediated amplification of RNA technology, and RNA-primed rolling circle amplification. Thus, SATIC methodology may serve as an on-site and real-time measurement technique for transcriptomic biomarkers for various diseases.

  3. Novel One-Tube-One-Step Real-Time Methodology for Rapid Transcriptomic Biomarker Detection: Signal Amplification by Ternary Initiation Complexes.

    PubMed

    Fujita, Hiroto; Kataoka, Yuka; Tobita, Seiji; Kuwahara, Masayasu; Sugimoto, Naoki

    2016-07-19

    We have developed a novel RNA detection method, termed signal amplification by ternary initiation complexes (SATIC), in which an analyte sample is simply mixed with the relevant reagents and allowed to stand for a short time under isothermal conditions (37 °C). The advantage of the technique is that there is no requirement for (i) heat annealing, (ii) thermal cycling during the reaction, (iii) a reverse transcription step, or (iv) enzymatic or mechanical fragmentation of the target RNA. SATIC involves the formation of a ternary initiation complex between the target RNA, a circular DNA template, and a DNA primer, followed by rolling circle amplification (RCA) to generate multiple copies of G-quadruplex (G4) on a long DNA strand like beads on a string. The G4s can be specifically fluorescence-stained with N(3)-hydroxyethyl thioflavin T (ThT-HE), which emits weakly with single- and double-stranded RNA/DNA but strongly with parallel G4s. An improved dual SATIC system, which involves the formation of two different ternary initiation complexes in the RCA process, exhibited a wide quantitative detection range of 1-5000 pM. Furthermore, this enabled visual observation-based RNA detection, which is more rapid and convenient than conventional isothermal methods, such as reverse transcription-loop-mediated isothermal amplification, signal mediated amplification of RNA technology, and RNA-primed rolling circle amplification. Thus, SATIC methodology may serve as an on-site and real-time measurement technique for transcriptomic biomarkers for various diseases. PMID:27347743

  4. A high-order solver for unsteady incompressible Navier-Stokes equations using the flux reconstruction method on unstructured grids with implicit dual time stepping

    NASA Astrophysics Data System (ADS)

    Cox, Christopher; Liang, Chunlei; Plesniak, Michael

    2015-11-01

    This paper reports development of a high-order compact method for solving unsteady incompressible flow on unstructured grids with implicit time stepping. The method falls under the class of methods now referred to as flux reconstruction/correction procedure via reconstruction. The governing equations employ the classical artificial compressibility treatment, where dual time stepping is needed to solve unsteady flow problems. An implicit non-linear lower-upper symmetric Gauss-Seidel scheme with backward Euler discretization is used to efficiently march the solution in pseudo time, while a second-order backward Euler discretization is used to march in physical time. We verify and validate implementation of the high-order method coupled with our implicit time-stepping scheme. Three-dimensional results computed on many processing elements will be presented. The high-order method is very suitable for parallel computing and can easily be extended to moving and deforming grids. The current implicit time stepping scheme is proven effective in satisfying the divergence-free constraint on the velocity field in the artificial compressibility formulation within the context of the high-order flux reconstruction method. Financial support provided under the GW Presidential Merit Fellowship.

  5. A high-order solver for unsteady incompressible Navier-Stokes equations using the flux reconstruction method on unstructured grids with implicit dual time stepping

    NASA Astrophysics Data System (ADS)

    Cox, Christopher; Liang, Chunlei; Plesniak, Michael W.

    2016-06-01

    We report development of a high-order compact flux reconstruction method for solving unsteady incompressible flow on unstructured grids with implicit dual time stepping. The method falls under the class of methods now referred to as flux reconstruction/correction procedure via reconstruction. The governing equations employ Chorin's classic artificial compressibility formulation with dual time stepping to solve unsteady flow problems. An implicit non-linear lower-upper symmetric Gauss-Seidel scheme with backward Euler discretization is used to efficiently march the solution in pseudo time, while a second-order backward Euler discretization is used to march in physical time. We verify and validate implementation of the high-order method coupled with our implicit time stepping scheme using both steady and unsteady incompressible flow problems. The current implicit time stepping scheme is proven effective in satisfying the divergence-free constraint on the velocity field in the artificial compressibility formulation within the context of the high-order flux reconstruction method. This compact high-order method is very suitable for parallel computing and can easily be extended to moving and deforming grids.

  6. Canadian children's and youth's pedometer-determined steps/day, parent-reported TV watching time, and overweight/obesity: The CANPLAY Surveillance Study

    PubMed Central

    2011-01-01

    Background This study examines associations between pedometer-determined steps/day and parent-reported child's Body Mass Index (BMI) and time typically spent watching television between school and dinner. Methods Young people (aged 5-19 years) were recruited through their parents by random digit dialling and mailed a data collection package. Information on height and weight and time spent watching television between school and dinner on a typical school day was collected from parents. In total, 5949 boys and 5709 girls reported daily steps. BMI was categorized as overweight or obese using Cole's cut points. Participants wore pedometers for 7 days and logged daily steps. The odds of being overweight and obese by steps/day and parent-reported time spent television watching were estimated using logistic regression for complex samples. Results Girls had a lower median steps/day (10682 versus 11059 for boys) and also a narrower variation in steps/day (interquartile range, 4410 versus 5309 for boys). 11% of children aged 5-19 years were classified as obese; 17% of boys and girls were overweight. Both boys and girls watched, on average, < 40 minutes of television between school and dinner on school days. Adjusting for child's age and sex and parental education, the odds of a child being obese decreased by 20% for every extra 3000 steps/day and increased by 21% for every 30 minutes of television watching. There was no association of being overweight with steps/day, however the odds of being overweight increased by 8% for every 30 minutes of additional time spent watching television between school and dinner on a typical school day. Discussion Television viewing is the more prominent factor in terms of predicting overweight, and it contributes to obesity, but steps/day attenuates the association between television viewing and obesity, and therefore can be considered protective against obesity. In addition to replacing opportunities for active alternative behaviours

  7. A sensitive one-step real-time PCR for detection of avian influenza viruses using a MGB probe and an internal positive control

    PubMed Central

    Di Trani, Livia; Bedini, Barbara; Donatelli, Isabella; Campitelli, Laura; Chiappini, Barbara; De Marco, Maria Alessandra; Delogu, Mauro; Buonavoglia, Canio; Vaccari, Gabriele

    2006-01-01

    Background Avian influenza viruses (AIVs) are endemic in wild birds and their introduction and conversion to highly pathogenic avian influenza virus in domestic poultry is a cause of serious economic losses as well as a risk for potential transmission to humans. The ability to rapidly recognise AIVs in biological specimens is critical for limiting further spread of the disease in poultry. The advent of molecular methods such as real time polymerase chain reaction has allowed improvement of detection methods currently used in laboratories, although not all of these methods include an Internal Positive Control (IPC) to monitor for false negative results. Therefore we developed a one-step reverse transcription real time PCR (RRT-PCR) with a Minor Groove Binder (MGB) probe for the detection of different subtypes of AIVs. This technique also includes an IPC. Methods RRT-PCR was developed using an improved TaqMan technology with a MGB probe to detect AI from reference viruses. Primers and probe were designed based on the matrix gene sequences from most animal and human A influenza virus subtypes. The specificity of RRT-PCR was assessed by detecting influenza A virus isolates belonging to subtypes from H1–H13 isolated in avian, human, swine and equine hosts. The analytical sensitivity of the RRT-PCR assay was determined using serial dilutions of in vitro transcribed matrix gene RNA. The use of a rodent RNA as an IPC in order not to reduce the efficiency of the assay was adopted. Results The RRT-PCR assay is capable to detect all tested influenza A viruses. The detection limit of the assay was shown to be between 5 and 50 RNA copies per reaction and the standard curve demonstrated a linear range from 5 to 5 × 108 copies as well as excellent reproducibility. The analytical sensitivity of the assay is 10–100 times higher than conventional RT-PCR. Conclusion The high sensitivity, rapidity, reproducibility and specificity of the AIV RRT-PCR with the use of IPC to monitor

  8. THE INFLUENCE OF MODEL TIME STEP ON THE RELATIVE SENSITIVITY OF POPULATION GROWTH TO SURVIVAL, GROWTH AND REPRODUCTION

    EPA Science Inventory

    Matrix population models are often used to extrapolate from life stage-specific stressor effects on survival and reproduction to population-level effects. Demographic elasticity analysis of a matrix model allows an evaluation of the relative sensitivity of population growth rate ...

  9. Summary of Simplified Two Time Step Method for Calculating Combustion Rates and Nitrogen Oxide Emissions for Hydrogen/Air and Hydrogen/Oxygen

    NASA Technical Reports Server (NTRS)

    Marek, C. John; Molnar, Melissa

    2005-01-01

    A simplified single rate expression for hydrogen combustion and nitrogen oxide production was developed. Detailed kinetics are predicted for the chemical kinetic times using the complete chemical mechanism over the entire operating space. These times are then correlated to the reactor conditions using an exponential fit. Simple first order reaction expressions are then used to find the conversion in the reactor. The method uses a two time step kinetic scheme. The first time averaged step is used at the initial times with smaller water concentrations. This gives the average chemical kinetic time as a function of initial overall fuel air ratio, temperature, and pressure. The second instantaneous step is used at higher water concentrations (greater than l x 10(exp -20)) moles per cc) in the mixture which gives the chemical kinetic time as a function of the instantaneous fuel and water mole concentrations, pressure and temperature (T(sub 4)). The simple correlations are then compared to the turbulent mixing times to determine the limiting properties of the reaction. The NASA Glenn GLSENS kinetics code calculates the reaction rates and rate constants for each species in a kinetic scheme for finite kinetic rates. These reaction rates are used to calculate the necessary chemical kinetic times. This time is regressed over the complete initial conditions using the Excel regression routine. Chemical kinetic time equations for H2 and NOx are obtained for H2/Air fuel and for H2/O2. A similar correlation is also developed using data from NASA's Chemical Equilibrium Applications (CEA) code to determine the equilibrium temperature (T(sub 4)) as a function of overall fuel/air ratio, pressure and initial temperature (T(sub 3)). High values of the regression coefficient R squared are obtained.

  10. Simplified Two-Time Step Method for Calculating Combustion Rates and Nitrogen Oxide Emissions for Hydrogen/Air and Hydorgen/Oxygen

    NASA Technical Reports Server (NTRS)

    Molnar, Melissa; Marek, C. John

    2005-01-01

    A simplified single rate expression for hydrogen combustion and nitrogen oxide production was developed. Detailed kinetics are predicted for the chemical kinetic times using the complete chemical mechanism over the entire operating space. These times are then correlated to the reactor conditions using an exponential fit. Simple first order reaction expressions are then used to find the conversion in the reactor. The method uses a two-time step kinetic scheme. The first time averaged step is used at the initial times with smaller water concentrations. This gives the average chemical kinetic time as a function of initial overall fuel air ratio, temperature, and pressure. The second instantaneous step is used at higher water concentrations (> 1 x 10(exp -20) moles/cc) in the mixture which gives the chemical kinetic time as a function of the instantaneous fuel and water mole concentrations, pressure and temperature (T4). The simple correlations are then compared to the turbulent mixing times to determine the limiting properties of the reaction. The NASA Glenn GLSENS kinetics code calculates the reaction rates and rate constants for each species in a kinetic scheme for finite kinetic rates. These reaction rates are used to calculate the necessary chemical kinetic times. This time is regressed over the complete initial conditions using the Excel regression routine. Chemical kinetic time equations for H2 and NOx are obtained for H2/air fuel and for the H2/O2. A similar correlation is also developed using data from NASA s Chemical Equilibrium Applications (CEA) code to determine the equilibrium temperature (T4) as a function of overall fuel/air ratio, pressure and initial temperature (T3). High values of the regression coefficient R2 are obtained.

  11. Beamforming of aeroacoustic sources in the time domain: An investigation of the intermittency of the noise radiated by a forward-facing step

    NASA Astrophysics Data System (ADS)

    Fischer, J.; Valeau, V.; Brizzi, L.-E.

    2016-11-01

    The present study investigates the intermittency of the broadband aeroacoustic noise produced by a forward-facing step in a flow. The noise source is viewed as a random succession of the so-called intermittent events of short duration distributed spatially in a source region in the flow. An array processing method based on time-domain beamforming has been developed in order to track systematically the intermittent events, both in the time and space domains. Based on a simulated model of the far-field pressure field, the method is validated in terms of event detection and of performance for recovering the pressure spectrum. The method is then applied to experimental array data taken in an anechoic wind-tunnel at low Mach numbers (not exceeding 0.15) for a forward-facing step of height 30 mm. The results show that some very short intermittent events (with a mean duration of the order of 0.15 ms) can be identified from the array data. The spatial distribution of the intermittent events is found to be in agreement with the frequency domain beamform maps. The probability density functions of the events, in terms of widths and apparition times, are shown to be governed by Gamma laws and indicate random phenomena; it is observed that the statistical distributions vary with the streamwise position downstream and upstream of the step, the trends being in agreement with the source behavior as evidenced by using the frequency-domain beamforming methods. The proposed method is then shown to identify, in terms of emission time, location and temporal width, a succession of short acoustic events that participate to the broadband aeroacoustic noise produced by the step; those random events are likely to be linked to the dynamics of the flow interacting with the step.

  12. Conventional and Real-Time PCRs for Detection of Erwinia piriflorinigrans Allow Its Distinction from the Fire Blight Pathogen, Erwinia amylovora

    PubMed Central

    Barbé, Silvia; Bertolini, Edson; Roselló, Montserrat; Llop, Pablo

    2014-01-01

    Erwinia piriflorinigrans is a new pathogenic species of the bacterial genus Erwinia that has been described recently in Spain. Accurate detection and identification of E. piriflorinigrans are challenging because its symptoms on pear blossoms are similar to those caused by Erwinia amylovora, the causal agent of fire blight. Moreover, these two species share phenotypic and molecular characteristics. Two specific and sensitive conventional and real-time PCR protocols were developed to identify and detect E. piriflorinigrans and to differentiate it from E. amylovora and other species of this genus. These protocols were based on sequences from plasmid pEPIR37, which is present in all strains of E. piriflorinigrans analyzed. After the stability of the plasmid was demonstrated, the specificities of the protocols were confirmed by the amplification of all E. piriflorinigrans strains tested, whereas 304 closely related pathogenic and nonpathogenic Erwinia strains and microbiota from pear trees were not amplified. In sensitivity assays, 103 cells/ml extract were detected in spiked plant material by conventional or real-time PCR, and 102 cells/ml were detected in DNA extracted from spiked plant material by real-time PCR. The protocols developed here succeeded in detecting E. piriflorinigrans in 102 out of 564 symptomatic and asymptomatic naturally infected pear samples (flowers, cortex stem tissue, leaves, shoots, and fruitlets), in necrotic Pyracantha sp. blossoms, and in necrotic pear and apple tissues infected with both E. amylovora and E. piriflorinigrans. Therefore, these new tools can be used in epidemiological studies that will enhance our understanding of the life cycle of E. piriflorinigrans in different hosts and plant tissues and its interaction with E. amylovora. PMID:24509928

  13. Conventional and real-time PCRs for detection of Erwinia piriflorinigrans allow its distinction from the fire blight pathogen, Erwinia amylovora.

    PubMed

    Barbé, Silvia; Bertolini, Edson; Roselló, Montserrat; Llop, Pablo; López, María M

    2014-04-01

    Erwinia piriflorinigrans is a new pathogenic species of the bacterial genus Erwinia that has been described recently in Spain. Accurate detection and identification of E. piriflorinigrans are challenging because its symptoms on pear blossoms are similar to those caused by Erwinia amylovora, the causal agent of fire blight. Moreover, these two species share phenotypic and molecular characteristics. Two specific and sensitive conventional and real-time PCR protocols were developed to identify and detect E. piriflorinigrans and to differentiate it from E. amylovora and other species of this genus. These protocols were based on sequences from plasmid pEPIR37, which is present in all strains of E. piriflorinigrans analyzed. After the stability of the plasmid was demonstrated, the specificities of the protocols were confirmed by the amplification of all E. piriflorinigrans strains tested, whereas 304 closely related pathogenic and nonpathogenic Erwinia strains and microbiota from pear trees were not amplified. In sensitivity assays, 10(3) cells/ml extract were detected in spiked plant material by conventional or real-time PCR, and 10(2) cells/ml were detected in DNA extracted from spiked plant material by real-time PCR. The protocols developed here succeeded in detecting E. piriflorinigrans in 102 out of 564 symptomatic and asymptomatic naturally infected pear samples (flowers, cortex stem tissue, leaves, shoots, and fruitlets), in necrotic Pyracantha sp. blossoms, and in necrotic pear and apple tissues infected with both E. amylovora and E. piriflorinigrans. Therefore, these new tools can be used in epidemiological studies that will enhance our understanding of the life cycle of E. piriflorinigrans in different hosts and plant tissues and its interaction with E. amylovora.

  14. Real-time PCR assay allows detection of the New Delhi metallo-β-lactamase (NDM-1)-encoding gene in France.

    PubMed

    Diene, Seydina M; Bruder, Nicolas; Raoult, Didier; Rolain, Jean-Marc

    2011-06-01

    In this study, we report the development of a rapid real-time polymerase chain reaction (PCR) assay with TaqMan probe to detect the New Delhi metallo-β-lactamase (NDM-1)-encoding gene directly from bacterial isolates. The specificity of the assay was verified in silico as well as with a large panel of 84 clinically relevant bacteria, including the Klebsiella pneumoniae NCTC 13443 NDM-1-positive reference strain. Using this assay retrospectively on a local series of 44 K. pneumoniae isolates from Marseille Hospitals (France), it was possible to detect and identify an NDM-1-producing K. pneumoniae strain isolated from bronchoalveolar lavage in April 2010 from a French patient repatriated from India after a motorbike accident. Standard PCR amplification and sequencing of the entire NDM-1 gene from this isolate was also performed and the amino acid sequence showed 100% homology with the NDM-1 protein from the K. pneumoniae reference strain. We believe that this real-time PCR assay would be a powerful tool that could be added to other molecular detection assays such as detection of KPC- or OXA-encoding genes for rapid screening and/or identification of carbapenem-resistant bacterial isolates from patients returning from the Asian continent that could be implemented in a point-of-care strategy.

  15. Accurate molecular dynamics and nuclear quantum effects at low cost by multiple steps in real and imaginary time: Using density functional theory to accelerate wavefunction methods.

    PubMed

    Kapil, V; VandeVondele, J; Ceriotti, M

    2016-02-01

    The development and implementation of increasingly accurate methods for electronic structure calculations mean that, for many atomistic simulation problems, treating light nuclei as classical particles is now one of the most serious approximations. Even though recent developments have significantly reduced the overhead for modeling the quantum nature of the nuclei, the cost is still prohibitive when combined with advanced electronic structure methods. Here we present how multiple time step integrators can be combined with ring-polymer contraction techniques (effectively, multiple time stepping in imaginary time) to reduce virtually to zero the overhead of modelling nuclear quantum effects, while describing inter-atomic forces at high levels of electronic structure theory. This is demonstrated for a combination of MP2 and semi-local DFT applied to the Zundel cation. The approach can be seamlessly combined with other methods to reduce the computational cost of path integral calculations, such as high-order factorizations of the Boltzmann operator or generalized Langevin equation thermostats.

  16. Unconditionally energy stable time stepping scheme for Cahn-Morral equation: Application to multi-component spinodal decomposition and optimal space tiling

    NASA Astrophysics Data System (ADS)

    Tavakoli, Rouhollah

    2016-01-01

    An unconditionally energy stable time stepping scheme is introduced to solve Cahn-Morral-like equations in the present study. It is constructed based on the combination of David Eyre's time stepping scheme and Schur complement approach. Although the presented method is general and independent of the choice of homogeneous free energy density function term, logarithmic and polynomial energy functions are specifically considered in this paper. The method is applied to study the spinodal decomposition in multi-component systems and optimal space tiling problems. A penalization strategy is developed, in the case of later problem, to avoid trivial solutions. Extensive numerical experiments demonstrate the success and performance of the presented method. According to the numerical results, the method is convergent and energy stable, independent of the choice of time stepsize. Its MATLAB implementation is included in the appendix for the numerical evaluation of algorithm and reproduction of the presented results.

  17. Accurate molecular dynamics and nuclear quantum effects at low cost by multiple steps in real and imaginary time: Using density functional theory to accelerate wavefunction methods

    NASA Astrophysics Data System (ADS)

    Kapil, V.; VandeVondele, J.; Ceriotti, M.

    2016-02-01

    The development and implementation of increasingly accurate methods for electronic structure calculations mean that, for many atomistic simulation problems, treating light nuclei as classical particles is now one of the most serious approximations. Even though recent developments have significantly reduced the overhead for modeling the quantum nature of the nuclei, the cost is still prohibitive when combined with advanced electronic structure methods. Here we present how multiple time step integrators can be combined with ring-polymer contraction techniques (effectively, multiple time stepping in imaginary time) to reduce virtually to zero the overhead of modelling nuclear quantum effects, while describing inter-atomic forces at high levels of electronic structure theory. This is demonstrated for a combination of MP2 and semi-local DFT applied to the Zundel cation. The approach can be seamlessly combined with other methods to reduce the computational cost of path integral calculations, such as high-order factorizations of the Boltzmann operator or generalized Langevin equation thermostats.

  18. The effect of large-scale model time step and multiscale coupling frequency on cloud climatology, vertical structure, and rainfall extremes in a superparameterized GCM

    DOE PAGES

    Yu, Sungduk; Pritchard, Michael S.

    2015-12-17

    The effect of global climate model (GCM) time step—which also controls how frequently global and embedded cloud resolving scales are coupled—is examined in the Superparameterized Community Atmosphere Model ver 3.0. Systematic bias reductions of time-mean shortwave cloud forcing (~10 W/m2) and longwave cloud forcing (~5 W/m2) occur as scale coupling frequency increases, but with systematically increasing rainfall variance and extremes throughout the tropics. An overarching change in the vertical structure of deep tropical convection, favoring more bottom-heavy deep convection as a global model time step is reduced may help orchestrate these responses. The weak temperature gradient approximation is more faithfullymore » satisfied when a high scale coupling frequency (a short global model time step) is used. These findings are distinct from the global model time step sensitivities of conventionally parameterized GCMs and have implications for understanding emergent behaviors of multiscale deep convective organization in superparameterized GCMs. Lastly, the results may also be useful for helping to tune them.« less

  19. The effect of large-scale model time step and multiscale coupling frequency on cloud climatology, vertical structure, and rainfall extremes in a superparameterized GCM

    SciTech Connect

    Yu, Sungduk; Pritchard, Michael S.

    2015-12-17

    The effect of global climate model (GCM) time step—which also controls how frequently global and embedded cloud resolving scales are coupled—is examined in the Superparameterized Community Atmosphere Model ver 3.0. Systematic bias reductions of time-mean shortwave cloud forcing (~10 W/m2) and longwave cloud forcing (~5 W/m2) occur as scale coupling frequency increases, but with systematically increasing rainfall variance and extremes throughout the tropics. An overarching change in the vertical structure of deep tropical convection, favoring more bottom-heavy deep convection as a global model time step is reduced may help orchestrate these responses. The weak temperature gradient approximation is more faithfully satisfied when a high scale coupling frequency (a short global model time step) is used. These findings are distinct from the global model time step sensitivities of conventionally parameterized GCMs and have implications for understanding emergent behaviors of multiscale deep convective organization in superparameterized GCMs. Lastly, the results may also be useful for helping to tune them.

  20. A Compact Tandem Two-Step Laser Time-of-Flight Mass Spectrometer for In Situ Analysis of Non-Volatile Organics on Planetary Surfaces

    NASA Technical Reports Server (NTRS)

    Getty, Stephanie A.; Brinckerhoff, William B.; Li, Xiang; Elsila, Jamie; Cornish, Timothy; Ecelberger, Scott; Wu, Qinghao; Zare, Richard

    2014-01-01

    Two-step laser desorption mass spectrometry is a well suited technique to the analysis of high priority classes of organics, such as polycyclic aromatic hydrocarbons, present in complex samples. The use of decoupled desorption and ionization laser pulses allows for sensitive and selective detection of structurally intact organic species. We have recently demonstrated the implementation of this advancement in laser mass spectrometry in a compact, flight-compatible instrument that could feasibly be the centerpiece of an analytical science payload as part of a future spaceflight mission to a small body or icy moon.

  1. Implementation of time-resolved step-scan fourier transform infrared (FT-IR) spectroscopy using a kHz repetition rate pump laser.

    PubMed

    Magana, Donny; Parul, Dzmitry; Dyer, R Brian; Shreve, Andrew P

    2011-05-01

    Time-resolved step-scan Fourier transform infrared (FT-IR) spectroscopy has been shown to be invaluable for studying excited-state structures and dynamics in both biological and inorganic systems. Despite the established utility of this method, technical challenges continue to limit the data quality and more wide ranging applications. A critical problem has been the low laser repetition rate and interferometer stepping rate (both are typically 10 Hz) used for data acquisition. Here we demonstrate significant improvement in the quality of time-resolved spectra through the use of a kHz repetition rate laser to achieve kHz excitation and data collection rates while stepping the spectrometer at 200 Hz. We have studied the metal-to-ligand charge transfer excited state of Ru(bipyridine)(3)Cl(2) in deuterated acetonitrile to test and optimize high repetition rate data collection. Comparison of different interferometer stepping rates reveals an optimum rate of 200 Hz due to minimization of long-term baseline drift. With the improved collection efficiency and signal-to-noise ratio, better assignments of the MLCT excited-state bands can be made. Using optimized parameters, carbonmonoxy myoglobin in deuterated buffer is also studied by observing the infrared signatures of carbon monoxide photolysis upon excitation of the heme. We conclude from these studies that a substantial increase in performance of ss-FT-IR instrumentation is achieved by coupling commercial infrared benches with kHz repetition rate lasers.

  2. Meta-analysis and time series modeling allow a systematic review of primary HIV-1 drug-resistant prevalence in Latin America and Caribbean.

    PubMed

    Coelho, Antonio Victor Campos; De Moura, Ronald Rodrigues; Da Silva, Ronaldo Celerino; Kamada, Anselmo Jiro; Guimarães, Rafael Lima; Brandão, Lucas André Cavalcanti; Coelho, Hemílio Fernandes Campos; Crovella, Sergio

    2015-01-01

    Here we review the prevalence of HIV-1 primary drug resistance in Latin America and Caribbean using meta-analysis as well as time-series modeling. We also discuss whether there could be a drawback to HIV/AIDS programs due to drug resistance in Latin America and Caribbean in the next years. We observed that, although some studies report low or moderate primary drug resistance prevalence in Caribbean countries, this evidence needs to be updated. In other countries, such as Brazil and Argentina, the prevalence of drug resistance appears to be rising. Mutations conferring resistance against reverse transcriptase inhibitors were the most frequent in the analyzed populations (70% of all mutational events). HIV-1 subtype B was the most prevalent in Latin America and the Caribbean, although subtype C and B/F recombinants have significant contributions in Argentina and Brazil. Thus, we suggest that primary drug resistance in Latin America and the Caribbean could have been underestimated. Clinical monitoring should be improved to offer better therapy, reducing the risk for HIV-1 resistance emergence and spread, principally in vulnerable populations, such as men who have sex with men transmission group, sex workers and intravenous drug users.

  3. Visual deprivation leads to gait adaptations that are age- and context-specific: I. Step-time parameters.

    PubMed

    Hallemans, Ann; Beccu, Sofie; Van Loock, Kelly; Ortibus, Els; Truijen, Steven; Aerts, Peter

    2009-07-01

    In children, visual information is crucial for static postural control, although age-related differences exist in the impact of visual perturbation on postural sway. Since static postural control and locomotion are closely related, we expect age-related differences in the impact of visual deprivation on dynamic stability and gait. It is hypothesised that this is related to the important role of vision in postural control. Postural stability and gait was tested in 20 adults and 40 children (3-11 years old) under two different visual conditions: eyes open (EO) and eyes closed (EC). Significant differences were found between EO and EC for postural sway, dimensionless walking speed, dimensionless stride length and duration of double support. Thus, we can state that visual deprivation affects locomotion both in adults and children. Concerning walking speed a significant interaction effect was observed with age. The difference in walking speed between EO and EC is larger in children than in adults. Furthermore, we found significant correlations between postural sway and walking speed, step frequency and stride length. These observations support the hypothesis that gait adaptations in situations of visual deprivation are related to balance problems.

  4. Increase in family allowances.

    PubMed

    1989-01-01

    In July 1989 the family allowance structure in Australia was changed from a 4-rate to a 2-rate structure. The new rates were increased to $A9 a week for the 1st 3 children and $A12 for each additional child. The Family Allowance Supplment rate for children 13-15 years old was raised from $A31 to $A34.10/week. PMID:12344544

  5. ns-μs Time-Resolved Step-Scan FTIR of ba3 Oxidoreductase from Thermus thermophilus: Protonic Connectivity of w941-w946-w927

    PubMed Central

    Nicolaides, Antonis; Soulimane, Tewfik; Varotsis, Constantinos

    2016-01-01

    Time-resolved step-scan FTIR spectroscopy has been employed to probe the dynamics of the ba3 oxidoreductase from Thermus thermophilus in the ns-μs time range and in the pH/pD 6–9 range. The data revealed a pH/pD sensitivity of the D372 residue and of the ring-A propionate of heme a3. Based on the observed transient changes a model in which the protonic connectivity of w941-w946-927 to the D372 and the ring-A propionate of heme a3 is described. PMID:27690021

  6. Development of a time-stepping sediment budget model for assessing land use impacts in large river basins.

    PubMed

    Wilkinson, S N; Dougall, C; Kinsey-Henderson, A E; Searle, R D; Ellis, R J; Bartley, R

    2014-01-15

    The use of river basin modelling to guide mitigation of non-point source pollution of wetlands, estuaries and coastal waters has become widespread. To assess and simulate the impacts of alternate land use or climate scenarios on river washload requires modelling techniques that represent sediment sources and transport at the time scales of system response. Building on the mean-annual SedNet model, we propose a new D-SedNet model which constructs daily budgets of fine sediment sources, transport and deposition for each link in a river network. Erosion rates (hillslope, gully and streambank erosion) and fine sediment sinks (floodplains and reservoirs) are disaggregated from mean annual rates based on daily rainfall and runoff. The model is evaluated in the Burdekin basin in tropical Australia, where policy targets have been set for reducing sediment and nutrient loads to the Great Barrier Reef (GBR) lagoon from grazing and cropping land. D-SedNet predicted annual loads with similar performance to that of a sediment rating curve calibrated to monitored suspended sediment concentrations. Relative to a 22-year reference load time series at the basin outlet derived from a dynamic general additive model based on monitoring data, D-SedNet had a median absolute error of 68% compared with 112% for the rating curve. RMS error was slightly higher for D-SedNet than for the rating curve due to large relative errors on small loads in several drought years. This accuracy is similar to existing agricultural system models used in arable or humid environments. Predicted river loads were sensitive to ground vegetation cover. We conclude that the river network sediment budget model provides some capacity for predicting load time-series independent of monitoring data in ungauged basins, and for evaluating the impact of land management on river sediment load time-series, which is challenging across large regions in data-poor environments. PMID:23968738

  7. Development of a time-stepping sediment budget model for assessing land use impacts in large river basins.

    PubMed

    Wilkinson, S N; Dougall, C; Kinsey-Henderson, A E; Searle, R D; Ellis, R J; Bartley, R

    2014-01-15

    The use of river basin modelling to guide mitigation of non-point source pollution of wetlands, estuaries and coastal waters has become widespread. To assess and simulate the impacts of alternate land use or climate scenarios on river washload requires modelling techniques that represent sediment sources and transport at the time scales of system response. Building on the mean-annual SedNet model, we propose a new D-SedNet model which constructs daily budgets of fine sediment sources, transport and deposition for each link in a river network. Erosion rates (hillslope, gully and streambank erosion) and fine sediment sinks (floodplains and reservoirs) are disaggregated from mean annual rates based on daily rainfall and runoff. The model is evaluated in the Burdekin basin in tropical Australia, where policy targets have been set for reducing sediment and nutrient loads to the Great Barrier Reef (GBR) lagoon from grazing and cropping land. D-SedNet predicted annual loads with similar performance to that of a sediment rating curve calibrated to monitored suspended sediment concentrations. Relative to a 22-year reference load time series at the basin outlet derived from a dynamic general additive model based on monitoring data, D-SedNet had a median absolute error of 68% compared with 112% for the rating curve. RMS error was slightly higher for D-SedNet than for the rating curve due to large relative errors on small loads in several drought years. This accuracy is similar to existing agricultural system models used in arable or humid environments. Predicted river loads were sensitive to ground vegetation cover. We conclude that the river network sediment budget model provides some capacity for predicting load time-series independent of monitoring data in ungauged basins, and for evaluating the impact of land management on river sediment load time-series, which is challenging across large regions in data-poor environments.

  8. Gas flushing through hyper-acidic crater lakes: the next steps within a reframed monitoring time window

    NASA Astrophysics Data System (ADS)

    Rouwet, Dmitri

    2016-04-01

    Tracking variations in the chemical composition, water temperature and pH of brines from peak-activity crater lakes is the most obvious way to forecast phreatic activity. Volcano monitoring intrinsically implies a time window of observation that should be synchronised with the kinetics of magmatic processes, such as degassing and magma intrusion. To decipher "how much time ago" a variation in degassing regime actually occurred before eventually being detected in a crater lake is key, and depends on the lake water residence time. The above reasoning assumes that gas is preserved as anions in the lake water (SO4, Cl, F anions), in other words, that scrubbing of acid gases is complete and irreversible. Less is true. Recent work has confirmed, by direct MultiGas measurement from evaporative plumes, that even the strongest acid in liquid medium (i.e. SO2) degasses from hyper-acidic crater lakes. The less strong acid HCl has long been recognised as being more volatile than hydrophyle in extremely acidic solutions (pH near 0), through a long-term steady increase in SO4/Cl ratios in the vigorously evaporating crater lake of Poás volcano. We now know that acidic gases flush through hyper-acidic crater lake brines, but we don't know to which extend (completely or partially?), and with which speed. The chemical composition hence only reflects a transient phase of the gas flushing through the lake. In terms of volcanic surveillance this brings the advantage that the monitoring time window is definitely shorter than defined by the water chemistry, but yet, we do not know how much shorter. Empirical experiments by Capaccioni et al. (in press) have tried to tackle this kinetic problem for HCl degassing from a "lab-lake" on the short-term (2 days). With this state of the art in mind, two new monitoring strategies can be proposed to seek for precursory signals of phreatic eruptions from crater lakes: (1) Tracking variations in gas compositions, fluxes and ratios between species in

  9. Global surface mass time variations by using a two-step inversion for cumulating daily satellite gravity information

    NASA Astrophysics Data System (ADS)

    Ramillien, Guillaume; Frappart, Frappart; Seoane, Lucia

    2015-04-01

    We propose a new method to produce time series of global maps of surface mass variations by progressive integration of daily geopotential variations measured by orbiting satellites. In the case of the GRACE mission (2002 - 2012), these geopotential variations can be determined from very accurate inter-satellite K-Band Range Rate (KBRR) measurements of 5-second daily orbits. In particular, the along-track gravity contribution of hydrology is extracted by removing de-aliasing models for static field, atmosphere, oceans mass variations (including periodical tides), as well as polar movements. Our determination of surface mass sources consists of two successive dependent Kalman filter stages. The first one consists of reducing the satellite-based potential anomalies by adjusting the longest spatial wavelengths (i.e., low-degree spherical harmonics less than 5-6). In the second stage, the residual potential anomalies from the previous stage are used to recover surface mass density changes - in terms of Equivalent-Water Height (EWH) - over a global network of juxtaposed triangular elements. These surface tiles of ~40,000 km x km are imposed to be identical and homogeneously-distributed over the terrestrial sphere, however they can be adapted to the local geometry of the surface mass. Our global approach was tested by inverting simulated hydrology-related geopotential data, and successfully applied to estimate time-varying surface mass densities from real GRACE-based residuals. This strategy of combined Kalman filter-type inversions can also be useful for exploring the possibility of reaching better time and space resolutions for hydrology, that would be hopefully brought by future low altitude geodetic missions.

  10. Two-step Laser Time-of-Flight Mass Spectrometry to Elucidate Organic Diversity in Planetary Surface Materials.

    NASA Technical Reports Server (NTRS)

    Getty, Stephanie A.; Brinckerhoff, William B.; Cornish, Timothy; Li, Xiang; Floyd, Melissa; Arevalo, Ricardo Jr.; Cook, Jamie Elsila; Callahan, Michael P.

    2013-01-01

    Laser desorption/ionization time-of-flight mass spectrometry (LD-TOF-MS) holds promise to be a low-mass, compact in situ analytical capability for future landed missions to planetary surfaces. The ability to analyze a solid sample for both mineralogical and preserved organic content with laser ionization could be compelling as part of a scientific mission pay-load that must be prepared for unanticipated discoveries. Targeted missions for this instrument capability include Mars, Europa, Enceladus, and small icy bodies, such as asteroids and comets.

  11. Detection of Citrus leprosis virus C using specific primers and TaqMan probe in one-step real-time reverse-transcription polymerase chain reaction assays.

    PubMed

    Choudhary, Nandlal; Wei, G; Govindarajulu, A; Roy, Avijit; Li, Wenbin; Picton, Deric D; Nakhla, M K; Levy, L; Brlansky, R H

    2015-11-01

    Citrus leprosis virus C (CiLV-C), a causal agent of the leprosis disease in citrus, is mostly present in the South and Central America and spreading toward the North America. To enable better diagnosis and inhibit the further spread of this re-emerging virus a quantitative (q) real-time reverse transcription polymerase chain reaction (qRT-PCR) assay is needed for early detection of CiLV-C when the virus is present in low titer in citrus leprosis samples. Using the genomic sequence of CiLV-C, specific primers and probe were designed and synthesized to amplify a 73 nt amplicon from the movement protein (MP) gene. A standard curve of the 73 nt amplicon MP gene was developed using known 10(10)-10(1) copies of in vitro synthesized RNA transcript to estimate the copy number of RNA transcript in the citrus leprosis samples. The one-step qRT-PCR detection assays for CiLV-C were determined to be 1000 times more sensitive when compared to the one-step conventional reverse transcription polymerase chain reaction (RT-PCR) CiLV-C detection method. To evaluate the quality of the total RNA extracts, NADH dehydrogenase gene specific primers (nad5) and probe were included in reactions as an internal control. The one-step qRT-PCR specificity was successfully validated by testing for the presence of CiLV-C in the total RNA extracts of the citrus leprosis samples collected from Belize, Costa Rica, Mexico and Panama. Implementation of the one-step qRT-PCR assays for CiLV-C diagnosis should assist regulatory agencies in surveillance activities to monitor the distribution pattern of CiLV-C in countries where it is present and to prevent further dissemination into citrus growing countries where there is no report of CiLV-C presence. PMID:26341059

  12. Detection of Citrus leprosis virus C using specific primers and TaqMan probe in one-step real-time reverse-transcription polymerase chain reaction assays.

    PubMed

    Choudhary, Nandlal; Wei, G; Govindarajulu, A; Roy, Avijit; Li, Wenbin; Picton, Deric D; Nakhla, M K; Levy, L; Brlansky, R H

    2015-11-01

    Citrus leprosis virus C (CiLV-C), a causal agent of the leprosis disease in citrus, is mostly present in the South and Central America and spreading toward the North America. To enable better diagnosis and inhibit the further spread of this re-emerging virus a quantitative (q) real-time reverse transcription polymerase chain reaction (qRT-PCR) assay is needed for early detection of CiLV-C when the virus is present in low titer in citrus leprosis samples. Using the genomic sequence of CiLV-C, specific primers and probe were designed and synthesized to amplify a 73 nt amplicon from the movement protein (MP) gene. A standard curve of the 73 nt amplicon MP gene was developed using known 10(10)-10(1) copies of in vitro synthesized RNA transcript to estimate the copy number of RNA transcript in the citrus leprosis samples. The one-step qRT-PCR detection assays for CiLV-C were determined to be 1000 times more sensitive when compared to the one-step conventional reverse transcription polymerase chain reaction (RT-PCR) CiLV-C detection method. To evaluate the quality of the total RNA extracts, NADH dehydrogenase gene specific primers (nad5) and probe were included in reactions as an internal control. The one-step qRT-PCR specificity was successfully validated by testing for the presence of CiLV-C in the total RNA extracts of the citrus leprosis samples collected from Belize, Costa Rica, Mexico and Panama. Implementation of the one-step qRT-PCR assays for CiLV-C diagnosis should assist regulatory agencies in surveillance activities to monitor the distribution pattern of CiLV-C in countries where it is present and to prevent further dissemination into citrus growing countries where there is no report of CiLV-C presence.

  13. A high-order discontinuous Galerkin method for fluid–structure interaction with efficient implicit–explicit time stepping

    SciTech Connect

    Froehle, Bradley Persson, Per-Olof

    2014-09-01

    We present a high-order accurate scheme for coupled fluid–structure interaction problems. The fluid is discretized using a discontinuous Galerkin method on unstructured tetrahedral meshes, and the structure uses a high-order volumetric continuous Galerkin finite element method. Standard radial basis functions are used for the mesh deformation. The time integration is performed using a partitioned approach based on implicit–explicit Runge–Kutta methods. The resulting scheme fully decouples the implicit solution procedures for the fluid and the solid parts, which we perform using two separate efficient parallel solvers. We demonstrate up to fifth order accuracy in time on a non-trivial test problem, on which we also show that additional subiterations are not required. We solve a benchmark problem of a cantilever beam in a shedding flow, and show good agreement with other results in the literature. Finally, we solve for the flow around a thin membrane at a high angle of attack in both 2D and 3D, and compare with the results obtained with a rigid plate.

  14. Step-scan FTIR absorption difference time-resolved spectroscopy studies the excited state electronic structures and decay kinetics of d6 transition metal polypyridine complexes

    NASA Astrophysics Data System (ADS)

    Smith, G. D.; Paegel, B. M.; Palmer, R. A.; Chen, P.; Omberg, K. M.; Meyer, T. J.

    1998-06-01

    Step-scan FTIR absorption difference time-resolved spectroscopy (S2 FTIR ΔA TRS) has been used to study the photo-excited states of several low-spin d6 transition metal polypyridine complexes. Insight into the distribution of electron density in the excited states is obtained by comparing the ground and excited state vibrational frequencies of various bands sensitive to electronic structure. The multiplex, registration, and IR throughput advantages of this interferometric technique are significant in comparison with other methods currently used to probe photo-excited processes on the nanosecond time scale. The S2 FTIR ΔA TR spectra were obtained by use of a step-scan modified Bruker IFS 88 FTIR spectrometer equipped with an AC/DC-coupled photovoltaic Kolmar Technologies MCT detector with a 20 ns rise time and a 100/200 MHz PAD82a transient digitizer. The complexes were excited with frequency-tripled pulses from a Q-switched Quanta-Ray DCR1A Nd:YAG laser (355 nm, 10 ns, 10 Hz, 3 mJ/pulse). Data were collected with 10 ns time resolution.

  15. Time-Stepping Approximation of Rigid-Body Dynamics with Perfect Unilateral Constraints. I: The Inelastic Impact Case

    NASA Astrophysics Data System (ADS)

    Paoli, L.

    2010-11-01

    We consider a discrete mechanical system with a non-trivial mass matrix, subjected to perfect unilateral constraints described by the geometrical inequalities {f_{α} (q) ≥q 0, α in \\{1, dots, ν\\} (ν ≥q 1)}. We assume that the transmission of the velocities at impact is governed by Newton’s Law with a coefficient of restitution e = 0 (so that the impact is inelastic). We propose a time-discretization of the second order differential inclusion describing the dynamics, which generalizes the scheme proposed in Paoli (J Differ Equ 211:247-281, 2005) and, for any admissible data, we prove the convergence of approximate motions to a solution of the initial-value problem.

  16. Cyclic steps on ice

    NASA Astrophysics Data System (ADS)

    Yokokawa, M.; Izumi, N.; Naito, K.; Parker, G.; Yamada, T.; Greve, R.

    2016-05-01

    Boundary waves often form at the interface between ice and fluid flowing adjacent to it, such as ripples under river ice covers, and steps on the bed of supraglacial meltwater channels. They may also be formed by wind, such as the megadunes on the Antarctic ice sheet. Spiral troughs on the polar ice caps of Mars have been interpreted to be cyclic steps formed by katabatic wind blowing over ice. Cyclic steps are relatives of upstream-migrating antidunes. Cyclic step formation on ice is not only a mechanical but also a thermodynamic process. There have been very few studies on the formation of either cyclic steps or upstream-migrating antidunes on ice. In this study, we performed flume experiments to reproduce cyclic steps on ice by flowing water, and found that trains of steps form when the Froude number is larger than unity. The features of those steps allow them to be identified as ice-bed analogs of cyclic steps in alluvial and bedrock rivers. We performed a linear stability analysis and obtained a physical explanation of the formation of upstream-migrating antidunes, i.e., precursors of cyclic steps. We compared the results of experiments with the predictions of the analysis and found the observed steps fall in the range where the analysis predicts interfacial instability. We also found that short antidune-like undulations formed as a precursor to the appearance of well-defined steps. This fact suggests that such antidune-like undulations correspond to the instability predicted by the analysis and are precursors of cyclic steps.

  17. Detection of Langat virus by TaqMan real-time one-step qRT-PCR method.

    PubMed

    Muhd Radzi, Siti Fatimah; Rückert, Claudia; Sam, Sing-Sin; Teoh, Boon-Teong; Jee, Pui-Fong; Phoon, Wai-Hong; Abubakar, Sazaly; Zandi, Keivan

    2015-09-11

    Langat virus (LGTV), one of the members of the tick-borne encephalitis virus (TBEV) complex, was firstly isolated from Ixodes granulatus ticks in Malaysia. However, the prevalence of LGTV in ticks in the region remains unknown. Surveillance for LGTV is therefore important and thus a tool for specific detection of LGTV is needed. In the present study, we developed a real-time quantitative reverse-transcription-polymerase chain reaction (qRT-PCR) for rapid detection of LGTV. Our findings showed that the developed qRT-PCR could detect LGTV at a titre as low as 0.1 FFU/ml. The detection limit of the qRT-PCR assay at 95% probability was 0.28 FFU/ml as determined by probit analysis (p ≤ 0.05). Besides, the designed primers and probe did not amplify ORF of the E genes for some closely related and more pathogenic viruses including TBEV, Louping ill virus, Omsk hemorrhagic fever virus (OHFV), Alkhurma virus (ALKV), Kyasanur Forest Disease virus (KFDV) and Powassan virus (POWV) which showed the acceptable specificity of the developed assay. The sensitivity of the developed method also has been confirmed by determining the LGTV in infected tick cell line as well as LGTV- spiked tick tissues.

  18. Detection of Langat virus by TaqMan real-time one-step qRT-PCR method

    PubMed Central

    Muhd Radzi, Siti Fatimah; Rückert, Claudia; Sam, Sing-Sin; Teoh, Boon-Teong; Jee, Pui-Fong; Phoon, Wai-Hong; Abubakar, Sazaly; Zandi, Keivan

    2015-01-01

    Langat virus (LGTV), one of the members of the tick-borne encephalitis virus (TBEV) complex, was firstly isolated from Ixodes granulatus ticks in Malaysia. However, the prevalence of LGTV in ticks in the region remains unknown. Surveillance for LGTV is therefore important and thus a tool for specific detection of LGTV is needed. In the present study, we developed a real-time quantitative reverse-transcription-polymerase chain reaction (qRT-PCR) for rapid detection of LGTV. Our findings showed that the developed qRT-PCR could detect LGTV at a titre as low as 0.1 FFU/ml. The detection limit of the qRT-PCR assay at 95% probability was 0.28 FFU/ml as determined by probit analysis (p ≤ 0.05). Besides, the designed primers and probe did not amplify ORF of the E genes for some closely related and more pathogenic viruses including TBEV, Louping ill virus, Omsk hemorrhagic fever virus (OHFV), Alkhurma virus (ALKV), Kyasanur Forest Disease virus (KFDV) and Powassan virus (POWV) which showed the acceptable specificity of the developed assay. The sensitivity of the developed method also has been confirmed by determining the LGTV in infected tick cell line as well as LGTV- spiked tick tissues. PMID:26360297

  19. Investigation of a transonic axisymmetric backward-facing step flow by means of time-resolved PIV and PSP

    NASA Astrophysics Data System (ADS)

    Scharnowski, Sven; Bitter, Martin; Kähler, Christian J.

    2012-11-01

    The results presented here are obtained within a sub project of the SFB TRR 40 program (founded by the German research foundation), which focuses on the analysis and modeling of coupled liquid rocket propulsion systems and their integration into the space transportation system. The overall objective is to develop technological foundations for the design of thermally and mechanically highly loaded components of future space transportation systems. The interaction between the shear layer and the nozzle in the wake of the launcher is particularly important. Therefore, detailed analyses of a generic space launcher model's wake flow are the main emphasis of this sub project. The combination of time-resolved PIV and PSP provide deep insights into the flow physics: The separation at the end of the main body, the formation of the shear layer, its growth and its reattachment, as well as the surface pressure fluctuations, are analyzed in detail. The results reveal unsteady loads caused by shear layer motion which could interfere with structural modes of a space launcher main engines' nozzle.

  20. Heat-activatable primers for hot-start PCR and hot-start one-step RT-PCR: endpoint and real-time experiments.

    PubMed

    Ashrafi, Elena Hidalgo; Paul, Natasha

    2009-10-01

    Hot-start PCR is a technique that improves PCR performance by reducing nonspecific amplification during the initial setup stages of the PCR. This unit describes hot-start PCR protocols which utilize primers containing temperature-sensitive modifications. The introduction of 4-oxo-tetradecyl (OXT) phosphotriester groups onto the 3' end of the primer allows for primer-based hot-start PCR that is amenable for use in a number of PCR-based applications. The protocols described in this unit utilize OXT-modified primers in applications such as standard thermal cycling PCR, fast thermal cycling PCR, multiplex PCR, and one-step reverse-transcription PCR. This method is also advantageous for instances where improved PCR specificity is desired and a hot-start polymerase suitable for your application is not available.

  1. A two-step lyssavirus real-time polymerase chain reaction using degenerate primers with superior sensitivity to the fluorescent antigen test.

    PubMed

    Suin, Vanessa; Nazé, Florence; Francart, Aurélie; Lamoral, Sophie; De Craeye, Stéphane; Kalai, Michael; Van Gucht, Steven

    2014-01-01

    A generic two-step lyssavirus real-time reverse transcriptase polymerase chain reaction (qRT-PCR), based on a nested PCR strategy, was validated for the detection of different lyssavirus species. Primers with 17 to 30% of degenerate bases were used in both consecutive steps. The assay could accurately detect RABV, LBV, MOKV, DUVV, EBLV-1, EBLV-2, and ABLV. In silico sequence alignment showed a functional match with the remaining lyssavirus species. The diagnostic specificity was 100% and the sensitivity proved to be superior to that of the fluorescent antigen test. The limit of detection was ≤ 1 50% tissue culture infectious dose. The related vesicular stomatitis virus was not recognized, confirming the selectivity for lyssaviruses. The assay was applied to follow the evolution of rabies virus infection in the brain of mice from 0 to 10 days after intranasal inoculation. The obtained RNA curve corresponded well with the curves obtained by a one-step monospecific RABV-qRT-PCR, the fluorescent antigen test, and virus titration. Despite the presence of degenerate bases, the assay proved to be highly sensitive, specific, and reproducible.

  2. Linking search space structure, run-time dynamics, and problem difficulty : a step toward demystifying tabu search.

    SciTech Connect

    Whitley, L. Darrell; Howe, Adele E.; Watson, Jean-Paul

    2004-09-01

    Tabu search is one of the most effective heuristics for locating high-quality solutions to a diverse array of NP-hard combinatorial optimization problems. Despite the widespread success of tabu search, researchers have a poor understanding of many key theoretical aspects of this algorithm, including models of the high-level run-time dynamics and identification of those search space features that influence problem difficulty. We consider these questions in the context of the job-shop scheduling problem (JSP), a domain where tabu search algorithms have been shown to be remarkably effective. Previously, we demonstrated that the mean distance between random local optima and the nearest optimal solution is highly correlated with problem difficulty for a well-known tabu search algorithm for the JSP introduced by Taillard. In this paper, we discuss various shortcomings of this measure and develop a new model of problem difficulty that corrects these deficiencies. We show that Taillard's algorithm can be modeled with high fidelity as a simple variant of a straightforward random walk. The random walk model accounts for nearly all of the variability in the cost required to locate both optimal and sub-optimal solutions to random JSPs, and provides an explanation for differences in the difficulty of random versus structured JSPs. Finally, we discuss and empirically substantiate two novel predictions regarding tabu search algorithm behavior. First, the method for constructing the initial solution is highly unlikely to impact the performance of tabu search. Second, tabu tenure should be selected to be as small as possible while simultaneously avoiding search stagnation; values larger than necessary lead to significant degradations in performance.

  3. Multi-time-step ahead daily and hourly intermittent reservoir inflow prediction by artificial intelligent techniques using lumped and distributed data

    NASA Astrophysics Data System (ADS)

    Jothiprakash, V.; Magar, R. B.

    2012-07-01

    SummaryIn this study, artificial intelligent (AI) techniques such as artificial neural network (ANN), Adaptive neuro-fuzzy inference system (ANFIS) and Linear genetic programming (LGP) are used to predict daily and hourly multi-time-step ahead intermittent reservoir inflow. To illustrate the applicability of AI techniques, intermittent Koyna river watershed in Maharashtra, India is chosen as a case study. Based on the observed daily and hourly rainfall and reservoir inflow various types of time-series, cause-effect and combined models are developed with lumped and distributed input data. Further, the model performance was evaluated using various performance criteria. From the results, it is found that the performances of LGP models are found to be superior to ANN and ANFIS models especially in predicting the peak inflows for both daily and hourly time-step. A detailed comparison of the overall performance indicated that the combined input model (combination of rainfall and inflow) performed better in both lumped and distributed input data modelling. It was observed that the lumped input data models performed slightly better because; apart from reducing the noise in the data, the better techniques and their training approach, appropriate selection of network architecture, required inputs, and also training-testing ratios of the data set. The slight poor performance of distributed data is due to large variations and lesser number of observed values.

  4. A time-based potential step analysis of electrochemical impedance incorporating a constant phase element: a study of commercially pure titanium in phosphate buffered saline.

    PubMed

    Ehrensberger, Mark T; Gilbert, Jeremy L

    2010-05-01

    The measurement of electrochemical impedance is a valuable tool to assess the electrochemical environment that exists at the surface of metallic biomaterials. This article describes the development and validation of a new technique, potential step impedance analysis (PSIA), to assess the electrochemical impedance of materials whose interface with solution can be modeled as a simplified Randles circuit that is modified with a constant phase element. PSIA is based upon applying a step change in voltage to a working electrode and analyzing the subsequent current transient response in a combined time and frequency domain technique. The solution resistance, polarization resistance, and interfacial capacitance are found directly in the time domain. The experimental current transient is numerically transformed to the frequency domain to determine the constant phase exponent, alpha. This combined time and frequency approach was tested using current transients generated from computer simulations, from resistor-capacitor breadboard circuits, and from commercially pure titanium samples immersed in phosphate buffered saline and polarized at -800 mV or +1000 mV versus Ag/AgCl. It was shown that PSIA calculates equivalent admittance and impedance behavior over this range of potentials when compared to standard electrochemical impedance spectroscopy. This current transient approach characterizes the frequency response of the system without the need for expensive frequency response analyzers or software.

  5. Time-resolved spectral characterization of ring cavity surface emitting and ridge-type distributed feedback quantum cascade lasers by step-scan FT-IR spectroscopy.

    PubMed

    Brandstetter, Markus; Genner, Andreas; Schwarzer, Clemens; Mujagic, Elvis; Strasser, Gottfried; Lendl, Bernhard

    2014-02-10

    We present the time-resolved comparison of pulsed 2nd order ring cavity surface emitting (RCSE) quantum cascade lasers (QCLs) and pulsed 1st order ridge-type distributed feedback (DFB) QCLs using a step-scan Fourier transform infrared (FT-IR) spectrometer. Laser devices were part of QCL arrays and fabricated from the same laser material. Required grating periods were adjusted to account for the grating order. The step-scan technique provided a spectral resolution of 0.1 cm(-1) and a time resolution of 2 ns. As a result, it was possible to gain information about the tuning behavior and potential mode-hops of the investigated lasers. Different cavity-lengths were compared, including 0.9 mm and 3.2 mm long ridge-type and 0.97 mm (circumference) ring-type cavities. RCSE QCLs were found to have improved emission properties in terms of line-stability, tuning rate and maximum emission time compared to ridge-type lasers.

  6. Temporal averaging of phase measurements in the presence of spurious phase drift - Application to phase-stepped real-time holographic interferometry

    NASA Technical Reports Server (NTRS)

    Ovryn, B.; Haacke, E. M.

    1993-01-01

    A technique that compensates for low spatial frequency spurious phase changes during an interference experiment is developed; it permits temporal averaging of multiple-phase measurements, made before and after object displacement. The method is tested with phase-stepped real-time holographic interferometry applied to cantilever bending of a piezoelectric bimorph ceramic. Results indicate that temporal averaging of the corrected data significantly reduces the white noise in a phase measurement without incurring systematic errors or sacrificing spatial resolution. White noise is reduced from 3 deg to less than 1 deg using these methods.

  7. A variable multi-step method for transient heat conduction

    NASA Technical Reports Server (NTRS)

    Smolinski, Patrick

    1991-01-01

    A variable explicit time integration algorithm is developed for unsteady diffusion problems. The algorithm uses nodal partitioning and allows the nodal groups to be updated with different time steps. The stability of the algorithm is analyzed using energy methods and critical time steps are found in terms of element eigenvalues with no restrictions on element types. Several numerical examples are given to illustrate the accuracy of the method.

  8. Development of a one-step SYBR Green I real-time RT-PCR assay for the detection and quantitation of Araraquara and Rio Mamore hantavirus.

    PubMed

    Machado, Alex Martins; de Souza, William Marciel; de Pádua, Michelly; da Silva Rodrigues Machado, Aline Rafaela; Figueiredo, Luiz Tadeu Moraes

    2013-09-19

    Hantaviruses are members of the family Bunyaviridae and are an emerging cause of disease worldwide with high lethality in the Americas. In Brazil, the diagnosis for hantaviruses is based on immunologic techniques associated with conventional RT-PCR. A novel one-step SYBR Green real-time RT-PCR was developed for the detection and quantitation of Araraquara (ARAV) and Rio Mamore hantavirus (RIOMV). The detection limit of assay was 10 copies/μL of RNA in vitro transcribed of segment S. The specificity of assay was evaluated by melting curve analysis, which showed that the Araraquara virus amplified product generated a melt peak at 80.83 ± 0.89 °C without generating primer-dimers or non-specific products. The assay was more sensitive than conventional RT-PCR and we detected two samples undetected by conventional RT-PCR. The one-step SYBR Green real-time quantitative RT-PCR is specific, sensible and reproducible, which makes it a powerful tool in both diagnostic applications and general research of ARAV and RIOMV and possibly other Brazilian hantaviruses.

  9. Investigations on polyplex stability during the freezing step of lyophilization using controlled ice nucleation--the importance of residence time in the low-viscosity fluid state.

    PubMed

    Kasper, Julia C; Pikal, Michael J; Friess, Wolfgang

    2013-03-01

    The aim of the study was to comprehensively investigate the influence of the freezing step during lyophilization on the stability of gene-delivery particles in order to better understand particle stabilization during freezing. Particle size of plasmid/linear polyethylenimine (LPEI) polyplexes at two DNA concentrations and at increasing sucrose-DNA ratios was investigated separately as a function of freezing procedure, ice-nucleation temperature, residence time of the particles in a partially frozen state, or incomplete freezing. Using a numerical model, the increase in sucrose concentration and system viscosity and corresponding bimolecular reaction rates were theoretically estimated. Freezing with a temperature-hold step after ice nucleation negatively influenced particle stability. Ice-nucleation temperature had an impact only at low DNA concentrations. Particle stability was highly reduced during the early part of freezing (<-3°C), especially at low shelf-ramp rates. In this phase, bimolecular reaction rates increase greatly at still low system viscosity. Below a critical temperature (≤∼-18°C) and at high system viscosity, no further particle aggregation occurred. In conclusion, the initial sample viscosity rather than the unfrozen volume and the residence time of particles in the low-viscosity state are the predominant factors in particle stabilization, which likely apply to aggregation in any system.

  10. Time-stepping methods for the simulation of the self-assembly of nano-crystals in MATLAB on a GPU

    NASA Astrophysics Data System (ADS)

    Korzec, M. D.; Ahnert, T.

    2013-10-01

    Partial differential equations describing the patterning of thin crystalline films are typically of fourth or sixth order, they are quasi- or semilinear and they are mostly defined on simple geometries such as rectangular domains. For the numerical simulation of these kinds of problems spectral methods are an efficient approach. We apply several implicit-explicit schemes to one recently derived PDE that we express in terms of coefficients of trigonometric interpolants. While the simplest IMEX scheme turns out to have the mildest step-size restriction, higher order SBDF schemes tend to be more unstable and exponential time integrators are fastest for the calculation of very accurate solutions. We implemented a reduced model in the EXPINT package syntax [3] and compared various exponential schemes. A convexity splitting approach was employed to stabilize the SBDF1 scheme. We show that accuracy control is crucial when using this idea, therefore we present a time-adaptive SBDF1/SBDF1-2-step method that yields convincing results reflecting the change in timescales during topological changes of the nanostructures. The implementation of all presented methods is carried out in MATLAB. We used the open source GPUmat package to gain up to 5-fold runtime benefits by carrying out calculations on a low-cost GPU without having to prescribe any knowledge in low-level programming or CUDA implementations and found comparable speedups as with MATLAB's PCT or with GPUmat run on Octave.

  11. Development of a two-step SYBR Green I based real time RT-PCR assay for detecting and quantifying peste des petits ruminants virus in clinical samples.

    PubMed

    Abera, Tsegalem; Thangavelu, Ardhanary

    2014-12-01

    A two-step SYBR Green I based real time RT-PCR targeting the matrix (M) gene of Peste des petits ruminants virus (PPRV) was developed. The specificity of the assay was assessed against viral nucleic acid extracted from a range of animal viruses of clinical and structural similarities to PPRV including canine distemper virus, measles virus, bluetongue virus and Newcastle disease virus. But none of the viruses and no template control showed an amplification signal. Sensitivity of the same assay was assessed based on plasmid DNA copy number and with respect to infectivity titre. The lower detection limit achieved was 2.88 plasmid DNA copies/μl with corresponding Ct value of 35.93. Based on tissue culture infectivity titre the lower detection limits were 0.0001TCID50/ml and 1TCID50/ml for the SYBR green I based real time RT-PCR and conventional RT-PCR, respectively. The calculated coefficient of variations values for intra- and inter-assay variability were low, ranging from 0.21% to 1.83% and 0.44% to 1.97%, respectively. The performance of newly developed assay was evaluated on a total of 36 clinical samples suspected of PPR and compared with conventional RT-PCR. The SYBR Green I based real time RT-PCR assay detected PPRV in 32 (88.8%) of clinical samples compared to 19 (52.7%) by conventional RT-PCR. Thus, the two-step SYBR Green I based real time RT-PCR assay targeting the M gene of PPRV reported in this study was highly sensitive, specific and reproducible for detection and quantitation of PPRV nucleic acids.

  12. A real-time one-step reverse transcriptase-polymerase chain reaction method to quantify c-erbB-2 expression in human breast cancer.

    PubMed

    Pawlowski, V; Révillion, F; Hornez, L; Peyrat, J P

    2000-01-01

    We developed a real-time one-step reverse transcriptase-polymerase chain reaction (RT-PCR) method for the routine quantification of c-erbB-2 oncogene expression in breast cancer, using a 7700 ABI PRISM Sequence Detector System (Perkin Elmer-Applied Biosystems, Courtaboeuf, France). The real-time quantification of the polymerase chain reaction products is based on the TaqMan 5' nuclease assay. The optimal experimental conditions we determined were as follows: 6 mM MgCl2, 200 nM of fluorogenic probe, 200 nM of each primer, and 12.5 units MuLV reverse transcriptase. The GAPDH housekeeping gene was used for normalization of c-erbB-2 expression. In human breast cancer cell lines, the normalized expression of c-erbB-2 ranged from 8 x 10(-6) to 2,600 x 10(-6), the two highest values corresponding to the c-erbB-2 overexpressing cells MDA-MB-453 and SK-BR-3. In a series of 100 breast cancer samples, c-erbB-2 normalized expression was found to range from 0.4 x 10(-6) to 350 x 10(-6). A close correlation was observed between this real-time one-step quantitative RT-PCR method and both semiquantitative conventional RT-PCR (N = 22; r = 0.8543; P < .0001) and c-erbB-2 protein expression (p185) quantified by an enzyme immunoassay (EIA) (N = 27; r = 0.71; P < .0001). The current realtime RT-PCR assay is rapid, sensitive, and reproducible and appears particularly suitable to quantify gene expression in large series of samples.

  13. Evaluation of tcdB real-time PCR in a three-step diagnostic algorithm for detection of toxigenic Clostridium difficile.

    PubMed

    Larson, Ann M; Fung, Angela M; Fang, Ferric C

    2010-01-01

    Clostridium difficile is the most common infectious cause of diarrhea in hospitalized patients. The optimal approach for the detection of toxigenic C. difficile remains controversial because no single test is sensitive, specific, and affordable. We have developed a real-time PCR method (direct stool PCR [DPCR]) to detect the tcdB gene encoding toxin B directly from stool specimens and have combined it with enzyme immunoassays (EIAs) in a three-step protocol. DPCR was performed on 699 specimens that were positive for C. difficile glutamate dehydrogenase (GDH) by Wampole C Diff Quik Chek EIA (GDH-Q) and negative for toxins A and B by Wampole Tox A/B Quik Chek EIA (AB-Q), performed sequentially. The performance of this three-step algorithm was compared with a modified "gold standard" that combined tissue culture cytotoxicity (CYT) and DPCR. A separate investigation was performed to evaluate the sensitivity of the GDH-Q as a screening test, and toxigenic C. difficile was found in 1.9% of 211 GDH-Q-negative specimens. The overall sensitivity, specificity, and positive and negative predictive values, respectively, were as follows for an algorithm combining GDH-Q, AB-Q, and DPCR: 83.8%, 99.7%, 97.1%, and 97.9%. Those for CYT alone were 58.8%, 100%, 100%, and 94.9%, respectively. In comparison, the sensitivity and specificity of DPCR were estimated to be 97.5% and 99.7%, respectively, using the same modified gold standard. Neither CYT nor toxin EIA was sufficiently sensitive to exclude toxigenic C. difficile, and combining EIAs with CYT in a three-step algorithm failed to substantially improve sensitivity. DPCR is a sensitive and specific method for the detection of toxigenic C. difficile that can provide same-day results at a cost-per-positive test comparable to those of other methods. A three-step algorithm in which DPCR is used to analyze GDH EIA-positive, toxin EIA-negative specimens provides a convenient and specific alternative with rapid results for 87.7% of

  14. Evaluation of tcdB Real-Time PCR in a Three-Step Diagnostic Algorithm for Detection of Toxigenic Clostridium difficile▿

    PubMed Central

    Larson, Ann M.; Fung, Angela M.; Fang, Ferric C.

    2010-01-01

    Clostridium difficile is the most common infectious cause of diarrhea in hospitalized patients. The optimal approach for the detection of toxigenic C. difficile remains controversial because no single test is sensitive, specific, and affordable. We have developed a real-time PCR method (direct stool PCR [DPCR]) to detect the tcdB gene encoding toxin B directly from stool specimens and have combined it with enzyme immunoassays (EIAs) in a three-step protocol. DPCR was performed on 699 specimens that were positive for C. difficile glutamate dehydrogenase (GDH) by Wampole C Diff Quik Chek EIA (GDH-Q) and negative for toxins A and B by Wampole Tox A/B Quik Chek EIA (AB-Q), performed sequentially. The performance of this three-step algorithm was compared with a modified “gold standard” that combined tissue culture cytotoxicity (CYT) and DPCR. A separate investigation was performed to evaluate the sensitivity of the GDH-Q as a screening test, and toxigenic C. difficile was found in 1.9% of 211 GDH-Q-negative specimens. The overall sensitivity, specificity, and positive and negative predictive values, respectively, were as follows for an algorithm combining GDH-Q, AB-Q, and DPCR: 83.8%, 99.7%, 97.1%, and 97.9%. Those for CYT alone were 58.8%, 100%, 100%, and 94.9%, respectively. In comparison, the sensitivity and specificity of DPCR were estimated to be 97.5% and 99.7%, respectively, using the same modified gold standard. Neither CYT nor toxin EIA was sufficiently sensitive to exclude toxigenic C. difficile, and combining EIAs with CYT in a three-step algorithm failed to substantially improve sensitivity. DPCR is a sensitive and specific method for the detection of toxigenic C. difficile that can provide same-day results at a cost-per-positive test comparable to those of other methods. A three-step algorithm in which DPCR is used to analyze GDH EIA-positive, toxin EIA-negative specimens provides a convenient and specific alternative with rapid results for 87.7% of

  15. [Prediction models for ground surface fuels moisture content of Larix gmelinii stand in Daxing'anling of China based on one-hour time step].

    PubMed

    Yu, Hong-Zhou; Sen, Jin; Di, Xue-Ying

    2013-06-01

    By using the equilibrium moisture content-time lag methods of Nelson and Simard and the meteorological element regression method, this paper studied the dynamics of the moisture content of ground surface fine dead fuels under a Larix gmelinii stand on the sunny slope in Daxing' anling with a time interval of one hour, established the corresponding prediction models, and analyzed the prediction errors under different understory densities. The results showed that the prediction methods of the fuels moisture content based on one-hour time step were applicable for the typical Larix gmelinii stand in Daxing' anling. The mean absolute error and the mean relative error of Simard method was 1.1% and 8.5%, respectively, being lower than those of Nelson method and meteorological element regression method, and close to those of similar studies. On the same slopes and slope positions, the fuel moisture content varied with different understory densities, and thus, it would be necessary to select the appropriate equilibrium moisture content model for specific regional stand and position, or establish the fuel moisture content model based on specific stand when the dynamics of fuel moisture content would be investigated with a time interval of one hour.

  16. A parallel numerical simulation for supersonic flows using zonal overlapped grids and local time steps for common and distributed memory multiprocessors

    SciTech Connect

    Patel, N.R.; Sturek, W.B.; Hiromoto, R.

    1989-01-01

    Parallel Navier-Stokes codes are developed to solve both two- dimensional and three-dimensional flow fields in and around ramjet and nose tip configurations. A multi-zone overlapped grid technique is used to extend an explicit finite-difference method to more complicated geometries. Parallel implementations are developed for execution on both distributed and common-memory multiprocessor architectures. For the steady-state solutions, the use of the local time-step method has the inherent advantage of reducing the communications overhead commonly incurred by parallel implementations. Computational results of the codes are given for a series of test problems. The parallel partitioning of computational zones is also discussed. 5 refs., 18 figs.

  17. Establishment and validation of two duplex one-step real-time RT-PCR assays for diagnosis of foot-and-mouth disease.

    PubMed

    Gorna, K; Relmy, A; Romey, A; Zientara, S; Blaise-Boisseau, S; Bakkali-Kassimi, L

    2016-09-01

    Two duplex one-step TaqMan-based RT-PCR protocols for detection of foot-and-mouth disease virus (FMDV) were established and validated. Each RT-PCR test consists of a ready-to-use master mix for simultaneous detection of the well established 3D or IRES FMDV targets and incorporates the host β-actin mRNA as an internal control target, in a single-tube assay. The two real-time RT-PCR 3D/β-actin and IRES/β-actin tests are highly sensitive and able to detect up to 7TCID50/ml of FMDV and 10 copies/1μl of viral RNA. In field epithelium samples, the diagnostic sensitivity was 100% (95% CI; 91-100%) for the 3D/β-actin test and 97% (95% CI; 87-100%) for the IRES/β-actin test. The diagnostic specificity was 100% (95% CI; 95-100%) for both RT-PCRs. In addition, the two protocols proved to be robust, showing inter-assay coefficients of variation ranging from 1.94% to 6.73% for the IRES target and from 2.33% to 5.42% for the 3D target for different RNA extractions and different RT-PCR conditions. The internally controlled one-step real-time RT-PCR protocols described in this study provide a rapid, effective and reliable method for the detection of FMDV and thus may improve the routine diagnosis for foot-and-mouth disease. PMID:27317973

  18. Establishment and validation of two duplex one-step real-time RT-PCR assays for diagnosis of foot-and-mouth disease.

    PubMed

    Gorna, K; Relmy, A; Romey, A; Zientara, S; Blaise-Boisseau, S; Bakkali-Kassimi, L

    2016-09-01

    Two duplex one-step TaqMan-based RT-PCR protocols for detection of foot-and-mouth disease virus (FMDV) were established and validated. Each RT-PCR test consists of a ready-to-use master mix for simultaneous detection of the well established 3D or IRES FMDV targets and incorporates the host β-actin mRNA as an internal control target, in a single-tube assay. The two real-time RT-PCR 3D/β-actin and IRES/β-actin tests are highly sensitive and able to detect up to 7TCID50/ml of FMDV and 10 copies/1μl of viral RNA. In field epithelium samples, the diagnostic sensitivity was 100% (95% CI; 91-100%) for the 3D/β-actin test and 97% (95% CI; 87-100%) for the IRES/β-actin test. The diagnostic specificity was 100% (95% CI; 95-100%) for both RT-PCRs. In addition, the two protocols proved to be robust, showing inter-assay coefficients of variation ranging from 1.94% to 6.73% for the IRES target and from 2.33% to 5.42% for the 3D target for different RNA extractions and different RT-PCR conditions. The internally controlled one-step real-time RT-PCR protocols described in this study provide a rapid, effective and reliable method for the detection of FMDV and thus may improve the routine diagnosis for foot-and-mouth disease.

  19. A journey of a thousand miles begins with one small step - human agency, hydrological processes and time in socio-hydrology

    NASA Astrophysics Data System (ADS)

    Ertsen, M. W.; Murphy, J. T.; Purdue, L. E.; Zhu, T.

    2014-04-01

    When simulating social action in modeling efforts, as in socio-hydrology, an issue of obvious importance is how to ensure that social action by human agents is well-represented in the analysis and the model. Generally, human decision-making is either modeled on a yearly basis or lumped together as collective social structures. Both responses are problematic, as human decision-making is more complex and organizations are the result of human agency and cannot be used as explanatory forces. A way out of the dilemma of how to include human agency is to go to the largest societal and environmental clustering possible: society itself and climate, with time steps of years or decades. In the paper, another way out is developed: to face human agency squarely, and direct the modeling approach to the agency of individuals and couple this with the lowest appropriate hydrological level and time step. This approach is supported theoretically by the work of Bruno Latour, the French sociologist and philosopher. We discuss irrigation archaeology, as it is in this discipline that the issues of scale and explanatory force are well discussed. The issue is not just what scale to use: it is what scale matters. We argue that understanding the arrangements that permitted the management of irrigation over centuries requires modeling and understanding the small-scale, day-to-day operations and personal interactions upon which they were built. This effort, however, must be informed by the longer-term dynamics, as these provide the context within which human agency is acted out.

  20. A journey of a thousand miles begins with one small step - human agency, hydrological processes and time in socio-hydrology

    NASA Astrophysics Data System (ADS)

    Ertsen, M. W.; Murphy, J. T.; Purdue, L. E.; Zhu, T.

    2013-11-01

    When simulating social action in modeling efforts, as in socio-hydrology, an issue of obvious importance is how to ensure that social action by human agents is well-represented in the analysis and the model. Generally, human decision-making is either modeled on a yearly basis or lumped together as collective social structures. Both responses are problematic, as human decision making is more complex and organizations are the result of human agency and cannot be used as explanatory forces. A way out of the dilemma how to include human agency is to go to the largest societal and environmental clustering possible: society itself and climate, with time steps of years or decades. In the paper, the other way out is developed: to face human agency squarely, and direct the modeling approach to the human agency of individuals and couple this with the lowest appropriate hydrological level and time step. This approach is supported theoretically by the work of Bruno Latour, the French sociologist and philosopher. We discuss irrigation archaeology, as it is in this discipline that the issues of scale and explanatory force are well discussed. The issue is not just what scale to use: it is what scale matters. We argue that understanding the arrangements that permitted the management of irrigation over centuries, requires modeling and understanding the small-scale, day-to-day operations and personal interactions upon which they were built. This effort, however, must be informed by the longer-term dynamics as these provide the context within which human agency, is acted out.

  1. Using a generational time-step model to simulate dynamics of adaptation to transgenic corn and crop rotation by western corn rootworm (Coleoptera: Chrysomelidae).

    PubMed

    Crowder, D W; Onstad, D W

    2005-04-01

    We expanded a simulation model of the population dynamics and genetics of the western corn rootworm for a landscape of corn, soybean, and other crops to study the simultaneous development of resistance to both crop rotation and transgenic corn. Transgenic corn effective against corn rootworm was recently approved in 2003 and may be a very effective new technology for control of western corn rootworm in areas with or without the rotation-resistant variant. In simulations of areas with rotation-resistant populations, planting transgenic corn to only rotated cornfields was a robust strategy to prevent resistance to both traits. In these areas, planting transgenic corn to only continuous fields was not an effective strategy for preventing adaptation to crop rotation or transgenic corn. In areas without rotation-resistant phenotypes, gene expression of the allele for resistance to transgenic corn was the most important factor affecting the development of resistance to transgenic corn. If the allele for resistance to transgenic corn is recessive, resistance can be delayed longer than 15 yr, but if the resistant allele is dominant then resistance usually developed within 15 yr. In a sensitivity analysis, among the parameters investigated, initial allele frequency and density dependence were the two most important factors affecting the evolution of resistance. We compared the results of this simulation model with a more complicated model and results between the two were similar. This indicates that results from a simpler model with a generational time-step can compare favorably with a more complex model with a daily time-step.

  2. Development of one-step real-time reverse transcriptase-PCR-based assays for the rapid and simultaneous detection of four viruses causing porcine diarrhea.

    PubMed

    Masuda, Tsuneyuki; Tsuchiaka, Shinobu; Ashiba, Tomoko; Yamasato, Hiroshi; Fukunari, Kazuhiro; Omatsu, Tsutomu; Furuya, Tetsuya; Shirai, Junsuke; Mizutani, Tetsuya; Nagai, Makoto

    2016-02-01

    Porcine diarrhea caused by viruses is a major problem of the pig farming industry and can result in substantial losses of revenue. Thus, diagnosing the infectious agents is important to prevent and control diseases in pigs. We developed novel one-step real-time quantitative RT-PCR (qPCR) assays that can detect four porcine diarrheal viruses simultaneously: porcine epidemic diarrhea virus (PEDV), transmissible gastroenteritis virus (TGEV), porcine deltacoronavirus (PDCoV), and porcine group A rotavirus (PRVA). The qPCR analysis takes only 75 minutes to detect the presence of the four viruses. The limits of detection of our new assays for PEDV, TGEV, PDCoV, and PRVA were 100, 10, 10 and 10 copies per reaction, respectively. The sensitivity of qPCR was 1-1000 times higher than that of published gel-based RT-PCR. We used our qPCR method to successfully diagnose clinical samples from infected pigs, and no false positive results were obtained. In conclusion, qPCR can drastically reduce the diagnostic time to detect viruses compared to currently employed methods. We predict that the qPCR assays will become a useful tool for detecting viral infections that cause diarrhea and other complications in pigs. PMID:27348884

  3. The validation and utility of a quantitative one-step multiplex RT real-time PCR targeting rotavirus A and norovirus.

    PubMed

    Dung, Tran Thi Ngoc; Phat, Voong Vinh; Nga, Tran Vu Thieu; My, Phan Vu Tra; Duy, Pham Thanh; Campbell, James I; Thuy, Cao Thu; Hoang, Nguyen Van Minh; Van Minh, Pham; Le Phuc, Hoang; Tuyet, Pham Thi Ngoc; Vinh, Ha; Kien, Duong Thi Hue; Huy, Huynh Le Anh; Vinh, Nguyen Thanh; Nga, Tran Thi Thu; Hau, Nguyen Thi Thu; Chinh, Nguyen Tran; Thuong, Tang Chi; Tuan, Ha Manh; Simmons, Cameron; Farrar, Jeremy J; Baker, Stephen

    2013-01-01

    Rotavirus (RoV) and Norovirus (NoV) are the main causes of viral gastroenteritis. Currently, there is no validated multiplex real-time PCR that can detect and quantify RoV and NoV simultaneously. The aim of the study was to develop, validate, and internally control a multiplex one-step RT real-time PCR to detect and quantify RoV and NoV in stool samples. PCR sensitivity was assessed by comparing amplification against the current gold standard, enzyme immunoassay (EIA), on stool samples from 94 individuals with diarrhea and 94 individuals without diarrhea. PCR detected 10% more RoV positive samples than EIA in stools samples from patients with diarrhea. PCR detected 23% more NoV genogroup II positive samples from individuals with diarrhea and 9% more from individuals without diarrhea than EIA, respectively. Genotyping of the PCR positive/EIA negative samples suggested the higher rate of PCR positivity, in comparison to EIA, was due to increased sensitivity, rather than nonspecific hybridization. Quantitation demonstrated that the viral loads of RoV and NoV in the stools of diarrheal patients were an order of magnitude greater than in individuals without diarrhea. This internally controlled real-time PCR method is robust, exhibits a high degree of reproducibility, and may have a greater utility and sensitivity than commercial EIA kits. PMID:23046990

  4. Development of a rapid Buffer-exchange system for time-resolved ATR-FTIR spectroscopy with the step-scan mode

    PubMed Central

    Furutani, Yuji; Kimura, Tetsunari; Okamoto, Kido

    2013-01-01

    Attenuated total reflectance (ATR)-FTIR spectroscopy has been widely used to probe protein structural changes under various stimuli, such as light absorption, voltage change, and ligand binding, in aqueous conditions. Time-resolved measurements require a trigger, which can be controlled electronically; therefore, light and voltage changes are suitable. Here we developed a novel, rapid buffer-exchange system for time-resolved ATR-FTIR spectroscopy to monitor the ligand- or ion-binding re-action of a protein. By using the step-scan mode (time resolution; 2.5 ms), we confirmed the completion of the buffer-exchange reaction within ∼25 ms; the process was monitored by the infrared absorption change of a nitrate band at 1,350 cm−1. We also demonstrated the anion-binding reaction of a membrane protein, Natronomonas pharaonis halorhodopsin (pHR), which binds a chloride ion in the initial anion-binding site near the retinal chromophore. The formation of chloride- or nitrate-bound pHR was confirmed by an increase of the retinal absorption band at 1,528 cm−1. It also should be noted that low sample consumption (∼1 µg of protein) makes this new method a powerful technique to understand ligand–protein and ion–protein interactions, particularly for membrane proteins. PMID:27493550

  5. Rapid diagnosis of acute hemorrhagic conjunctivitis due to coxsackievirus A24 variant by real-time one-step RT-PCR.

    PubMed

    Lévêque, Nicolas; Lahlou Amine, Idriss; Tcheng, Remy; Falcon, Delphine; Rivat, Nathalie; Dussart, Philippe; Muyembe, Jean-Jacques; Chomel, Jean-Jacques; Norder, Helene; Eugene, Maxime; Lina, Bruno

    2007-06-01

    Coxsackievirus A24 variant is, together with enterovirus 70 and adenoviruses, the major etiological agent involved in acute hemorrhagic conjunctivitis outbreaks worldwide. However, the standard virus isolation method followed by serotyping or VP1 region sequencing is time-consuming. A rapid method for the detection of coxsackievirus A24 variant from conjunctival swab specimens would be useful in the context of explosive and extensive outbreaks. A one-step real-time RT-PCR assay based on TaqMan technology was thus developed and assessed on 36 conjunctival swabs from outbreaks of conjunctivitis in Morocco in 2004 due to a coxsackievirus A24 variant and in Corsica in 2006 due to adenovirus type 3, and 83 virus strains including 41 coxsackievirus A24 variant collected in French Guiana and Guadeloupe in 2003, in the Democratic Republic of the Congo in 2003, in Morocco in 2004 and 42 other virus species genetically close or known to be responsible for conjunctivitis. All the conjunctival swabs from coxsackievirus A24 variant related outbreak and the 41 coxsackievirus A24 variant strains were tested positive by the RT-PCR assay within 4h. This novel single-tube real-time RT-PCR assay is sensitive and specific, and consists in a reliable and faster alternative to the viral culture for recent and future acute hemorrhagic conjunctivitis outbreaks caused by coxsackievirus A24 variant.

  6. Comprehensive Multiplex One-Step Real-Time TaqMan qRT-PCR Assays for Detection and Quantification of Hemorrhagic Fever Viruses

    PubMed Central

    Li, Jiandong; Qu, Jing; He, Chengcheng; Zhang, Shuo; Li, Chuan; Zhang, Quanfu; Liang, Mifang; Li, Dexin

    2014-01-01

    Background Viral hemorrhagic fevers (VHFs) are a group of animal and human illnesses that are mostly caused by several distinct families of viruses including bunyaviruses, flaviviruses, filoviruses and arenaviruses. Although specific signs and symptoms vary by the type of VHF, initial signs and symptoms are very similar. Therefore rapid immunologic and molecular tools for differential diagnosis of hemorrhagic fever viruses (HFVs) are important for effective case management and control of the spread of VHFs. Real-time quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) assay is one of the reliable and desirable methods for specific detection and quantification of virus load. Multiplex PCR assay has the potential to produce considerable savings in time and resources in the laboratory detection. Results Primers/probe sets were designed based on appropriate specific genes for each of 28 HFVs which nearly covered all the HFVs, and identified with good specificity and sensitivity using monoplex assays. Seven groups of multiplex one-step real-time qRT-PCR assays in a universal experimental system were then developed by combining all primers/probe sets into 4-plex reactions and evaluated with serial dilutions of synthesized viral RNAs. For all the multiplex assays, no cross-reactivity with other HFVs was observed, and the limits of detection were mainly between 45 and 150 copies/PCR. The reproducibility was satisfactory, since the coefficient of variation of Ct values were all less than 5% in each dilution of synthesized viral RNAs for both intra-assays and inter-assays. Evaluation of the method with available clinical serum samples collected from HFRS patients, SFTS patients and Dengue fever patients showed high sensitivity and specificity of the related multiplex assays on the clinical specimens. Conclusions Overall, the comprehensive multiplex one-step real-time qRT-PCR assays were established in this study, and proved to be specific, sensitive

  7. A One-Step Real-Time RT-PCR Assay for the Detection and Quantitation of Sugarcane Streak Mosaic Virus

    PubMed Central

    Fu, Wei-Lin; Sun, Sheng-Ren; Fu, Hua-Ying; Chen, Ru-Kai; Su, Jin-Wei; Gao, San-Ji

    2015-01-01

    Sugarcane mosaic disease is caused by the Sugarcane streak mosaic virus (SCSMV; genus Poacevirus, family Potyviridae) which is common in some Asian countries. Here, we established a protocol of a one-step real-time quantitative reverse transcription PCR (real-time qRT-PCR) using the TaqMan probe for the detection of SCSMV in sugarcane. Primers and probes were designed within the conserved region of the SCSMV coat protein (CP) gene sequences. Standard single-stranded RNA (ssRNA) generated by PCR-based gene transcripts of recombinant pGEM-CP plasmid in vitro and total RNA extracted from SCSMV-infected sugarcane were used as templates of qRT-PCR. We further performed a sensitivity assay to show that the detection limit of the assay was 100 copies of ssRNA and 2 pg of total RNA with good reproducibility. The values obtained were approximately 100-fold more sensitive than those of the conventional RT-PCR. A higher incidence (68.6%) of SCSMV infection was detected by qRT-PCR than that (48.6%) with conventional RT-PCR in samples showing mosaic symptoms. SCSMV-free samples were verified by infection with Sugarcane mosaic virus (SCMV) or Sorghum mosaic virus (SrMV) or a combination of both. The developed qRT-PCR assay may become an alternative molecular tool for an economical, rapid, and efficient detection and quantification of SCSMV. PMID:26185758

  8. Golgi-Cox Staining Step by Step

    PubMed Central

    Zaqout, Sami; Kaindl, Angela M.

    2016-01-01

    Golgi staining remains a key method to study neuronal morphology in vivo. Since most protocols delineating modifications of the original staining method lack details on critical steps, establishing this method in a laboratory can be time-consuming and frustrating. Here, we describe the Golgi-Cox staining in such detail that should turn the staining into an easily feasible method for all scientists working in the neuroscience field. PMID:27065817

  9. Diablo 2.0: A modern DNS/LES code for the incompressible NSE leveraging new time-stepping and multigrid algorithms

    NASA Astrophysics Data System (ADS)

    Cavaglieri, Daniele; Bewley, Thomas; Mashayek, Ali

    2015-11-01

    We present a new code, Diablo 2.0, for the simulation of the incompressible NSE in channel and duct flows with strong grid stretching near walls. The code leverages the fractional step approach with a few twists. New low-storage IMEX (implicit-explicit) Runge-Kutta time-marching schemes are tested which are superior to the traditional and widely-used CN/RKW3 (Crank-Nicolson/Runge-Kutta-Wray) approach; the new schemes tested are L-stable in their implicit component, and offer improved overall order of accuracy and stability with, remarkably, similar computational cost and storage requirements. For duct flow simulations, our new code also introduces a new smoother for the multigrid solver for the pressure Poisson equation. The classic approach, involving alternating-direction zebra relaxation, is replaced by a new scheme, dubbed tweed relaxation, which achieves the same convergence rate with roughly half the computational cost. The code is then tested on the simulation of a shear flow instability in a duct, a classic problem in fluid mechanics which has been the object of extensive numerical modelling for its role as a canonical pathway to energetic turbulence in several fields of science and engineering.

  10. The effect of time step, thermostat, and strain rate on ReaxFF simulations of mechanical failure in diamond, graphene, and carbon nanotube.

    PubMed

    Jensen, Benjamin D; Wise, Kristopher E; Odegard, Gregory M

    2015-08-01

    As the sophistication of reactive force fields for molecular modeling continues to increase, their use and applicability has also expanded, sometimes beyond the scope of their original development. Reax Force Field (ReaxFF), for example, was originally developed to model chemical reactions, but is a promising candidate for modeling fracture because of its ability to treat covalent bond cleavage. Performing reliable simulations of a complex process like fracture, however, requires an understanding of the effects that various modeling parameters have on the behavior of the system. This work assesses the effects of time step size, thermostat algorithm and coupling coefficient, and strain rate on the fracture behavior of three carbon-based materials: graphene, diamond, and a carbon nanotube. It is determined that the simulated stress-strain behavior is relatively independent of the thermostat algorithm, so long as coupling coefficients are kept above a certain threshold. Likewise, the stress-strain response of the materials was also independent of the strain rate, if it is kept below a maximum strain rate. Finally, the mechanical properties of the materials predicted by the Chenoweth C/H/O parameterization for ReaxFF are compared with literature values. Some deficiencies in the Chenoweth C/H/O parameterization for predicting mechanical properties of carbon materials are observed.

  11. Whole genome alignment based one-step real-time RT-PCR for universal detection of avian orthoreoviruses of chicken, pheasant and turkey origins.

    PubMed

    Tang, Yi; Lu, Huaguang

    2016-04-01

    Newly emerging avian orthoreovirus (ARV) variants have been continuously detected in Pennsylvania poultry since 2011. In this paper, we report our recent diagnostic assay development of one-step real-time RT-PCR (rRT-PCR) for the rapid and universal detection of all ARVs or reference strains of chicken, pheasant and turkey origins and six σC genotypes of the newly emerging field ARV variants in Pennsylvania (PA) poultry. Primers and probes for the rRT-PCR were designed from the conserved region of the M1 genome segment 5' end based on the whole-genome alignment of various ARV strains, including six field variants or novel strains obtained in PA poultry. The detection limit of the newly developed rRT-PCR for ARV was as low as 10 copies/reaction of viral RNA, and 10(0.50)-10(0.88) tissue culture infectious dose (TCID50)/100 μL of viruses. This new rRT-PCR detected all six σC genotypes from the 66 ARV field variant strains and reference strains tested in this study. There were no cross-reactions with other avian viruses. Reproducibility of the assay was confirmed by intra- and inter-assay tests with variability from 0.12% to 2.19%. Sensitivity and specificity of this new rRT-PCR for ARV were achieved at 100% and 88%, respectively, in comparison with virus isolation as the "gold standard" in testing poultry tissue specimen. PMID:26812128

  12. Whole genome alignment based one-step real-time RT-PCR for universal detection of avian orthoreoviruses of chicken, pheasant and turkey origins.

    PubMed

    Tang, Yi; Lu, Huaguang

    2016-04-01

    Newly emerging avian orthoreovirus (ARV) variants have been continuously detected in Pennsylvania poultry since 2011. In this paper, we report our recent diagnostic assay development of one-step real-time RT-PCR (rRT-PCR) for the rapid and universal detection of all ARVs or reference strains of chicken, pheasant and turkey origins and six σC genotypes of the newly emerging field ARV variants in Pennsylvania (PA) poultry. Primers and probes for the rRT-PCR were designed from the conserved region of the M1 genome segment 5' end based on the whole-genome alignment of various ARV strains, including six field variants or novel strains obtained in PA poultry. The detection limit of the newly developed rRT-PCR for ARV was as low as 10 copies/reaction of viral RNA, and 10(0.50)-10(0.88) tissue culture infectious dose (TCID50)/100 μL of viruses. This new rRT-PCR detected all six σC genotypes from the 66 ARV field variant strains and reference strains tested in this study. There were no cross-reactions with other avian viruses. Reproducibility of the assay was confirmed by intra- and inter-assay tests with variability from 0.12% to 2.19%. Sensitivity and specificity of this new rRT-PCR for ARV were achieved at 100% and 88%, respectively, in comparison with virus isolation as the "gold standard" in testing poultry tissue specimen.

  13. Development and Validation of a Quantitative, One-Step, Multiplex, Real-Time Reverse Transcriptase PCR Assay for Detection of Dengue and Chikungunya Viruses.

    PubMed

    Simmons, Monika; Myers, Todd; Guevara, Carolina; Jungkind, Donald; Williams, Maya; Houng, Huo-Shu

    2016-07-01

    Dengue virus (DENV) and chikungunya virus (CHIKV) are important human pathogens with common transmission vectors and similar clinical presentations. Patient care may be impacted by the misdiagnosis of DENV and CHIKV in areas where both viruses cocirculate. In this study, we have developed and validated a one-step multiplex reverse transcriptase PCR (RT-PCR) to simultaneously detect, quantify, and differentiate between four DENV serotypes (pan-DENV) and chikungunya virus. The assay uses TaqMan technology, employing two forward primers, three reverse primers, and four fluorophore-labeled probes in a single-reaction format. Coextracted and coamplified RNA was used as an internal control (IC), and in vitro-transcribed DENV and CHIKV RNAs were used to generate standard curves for absolute quantification. The diagnostic 95% limits of detection (LOD) within the linear range were 50 and 60 RNA copies/reaction for DENV (serotypes 1 to 4) and CHIKV, respectively. Our assay was able to detect 53 different strains of DENV, representing four serotypes, and six strains of CHIKV. No cross-reactivity was observed with related flaviviruses and alphaviruses, To evaluate diagnostic sensitivity and specificity, 89 clinical samples positive or negative for DENV (serotypes 1 to 4) and CHIKV by the standard virus isolation method were tested in our assay. The multiplex RT-PCR assay showed 95% sensitivity and 100% specificity for DENV and 100% sensitivity and specificity for CHIKV. With an assay turnaround time of less than 2 h, including extraction of RNA, the multiplex quantitative RT-PCR assay provides rapid diagnosis for the differential detection of two clinically indistinguishable diseases, whose geographical occurrence is increasingly overlapping. PMID:27098955

  14. Step-changes in the physical, chemical and biological characteristics of the Gulf of Maine, as documented by the GNATS time series

    USGS Publications Warehouse

    Balch, William M.; Drapeau, D.T.; Bowler, B.C.; Huntington, Thomas G.

    2012-01-01

    We identify step-changes in the physical, chemical and biological characteristics of the Gulf of Maine (GoM) using the Gulf of Maine North Atlantic Time Series (GNATS), a series of oceanographic measurements obtained between September 1998 and December 2010 along a transect in the GoM running from Portland, ME, to Yarmouth, NS. GNATS sampled a period of extremes in precipitation and river discharge (4 of the 8 wettest years of the last century occurred between 2005 and 2010). Coincident with increased precipitation, we observed the following shifts: (1) decreased salinity and density within the surface waters of the western GoM; (2) both reduced temperature and vertical temperature gradients in the upper 50 m; (3) increased colored dissolved organic matter (CDOM) concentrations and particle scattering in the western GoM; (4) increased concentrations of nitrate and phosphate across all but the eastern GoM; (5) increased silicate, particularly in the western GoM, with a sharp increase in the ratio of silicate to dissolved inorganic nitrogen; (6) sharply decreased carbon fixation by phytoplankton; (7) moderately decreased chlorophyll, particulate organic carbon (POC) and particulate inorganic carbon (PIC) in the central GoM and (8) decreased POC- and PIC-specific growth rates. Gulf-wide anomaly analyses suggest that (1) the surface density changes were predominantly driven by temperature, (2) dissolved nutrients, as well as POC/PON, varied in Redfield ratios and (3) anomalies for salinity, density, CDOM, particle backscattering and silicate were significantly correlated with river discharge. Precipitation and river discharge appear to be playing a critical role in controlling the long-term productivity of the Gulf of Maine by supplying CDOM and detrital material, which ultimately competes with phytoplankton for light absorption.

  15. Development of a real-time PCR method coupled with a selective pre-enrichment step for quantification of Morganella morganii and Morganella psychrotolerans in fish products.

    PubMed

    Podeur, Gaëtan; Dalgaard, Paw; Leroi, Francoise; Prévost, Hervé; Emborg, Jette; Martinussen, Jan; Hansen, Lars Hestbjerg; Pilet, Marie-France

    2015-06-16

    Histamine fish poisoning is common and due to toxic concentrations of histamine often produced by Gram-negative bacteria in fin-fish products with a high content of the free amino acid histidine. The genus Morganella includes two species previously reported to cause incidents of histamine fish poisoning. Morganella morganii and Morganella psychrotolerans are both strong producer of histamine. However, little is known about the occurrence and critical stages for fish contamination with these bacteria. To elucidate contamination routes of Morganella, specific real-time quantitative PCR (RTi qPCR) methods for quantification of M. morganii and M. psychrotolerans have been developed. Selective primers amplified a 110 bp region of the vasD gene for M. psychrotolerans and a 171 bp region of the galactokinase gene for M. morganii. These primer-sets showed high specificity as demonstrated by using purified DNA from 23 other histamine producing bacteria and 26 isolates with no or limited histamine production. The efficiency of the qPCR reactions on artificially contaminated fish samples were 100.8% and 96.3% respectively. The limit of quantification (LOQ) without enrichment was 4 log CFU/g. A quantitative enrichment step with a selective medium was included and improved the sensitivity of the methods to a LOQ of below 50 CFU/g in seafood. RTi qPCR methods with or without enrichment were evaluated for enumeration of Morganella species in naturally contaminated fresh fish and lightly preserved seafood from Denmark. These new methods will contribute to a better understanding of the occurrence and histamine production by Morganella species in fish products, information that is essential to reduce the unacceptably high frequency of histamine fish poisoning.

  16. The Tangle of Student Allowances.

    ERIC Educational Resources Information Center

    Thomson, Norman J.

    1980-01-01

    A discussion of the distribution of student financial aid in Australia focuses on these issues: direct vs. indirect payment to students; inequality in living allowances given to secondary and postsecondary students; and distribution of expense allowances by state government and living allowances by the Commonwealth. (MSE)

  17. Identification of different respiratory viruses, after a cell culture step, by matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS)

    PubMed Central

    Calderaro, Adriana; Arcangeletti, Maria Cristina; Rodighiero, Isabella; Buttrini, Mirko; Montecchini, Sara; Vasile Simone, Rosita; Medici, Maria Cristina; Chezzi, Carlo; De Conto, Flora

    2016-01-01

    In this study matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS), a reliable identification method for the diagnosis of bacterial and fungal infections, is presented as an innovative tool to investigate the protein profile of cell cultures infected by the most common viruses causing respiratory tract infections in humans. MALDI-TOF MS was applied to the identification of influenza A and B viruses, adenovirus C species, parainfluenza virus types 1, 2 and 3, respiratory syncytial virus, echovirus, cytomegalovirus and metapneumovirus. In this study MALDI-TOF MS was proposed as a model to be applied to the identification of cultivable respiratory viruses using cell culture as a viral proteins enrichment method to the proteome profiling of virus infected and uninfected cell cultures. The reference virus strains and 58 viruses identified from respiratory samples of subjects with respiratory diseases positive for one of the above mentioned viral agents by cell culture were used for the in vitro infection of suitable cell cultures. The isolated viral particles, concentrated by ultracentrifugation, were used for subsequent protein extraction and their spectra profiles were generated by MALDI-TOF MS analysis. The newly created library allowed us to discriminate between uninfected and respiratory virus infected cell cultures. PMID:27786297

  18. One-step multiplex real time RT-PCR for the detection of bovine respiratory syncytial virus, bovine herpesvirus 1 and bovine parainfluenza virus 3

    PubMed Central

    2012-01-01

    Background Detection of respiratory viruses in veterinary species has traditionally relied on virus detection by isolation or immunofluorescence and/or detection of circulating antibody using ELISA or serum neutralising antibody tests. Multiplex real time PCR is increasingly used to diagnose respiratory viruses in humans and has proved to be superior to traditional methods. Bovine respiratory disease (BRD) is one of the most common causes of morbidity and mortality in housed cattle and virus infections can play a major role. We describe here a one step multiplex reverse transcriptase quantitative polymerase chain reaction (mRT-qPCR) to detect the viruses commonly implicated in BRD. Results A mRT-qPCR assay was developed and optimised for the simultaneous detection of bovine respiratory syncytial virus (BRSV), bovine herpes virus type 1 (BoHV-1) and bovine parainfluenza virus type 3 (BPI3 i & ii) nucleic acids in clinical samples from cattle. The assay targets the highly conserved glycoprotein B gene of BoHV-1, nucleocapsid gene of BRSV and nucleoprotein gene of BPI3. This mRT-qPCR assay was assessed for sensitivity, specificity and repeatability using in vitro transcribed RNA and recent field isolates. For clinical validation, 541 samples from clinically affected animals were tested and mRT-qPCR result compared to those obtained by conventional testing using virus isolation (VI) and/or indirect fluorescent antibody test (IFAT). Conclusions The mRT-qPCR assay was rapid, highly repeatable, specific and had a sensitivity of 97% in detecting 102 copies of BRSV, BoHV-1 and BPI3 i & ii. This is the first mRT-qPCR developed to detect the three primary viral agents of BRD and the first multiplex designed using locked nucleic acid (LNA), minor groove binding (MGB) and TaqMan probes in one reaction mix. This test was more sensitive than both VI and IFAT and can replace the aforesaid methods for virus detection during outbreaks of BRD. PMID:22455597

  19. 45 CFR 34.4 - Allowable claims.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... occurred. (7) Claims for automobiles, only when required to perform official business or parked on a... amount allowed is the value of the vehicle at the time of loss as determined by the National...

  20. 76 FR 70883 - Clothing Allowance

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-11-16

    ... published in the Federal Register on February 2, 2011 (76 FR 5733-5734), VA proposed to amend its... appliances affecting different articles of clothing. 76 FR 5733; Sursely, 551 F.3d at 1356. VA will make the... allowances. The amendment provides for an annual clothing allowance for each qualifying prosthetic...

  1. Medical Preparedness Allowable Use Act

    THOMAS, 112th Congress

    Rep. Bilirakis, Gus M. [R-FL-9

    2012-06-21

    11/28/2012 Received in the Senate and Read twice and referred to the Committee on Homeland Security and Governmental Affairs. (All Actions) Tracker: This bill has the status Passed HouseHere are the steps for Status of Legislation:

  2. Medical Preparedness Allowable Use Act

    THOMAS, 113th Congress

    Rep. Bilirakis, Gus M. [R-FL-12

    2013-04-26

    02/04/2014 Received in the Senate and Read twice and referred to the Committee on Homeland Security and Governmental Affairs. (All Actions) Tracker: This bill has the status Passed HouseHere are the steps for Status of Legislation:

  3. Micromachine Wedge Stepping Motor

    SciTech Connect

    Allen, J.J.; Schriner, H.K.

    1998-11-04

    A wedge stepping motor, which will index a mechanism, has been designed and fabricated in the surface rnicromachine SUMMiT process. This device has demonstrated the ability to index one gear tooth at a time with speeds up to 205 teeth/see. The wedge stepper motor has the following features, whi:h will be useful in a number of applications. o The ability to precisely position mechanical components. . Simple pulse signals can be used for operation. o Only 2 drive signals are requixed for operation. o Torque and precision capabilities increase with device size . The device to be indexed is restrained at all times by the wedge shaped tooth that is used for actuation. This paper will discuss the theory of operation and desi=m of the wedge stepping motor. The fabrication and testing of I he device will also be presented.

  4. Proton Transfer and Protein Conformation Dynamics in Photosensitive Proteins by Time-resolved Step-scan Fourier-transform Infrared Spectroscopy

    PubMed Central

    Lórenz-Fonfría, Víctor A.; Heberle, Joachim

    2014-01-01

    Monitoring the dynamics of protonation and protein backbone conformation changes during the function of a protein is an essential step towards understanding its mechanism. Protonation and conformational changes affect the vibration pattern of amino acid side chains and of the peptide bond, respectively, both of which can be probed by infrared (IR) difference spectroscopy. For proteins whose function can be repetitively and reproducibly triggered by light, it is possible to obtain infrared difference spectra with (sub)microsecond resolution over a broad spectral range using the step-scan Fourier transform infrared technique. With ~102-103 repetitions of the photoreaction, the minimum number to complete a scan at reasonable spectral resolution and bandwidth, the noise level in the absorption difference spectra can be as low as ~10-4, sufficient to follow the kinetics of protonation changes from a single amino acid. Lower noise levels can be accomplished by more data averaging and/or mathematical processing. The amount of protein required for optimal results is between 5-100 µg, depending on the sampling technique used. Regarding additional requirements, the protein needs to be first concentrated in a low ionic strength buffer and then dried to form a film. The protein film is hydrated prior to the experiment, either with little droplets of water or under controlled atmospheric humidity. The attained hydration level (g of water / g of protein) is gauged from an IR absorption spectrum. To showcase the technique, we studied the photocycle of the light-driven proton-pump bacteriorhodopsin in its native purple membrane environment, and of the light-gated ion channel channelrhodopsin-2 solubilized in detergent. PMID:24998200

  5. Proton transfer and protein conformation dynamics in photosensitive proteins by time-resolved step-scan Fourier-transform infrared spectroscopy.

    PubMed

    Lórenz-Fonfría, Víctor A; Heberle, Joachim

    2014-06-27

    Monitoring the dynamics of protonation and protein backbone conformation changes during the function of a protein is an essential step towards understanding its mechanism. Protonation and conformational changes affect the vibration pattern of amino acid side chains and of the peptide bond, respectively, both of which can be probed by infrared (IR) difference spectroscopy. For proteins whose function can be repetitively and reproducibly triggered by light, it is possible to obtain infrared difference spectra with (sub)microsecond resolution over a broad spectral range using the step-scan Fourier transform infrared technique. With -10(2)-10(3) repetitions of the photoreaction, the minimum number to complete a scan at reasonable spectral resolution and bandwidth, the noise level in the absorption difference spectra can be as low as -10(-) (4), sufficient to follow the kinetics of protonation changes from a single amino acid. Lower noise levels can be accomplished by more data averaging and/or mathematical processing. The amount of protein required for optimal results is between 5-100 µg, depending on the sampling technique used. Regarding additional requirements, the protein needs to be first concentrated in a low ionic strength buffer and then dried to form a film. The protein film is hydrated prior to the experiment, either with little droplets of water or under controlled atmospheric humidity. The attained hydration level (g of water / g of protein) is gauged from an IR absorption spectrum. To showcase the technique, we studied the photocycle of the light-driven proton-pump bacteriorhodopsin in its native purple membrane environment, and of the light-gated ion channel channelrhodopsin-2 solubilized in detergent.

  6. New quick method for isolating RNA from laser captured cells stained by immunofluorescent immunohistochemistry; RNA suitable for direct use in fluorogenic TaqMan one-step real-time RT-PCR.

    PubMed

    Gallup, Jack M; Kawashima, Kenji; Lucero, Ginger; Ackermann, Mark R

    2005-01-01

    We describe a new approach for reliably isolating one-step real-time quantitative RT-PCR-quality RNA from laser captured cells retrieved from frozen sections previously subjected to immunofluorescent immunohistochemistry (IF-IHC) and subsequently subjected to fluorogenic one-step real-time RT-PCR analysis without the need for costly, time-consuming linear amplification. One cell's worth of RNA can now be interrogated with confidence. This approach represents an amalgam of technologies already offered commercially by Applied Biosystems, Arcturus and Invitrogen. It is the primary focus of this communication to expose the details and execution of an important new LCM RNA isolation technique, but also provide a detailed account of the IF-IHC procedure preceding RNA isolation, and provide information regarding our approach to fluorogenic one-step real-time RT-PCR in general. Experimental results shown here are meant to supplement the primary aim and are not intended to represent a complete scientific study. It is important to mention, that since LCM-RT-PCR is still far less expensive than micro-array analysis, we feel this approach to isolating RNA from LCM samples will be of continuing use to many researchers with limited budgets in the years ahead. PMID:16136226

  7. New quick method for isolating RNA from laser captured cells stained by immunofluorescent immunohistochemistry; RNA suitable for direct use in fluorogenic TaqMan one-step real-time RT-PCR

    PubMed Central

    Kawashima, Kenji; Lucero, Ginger; Ackermann, Mark R.

    2005-01-01

    We describe a new approach for reliably isolating one-step real-time quantitative RT-PCR-quality RNA from laser captured cells retrieved from frozen sections previously subjected to immunofluorescent immunohistochemistry (IF-IHC) and subsequently subjected to fluorogenic one-step real-time RT-PCR analysis without the need for costly, time-consuming linear amplification. One cell’s worth of RNA can now be interrogated with confidence. This approach represents an amalgam of technologies already offered commercially by Applied Biosystems, Arcturus and Invitrogen. It is the primary focus of this communication to expose the details and execution of an important new LCM RNA isolation technique, but also provide a detailed account of the IF-IHC procedure preceding RNA isolation, and provide information regarding our approach to fluorogenic one-step real-time RT-PCR in general. Experimental results shown here are meant to supplement the primary aim and are not intended to represent a complete scientific study. It is important to mention, that since LCM-RT-PCR is still far less expensive than micro-array analysis, we feel this approach to isolating RNA from LCM samples will be of continuing use to many researchers with limited budgets in the years ahead. PMID:16136226

  8. 38 CFR 21.4145 - Work-study allowance.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2013-07-01 2013-07-01 false Work-study allowance. 21...; Educational Assistance Allowance § 21.4145 Work-study allowance. (a) Eligibility. (1) A veteran or reservist... rate of three-quarter time or full time is eligible to receive a work-study allowance. (2) An...

  9. 38 CFR 21.4145 - Work-study allowance.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2012-07-01 2012-07-01 false Work-study allowance. 21...; Educational Assistance Allowance § 21.4145 Work-study allowance. (a) Eligibility. (1) A veteran or reservist... rate of three-quarter time or full time is eligible to receive a work-study allowance. (2) An...

  10. 38 CFR 21.4145 - Work-study allowance.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2014-07-01 2014-07-01 false Work-study allowance. 21...; Educational Assistance Allowance § 21.4145 Work-study allowance. (a) Eligibility. (1) A veteran or reservist... rate of three-quarter time or full time is eligible to receive a work-study allowance. (2) An...

  11. 38 CFR 21.4145 - Work-study allowance.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 38 Pensions, Bonuses, and Veterans' Relief 2 2011-07-01 2011-07-01 false Work-study allowance. 21...; Educational Assistance Allowance § 21.4145 Work-study allowance. (a) Eligibility. (1) A veteran or reservist... rate of three-quarter time or full time is eligible to receive a work-study allowance. (2) An...

  12. Resolution and Characterization of Chemical Steps in Enzyme Catalytic Sequences by Using Low-Temperature and Time-Resolved, Full-Spectrum EPR Spectroscopy in Fluid Cryosolvent and Frozen Solution Systems.

    PubMed

    Wang, Miao; Zhu, Chen; Kohne, Meghan; Warncke, Kurt

    2015-01-01

    Approaches to the resolution and characterization of individual chemical steps in enzyme catalytic sequences, by using temperatures in the cryogenic range of 190-250 K, and kinetics measured by time-resolved, full-spectrum electron paramagnetic resonance spectroscopy in fluid cryosolvent and frozen solution systems, are described. The preparation and performance of the adenosylcobalamin-dependent ethanolamine ammonia-lyase enzyme from Salmonella typhimurium in the two systems exemplifies the biochemical and spectroscopic methods. General advantages of low-temperature studies are (1) slowing of reaction steps, so that measurements can be made by using straightforward T-step kinetic methods and commercial instrumentation, (2) resolution of individual reaction steps, so that first-order kinetic analysis can be applied, and (3) accumulation of intermediates that are not detectable at room temperatures. The broad temperature range from room temperature to 190 K encompasses three regimes: (1) temperature-independent mean free energy surface (corresponding to native behavior); (2) the narrow temperature region of a glass-like transition in the protein, over which the free energy surface changes, revealing dependence of the native reaction on collective protein/solvent motions; and (3) the temperature range below the glass transition region, for which persistent reaction corresponds to nonnative, alternative reaction pathways, in the vicinity of the native configurational envelope. Representative outcomes of low-temperature kinetics studies are portrayed on Eyring and free energy surface (landscape) plots, and guidelines for interpretations are presented.

  13. Step-Growth Polymerization.

    ERIC Educational Resources Information Center

    Stille, J. K.

    1981-01-01

    Following a comparison of chain-growth and step-growth polymerization, focuses on the latter process by describing requirements for high molecular weight, step-growth polymerization kinetics, synthesis and molecular weight distribution of some linear step-growth polymers, and three-dimensional network step-growth polymers. (JN)

  14. Tough Choices or Tough Times: Bolder Steps for Education Philanthropy? Notes and Resources from the GFE Foundation Leaders Institute (Tamaya, New Mexico, October 19, 2007)

    ERIC Educational Resources Information Center

    Mackinnon, Anne

    2007-01-01

    In late 2006, the National Center on Education and the Economy released "Tough Choices or Tough Times: The Report of the New Commission on the Skills of the American Workforce." With compelling language, the report updated and sharpened the findings of the center's influential 1990 report, "America's Choice: High Skills or Low Wages," which called…

  15. Behavioural Repertoire of Working Donkeys and Consistency of Behaviour over Time, as a Preliminary Step towards Identifying Pain-Related Behaviours

    PubMed Central

    Regan, Fran H.; Hockenhull, Jo; Pritchard, Joy C.; Waterman-Pearson, Avril E.; Whay, Helen R.

    2014-01-01

    Background The donkey has a reputation for stoicism and its behavioural repertoire in clinical contexts is under-reported. Lack of understanding of the norms of donkey behaviour and how it may vary over time can compromise use of behavioural measures as indicators of pain or emotional state. The objective of this study was to find out whether the behaviour of working donkeys was influenced by gender, the time of day or differed between days with a view to assessing how robust these measures are for inclusion in a working donkey ethogram. Methodology/Principal Findings Frequency and consistency of postural and event behaviours were measured in 21 adult working donkeys (12 females; 9 males). Instantaneous (scan) and focal sampling were used to measure maintenance, lying, ingestive and investigative behaviours at hourly intervals for ten sessions on each of two consecutive days. High head carriage and biting were seen more frequently in male donkeys than females (P<0.001). Level head carriage, licking/chewing and head-shaking were observed more frequently in female donkeys (P<0.001). Tail position, ear orientation, foot stamping, rolling/lying and head-shaking behaviours were affected by time of day (P<0.001). However, only two variations in ear orientation were found to be significantly different over the two days of observations (P<0.001). Tail swishing, head shaking, foot stamping, and ears held sideways and downwards were significantly correlated (P<0.001) and are assumed to be behaviours to discourage flies. Conclusions/Significance All donkeys expressed an extensive behavioural repertoire, although some differences in behaviour were evident between genders. While most behaviours were consistent over time, some behaviours were influenced by time of day. Few behaviours differed between the two test days. The findings can be used to inform the development of a robust, evidence-based ethogram for working donkeys. PMID:25076209

  16. Does the real-time thermal damage estimate allow for estimation of tumor control after MRI-guided laser-induced thermal therapy? Initial experience with recurrent intracranial ependymomas.

    PubMed

    Patel, Nitesh V; Jethwa, Pinakin R; Shetty, Anil; Danish, Shabbar F

    2015-04-01

    OBJECT Although control of intracranial ependymomas is highly correlated with degree of resection, it is unknown if the same is true for MRI-guided laser-induced thermal therapy (MRgLITT). The authors report their experience with MRgLITT for ependymoma and examine the utility of the real-time thermal damage estimate (TDE), a recent software advance, with respect to completeness of ablation and impact on tumor control. To the authors' knowledge, this is the largest single-center experience utilizing MRgLITT for recurrent ependymomas. METHODS Five tumors in 4 patients were treated with the Visualase Thermal Therapy System. Two tumors were treated similarly on recurrence. Ablation was performed using a 980-nm diode laser with a real-time image acquisition system. Single-plane TDEs were calculated and compared with the original lesion area to compute percentage area ablated (PAA). Volumetric analysis was performed, and percentage volume ablated (PVA) was estimated and correlated with the TDE. Tumor control was correlated with the TDE and volumetric data during treatment. RESULTS Nine ablations were performed on 5 tumors, 2 of which had multiple recurrences. The average pretreatment lesion volume was 8.4 ± 6.3 cm(3), and the average largest 2D area was 5.3 ± 2.7 cm(2). The averaged TDE was 3.9 ± 2.1 cm(2), average PAA was 80.1% ± 34.3%, and average PVA was 64.4% ± 23.5%. For subtotal ablations, average recurrence time was 4.4 ± 5.3 months; 1 adult case remains recurrence-free at 40 months. Using TDEs, the correlation between recurrence time and PAA was r = 0.93 (p = 0.01), and for PVA was r = 0.88 (p = 0.02). Furthermore, PVA and PAA were strongly correlated (r = 0.88, p = 0.02). CONCLUSIONS Through using the PAA, the real-time TDE correlated with the volume of ablation in this initial investigation. Furthermore, the TDE and volumetric data corresponded to the level of tumor control, with time to recurrence dependent on ablation completeness. MRgLITT may have a

  17. Real-Time Measurement of the Tool-Tissue Interaction in Minimally Invasive Abdominal Surgery: The First Step to Developing the Next Generation of Smart Laparoscopic Instruments.

    PubMed

    Barrie, Jenifer; Jayne, David G; Neville, Anne; Hunter, Louise; Hood, Adrian J; Culmer, Peter R

    2016-10-01

    Introduction Analysis of force application in laparoscopic surgery is critical to understanding the nature of the tool-tissue interaction. The aim of this study is to provide real-time data about manipulations to abdominal organs. Methods An instrumented short fenestrated grasper was used in an in vivo porcine model, measuring force at the grasper handle. Grasping force and duration over 5 small bowel manipulation tasks were analyzed. Forces required to retract gallbladder, bladder, small bowel, large bowel, and rectum were measured over 30 seconds. Four parameters were calculated-T(hold), the grasp time; T(close), time taken for the jaws to close; F(max), maximum force reached; and F(rms), root mean square force (representing the average force across the grasp time). Results Mean F(max) to manipulate the small bowel was 20.5 N (±7.2) and F(rms) was 13.7 N (±5.4). Mean T(close) was 0.52 seconds (±0.26) and T(hold) was 3.87 seconds (±1.5). In individual organs, mean F(max) was 49 N (±15) to manipulate the rectum and 59 N (±13.4) for the colon. The mean F(max) for bladder and gallbladder retraction was 28.8 N (±7.4) and 50.7 N (±3.8), respectively. All organs exhibited force relaxation, the F(rms) reduced to below 25 N for all organs except the small bowel, with a mean F(rms) of less than 10 N. Conclusion This study has commenced the process of quantifying tool-tissue interaction. The static measurements discussed here should evolve to include dynamic measurements such as shear, torque, and retraction forces, and be correlated with evidence of histological damage to tissue.

  18. A tiny step towards a theory of functional derivative equations —A strong solution of the space-time hopf equation

    NASA Astrophysics Data System (ADS)

    Inoue, Atsushi

    In this note, we construct a strong solution of the space-time Hopf equation, (partial /{partial t} - vΔ ){δ Z(η )}/{δ η _ell (x,t)} = ileft[ {tilde T^* left\\{ {{δ ^2 Z(η )}/{δ η _j (x,t)δ η _k (x,t)}} right\\}} right]^ell + if^ell (x,t)Z(η ) with certain subsidary conditions, which is an example of functional derivative equations and is manageable using a tiny part of "analysis in functional spaces".

  19. Transoral Robotic Surgery: Step-by-Step Radical Tonsillectomy

    PubMed Central

    Millas, Teresa

    2014-01-01

    Introduction. Transoral robotic surgery (TORS) radical tonsillectomy is an emerging minimally invasive surgical procedure for the treatment of cancer of the tonsil. The detailed surgical technique and claims for its reproducibility have been previously published. Case Presentation. We present a patient with a T2N2bM0 epidermoid carcinoma of the tonsil to illustrate step by step the surgical procedure for TORS radical tonsillectomy. Neck dissection and TORS were staged. No surgical reconstruction of the defect was required. No tracheostomy was necessary. The patient could eat without any feeding tube and was on full oral diet on the fifth postoperative day. Discussion. The transoral approach offers the benefits of minimally invasive surgery to patients with cancer of the tonsil. The excellent exposure and high precision provided by robotic instrumentation allow the surgeon to closely follow and accomplish the surgical steps, which is the best warranty for safety and effectiveness. PMID:24808963

  20. One Step Quantum Key Distribution Based on EPR Entanglement.

    PubMed

    Li, Jian; Li, Na; Li, Lei-Lei; Wang, Tao

    2016-01-01

    A novel quantum key distribution protocol is presented, based on entanglement and dense coding and allowing asymptotically secure key distribution. Considering the storage time limit of quantum bits, a grouping quantum key distribution protocol is proposed, which overcomes the vulnerability of first protocol and improves the maneuverability. Moreover, a security analysis is given and a simple type of eavesdropper's attack would introduce at least an error rate of 46.875%. Compared with the "Ping-pong" protocol involving two steps, the proposed protocol does not need to store the qubit and only involves one step. PMID:27357865

  1. One Step Quantum Key Distribution Based on EPR Entanglement

    PubMed Central

    Li, Jian; Li, Na; Li, Lei-Lei; Wang, Tao

    2016-01-01

    A novel quantum key distribution protocol is presented, based on entanglement and dense coding and allowing asymptotically secure key distribution. Considering the storage time limit of quantum bits, a grouping quantum key distribution protocol is proposed, which overcomes the vulnerability of first protocol and improves the maneuverability. Moreover, a security analysis is given and a simple type of eavesdropper’s attack would introduce at least an error rate of 46.875%. Compared with the “Ping-pong” protocol involving two steps, the proposed protocol does not need to store the qubit and only involves one step. PMID:27357865

  2. Simultaneous detection of influenza viruses A, B, and swine origin influenza A using multiplex one-step real-time RT-PCR assay.

    PubMed

    Monavari, S H R; Mollaie, H R; Fazlalipour, M

    2014-01-01

    Every year, seasonal epidemics of influenza viruses are causing considerable morbidity and mortality worldwide. Also infrequent novel and rearranged strains of influenza viruses have caused quick, acute universal pandemics resulting in millions of mortalities. The usage of efficient and accurate detection is superior for infection control, effective treatment, and epidemiological supervision. Therefore, evaluation of useful real-time PCR molecular tests for the detection of pandemic viruses is important before the next wave of the pandemic. A novel quantitative real-time reverse-transcription polymerase chain reaction (qRT-PCR) assay with specific primers was used successfully for detection and monitoring of the influenza A, B, and swine influenza. The newly designed primers target highly conserved regions in influenza viruses. Our qRT-PCR assay is highly specific for detecting influenza A, B, and swine influenza viruses. The cutoff CT value was determined <38 for domestic human diagnostic test, under conditions of FDA emergency, and the reaction efficiency of the InfA, swInfA, and InfB assays were thereby estimated to be 97.9 % (R2 = 0.998), 98.3 % (R2 = 0.986), and 99.5 % (R2 = 0.995), respectively. Interestingly, based on our finding, there is no cross reactivity of detecting other viruses.

  3. Training in the step-down inhibitory avoidance task time-dependently increases cAMP-dependent protein kinase activity in the entorhinal cortex.

    PubMed

    Pereira, P; Ardenghi, P; Mello e Souza, T; Medina, J H; Izquierdo, I

    2001-06-01

    The cAMP/cAMP-dependent protein kinase (PKA) signaling pathway has been implicated in synaptic plasticity changes and memory consolidation. Several cortical structures are involved in the consolidation of memory for inhibitory avoidance. The aim of the present work was to observe the effects of training in the inhibitory avoidance task on the levels of PKA activity in the entorhinal, parietal and posterior cingulate cortex (EC, PARIET and PC), and the medial precentral area (Fr2) of the rat, at different post-training times (0, 1.5, 3 and 6h). PKA activity, assayed using [gamma-32P]ATP and kemptide, a selective substrate, increased in the EC 3 h after training, but no changes were observed in PARIET, PC and Fr2. These results suggest that the late phase of memory consolidation of inhibitory avoidance requires a functional PKA signaling pathway in the EC in a way that a 'peak' of PKA activity is observed.

  4. The Satellite Test of the Equivalence Principle (STEP)

    NASA Technical Reports Server (NTRS)

    2004-01-01

    STEP will carry concentric test masses to Earth orbit to test a fundamental assumption underlying Einstein's theory of general relativity: that gravitational mass is equivalent to inertial mass. STEP is a 21st-century version of the test that Galileo is said to have performed by dropping a carnon ball and a musket ball simultaneously from the top of the Leaning Tower of Pisa to compare their accelerations. During the STEP experiment, four pairs of test masses will be falling around the Earth, and their accelerations will be measured by superconducting quantum interference devices (SQUIDS). The extended time sensitivity of the instruments will allow the measurements to be a million times more accurate than those made in modern ground-based tests.

  5. Effect of reaction temperature and time during two-step selenization and sulfurization of Se-Coated CuGa/In precursors

    NASA Astrophysics Data System (ADS)

    Koo, Jaseok; Kwon, Sunmo; Roh, Yong-Suk; Lee, Seok-Jin; Jung, Ki-Young; Shafarman, William N.; Park, Ji-Hyeon; Kim, Do Hoon; Myoung, Jae-Min; Kim, Woo Kyoung

    2016-07-01

    In this work, the selenization of Mo/CuGa/In/Se (Se layer thickness: 1 μm) precursors followed by sulfurization was investigated. Particular emphasis was placed on the effect of the variation of the selenization temperature and sulfurization time on the morphology and compositional depth profiles of the resulting Cu(InGa)(SeS)2 (CIGSS) absorber; in addition, the current-voltage characteristics of the corresponding devices were investigated. The selenization of the precursors was achieved by using a tube-type rapid thermal annealing system at various temperatures (500, 550, and 600 °C). Post-sulfurization of Cu(InGa)Se2 (CIGS) was performed in the same system by flowing H2S/He gas at 600 °C for different periods of time (5, 10, and 15 min). Post-sulfurization can improve the open-circuit voltage of a solar cell by attracting Ga toward the surface region of the light absorber and incorporating S into the absorber to yield quinary CIGSS compounds. In addition, the voids at the Mo/CIGS interface, produced during the selenization of the CuGa/In/Se precursors, were effectively removed after post-sulfurization. Among the process conditions explored in this study, the selenization of Mo/CuGa/In/Se at 550 °C for 7 min followed by sulfurization at 600 °C for 10 min produced the device with the best performance, providing also good material properties in terms of morphology and compositional homogeneity. [Figure not available: see fulltext.

  6. Water Structural Changes in the L and M Photocycle Intermediates of Bacteriorhodopsin as Revealed by Time-Resolved Step-Scan FTIR Spectroscopy+

    PubMed Central

    Morgan, Joel E.; Vakkasoglu, Ahmet S.; Gennis, Robert B.; Maeda, Akio

    2014-01-01

    In previous FTIR studies of the photocycle intermediates of bacteriorhodopsin at cryogenic temperatures, water molecules were observed in the L intermediate, in the region surrounded by protein residues between the Schiff base and Asp96. In the M intermediate, the water molecules had moved away towards the Phe219-Thr46 region, but in the N intermediate they were again observed near the Schiff base. In order to evaluate the relevance of this scheme at room temperature, time resolved FTIR difference spectra of bacteriorhodopsin, including the water O–H stretching vibration frequency regions, were recorded in the μsec and msec time ranges. Vibrational changes of weakly-H-bonded water molecules were observed in L, M, and N. In each of these intermediates, the depletion of a water O–H stretching vibration at 3645 cm−1 originating from the initial unphotolzyed bacteriorhodopsin was observed as a trough in the difference spectrum. This vibration is due to the dangling O–H group of a water molecule which interacts with Asp85, and its absence in each of these intermediates indicates that there is perturbation of this O–H group. The formation of M is accompanied by the appearance of water O–H stretching vibrations at 3670 and 3657 cm−1. These bands are due to water molecules present in the region surrounded by Thr46, Asp96 and Phe219. Formation of L at 298 K is accompanied by the perturbations of Asp96 and the Schiff base, though in different ways from what is observed at 170 K. Changes in a broad water vibrational feature, centered around 3610 cm−1, are kinetically correlated with the L-to-M transition. These results imply that even at room temperature, water molecules interact with Asp96 and the Schiff base in L, though with a less rigid structure than at cryogenic temperatures. PMID:17300175

  7. Step by Step: Avoiding Spiritual Bypass in 12-Step Work

    ERIC Educational Resources Information Center

    Cashwell, Craig S.; Clarke, Philip B.; Graves, Elizabeth G.

    2009-01-01

    With spirituality as a cornerstone, 12-step groups serve a vital role in the recovery community. It is important for counselors to be mindful, however, of the potential for clients to be in spiritual bypass, which likely will undermine the recovery process.

  8. Transformation of serum-susceptible Escherichia coli O111 with p16Slux plasmid to allow for real-time monitoring of complement-based inactivation of bacterial growth in bovine milk.

    PubMed

    Maye, S; Stanton, C; Fitzgerald, G F; Kelly, P M

    2016-01-01

    Complement activity has only recently been characterized in raw bovine milk. However, the activity of this component of the innate immune system was found to diminish as milk was subjected to heat or partitioning during cream separation. Detection of complement in milk relies on a bactericidal assay. This assay exploits the specific growth susceptibility of Escherichia coli O111 to the presence of complement. Practical application of the assay was demonstrated when a reduction in complement activity was recorded in the case of pasteurized and reduced-fat milks. This presented an opportunity to improve the functionality of the bactericidal assay by incorporating bioluminescence capability into the target organism. Following some adaptation, the strain was transformed by correctly integrating the p16Slux plasmid. Growth properties of the transformed strain of E. coli O111 were unaffected by the modification. The efficacy of the strain adaptation was correlated using the LINEST function analysis [r=0.966; standard error of prediction (SEy)=0.957] bioluminescence with that of bactericidal assay total plate counts within the range of 7.5 to 9.2 log cfu/mL using a combination of raw and processed milk samples. Importantly, the transformed E. coli O111 p16Slux strain could be identified in milk and broth samples using bioluminescence measurement, thus enabling the bactericidal assay-viability test to be monitored in real time throughout incubation.

  9. The pneumoplex assays, a multiplex PCR-enzyme hybridization assay that allows simultaneous detection of five organisms, Mycoplasma pneumoniae, Chlamydia (Chlamydophila) pneumoniae, Legionella pneumophila, Legionella micdadei, and Bordetella pertussis, and its real-time counterpart.

    PubMed

    Khanna, M; Fan, J; Pehler-Harrington, K; Waters, C; Douglass, P; Stallock, J; Kehl, S; Henrickson, K J

    2005-02-01

    Respiratory disease caused by atypical bacteria remains an important cause of morbidity and mortality for adults and children, despite the widespread use of effective antimicrobials agents. Culture remains the "gold standard" for the detection of these agents. However, culture is labor-intensive, takes several days to weeks for growth, and can be very insensitive for the detection of some of these organisms. Newer singleplex PCR diagnostic tests are sensitive and specific, but multiple assays would be needed to detect all of the common pathogens. Therefore, we developed the Pneumoplex assays, a multiplex PCR-enzyme hybridization assay (the standard assay) and a multiplex real-time assay to detect the most common atypical pathogens in a single test. Primer and probe sequences were designed from conserved regions of specific genes for each of these organisms. The limits of detection were as follows: for Bordetella pertussis, 2 CFU/ml; for Legionella pneumophila (serotypes 1 to 15) and Legionella micdadei, 9 and 80 CFU/ml, respectively; for Mycoplasma pneumoniae, 5 CFU/ml; and for Chlamydia (Chlamydophila) pneumoniae, 0.01 50% tissue culture infective doses. Recombinant DNA controls for each of these organisms were constructed, and the number of copies for each DNA control was calculated. The Pneumoplex could detect each DNA control down to 10 copies/ml. The analytical specificity demonstrated no cross-reactivity between 23 common respiratory pathogens. One hundred twenty-five clinical bronchoalveolar lavage fluid samples tested by the standard assay demonstrated that the Pneumoplex yielded a sensitivity and a specificity of 100 and 98.5%, respectively. This test has the potential to assist clinicians in establishing a specific etiologic diagnosis before initiating therapy, to decrease hospital costs, and to prevent inappropriate antimicrobial therapy.

  10. Stair-stepped Mound

    NASA Technical Reports Server (NTRS)

    2003-01-01

    MGS MOC Release No. MOC2-429, 22 July 2003

    This April 2003 Mars Global Surveyor (MGS) Mars Orbiter Camera (MOC) image shows a stair-stepped mound of sedimentary rock (right of center) on the floor of a large impact crater in western Arabia Terra near 11.0oN, 4.4oW. Sedimentary rock outcrops are common in the craters of this region. The repeated thickness and uniformity of the layers that make up this mound suggest that their depositional environment was one in which cyclic or episodic events occurred over some period of time. The sediments might have been deposited in a lake, or they may have settled directly out of the atmosphere. Most of the layered material was later eroded away, leaving this circular mound and the other nearby mesas and knobs. The image is illuminated by sunlight from the lower left.

  11. Comment on 'Shang S. 2012. Calculating actual crop evapotranspiration under soil water stress conditions with appropriate numerical methods and time step. Hydrological Processes 26: 3338-3343. DOI: 10.1002/hyp.8405'

    NASA Technical Reports Server (NTRS)

    Yatheendradas, Soni; Narapusetty, Balachandrudu; Peters-Lidard, Christa; Funk, Christopher; Verdin, James

    2014-01-01

    A previous study analyzed errors in the numerical calculation of actual crop evapotranspiration (ET(sub a)) under soil water stress. Assuming no irrigation or precipitation, it constructed equations for ET(sub a) over limited soil-water ranges in a root zone drying out due to evapotranspiration. It then used a single crop-soil composite to provide recommendations about the appropriate usage of numerical methods under different values of the time step and the maximum crop evapotranspiration (ET(sub c)). This comment reformulates those ET(sub a) equations for applicability over the full range of soil water values, revealing a dependence of the relative error in numerical ET(sub a) on the initial soil water that was not seen in the previous study. It is shown that the recommendations based on a single crop-soil composite can be invalid for other crop-soil composites. Finally, a consideration of the numerical error in the time-cumulative value of ET(sub a) is discussed besides the existing consideration of that error over individual time steps as done in the previous study. This cumulative ET(sub a) is more relevant to the final crop yield.

  12. Stepped-Pin Clevis Resists Jamming

    NASA Technical Reports Server (NTRS)

    Killgrove, T. O.

    1985-01-01

    Pin modification allows pyrotechnic release devices to operate more smoothly. New clevis pin has stepped diameters to prevent bending as it exits yoke. In contrast, conventional unstepped clevis pin bends and jams as it is withdrawn. Stepped pin design suitable for explosive and possible hammer driven pin sullers.

  13. Two-step phase-shifting SPIDER

    NASA Astrophysics Data System (ADS)

    Zheng, Shuiqin; Cai, Yi; Pan, Xinjian; Zeng, Xuanke; Li, Jingzhen; Li, Ying; Zhu, Tianlong; Lin, Qinggang; Xu, Shixiang

    2016-09-01

    Comprehensive characterization of ultrafast optical field is critical for ultrashort pulse generation and its application. This paper combines two-step phase-shifting (TSPS) into the spectral phase interferometry for direct electric-field reconstruction (SPIDER) to improve the reconstruction of ultrafast optical-fields. This novel SPIDER can remove experimentally the dc portion occurring in traditional SPIDER method by recording two spectral interferograms with π phase-shifting. As a result, the reconstructed results are much less disturbed by the time delay between the test pulse replicas and the temporal widths of the filter window, thus more reliable. What is more, this SPIDER can work efficiently even the time delay is so small or the measured bandwidth is so narrow that strong overlap happens between the dc and ac portions, which allows it to be able to characterize the test pulses with complicated temporal/spectral structures or narrow bandwidths.

  14. Two-step phase-shifting SPIDER

    PubMed Central

    Zheng, Shuiqin; Cai, Yi; Pan, Xinjian; Zeng, Xuanke; Li, Jingzhen; Li, Ying; Zhu, Tianlong; Lin, Qinggang; Xu, Shixiang

    2016-01-01

    Comprehensive characterization of ultrafast optical field is critical for ultrashort pulse generation and its application. This paper combines two-step phase-shifting (TSPS) into the spectral phase interferometry for direct electric-field reconstruction (SPIDER) to improve the reconstruction of ultrafast optical-fields. This novel SPIDER can remove experimentally the dc portion occurring in traditional SPIDER method by recording two spectral interferograms with π phase-shifting. As a result, the reconstructed results are much less disturbed by the time delay between the test pulse replicas and the temporal widths of the filter window, thus more reliable. What is more, this SPIDER can work efficiently even the time delay is so small or the measured bandwidth is so narrow that strong overlap happens between the dc and ac portions, which allows it to be able to characterize the test pulses with complicated temporal/spectral structures or narrow bandwidths. PMID:27666528

  15. STEPS: Moving from Welfare to Work.

    ERIC Educational Resources Information Center

    Vail, Ann; Cummings, Merrilyn; Kratzer, Connie; Galindo, Vickie

    Cooperative extension service faculty at New Mexico State University started the Steps to Employment and Personal Success (STEPS) program to help Temporary Assistance for Needy Families (TANF) clients qualify for and maintain full-time employment and strengthen their families for long-term success. Clients are referred to STEPS by New Mexico…

  16. Assignment of IR bands of isolated and protein-bound Peridinin in its fundamental and triplet state by static FTIR, time-resolved step-scan FTIR and DFT calculations

    NASA Astrophysics Data System (ADS)

    Mezzetti, Alberto; Kish, Elizabeth; Robert, Bruno; Spezia, Riccardo

    2015-06-01

    The vibrational properties of Peridinin in its fundamental state and in the excited triplet state have been investigated by DFT calculations and static and time-resolved FTIR spectroscopy. The infrared spectrum of Peridinin in its fundamental state has been explored in the whole 2000-600 cm-1 range, and interpreted in term of molecular vibrations. In particular, new infrared bands have been identified and assigned to specific molecular vibrations. 3Peridinin molecular vibrations have also been investigated by DFT calculations. In addition, putative IR bands belonging to Peridinin and 3Peridinin have been identified in the step-scan FTIR difference spectrum of the Peridinin-Chlorophyll a-Protein from Amphidinium carterae, where light induce formation of a triplet state localized on one or more Peridinins. The exact nature of the triplet state formed in Peridinin-Chlorophyll a-Protein from dinoflagellates, in particular the possible involvement in this triplet state of 3Chlorophyll a, has been largely debated in the last few years (see Carbonera et al., 2014 [3]); time-resolved differential FTIR experiments have played a key role in this debate. Identification of IR marker bands for the main molecule (Peridinin) implicated in this photophysical process is therefore particularly important and makes this study a significant step towards the full understanding of Peridinin-Chlorophyll-a-Proteins photophysics.

  17. 40 CFR 264.113 - Closure; time allowed for closure.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... permit requirements; and (2) The request to modify the permit includes an amended waste analysis plan... longer than the allotted period to complete and that an extension will not pose a threat to human...

  18. 40 CFR 265.113 - Closure; time allowed for closure.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... owner or operator submits an amended part B application, or a part B application, if not previously... application to receive non-hazardous wastes; and (ii) There is a reasonable likelihood that the owner or... operate in compliance with all applicable interim status requirements; and (2) The part B...

  19. Numerical Integration: One Step at a Time

    ERIC Educational Resources Information Center

    Yang, Yajun; Gordon, Sheldon P.

    2016-01-01

    This article looks at the effects that adding a single extra subdivision has on the level of accuracy of some common numerical integration routines. Instead of automatically doubling the number of subdivisions for a numerical integration rule, we investigate what happens with a systematic method of judiciously selecting one extra subdivision for…

  20. A Step or Two Back in Time.

    ERIC Educational Resources Information Center

    Thomson, Peggy

    1979-01-01

    Describes the National Park Service's Environmental Living Program for elementary school children in the San Francisco Bay Area, where teachers, parents, and children stay overnight in a historic fort and schooner, experience living in a past age, use candles and oil stoves, and engage in mock military and shipboard activities. (MF)

  1. Brief Azacytidine Step Allows The Conversion of Suspension Human Fibroblasts into Neural Progenitor-Like Cells

    PubMed Central

    Mirakhori, Fahimeh; Zeynali, Bahman; Kiani, Sahar; Baharvand, Hossein

    2015-01-01

    In recent years transdifferentiation technology has enabled direct conversion of human fibroblasts to become a valuable, abundant and accessible cell source for patient-specific induced cell generation in biomedical research. The majority of transdifferentiation approaches rely upon viral gene delivery which due to random integration with the host genome can cause genome instability and tumorigenesis upon transplantation. Here, we provide a simple way to induce neural progenitor-like cells from human fibroblasts without genetic manipulation by changing physicochemical culture properties from monolayer culture into a suspension in the presence of a chemical DNA methyltransferase inhibitor agent, Azacytidine. We have demonstrated the expression of neural progenitor-like markers, morphology and the ability to spontaneously differentiate into neural-like cells. This approach is simple, inexpensive, lacks genetic manipulation and could be a foundation for future chemical neural transdifferentiation and a safe induction of neural progenitor cells from human fibroblasts for clinical applications. PMID:25870845

  2. Extended Follow-up Confirms Early Vaccine-Enhanced Risk of HIV Acquisition and Demonstrates Waning Effect Over Time Among Participants in a Randomized Trial of Recombinant Adenovirus HIV Vaccine (Step Study)

    PubMed Central

    Duerr, Ann; Huang, Yunda; Buchbinder, Susan; Coombs, Robert W.; Sanchez, Jorge; del Rio, Carlos; Casapia, Martin; Santiago, Steven; Gilbert, Peter; Corey, Lawrence; Robertson, Michael N.

    2012-01-01

    Background. The Step Study tested whether an adenovirus serotype 5 (Ad5)–vectored human immunodeficiency virus (HIV) vaccine could prevent HIV acquisition and/or reduce viral load set-point after infection. At the first interim analysis, nonefficacy criteria were met. Vaccinations were halted; participants were unblinded. In post hoc analyses, more HIV infections occurred in vaccinees vs placebo recipients in men who had Ad5-neutralizing antibodies and/or were uncircumcised. Follow-up was extended to assess relative risk of HIV acquisition in vaccinees vs placebo recipients over time. Methods. We used Cox proportional hazard models for analyses of vaccine effect on HIV acquisition and vaccine effect modifiers, and nonparametric and semiparametric methods for analysis of constancy of relative risk over time. Results. One hundred seventy-two of 1836 men were infected. The adjusted vaccinees vs placebo recipients hazard ratio (HR) for all follow-up time was 1.40 (95% confidence interval [CI], 1.03–1.92; P = .03). Vaccine effect differed by baseline Ad5 or circumcision status during first 18 months, but neither was significant for all follow-up time. The HR among uncircumcised and/or Ad5-seropositive men waned with time since vaccination. No significant vaccine-associated risk was seen among circumcised, Ad5-negative men (HR, 0.97; P = 1.0) over all follow-up time. Conclusions. The vaccine-associated risk seen in interim analysis was confirmed but waned with time from vaccination. Clinical Trials Registration. NCT00095576. PMID:22561365

  3. STEP Experiment Requirements

    NASA Technical Reports Server (NTRS)

    Brumfield, M. L. (Compiler)

    1984-01-01

    A plan to develop a space technology experiments platform (STEP) was examined. NASA Langley Research Center held a STEP Experiment Requirements Workshop on June 29 and 30 and July 1, 1983, at which experiment proposers were invited to present more detailed information on their experiment concept and requirements. A feasibility and preliminary definition study was conducted and the preliminary definition of STEP capabilities and experiment concepts and expected requirements for support services are presented. The preliminary definition of STEP capabilities based on detailed review of potential experiment requirements is investigated. Topics discussed include: Shuttle on-orbit dynamics; effects of the space environment on damping materials; erectable beam experiment; technology for development of very large solar array deployers; thermal energy management process experiment; photovoltaic concentrater pointing dynamics and plasma interactions; vibration isolation technology; flight tests of a synthetic aperture radar antenna with use of STEP.

  4. Time?

    NASA Astrophysics Data System (ADS)

    Amoroso, Richard L.

    2013-09-01

    The concept of time in the `clockwork' Newtonian world was irrelevant; and has generally been ignored until recently by several generations of physicists since the implementation of quantum mechanics. We will set aside the utility of time as a property relating to physical calculations of events relating to a metrics line element or as an aspect of the transformation of a particles motion/interaction in a coordinate system or in relation to thermodynamics etc., i.e. we will discard all the usual uses of time as a concept used to circularly define physical parameters in terms of other physical parameters; concentrating instead on time as an aspect of the fundamental cosmic topology of our virtual reality especially as it inseparably relates to the nature and role of the observer in natural science.

  5. Detection of Steps in Single Molecule Data

    PubMed Central

    Aggarwal, Tanuj; Materassi, Donatello; Davison, Robert; Hays, Thomas; Salapaka, Murti

    2013-01-01

    Over the past few decades, single molecule investigations employing optical tweezers, AFM and TIRF microscopy have revealed that molecular behaviors are typically characterized by discrete steps or events that follow changes in protein conformation. These events, that manifest as steps or jumps, are short-lived transitions between otherwise more stable molecular states. A major limiting factor in determining the size and timing of the steps is the noise introduced by the measurement system. To address this impediment to the analysis of single molecule behaviors, step detection algorithms incorporate large records of data and provide objective analysis. However, existing algorithms are mostly based on heuristics that are not reliable and lack objectivity. Most of these step detection methods require the user to supply parameters that inform the search for steps. They work well, only when the signal to noise ratio (SNR) is high and stepping speed is low. In this report, we have developed a novel step detection method that performs an objective analysis on the data without input parameters, and based only on the noise statistics. The noise levels and characteristics can be estimated from the data providing reliable results for much smaller SNR and higher stepping speeds. An iterative learning process drives the optimization of step-size distributions for data that has unimodal step-size distribution, and produces extremely low false positive outcomes and high accuracy in finding true steps. Our novel methodology, also uniquely incorporates compensation for the smoothing affects of probe dynamics. A mechanical measurement probe typically takes a finite time to respond to step changes, and when steps occur faster than the probe response time, the sharp step transitions are smoothed out and can obscure the step events. To address probe dynamics we accept a model for the dynamic behavior of the probe and invert it to reveal the steps. No other existing method addresses

  6. Step-by-Step Simulation of Radiation Chemistry Using Green Functions for Diffusion-Influenced Reactions

    NASA Technical Reports Server (NTRS)

    Plante, Ianik; Cucinotta, Francis A.

    2011-01-01

    Radiolytic species are formed approximately 1 ps after the passage of ionizing radiation through matter. After their formation, they diffuse and chemically react with other radiolytic species and neighboring biological molecules, leading to various oxidative damage. Therefore, the simulation of radiation chemistry is of considerable importance to understand how radiolytic species damage biological molecules [1]. The step-by-step simulation of chemical reactions is difficult, because the radiolytic species are distributed non-homogeneously in the medium. Consequently, computational approaches based on Green functions for diffusion-influenced reactions should be used [2]. Recently, Green functions for more complex type of reactions have been published [3-4]. We have developed exact random variate generators of these Green functions [5], which will allow us to use them in radiation chemistry codes. Moreover, simulating chemistry using the Green functions is which is computationally very demanding, because the probabilities of reactions between each pair of particles should be evaluated at each timestep [2]. This kind of problem is well adapted for General Purpose Graphic Processing Units (GPGPU), which can handle a large number of similar calculations simultaneously. These new developments will allow us to include more complex reactions in chemistry codes, and to improve the calculation time. This code should be of importance to link radiation track structure simulations and DNA damage models.

  7. The Next Giant Step

    NASA Video Gallery

    Artist Robert McCall painted "The Next Giant Step" in 1979 to commemorate the heroism and courage of spaceflight pioneers. Located in the lobby of Johnson's building 2, the mural depicts America's ...

  8. 49 CFR 266.11 - Allowable costs.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 49 Transportation 4 2010-10-01 2010-10-01 false Allowable costs. 266.11 Section 266.11... TRANSPORTATION ACT § 266.11 Allowable costs. Allowable costs include only the following costs which are properly allocable to the work performed: Planning and program operation costs which are allowed under...

  9. 46 CFR 154.421 - Allowable stress.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 5 2010-10-01 2010-10-01 false Allowable stress. 154.421 Section 154.421 Shipping COAST... § 154.421 Allowable stress. The allowable stress for the integral tank structure must meet the American Bureau of Shipping's allowable stress for the vessel's hull published in “Rules for Building and...

  10. 46 CFR 154.421 - Allowable stress.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 46 Shipping 5 2012-10-01 2012-10-01 false Allowable stress. 154.421 Section 154.421 Shipping COAST... § 154.421 Allowable stress. The allowable stress for the integral tank structure must meet the American Bureau of Shipping's allowable stress for the vessel's hull published in “Rules for Building and...

  11. 46 CFR 154.421 - Allowable stress.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 46 Shipping 5 2013-10-01 2013-10-01 false Allowable stress. 154.421 Section 154.421 Shipping COAST... § 154.421 Allowable stress. The allowable stress for the integral tank structure must meet the American Bureau of Shipping's allowable stress for the vessel's hull published in “Rules for Building and...

  12. 46 CFR 154.440 - Allowable stress.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 46 Shipping 5 2011-10-01 2011-10-01 false Allowable stress. 154.440 Section 154.440 Shipping COAST... Tank Type A § 154.440 Allowable stress. (a) The allowable stresses for an independent tank type A must... Commandant (CG-522). (b) A greater allowable stress than required in paragraph (a)(1) of this section may...

  13. 46 CFR 154.421 - Allowable stress.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 46 Shipping 5 2014-10-01 2014-10-01 false Allowable stress. 154.421 Section 154.421 Shipping COAST... § 154.421 Allowable stress. The allowable stress for the integral tank structure must meet the American Bureau of Shipping's allowable stress for the vessel's hull published in “Rules for Building and...

  14. 46 CFR 154.421 - Allowable stress.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 46 Shipping 5 2011-10-01 2011-10-01 false Allowable stress. 154.421 Section 154.421 Shipping COAST... § 154.421 Allowable stress. The allowable stress for the integral tank structure must meet the American Bureau of Shipping's allowable stress for the vessel's hull published in “Rules for Building and...

  15. 46 CFR 154.440 - Allowable stress.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 46 Shipping 5 2013-10-01 2013-10-01 false Allowable stress. 154.440 Section 154.440 Shipping COAST... Tank Type A § 154.440 Allowable stress. (a) The allowable stresses for an independent tank type A must... Commandant (CG-ENG). (b) A greater allowable stress than required in paragraph (a)(1) of this section may...

  16. 46 CFR 154.440 - Allowable stress.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 46 Shipping 5 2012-10-01 2012-10-01 false Allowable stress. 154.440 Section 154.440 Shipping COAST... Tank Type A § 154.440 Allowable stress. (a) The allowable stresses for an independent tank type A must... Commandant (CG-ENG). (b) A greater allowable stress than required in paragraph (a)(1) of this section may...

  17. 46 CFR 154.440 - Allowable stress.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 46 Shipping 5 2014-10-01 2014-10-01 false Allowable stress. 154.440 Section 154.440 Shipping COAST... Tank Type A § 154.440 Allowable stress. (a) The allowable stresses for an independent tank type A must... Commandant (CG-ENG). (b) A greater allowable stress than required in paragraph (a)(1) of this section may...

  18. A big first step.

    PubMed

    Jones, Howard W

    2004-11-01

    The singleton, term gestation, live birth rate per cycle initiated (BESST) endpoint proposed at the beginning of 2004 is a first big step which should be added to by the consideration of multiple pregnancy rates in relation to singleton rates, by recording of fetal reductions and of pregnancies resulting from cryopreserved material. After three or more steps we may have an accurate reporting system which helps patients to distinguish the pros and cons for singleton term delivery. PMID:15479704

  19. Control Circuit For Two Stepping Motors

    NASA Technical Reports Server (NTRS)

    Ratliff, Roger; Rehmann, Kenneth; Backus, Charles

    1990-01-01

    Control circuit operates two independent stepping motors, one at a time. Provides following operating features: After selected motor stepped to chosen position, power turned off to reduce dissipation; Includes two up/down counters that remember at which one of eight steps each motor set. For selected motor, step indicated by illumination of one of eight light-emitting diodes (LED's) in ring; Selected motor advanced one step at time or repeatedly at rate controlled; Motor current - 30 mA at 90 degree positions, 60 mA at 45 degree positions - indicated by high or low intensity of LED that serves as motor-current monitor; Power-on reset feature provides trouble-free starts; To maintain synchronism between control circuit and motors, stepping of counters inhibited when motor power turned off.

  20. Step fluctuations and step interactions on Mo(0 1 1)

    NASA Astrophysics Data System (ADS)

    Ondrejcek, M.; Swiech, W.; Durfee, C. S.; Flynn, C. P.

    2003-09-01

    Step fluctuations have been studied on Mo(0 1 1) thin single crystal films with various orientations of miscut, in order to determine the step stiffnesses. Effects of unseen defect structures were clearly visible in some data. Measurements of fluctuation amplitudes and relaxation times were made in the temperature range 1100-1680 K. The results show an anisotropic stiffness of about 0.36 eV/nm along [0 1¯ 1] and about 0.15 eV/nm along [1 0 0]. No temperature dependence of the stiffness was detected. The step free energies derived from the stiffnesses average about 0.27 eV/nm and are less anisotropic by about a factor 3. From the temperature dependence of the relaxation rates, an activation energy of 0.8 ± 0.2 eV was determined for the mass diffusion of the mobile defects responsible for the fluctuations. An appendix details an investigation of correlations induced in the motions of neighboring steps by diffusion and by energetic interactions.

  1. Efficient photoheating algorithms in time-dependent photoionization simulations

    NASA Astrophysics Data System (ADS)

    Lee, Kai-Yan; Mellema, Garrelt; Lundqvist, Peter

    2016-02-01

    We present an extension to the time-dependent photoionization code C2-RAY to calculate photoheating in an efficient and accurate way. In C2-RAY, the thermal calculation demands relatively small time-steps for accurate results. We describe two novel methods to reduce the computational cost associated with small time-steps, namely, an adaptive time-step algorithm and an asynchronous evolution approach. The adaptive time-step algorithm determines an optimal time-step for the next computational step. It uses a fast ray-tracing scheme to quickly locate the relevant cells for this determination and only use these cells for the calculation of the time-step. Asynchronous evolution allows different cells to evolve with different time-steps. The asynchronized clocks of the cells are synchronized at the times where outputs are produced. By only evolving cells which may require short time-steps with these short time-steps instead of imposing them to the whole grid, the computational cost of the calculation can be substantially reduced. We show that our methods work well for several cosmologically relevant test problems and validate our results by comparing to the results of another time-dependent photoionization code.

  2. 40 CFR 35.2109 - Step 2+3.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 40 Protection of Environment 1 2011-07-01 2011-07-01 false Step 2+3. 35.2109 Section 35.2109... ASSISTANCE Grants for Construction of Treatment Works § 35.2109 Step 2+3. The Regional Administrator may award a Step 2+3 grant which will provide the Federal share of an allowance under appendix B and...

  3. 40 CFR 35.2109 - Step 2+3.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 1 2010-07-01 2010-07-01 false Step 2+3. 35.2109 Section 35.2109... ASSISTANCE Grants for Construction of Treatment Works § 35.2109 Step 2+3. The Regional Administrator may award a Step 2+3 grant which will provide the Federal share of an allowance under appendix B and...

  4. Two-Step Incision for Periarterial Sympathectomy of the Hand

    PubMed Central

    Jeon, Seung Bae; Ahn, Yong Su; Choi, Matthew Seung Suk

    2015-01-01

    Background Surgical scars on the palmar surface of the hand may lead to functional and also aesthetic and psychological consequences. The objective of this study was to introduce a new incision technique for periarterial sympathectomy of the hand and to compare the results of the new two-step incision technique with those of a Koman incision by using an objective questionnaire. Methods A total of 40 patients (17 men and 23 women) with intractable Raynaud's disease or syndrome underwent surgery in our hospital, conducted by a single surgeon, between January 2008 and January 2013. Patients who had undergone extended sympathectomy or vessel graft were excluded. Clinical evaluation of postoperative scars was performed in both groups one year after surgery using the patient and observer scar assessment scale (POSAS) and the Wake Forest University rating scale. Results The total patient score was 8.59 (range, 6-15) in the two-step incision group and 9.62 (range, 7-18) in the Koman incision group. A significant difference was found between the groups in the total PS score (P-value=0.034) but not in the total observer score. Our analysis found no significant difference in preoperative and postoperative Wake Forest University rating scale scores between the two-step and Koman incision groups. The time required for recovery prior to returning to work after surgery was shorter in the two-step incision group, with a mean of 29.48 days in the two-step incision group and 34.15 days in the Koman incision group (P=0.03). Conclusions Compared to the Koman incision, the new two-step incision technique provides better aesthetic results, similar symptom improvement, and a reduction in the recovery time required before returning to work. Furthermore, this incision allows the surgeon to access a wide surgical field and a sufficient exposure of anatomical structures. PMID:26618125

  5. One-step multiplex real-time RT-PCR assay for detecting and genotyping wild-type group A rotavirus strains and vaccine strains (Rotarix® and RotaTeq®) in stool samples.

    PubMed

    Gautam, Rashi; Mijatovic-Rustempasic, Slavica; Esona, Mathew D; Tam, Ka Ian; Quaye, Osbourne; Bowen, Michael D

    2016-01-01

    Background. Group A rotavirus (RVA) infection is the major cause of acute gastroenteritis (AGE) in young children worldwide. Introduction of two live-attenuated rotavirus vaccines, RotaTeq® and Rotarix®, has dramatically reduced RVA associated AGE and mortality in developed as well as in many developing countries. High-throughput methods are needed to genotype rotavirus wild-type strains and to identify vaccine strains in stool samples. Quantitative RT-PCR assays (qRT-PCR) offer several advantages including increased sensitivity, higher throughput, and faster turnaround time. Methods. In this study, a one-step multiplex qRT-PCR assay was developed to detect and genotype wild-type strains and vaccine (Rotarix® and RotaTeq®) rotavirus strains along with an internal processing control (Xeno or MS2 RNA). Real-time RT-PCR assays were designed for VP7 (G1, G2, G3, G4, G9, G12) and VP4 (P[4], P[6] and P[8]) genotypes. The multiplex qRT-PCR assay also included previously published NSP3 qRT-PCR for rotavirus detection and Rotarix® NSP2 and RotaTeq® VP6 qRT-PCRs for detection of Rotarix® and RotaTeq® vaccine strains respectively. The multiplex qRT-PCR assay was validated using 853 sequence confirmed stool samples and 24 lab cultured strains of different rotavirus genotypes. By using thermostable rTth polymerase enzyme, dsRNA denaturation, reverse transcription (RT) and amplification (PCR) steps were performed in single tube by uninterrupted thermocycling profile to reduce chances of sample cross contamination and for rapid generation of results. For quantification, standard curves were generated using dsRNA transcripts derived from RVA gene segments. Results. The VP7 qRT-PCRs exhibited 98.8-100% sensitivity, 99.7-100% specificity, 85-95% efficiency and a limit of detection of 4-60 copies per singleplex reaction. The VP7 qRT-PCRs exhibited 81-92% efficiency and limit of detection of 150-600 copies in multiplex reactions. The VP4 qRT-PCRs exhibited 98

  6. One-step multiplex real-time RT-PCR assay for detecting and genotyping wild-type group A rotavirus strains and vaccine strains (Rotarix® and RotaTeq®) in stool samples

    PubMed Central

    Mijatovic-Rustempasic, Slavica; Esona, Mathew D.; Tam, Ka Ian; Quaye, Osbourne; Bowen, Michael D.

    2016-01-01

    Background. Group A rotavirus (RVA) infection is the major cause of acute gastroenteritis (AGE) in young children worldwide. Introduction of two live-attenuated rotavirus vaccines, RotaTeq® and Rotarix®, has dramatically reduced RVA associated AGE and mortality in developed as well as in many developing countries. High-throughput methods are needed to genotype rotavirus wild-type strains and to identify vaccine strains in stool samples. Quantitative RT-PCR assays (qRT-PCR) offer several advantages including increased sensitivity, higher throughput, and faster turnaround time. Methods. In this study, a one-step multiplex qRT-PCR assay was developed to detect and genotype wild-type strains and vaccine (Rotarix® and RotaTeq®) rotavirus strains along with an internal processing control (Xeno or MS2 RNA). Real-time RT-PCR assays were designed for VP7 (G1, G2, G3, G4, G9, G12) and VP4 (P[4], P[6] and P[8]) genotypes. The multiplex qRT-PCR assay also included previously published NSP3 qRT-PCR for rotavirus detection and Rotarix® NSP2 and RotaTeq® VP6 qRT-PCRs for detection of Rotarix® and RotaTeq® vaccine strains respectively. The multiplex qRT-PCR assay was validated using 853 sequence confirmed stool samples and 24 lab cultured strains of different rotavirus genotypes. By using thermostable rTth polymerase enzyme, dsRNA denaturation, reverse transcription (RT) and amplification (PCR) steps were performed in single tube by uninterrupted thermocycling profile to reduce chances of sample cross contamination and for rapid generation of results. For quantification, standard curves were generated using dsRNA transcripts derived from RVA gene segments. Results. The VP7 qRT-PCRs exhibited 98.8–100% sensitivity, 99.7–100% specificity, 85–95% efficiency and a limit of detection of 4–60 copies per singleplex reaction. The VP7 qRT-PCRs exhibited 81–92% efficiency and limit of detection of 150–600 copies in multiplex reactions. The VP4 qRT-PCRs exhibited 98.8

  7. Melatonin: a universal time messenger.

    PubMed

    Erren, Thomas C; Reiter, Russel J

    2015-01-01

    Temporal organization plays a key role in humans, and presumably all species on Earth. A core building block of the chronobiological architecture is the master clock, located in the suprachi asmatic nuclei [SCN], which organizes "when" things happen in sub-cellular biochemistry, cells, organs and organisms, including humans. Conceptually, time messenging should follow a 5 step-cascade. While abundant evidence suggests how steps 1 through 4 work, step 5 of "how is central time information transmitted througout the body?" awaits elucidation. Step 1: Light provides information on environmental (external) time; Step 2: Ocular interfaces between light and biological (internal) time are intrinsically photosensitive retinal ganglion cells [ipRGS] and rods and cones; Step 3: Via the retinohypothalamic tract external time information reaches the light-dependent master clock in the brain, viz the SCN; Step 4: The SCN translate environmental time information into biological time and distribute this information to numerous brain structures via a melanopsin-based network. Step 5: Melatonin, we propose, transmits, or is a messenger of, internal time information to all parts of the body to allow temporal organization which is orchestrated by the SCN. Key reasons why we expect melatonin to have such role include: First, melatonin, as the chemical expression of darkness, is centrally involved in time- and timing-related processes such as encoding clock and calendar information in the brain; Second, melatonin travels throughout the body without limits and is thus a ubiquitous molecule. The chemial conservation of melatonin in all tested species could make this molecule a candidate for a universal time messenger, possibly constituting a legacy of an all-embracing evolutionary history.

  8. 10 CFR 600.317 - Allowable costs.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... OMB Circular A-122 is determined in accordance with the for-profit costs principles in 48 CFR part 31... Organizations.” (iii) Hospitals. Allowability is determined in accordance with the provisions of 45 CFR part 74... Allowable costs. (a) DOE determines allowability of costs in accordance with the cost principles...

  9. 7 CFR 550.25 - Allowable costs.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... at 2 CFR part 230. The allowability of costs incurred by institutions of higher education is... at 2 CFR part 225. The allowability of costs incurred by non-profit organizations is determined in... Institutions” codified at 2 CFR 220. The allowability of costs incurred by hospitals is determined...

  10. 20 CFR 211.8 - Displacement allowance.

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 20 Employees' Benefits 1 2012-04-01 2012-04-01 false Displacement allowance. 211.8 Section 211.8 Employees' Benefits RAILROAD RETIREMENT BOARD REGULATIONS UNDER THE RAILROAD RETIREMENT ACT CREDITABLE RAILROAD COMPENSATION § 211.8 Displacement allowance. An allowance paid to an employee because he has...

  11. 20 CFR 211.8 - Displacement allowance.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 20 Employees' Benefits 1 2014-04-01 2012-04-01 true Displacement allowance. 211.8 Section 211.8 Employees' Benefits RAILROAD RETIREMENT BOARD REGULATIONS UNDER THE RAILROAD RETIREMENT ACT CREDITABLE RAILROAD COMPENSATION § 211.8 Displacement allowance. An allowance paid to an employee because he has...

  12. 20 CFR 211.8 - Displacement allowance.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 20 Employees' Benefits 1 2010-04-01 2010-04-01 false Displacement allowance. 211.8 Section 211.8 Employees' Benefits RAILROAD RETIREMENT BOARD REGULATIONS UNDER THE RAILROAD RETIREMENT ACT CREDITABLE RAILROAD COMPENSATION § 211.8 Displacement allowance. An allowance paid to an employee because he has...

  13. 20 CFR 211.8 - Displacement allowance.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 20 Employees' Benefits 1 2011-04-01 2011-04-01 false Displacement allowance. 211.8 Section 211.8 Employees' Benefits RAILROAD RETIREMENT BOARD REGULATIONS UNDER THE RAILROAD RETIREMENT ACT CREDITABLE RAILROAD COMPENSATION § 211.8 Displacement allowance. An allowance paid to an employee because he has...

  14. 20 CFR 211.8 - Displacement allowance.

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 20 Employees' Benefits 1 2013-04-01 2012-04-01 true Displacement allowance. 211.8 Section 211.8 Employees' Benefits RAILROAD RETIREMENT BOARD REGULATIONS UNDER THE RAILROAD RETIREMENT ACT CREDITABLE RAILROAD COMPENSATION § 211.8 Displacement allowance. An allowance paid to an employee because he has...

  15. 44 CFR 206.228 - Allowable costs.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... Allowable costs. General policies for determining allowable costs are established in 44 CFR 13.22. Exceptions to those policies as allowed in 44 CFR 13.4 and 13.6 are explained below. (a) Eligible direct... accordance with 44 CFR part 207. (b)...

  16. 44 CFR 204.63 - Allowable costs.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ....63 Allowable costs. 44 CFR 13.22 establishes general policies for determining allowable costs. (a) We will reimburse direct costs for the administration of a fire management assistance grant under 44 CFR... 44 Emergency Management and Assistance 1 2010-10-01 2010-10-01 false Allowable costs....

  17. 50 CFR 80.15 - Allowable costs.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ..., see 5 CFR 1310.3.). (b) What is required to determine the allowability of costs? Source documents or... 50 Wildlife and Fisheries 6 2010-10-01 2010-10-01 false Allowable costs. 80.15 Section 80.15... WILDLIFE RESTORATION AND DINGELL-JOHNSON SPORT FISH RESTORATION ACTS § 80.15 Allowable costs. (a) What...

  18. 50 CFR 85.41 - Allowable costs.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... applicable Federal cost principles in 43 CFR 12.60(b). Purchase of informational signs, program signs, and... 50 Wildlife and Fisheries 6 2010-10-01 2010-10-01 false Allowable costs. 85.41 Section 85.41... Use/Acceptance of Funds § 85.41 Allowable costs. (a) Allowable grant costs are limited to those...

  19. 34 CFR 675.33 - Allowable costs.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... 34 Education 3 2011-07-01 2011-07-01 false Allowable costs. 675.33 Section 675.33 Education... costs. (a)(1) Allowable and unallowable costs. Except as provided in paragraph (a)(2) of this section, costs reasonably related to carrying out the programs described in § 675.32 are allowable. (2)...

  20. 42 CFR 417.534 - Allowable costs.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 42 Public Health 3 2011-10-01 2011-10-01 false Allowable costs. 417.534 Section 417.534 Public... PLANS Medicare Payment: Cost Basis § 417.534 Allowable costs. (a) Definition—Allowable costs means the direct and indirect costs, including normal standby costs incurred by the HMO or CMP, that are proper...

  1. 42 CFR 417.802 - Allowable costs.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 42 Public Health 3 2010-10-01 2010-10-01 false Allowable costs. 417.802 Section 417.802 Public... PLANS Health Care Prepayment Plans § 417.802 Allowable costs. (a) General rule. The costs that are considered allowable for HCPP reimbursement are the same as those for reasonable cost HMOs and CMPs...

  2. 45 CFR 1180.56 - Allowable costs.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 45 Public Welfare 3 2010-10-01 2010-10-01 false Allowable costs. 1180.56 Section 1180.56 Public... by a Grantee General Administrative Responsibilities § 1180.56 Allowable costs. (a) Determination of costs allowable under a grant is made in accordance with government-wide cost principles in...

  3. 34 CFR 304.21 - Allowable costs.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Grantee § 304.21 Allowable costs. In addition to the allowable costs established in the Education Department General Administrative Regulations in 34 CFR 75.530 through 75.562, the following items are... 34 Education 2 2011-07-01 2010-07-01 true Allowable costs. 304.21 Section 304.21...

  4. 34 CFR 80.22 - Allowable costs.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... CFR part 31. Contract Cost Principles and Procedures, or uniform cost accounting standards that comply... 34 Education 1 2010-07-01 2010-07-01 false Allowable costs. 80.22 Section 80.22 Education Office... Allowable costs. (a) Limitation on use of funds. Grant funds may be used only for: (1) The allowable...

  5. 34 CFR 80.22 - Allowable costs.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... CFR part 31. Contract Cost Principles and Procedures, or uniform cost accounting standards that comply... 34 Education 1 2011-07-01 2011-07-01 false Allowable costs. 80.22 Section 80.22 Education Office... Allowable costs. (a) Limitation on use of funds. Grant funds may be used only for: (1) The allowable...

  6. 42 CFR 417.802 - Allowable costs.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 42 Public Health 3 2011-10-01 2011-10-01 false Allowable costs. 417.802 Section 417.802 Public... PLANS Health Care Prepayment Plans § 417.802 Allowable costs. (a) General rule. The costs that are considered allowable for HCPP reimbursement are the same as those for reasonable cost HMOs and CMPs...

  7. 34 CFR 304.21 - Allowable costs.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Grantee § 304.21 Allowable costs. In addition to the allowable costs established in the Education Department General Administrative Regulations in 34 CFR 75.530 through 75.562, the following items are... 34 Education 2 2010-07-01 2010-07-01 false Allowable costs. 304.21 Section 304.21...

  8. 42 CFR 417.534 - Allowable costs.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 42 Public Health 3 2010-10-01 2010-10-01 false Allowable costs. 417.534 Section 417.534 Public... PLANS Medicare Payment: Cost Basis § 417.534 Allowable costs. (a) Definition—Allowable costs means the direct and indirect costs, including normal standby costs incurred by the HMO or CMP, that are proper...

  9. 45 CFR 1157.22 - Allowable costs.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... named in OBM Circular A-122 as not subject to that circular 48 CFR part 31. Contract Cost Principles and... 45 Public Welfare 3 2010-10-01 2010-10-01 false Allowable costs. 1157.22 Section 1157.22 Public... Allowable costs. (a) Limitation on use of funds. Grant funds may be used only for: (1) The allowable...

  10. 24 CFR 17.43 - Allowable claims.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... Allowable claims. (a) A claim may be allowed only if: (1) The damage or loss was not caused wholly or partly...) of this section, and the other provisions of this subpart, any claim for damage to, or loss of... types of claims may be allowed, unless excluded by §§ 17.44 and 17.45: (1) Property loss or damage...

  11. 44 CFR 206.228 - Allowable costs.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 44 Emergency Management and Assistance 1 2010-10-01 2010-10-01 false Allowable costs. 206.228... Allowable costs. General policies for determining allowable costs are established in 44 CFR 13.22... costs for major disasters and emergencies will be paid in accordance with 44 CFR part 207. (b)...

  12. 44 CFR 206.439 - Allowable costs.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 44 Emergency Management and Assistance 1 2010-10-01 2010-10-01 false Allowable costs. 206.439... Allowable costs. (a) General requirements for determining allowable costs are established in 44 CFR 13.22... section. (b) Administrative and management costs for major disasters will be paid in accordance with...

  13. 46 CFR 154.447 - Allowable stress.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 5 2010-10-01 2010-10-01 false Allowable stress. 154.447 Section 154.447 Shipping COAST... Tank Type B § 154.447 Allowable stress. (a) An independent tank type B designed from bodies of revolution must have allowable stresses 3 determined by the following formulae: 3 See Appendix B for...

  14. 46 CFR 154.447 - Allowable stress.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 46 Shipping 5 2013-10-01 2013-10-01 false Allowable stress. 154.447 Section 154.447 Shipping COAST... Tank Type B § 154.447 Allowable stress. (a) An independent tank type B designed from bodies of revolution must have allowable stresses 3 determined by the following formulae: 3 See Appendix B for...

  15. 46 CFR 154.447 - Allowable stress.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 46 Shipping 5 2011-10-01 2011-10-01 false Allowable stress. 154.447 Section 154.447 Shipping COAST... Tank Type B § 154.447 Allowable stress. (a) An independent tank type B designed from bodies of revolution must have allowable stresses 3 determined by the following formulae: 3 See Appendix B for...

  16. 46 CFR 154.428 - Allowable stress.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 46 Shipping 5 2011-10-01 2011-10-01 false Allowable stress. 154.428 Section 154.428 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) CERTAIN BULK DANGEROUS CARGOES SAFETY STANDARDS FOR... § 154.428 Allowable stress. The membrane tank and the supporting insulation must have allowable...

  17. 46 CFR 154.428 - Allowable stress.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 46 Shipping 5 2012-10-01 2012-10-01 false Allowable stress. 154.428 Section 154.428 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) CERTAIN BULK DANGEROUS CARGOES SAFETY STANDARDS FOR... § 154.428 Allowable stress. The membrane tank and the supporting insulation must have allowable...

  18. 46 CFR 154.428 - Allowable stress.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 46 Shipping 5 2013-10-01 2013-10-01 false Allowable stress. 154.428 Section 154.428 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) CERTAIN BULK DANGEROUS CARGOES SAFETY STANDARDS FOR... § 154.428 Allowable stress. The membrane tank and the supporting insulation must have allowable...

  19. 46 CFR 154.428 - Allowable stress.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 46 Shipping 5 2010-10-01 2010-10-01 false Allowable stress. 154.428 Section 154.428 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) CERTAIN BULK DANGEROUS CARGOES SAFETY STANDARDS FOR... § 154.428 Allowable stress. The membrane tank and the supporting insulation must have allowable...

  20. 46 CFR 154.428 - Allowable stress.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 46 Shipping 5 2014-10-01 2014-10-01 false Allowable stress. 154.428 Section 154.428 Shipping COAST GUARD, DEPARTMENT OF HOMELAND SECURITY (CONTINUED) CERTAIN BULK DANGEROUS CARGOES SAFETY STANDARDS FOR... § 154.428 Allowable stress. The membrane tank and the supporting insulation must have allowable...

  1. 46 CFR 154.447 - Allowable stress.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 46 Shipping 5 2012-10-01 2012-10-01 false Allowable stress. 154.447 Section 154.447 Shipping COAST... Tank Type B § 154.447 Allowable stress. (a) An independent tank type B designed from bodies of revolution must have allowable stresses 3 determined by the following formulae: 3 See Appendix B for...

  2. 46 CFR 154.447 - Allowable stress.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... 46 Shipping 5 2014-10-01 2014-10-01 false Allowable stress. 154.447 Section 154.447 Shipping COAST... Tank Type B § 154.447 Allowable stress. (a) An independent tank type B designed from bodies of revolution must have allowable stresses 3 determined by the following formulae: 3 See Appendix B for...

  3. 34 CFR 304.21 - Allowable costs.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 34 Education 2 2012-07-01 2012-07-01 false Allowable costs. 304.21 Section 304.21 Education... Grantee § 304.21 Allowable costs. In addition to the allowable costs established in the Education Department General Administrative Regulations in 34 CFR 75.530 through 75.562, the following items...

  4. 34 CFR 304.21 - Allowable costs.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 34 Education 2 2014-07-01 2013-07-01 true Allowable costs. 304.21 Section 304.21 Education... Grantee § 304.21 Allowable costs. In addition to the allowable costs established in the Education Department General Administrative Regulations in 34 CFR 75.530 through 75.562, the following items...

  5. 34 CFR 304.21 - Allowable costs.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 34 Education 2 2013-07-01 2013-07-01 false Allowable costs. 304.21 Section 304.21 Education... Grantee § 304.21 Allowable costs. In addition to the allowable costs established in the Education Department General Administrative Regulations in 34 CFR 75.530 through 75.562, the following items...

  6. Quantification of melanoma mRNA markers in sentinel nodes: pre-clinical evaluation of a single-step real-time reverse transcriptase-polymerase chain reaction assay.

    PubMed

    Abrahamsen, Helene N; Nexo, Ebba; Steiniche, Torben; Hamilton-Dutoit, Stephen J; Sorensen, Boe S

    2004-08-01

    Although reverse transcriptase-polymerase chain reaction (RT-PCR) analysis of melanocyte-associated mRNA can detect sentinel node melanoma metastases, most published assays are semi-quantitative methods of unknown sensitivity and precision, unsuitable for clinical use. We describe a single-step real-time quantitative RT-PCR assay for MART-1 and tyrosinase mRNAs, suitable for sentinel node analysis in a clinical setting. Using serial dilutions of melanoma cell line SK-MEL-28 RNA in water as a calibrator, we obtained linear calibration curves covering the range 0.5 to 10,000 arbitrary units (SK-MEL-28 melanoma cell equivalents). The sensitivity limit was 0.32 (MART-1) and 5 (tyrosinase) arbitrary units. Analytical imprecision was between 11% and 34%. MART-1 PCR efficiency was unaffected when samples were diluted with negative lymph node RNA rather than water, whereas tyrosinase PCR efficiency was halved. To evaluate the clinical suitability of our assay, we quantified melanocyte mRNAs in sentinel nodes with histologically verified micrometastases (n = 10) and benign nevus inclusions (n = 10), and in sentinel nodes without evidence of intranodal melanocytes (n = 10). We found significant differences in median melanocyte-derived mRNA levels comparing the three types of lymph nodes, suggesting that this quantitative molecular protocol may increase assay precision and be useful for the clinical evaluation of sentinel nodes.

  7. The next step in Earth radiation budget measurements

    NASA Astrophysics Data System (ADS)

    Wiscombe, Warren; Chiu, Christine

    2013-05-01

    Space-based Earth Radiation Budget (ERB) measurements are ready to take their next major evolutionary step beyond the ERBE three-satellite constellation of the 1980s. This step would complete the ERBE vision by using not just three but dozens of satellites, and it would complete the GERB vision by providing global diurnal cycle. Such a large constellation would measure true diurnal cycle, without long chains of assumptions and extrapolations, allowing ERB to take its place alongside the other synoptic variables that are assimilated in weather and climate models, and bringing ERB back to a forefront research area. This constellation approach would make it possible to study ERB for rapidly evolving large-scale phenomena. It would also allow, for the first time, the measurement of the true Earth Radiation Imbalance, a crucial quantity, much in the news of late, for testing climate models and for predicting the future course of global warming. Among many side benefits, the greatest would be that all interested nations could participate. Such nations would merely need to meet the instrument functional requirements and find rides to space, and the system could thus grow with time, allowing continuously improved sampling, rapid deployment of new technologies with minimal damage to data continuity, and economies of scale. This is really the perfect ERB system for a budget-constrained decade.

  8. Teaching BASIC. A Step by Step Guide.

    ERIC Educational Resources Information Center

    Allen, M. F.

    This three-chapter guide provides simple explanations about BASIC programming for a teacher to use in a classroom situation, and suggests procedures for a "hands-on" course. Numerous examples are presented of the questions, problems, and level of understanding to expect from first-time, adult users (ages 13 and up). The course materials are…

  9. Time-resolved Fourier transform infrared spectroscopy of the nucleotide-binding domain from the ATP-binding Cassette transporter MsbA: ATP hydrolysis is the rate-limiting step in the catalytic cycle.

    PubMed

    Syberg, Falk; Suveyzdis, Yan; Kötting, Carsten; Gerwert, Klaus; Hofmann, Eckhard

    2012-07-01

    MsbA is an essential Escherichia coli ATP-binding cassette (ABC) transporter involved in the flipping of lipid A across the cytoplasmic membrane. It is a close homologue of human P-glycoprotein involved in multidrug resistance, and it similarly accepts a variety of small hydrophobic xenobiotics as transport substrates. X-ray structures of three full-length ABC multidrug exporters (including MsbA) have been published recently and reveal large conformational changes during the transport cycle. However, how ATP hydrolysis couples to these conformational changes and finally the transport is still an open question. We employed time-resolved FTIR spectroscopy, a powerful method to elucidate molecular reaction mechanisms of soluble and membrane proteins, to address this question with high spatiotemporal resolution. Here, we monitored the hydrolysis reaction in the nucleotide-binding domain of MsbA at the atomic level. The isolated MsbA nucleotide-binding domain hydrolyzed ATP with V(max) = 45 nmol mg(-1) min(-1), similar to the full-length transporter. A Hill coefficient of 1.49 demonstrates positive cooperativity between the two catalytic sites formed upon dimerization. Global fit analysis of time-resolved FTIR data revealed two apparent rate constants of ~1 and 0.01 s(-1), which were assigned to formation of the catalytic site and hydrolysis, respectively. Using isotopically labeled ATP, we identified specific marker bands for protein-bound ATP (1245 cm(-1)), ADP (1101 and 1205 cm(-1)), and free phosphate (1078 cm(-1)). Cleavage of the β-phosphate-γ-phosphate bond was found to be the rate-limiting step; no protein-bound phosphate intermediate was resolved.

  10. Stepped inlet optical panel

    DOEpatents

    Veligdan, James T.

    2001-01-01

    An optical panel includes stacked optical waveguides having stepped inlet facets collectively defining an inlet face for receiving image light, and having beveled outlet faces collectively defining a display screen for displaying the image light channeled through the waveguides by internal reflection.

  11. A time-accurate multiple-grid algorithm

    NASA Technical Reports Server (NTRS)

    Jespersen, D. C.

    1985-01-01

    A time-accurate multiple-grid algorithm is described. The algorithm allows one to take much larger time steps with an explicit time-marching scheme than would otherwise be the case. Sample calculations of a scalar advection equation and the Euler equations for an oscillating airfoil are shown. For the oscillating airfoil, time steps an order of magnitude larger than the single-grid algorithm are possible.

  12. 5 CFR 591.306 - Employee eligibility for an allowance.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... REGULATIONS ALLOWANCES AND DIFFERENTIALS Allowance Based on Duty at Remote Worksites § 591.306 Employee... duty station at or within a remote post of duty approved under § 591.304, regardless of type of appointment or work schedule, only (1) when the employee travels the prescribed minimum distance and time,...

  13. 40 CFR 14.11 - Principal types of allowable claims.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... employee to possess under the circumstances at the time of the loss or damage. In evaluating whether a... allowable. Claims which are ordinarily allowed include loss or damage which occurred: (1) In a place... property was a vehicle which was subjected to an extraordinary risk in the employee's performance of...

  14. One step geometrical calibration method for optical coherence tomography

    NASA Astrophysics Data System (ADS)

    Díaz Díaz, Jesús; Stritzel, Jenny; Rahlves, Maik; Majdani, Omid; Reithmeier, Eduard; Ortmaier, Tobias; Roth, Bernhard

    2016-01-01

    We present a novel one-step calibration methodology for geometrical distortion correction for optical coherence tomography (OCT). A calibration standard especially designed for OCT is introduced, which consists of an array of inverse pyramidal structures. The use of multiple landmarks situated on four different height levels on the pyramids allow performing a 3D geometrical calibration. The calibration procedure itself is based on a parametric model of the OCT beam propagation. It is validated by experimental results and enables the reduction of systematic errors by more than one order of magnitude. In future, our results can improve OCT image reconstruction and interpretation for medical applications such as real time monitoring of surgery.

  15. Rapid Construction of Recombinant Plasmids by QuickStep-Cloning.

    PubMed

    Jajesniak, Pawel; Wong, Tuck Seng

    2017-01-01

    QuickStep-Cloning is a novel molecular cloning technique that builds upon the concepts of asymmetric PCR and megaprimer-based amplification of whole plasmid. It was designed specifically to address the major drawbacks of previously reported cloning methods. The fully optimized protocol allows for a seamless integration of a long DNA fragment into any position within a plasmid of choice, in a time-efficient and cost-effective manner, without the need of a tedious DNA gel purification, a restriction digestion, and an enzymatic ligation. QuickStep-Cloning can be completed in less than 6 h, significantly faster than most of the existing cloning methods, while retaining high efficiency. PMID:27671943

  16. Stepped heating procedure for experimental SAR evaluation of ferrofluids.

    PubMed

    Iacob, N; Schinteie, G; Palade, P; Ticos, C M; Kuncser, V

    2015-06-01

    The aim of this paper is to present a reliable procedure for the experimental determination of the specific absorption rate (SAR) in case of superparamagnetic Fe oxide nanoparticles dispersed in liquid environments. It is based on the acquisition of consecutive steps of time-temperature dependences along of both heating and cooling processes. Linear fitting of these recorded steps provides the heating and cooling speeds at different temperatures, which finally allow the determination of the heating profile in adiabatic-like conditions over a broad temperature range. The presented methodology represents on one hand, a useful alternative tool for the experimental evaluation of the heating capability of nanoparticulate systems for magnetic hyperthermia applications and on the other hand, gives support for a more accurate modeling of bio-heat transfer phenomena. PMID:26087918

  17. 9 CFR 51.32 - Claims not allowed.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... Indemnity for Sheep, Goats, and Horses § 51.32 Claims not allowed. Claims for indemnity for goats, sheep..., authorized, or certified at the time of the test; (c) Testing of goats, sheep, and horses in the herd...

  18. 9 CFR 51.32 - Claims not allowed.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... Indemnity for Sheep, Goats, and Horses § 51.32 Claims not allowed. Claims for indemnity for goats, sheep..., authorized, or certified at the time of the test; (c) Testing of goats, sheep, and horses in the herd...

  19. 9. DREDGE ARRANGEMENT ALLOWS FOR TWO DREDGE BASKETS TO BE ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    9. DREDGE ARRANGEMENT ALLOWS FOR TWO DREDGE BASKETS TO BE OUT AT ALTERNATING TIMES. WHILE STARBOARD IS HAULED IN, PORT IS RELEASED OUT TO DREDGE. - KATHRYN-Two-sail Bateau "Skipjack", Dogwood Harbor, Chesapeake Bay, Tilghman, Talbot County, MD

  20. Serial FBG sensor network allowing overlapping spectra

    NASA Astrophysics Data System (ADS)

    Abbenseth, S.; Lochmann, S.; Ahrens, A.; Rehm, B.

    2016-05-01

    For structure or material monitoring low impact serial fiber Bragg grating (FBG) networks have attracted increasing research interest. Common sensor networks using wavelength division multiplexing (WDM) for FBG interrogation are limited in their efficiency by the spectral width of their light source, the FBG tuning range and the spectral guard bands. Overlapping spectra are strictly forbidden in this case. Applying time division multiplexing (TDM) or active resonator schemes may overcome these restrictions. However, they introduce other substantial disadvantages like signal roundtrip dependency or sophisticated control of active resonating structures. Code division multiplexing (CDM) as a means of FBG interrogation by simple autocorrelation of appropriate codes has been shown to be superior in this respect. However, it came at the cost of a second spectrometer introducing additional equalization efforts. We demonstrate a new serial FBG sensor network utilizing CDM signal processing for efficient sensor interrogation without the need of a second spectrometer and additional state of polarization (SOP) controlling components. It allows overlapping spectra even when all sensing FBGs are positioned at the same centre wavelength and it shows a high degree of insensitivity to SOP. Sequence inversed keyed (SIK) serial signal processing utilizing quasi-orthogonal balanced codes ensures simple and quick sensor interrogation with high signal-to-interference/noise ratio.