Limitations of bootstrap current models

DOE PAGES

Belli, Emily A.; Candy, Jefferey M.; Meneghini, Orso; ...

2014-03-27

We assess the accuracy and limitations of two analytic models of the tokamak bootstrap current: (1) the well-known Sauter model and (2) a recent modification of the Sauter model by Koh et al. For this study, we use simulations from the first-principles kinetic code NEO as the baseline to which the models are compared. Tests are performed using both theoretical parameter scans as well as core- to-edge scans of real DIII-D and NSTX plasma profiles. The effects of extreme aspect ratio, large impurity fraction, energetic particles, and high collisionality are studied. In particular, the error in neglecting cross-species collisional couplingmore » – an approximation inherent to both analytic models – is quantified. Moreover, the implications of the corrections from kinetic NEO simulations on MHD equilibrium reconstructions is studied via integrated modeling with kinetic EFIT.« less

Coupling of PIES 3-D Equilibrium Code and NIFS Bootstrap Code with Applications to the Computation of Stellarator Equilibria

NASA Astrophysics Data System (ADS)

Monticello, D. A.; Reiman, A. H.; Watanabe, K. Y.; Nakajima, N.; Okamoto, M.

1997-11-01

The existence of bootstrap currents in both tokamaks and stellarators was confirmed, experimentally, more than ten years ago. Such currents can have significant effects on the equilibrium and stability of these MHD devices. In addition, stellarators, with the notable exception of W7-X, are predicted to have such large bootstrap currents that reliable equilibrium calculations require the self-consistent evaluation of bootstrap currents. Modeling of discharges which contain islands requires an algorithm that does not assume good surfaces. Only one of the two 3-D equilibrium codes that exist, PIES( Reiman, A. H., Greenside, H. S., Compt. Phys. Commun. 43), (1986)., can easily be modified to handle bootstrap current. Here we report on the coupling of the PIES 3-D equilibrium code and NIFS bootstrap code(Watanabe, K., et al., Nuclear Fusion 35) (1995), 335.

External heating and current drive source requirements towards steady-state operation in ITER

NASA Astrophysics Data System (ADS)

Poli, F. M.; Kessel, C. E.; Bonoli, P. T.; Batchelor, D. B.; Harvey, R. W.; Snyder, P. B.

2014-07-01

Steady state scenarios envisaged for ITER aim at optimizing the bootstrap current, while maintaining sufficient confinement and stability to provide the necessary fusion yield. Non-inductive scenarios will need to operate with internal transport barriers (ITBs) in order to reach adequate fusion gain at typical currents of 9 MA. However, the large pressure gradients associated with ITBs in regions of weak or negative magnetic shear can be conducive to ideal MHD instabilities, reducing the no-wall limit. The E × B flow shear from toroidal plasma rotation is expected to be low in ITER, with a major role in the ITB dynamics being played by magnetic geometry. Combinations of heating and current drive (H/CD) sources that sustain reversed magnetic shear profiles throughout the discharge are the focus of this work. Time-dependent transport simulations indicate that a combination of electron cyclotron (EC) and lower hybrid (LH) waves is a promising route towards steady state operation in ITER. The LH forms and sustains expanded barriers and the EC deposition at mid-radius freezes the bootstrap current profile stabilizing the barrier and leading to confinement levels 50% higher than typical H-mode energy confinement times. Using LH spectra with spectrum centred on parallel refractive index of 1.75-1.85, the performance of these plasma scenarios is close to the ITER target of 9 MA non-inductive current, global confinement gain H98 = 1.6 and fusion gain Q = 5.

Transport barriers in bootstrap-driven tokamaks

NASA Astrophysics Data System (ADS)

Staebler, G. M.; Garofalo, A. M.; Pan, C.; McClenaghan, J.; Van Zeeland, M. A.; Lao, L. L.

2018-05-01

Experiments have demonstrated improved energy confinement due to the spontaneous formation of an internal transport barrier in high bootstrap fraction discharges. Gyrokinetic analysis, and quasilinear predictive modeling, demonstrates that the observed transport barrier is caused by the suppression of turbulence primarily from the large Shafranov shift. It is shown that the Shafranov shift can produce a bifurcation to improved confinement in regions of positive magnetic shear or a continuous reduction in transport for weak or negative magnetic shear. Operation at high safety factor lowers the pressure gradient threshold for the Shafranov shift-driven barrier formation. Two self-organized states of the internal and edge transport barrier are observed. It is shown that these two states are controlled by the interaction of the bootstrap current with magnetic shear, and the kinetic ballooning mode instability boundary. Election scale energy transport is predicted to be dominant in the inner 60% of the profile. Evidence is presented that energetic particle-driven instabilities could be playing a role in the thermal energy transport in this region.

Three-dimensional magnetohydrodynamic equilibrium of quiescent H-modes in tokamak systems

NASA Astrophysics Data System (ADS)

Cooper, W. A.; Graves, J. P.; Duval, B. P.; Sauter, O.; Faustin, J. M.; Kleiner, A.; Lanthaler, S.; Patten, H.; Raghunathan, M.; Tran, T.-M.; Chapman, I. T.; Ham, C. J.

2016-06-01

Three dimensional free boundary magnetohydrodynamic equilibria that recover saturated ideal kink/peeling structures are obtained numerically. Simulations that model the JET tokamak at fixed < β > =1.7% with a large edge bootstrap current that flattens the q-profile near the plasma boundary demonstrate that a radial parallel current density ribbon with a dominant m /n  =  5/1 Fourier component at {{I}\\text{t}}=2.2 MA develops into a broadband spectrum when the toroidal current I t is increased to 2.5 MA.

Bootstrap and fast wave current drive for tokamak reactors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ehst, D.A.

1991-09-01

Using the multi-species neoclassical treatment of Hirshman and Sigmar we study steady state bootstrap equilibria with seed currents provided by low frequency (ICRF) fast waves and with additional surface current density driven by lower hybrid waves. This study applies to reactor plasmas of arbitrary aspect ratio. IN one limit the bootstrap component can supply nearly the total equilibrium current with minimal driving power (< 20 MW). However, for larger total currents considerable driving power is required (for ITER: I{sub o} = 18 MA needs P{sub FW} = 15 MW, P{sub LH} = 75 MW). A computational survey of bootstrap fractionmore » and current drive efficiency is presented. 11 refs., 8 figs.« less

From current-driven to neoclassically driven tearing modes.

PubMed

Reimerdes, H; Sauter, O; Goodman, T; Pochelon, A

2002-03-11

In the TCV tokamak, the m/n = 2/1 island is observed in low-density discharges with central electron-cyclotron current drive. The evolution of its width has two distinct growth phases, one of which can be linked to a "conventional" tearing mode driven unstable by the current profile and the other to a neoclassical tearing mode driven by a perturbation of the bootstrap current. The TCV results provide the first clear observation of such a destabilization mechanism and reconcile the theory of conventional and neoclassical tearing modes, which differ only in the dominant driving term.

High performance advanced tokamak regimes in DIII-D for next-step experiments

NASA Astrophysics Data System (ADS)

Greenfield, C. M.; Murakami, M.; Ferron, J. R.; Wade, M. R.; Luce, T. C.; Petty, C. C.; Menard, J. E.; Petrie, T. W.; Allen, S. L.; Burrell, K. H.; Casper, T. A.; DeBoo, J. C.; Doyle, E. J.; Garofalo, A. M.; Gorelov, I. A.; Groebner, R. J.; Hobirk, J.; Hyatt, A. W.; Jayakumar, R. J.; Kessel, C. E.; La Haye, R. J.; Jackson, G. L.; Lohr, J.; Makowski, M. A.; Pinsker, R. I.; Politzer, P. A.; Prater, R.; Strait, E. J.; Taylor, T. S.; West, W. P.; DIII-D Team

2004-05-01

Advanced Tokamak (AT) research in DIII-D [K. H. Burrell for the DIII-D Team, in Proceedings of the 19th Fusion Energy Conference, Lyon, France, 2002 (International Atomic Energy Agency, Vienna, 2002) published on CD-ROM] seeks to provide a scientific basis for steady-state high performance operation in future devices. These regimes require high toroidal beta to maximize fusion output and poloidal beta to maximize the self-driven bootstrap current. Achieving these conditions requires integrated, simultaneous control of the current and pressure profiles, and active magnetohydrodynamic stability control. The building blocks for AT operation are in hand. Resistive wall mode stabilization via plasma rotation and active feedback with nonaxisymmetric coils allows routine operation above the no-wall beta limit. Neoclassical tearing modes are stabilized by active feedback control of localized electron cyclotron current drive (ECCD). Plasma shaping and profile control provide further improvements. Under these conditions, bootstrap supplies most of the current. Steady-state operation requires replacing the remaining Ohmic current, mostly located near the half radius, with noninductive external sources. In DIII-D this current is provided by ECCD, and nearly stationary AT discharges have been sustained with little remaining Ohmic current. Fast wave current drive is being developed to control the central magnetic shear. Density control, with divertor cryopumps, of AT discharges with edge localized moding H-mode edges facilitates high current drive efficiency at reactor relevant collisionalities. A sophisticated plasma control system allows integrated control of these elements. Close coupling between modeling and experiment is key to understanding the separate elements, their complex nonlinear interactions, and their integration into self-consistent high performance scenarios. Progress on this development, and its implications for next-step devices, will be illustrated by results of recent experiment and simulation efforts.

Control of bootstrap current in the pedestal region of tokamaks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shaing, K. C.; Department of Engineering Physics, University of Wisconsin, Madison, Wisconsin 53796; Lai, A. L.

2013-12-15

The high confinement mode (H-mode) plasmas in the pedestal region of tokamaks are characterized by steep gradient of the radial electric field, and sonic poloidal U{sub p,m} flow that consists of poloidal components of the E×B flow and the plasma flow velocity that is parallel to the magnetic field B. Here, E is the electric field. The bootstrap current that is important for the equilibrium, and stability of the pedestal of H-mode plasmas is shown to have an expression different from that in the conventional theory. In the limit where ‖U{sub p,m}‖≫ 1, the bootstrap current is driven by themore » electron temperature gradient and inductive electric field fundamentally different from that in the conventional theory. The bootstrap current in the pedestal region can be controlled through manipulating U{sub p,m} and the gradient of the radial electric. This, in turn, can control plasma stability such as edge-localized modes. Quantitative evaluations of various coefficients are shown to illustrate that the bootstrap current remains finite when ‖U{sub p,m}‖ approaches infinite and to provide indications how to control the bootstrap current. Approximate analytic expressions for viscous coefficients that join results in the banana and plateau-Pfirsch-Schluter regimes are presented to facilitate bootstrap and neoclassical transport simulations in the pedestal region.« less

Electron transport fluxes in potato plateau regime

NASA Astrophysics Data System (ADS)

Shaing, K. C.; Hazeltine, R. D.

1997-12-01

Electron transport fluxes in the potato plateau regime are calculated from the solutions of the drift kinetic equation and fluid equations. It is found that the bootstrap current density remains finite in the region close to the magnetic axis, although it decreases with increasing collision frequency. This finite amount of the bootstrap current in the relatively collisional regime is important in modeling tokamak startup with 100% bootstrap current.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shaing, K.C.; Hazeltine, R.D.

Electron transport fluxes in the potato plateau regime are calculated from the solutions of the drift kinetic equation and fluid equations. It is found that the bootstrap current density remains finite in the region close to the magnetic axis, although it decreases with increasing collision frequency. This finite amount of the bootstrap current in the relatively collisional regime is important in modeling tokamak startup with 100{percent} bootstrap current. {copyright} {ital 1997 American Institute of Physics.}

Current/Pressure Profile Effects on Tearing Mode Stability in DIII-D Hybrid Discharges

NASA Astrophysics Data System (ADS)

Kim, K.; Park, J. M.; Murakami, M.; La Haye, R. J.; Na, Yong-Su

2015-11-01

It is important to understand the onset threshold and the evolution of tearing modes (TMs) for developing a high-performance steady state fusion reactor. As initial and basic comparisons to determine TM onset, the measured plasma profiles (such as temperature, density, rotation) were compared with the calculated current profiles between a pair of discharges with/without n=1 mode based on the database for DIII-D hybrid plasmas. The profiles were not much different, but the details were analyzed to determine their characteristics, especially near the rational surface. The tearing stability index calculated from PEST3, Δ' tends to increase rapidly just before the n=1 mode onset for these cases. The modeled equilibrium with varying pressure or current profiles parametrically based on the reference discharge is reconstructed for checking the onset dependency on Δ' or neoclassical effects such as bootstrap current. Simulations of TMs with the modeled equilibrium using resistive MHD codes will also be presented and compared with experiments to determine the sensibility for predicting TM onset. Work supported by US DOE under DE-FC02-04ER54698 and DE-AC52-07NA27344.

Investigation of the plasma shaping effects on the H-mode pedestal structure using coupled kinetic neoclassical/MHD stability simulations

NASA Astrophysics Data System (ADS)

Pankin, A. Y.; Rafiq, T.; Kritz, A. H.; Park, G. Y.; Snyder, P. B.; Chang, C. S.

2017-06-01

The effects of plasma shaping on the H-mode pedestal structure are investigated. High fidelity kinetic simulations of the neoclassical pedestal dynamics are combined with the magnetohydrodynamic (MHD) stability conditions for triggering edge localized mode (ELM) instabilities that limit the pedestal width and height in H-mode plasmas. The neoclassical kinetic XGC0 code [Chang et al., Phys. Plasmas 11, 2649 (2004)] is used in carrying out a scan over plasma elongation and triangularity. As plasma profiles evolve, the MHD stability limits of these profiles are analyzed with the ideal MHD ELITE code [Snyder et al., Phys. Plasmas 9, 2037 (2002)]. Simulations with the XGC0 code, which includes coupled ion-electron dynamics, yield predictions for both ion and electron pedestal profiles. The differences in the predicted H-mode pedestal width and height for the DIII-D discharges with different elongation and triangularities are discussed. For the discharges with higher elongation, it is found that the gradients of the plasma profiles in the H-mode pedestal reach semi-steady states. In these simulations, the pedestal slowly continues to evolve to higher pedestal pressures and bootstrap currents until the peeling-ballooning stability conditions are satisfied. The discharges with lower elongation do not reach the semi-steady state, and ELM crashes are triggered at earlier times. The plasma elongation is found to have a stronger stabilizing effect than the plasma triangularity. For the discharges with lower elongation and lower triangularity, the ELM frequency is large, and the H-mode pedestal evolves rapidly. It is found that the temperature of neutrals in the scrape-off-layer (SOL) region can affect the dynamics of the H-mode pedestal buildup. However, the final pedestal profiles are nearly independent of the neutral temperature. The elongation and triangularity affect the pedestal widths of plasma density and electron temperature profiles differently. This provides a new mechanism of controlling the pedestal bootstrap current and the pedestal stability.

Investigation of the plasma shaping effects on the H-mode pedestal structure using coupled kinetic neoclassical/MHD stability simulations

DOE PAGES

Pankin, A. Y.; Rafiq, T.; Kritz, A. H.; ...

2017-06-08

The effects of plasma shaping on the H-mode pedestal structure are investigated. High fidelity kinetic simulations of the neoclassical pedestal dynamics are combined with the magnetohydrodynamic (MHD) stability conditions for triggering edge localized mode (ELM) instabilities that limit the pedestal width and height in H-mode plasmas. We use the neoclassical kinetic XGC0 code [Chang et al., Phys. Plasmas 11, 2649 (2004)] to carry out a scan over plasma elongation and triangularity. As plasma profiles evolve, the MHD stability limits of these profiles are analyzed with the ideal MHD ELITE code [Snyder et al., Phys. Plasmas 9, 2037 (2002)]. In simulationsmore » with the XGC0 code, which includes coupled ion-electron dynamics, yield predictions for both ion and electron pedestal profiles. The differences in the predicted H-mode pedestal width and height for the DIII-D discharges with different elongation and triangularities are discussed. For the discharges with higher elongation, it is found that the gradients of the plasma profiles in the H-mode pedestal reach semi-steady states. In these simulations, the pedestal slowly continues to evolve to higher pedestal pressures and bootstrap currents until the peeling-ballooning stability conditions are satisfied. The discharges with lower elongation do not reach the semi-steady state, and ELM crashes are triggered at earlier times. The plasma elongation is found to have a stronger stabilizing effect than the plasma triangularity. For the discharges with lower elongation and lower triangularity, the ELM frequency is large, and the H-mode pedestal evolves rapidly. It is found that the temperature of neutrals in the scrape-off-layer (SOL) region can affect the dynamics of the H-mode pedestal buildup. But the final pedestal profiles are nearly independent of the neutral temperature. The elongation and triangularity affect the pedestal widths of plasma density and electron temperature profiles differently. This provides a new mechanism of controlling the pedestal bootstrap current and the pedestal stability.« less

Investigation of the plasma shaping effects on the H-mode pedestal structure using coupled kinetic neoclassical/MHD stability simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pankin, A. Y.; Rafiq, T.; Kritz, A. H.

The effects of plasma shaping on the H-mode pedestal structure are investigated. High fidelity kinetic simulations of the neoclassical pedestal dynamics are combined with the magnetohydrodynamic (MHD) stability conditions for triggering edge localized mode (ELM) instabilities that limit the pedestal width and height in H-mode plasmas. We use the neoclassical kinetic XGC0 code [Chang et al., Phys. Plasmas 11, 2649 (2004)] to carry out a scan over plasma elongation and triangularity. As plasma profiles evolve, the MHD stability limits of these profiles are analyzed with the ideal MHD ELITE code [Snyder et al., Phys. Plasmas 9, 2037 (2002)]. In simulationsmore » with the XGC0 code, which includes coupled ion-electron dynamics, yield predictions for both ion and electron pedestal profiles. The differences in the predicted H-mode pedestal width and height for the DIII-D discharges with different elongation and triangularities are discussed. For the discharges with higher elongation, it is found that the gradients of the plasma profiles in the H-mode pedestal reach semi-steady states. In these simulations, the pedestal slowly continues to evolve to higher pedestal pressures and bootstrap currents until the peeling-ballooning stability conditions are satisfied. The discharges with lower elongation do not reach the semi-steady state, and ELM crashes are triggered at earlier times. The plasma elongation is found to have a stronger stabilizing effect than the plasma triangularity. For the discharges with lower elongation and lower triangularity, the ELM frequency is large, and the H-mode pedestal evolves rapidly. It is found that the temperature of neutrals in the scrape-off-layer (SOL) region can affect the dynamics of the H-mode pedestal buildup. But the final pedestal profiles are nearly independent of the neutral temperature. The elongation and triangularity affect the pedestal widths of plasma density and electron temperature profiles differently. This provides a new mechanism of controlling the pedestal bootstrap current and the pedestal stability.« less

Transport Barriers in Bootstrap Driven Tokamaks

NASA Astrophysics Data System (ADS)

Staebler, Gary

2017-10-01

Maximizing the bootstrap current in a tokamak, so that it drives a high fraction of the total current, reduces the external power required to drive current by other means. Improved energy confinement, relative to empirical scaling laws, enables a reactor to more fully take advantage of the bootstrap driven tokamak. Experiments have demonstrated improved energy confinement due to the spontaneous formation of an internal transport barrier in high bootstrap fraction discharges. Gyrokinetic analysis, and quasilinear predictive modeling, demonstrates that the observed transport barrier is due to the suppression of turbulence primarily due to the large Shafranov shift. ExB velocity shear does not play a significant role in the transport barrier due to the high safety factor. It will be shown, that the Shafranov shift can produce a bifurcation to improved confinement in regions of positive magnetic shear or a continuous reduction in transport for weak or negative magnetic shear. Operation at high safety factor lowers the pressure gradient threshold for the Shafranov shift driven barrier formation. The ion energy transport is reduced to neoclassical and electron energy and particle transport is reduced, but still turbulent, within the barrier. Deeper into the plasma, very large levels of electron transport are observed. The observed electron temperature profile is shown to be close to the threshold for the electron temperature gradient (ETG) mode. A large ETG driven energy transport is qualitatively consistent with recent multi-scale gyrokinetic simulations showing that reducing the ion scale turbulence can lead to large increase in the electron scale transport. A new saturation model for the quasilinear TGLF transport code, that fits these multi-scale gyrokinetic simulations, can match the data if the impact of zonal flow mixing on the ETG modes is reduced at high safety factor. This work was supported by the U.S. Department of Energy under DE-FG02-95ER54309 and DE-FC02-04ER54698.

Heating and current drive requirements for ideal MHD stability and ITB sustainment in ITER steady state scenarios

NASA Astrophysics Data System (ADS)

Poli, Francesca

2012-10-01

Steady state scenarios envisaged for ITER aim at optimizing the bootstrap current, while maintaining sufficient confinement and stability to provide the necessary fusion yield. Non-inductive scenarios will need to operate with Internal Transport Barriers (ITBs) in order to reach adequate fusion gain at typical currents of 9 MA. However, the large pressure gradients associated with ITBs in regions of weak or negative magnetic shear can be conducive to ideal MHD instabilities in a wide range of βN, reducing the no-wall limit. Scenarios are established as relaxed flattop states with time-dependent transport simulations with TSC [1]. Fully non-inductive configurations with current in the range of 7-10 MA and various heating mixes (NB, EC, IC and LH) have been studied against variations of the pressure profile peaking and of the Greenwald fraction. It is found that stable equilibria have qmin> 2 and moderate ITBs at 2/3 of the minor radius [2]. The ExB flow shear from toroidal plasma rotation is expected to be low in ITER, with a major role in the ITB dynamics being played by magnetic geometry. Combinations of H&CD sources that maintain reverse or weak magnetic shear profiles throughout the discharge and ρ(qmin)>=0.5 are the focus of this work. The ITER EC upper launcher, designed for NTM control, can provide enough current drive off-axis to sustain moderate ITBs at mid-radius and maintain a non-inductive current of 8-9MA and H98>=1.5 with the day one heating mix. LH heating and current drive is effective in modifying the current profile off-axis, facilitating the formation of stronger ITBs in the rampup phase, their sustainment at larger radii and larger bootstrap fraction. The implications for steady state operation and fusion performance are discussed.[4pt] [1] Jardin S.C. et al, J. Comput. Phys. 66 (1986) 481[0pt] [2] Poli F.M. et al, Nucl. Fusion 52 (2012) 063027.

Some Aspects of Advanced Tokamak Modeling in DIII-D

NASA Astrophysics Data System (ADS)

St John, H. E.; Petty, C. C.; Murakami, M.; Kinsey, J. E.

2000-10-01

We extend previous work(M. Murakami, et al., General Atomics Report GA-A23310 (1999).) done on time dependent DIII-D advanced tokamak simulations by introducing theoretical confinement models rather than relying on power balance derived transport coefficients. We explore using NBCD and off axis ECCD together with a self-consistent aligned bootstrap current, driven by the internal transport barrier dynamics generated with the GLF23 confinement model, to shape the hollow current profile and to maintain MHD stable conditions. Our theoretical modeling approach uses measured DIII-D initial conditions to start off the simulations in a smooth consistent manner. This mitigates the troublesome long lived perturbations in the ohmic current profile that is normally caused by inconsistent initial data. To achieve this goal our simulation uses a sequence of time dependent eqdsks generated autonomously by the EFIT MHD equilibrium code in analyzing experimental data to supply the history for the simulation.

Formation and sustainment of internal transport barriers in the International Thermonuclear Experimental Reactor with the baseline heating mixa)

NASA Astrophysics Data System (ADS)

Poli, Francesca M.; Kessel, Charles E.

2013-05-01

Plasmas with internal transport barriers (ITBs) are a potential and attractive route to steady-state operation in ITER. These plasmas exhibit radially localized regions of improved confinement with steep pressure gradients in the plasma core, which drive large bootstrap current and generate hollow current profiles and negative magnetic shear. This work examines the formation and sustainment of ITBs in ITER with electron cyclotron heating and current drive. The time-dependent transport simulations indicate that, with a trade-off of the power delivered to the equatorial and to the upper launcher, the sustainment of steady-state ITBs can be demonstrated in ITER with the baseline heating configuration.

Improvement of Current Drive Efficiency in Projected FNSF Discharges

NASA Astrophysics Data System (ADS)

Prater, R.; Chan, V.; Garofalo, A.

2012-10-01

The Fusion Nuclear Science Facility - Advanced Tokamak (FNSF-AT) is envisioned as a facility that uses the tokamak approach to address the development of the AT path to fusion and fusion's energy objectives. It uses copper coils for a compact device with high βN and moderate power gain. The major radius is 2.7 m and central toroidal field is 5.44 T. Achieving the required confinement and stability at βN˜3.7 requires a current profile with negative central shear and qmin>1. Off-axis Electron Cyclotron Current Drive (ECCD), in addition to high bootstrap current fraction, can help support this current profile. Using the applied EC frequency and launch location as free parameters, a systematic study has been carried out to optimize the ECCD in the range ρ= 0.5-0.7. Using a top launch, making use of a large toroidal component to the launch direction, adjusting the vertical launch angle so that the rays propagate nearly parallel to the resonance, and adjusting the frequency for optimum total current give a high dimensionless efficiency of 0.44 for a broad ECCD profile peaked at ρ=0.7, and the driven current is 17 kA/MW for n20= 2.1 and Te= 10.3 keV locally.

Extrapolation of the DIII-D high poloidal beta scenario to ITER steady-state using transport modeling

NASA Astrophysics Data System (ADS)

McClenaghan, J.; Garofalo, A. M.; Meneghini, O.; Smith, S. P.

2016-10-01

Transport modeling of a proposed ITER steady-state scenario based on DIII-D high βP discharges finds that the core confinement may be improved with either sufficient rotation or a negative central shear q-profile. The high poloidal beta scenario is characterized by a large bootstrap current fraction( 80%) which reduces the demands on the external current drive, and a large radius internal transport barrier which is associated with improved normalized confinement. Typical temperature and density profiles from the non-inductive high poloidal beta scenario on DIII-D are scaled according to 0D modeling predictions of the requirements for achieving Q=5 steady state performance in ITER with ``day one'' H&CD capabilities. Then, TGLF turbulence modeling is carried out under systematic variations of the toroidal rotation and the core q-profile. Either strong negative central magnetic shear or rotation are found to successfully provide the turbulence suppression required to maintain the temperature and density profiles. This work supported by the US Department of Energy under DE-FC02-04ER54698.

Trapped fast particle destabilization of internal kink mode for the locally flattened q-profile with an inflection point

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Xian-Qu; Zhang, Rui-Bin; Meng, Guo

2016-07-15

The destabilization of ideal internal kink modes by trapped fast particles in tokamak plasmas with a “shoulder”-like equilibrium current is investigated. It is found that energetic particle branch of the mode is unstable with the driving of fast-particle precession drifts and corresponds to a precessional fishbone. The mode with a low stability threshold is also more easily excited than the conventional precessional fishbone. This is different from earlier studies for the same equilibrium in which the magnetohydrodynamic (MHD) branch of the mode is stable. Furthermore, the stability and characteristic frequency of the mode are analyzed by solving the dispersion relationmore » and comparing with the conventional fishbone. The results suggest that an equilibrium with a locally flattened q-profile, may be modified by localized current drive (or bootstrap current, etc.), is prone to the onset of the precessional fishbone branch of the mode.« less

Comparison of bootstrap approaches for estimation of uncertainties of DTI parameters.

PubMed

Chung, SungWon; Lu, Ying; Henry, Roland G

2006-11-01

Bootstrap is an empirical non-parametric statistical technique based on data resampling that has been used to quantify uncertainties of diffusion tensor MRI (DTI) parameters, useful in tractography and in assessing DTI methods. The current bootstrap method (repetition bootstrap) used for DTI analysis performs resampling within the data sharing common diffusion gradients, requiring multiple acquisitions for each diffusion gradient. Recently, wild bootstrap was proposed that can be applied without multiple acquisitions. In this paper, two new approaches are introduced called residual bootstrap and repetition bootknife. We show that repetition bootknife corrects for the large bias present in the repetition bootstrap method and, therefore, better estimates the standard errors. Like wild bootstrap, residual bootstrap is applicable to single acquisition scheme, and both are based on regression residuals (called model-based resampling). Residual bootstrap is based on the assumption that non-constant variance of measured diffusion-attenuated signals can be modeled, which is actually the assumption behind the widely used weighted least squares solution of diffusion tensor. The performances of these bootstrap approaches were compared in terms of bias, variance, and overall error of bootstrap-estimated standard error by Monte Carlo simulation. We demonstrate that residual bootstrap has smaller biases and overall errors, which enables estimation of uncertainties with higher accuracy. Understanding the properties of these bootstrap procedures will help us to choose the optimal approach for estimating uncertainties that can benefit hypothesis testing based on DTI parameters, probabilistic fiber tracking, and optimizing DTI methods.

Evaluation of dissolution profile similarity - Comparison between the f2, the multivariate statistical distance and the f2 bootstrapping methods.

PubMed

Paixão, Paulo; Gouveia, Luís F; Silva, Nuno; Morais, José A G

2017-03-01

A simulation study is presented, evaluating the performance of the f 2 , the model-independent multivariate statistical distance and the f 2 bootstrap methods in the ability to conclude similarity between two dissolution profiles. Different dissolution profiles, based on the Noyes-Whitney equation and ranging from theoretical f 2 values between 100 and 40, were simulated. Variability was introduced in the dissolution model parameters in an increasing order, ranging from a situation complying with the European guidelines requirements for the use of the f 2 metric to several situations where the f 2 metric could not be used anymore. Results have shown that the f 2 is an acceptable metric when used according to the regulatory requirements, but loses its applicability when variability increases. The multivariate statistical distance presented contradictory results in several of the simulation scenarios, which makes it an unreliable metric for dissolution profile comparisons. The bootstrap f 2 , although conservative in its conclusions is an alternative suitable method. Overall, as variability increases, all of the discussed methods reveal problems that can only be solved by increasing the number of dosage form units used in the comparison, which is usually not practical or feasible. Additionally, experimental corrective measures may be undertaken in order to reduce the overall variability, particularly when it is shown that it is mainly due to the dissolution assessment instead of being intrinsic to the dosage form. Copyright © 2016. Published by Elsevier B.V.

The effect of anisotropic heat transport on magnetic islands in 3-D configurations

NASA Astrophysics Data System (ADS)

Schlutt, M. G.; Hegna, C. C.

2012-08-01

An analytic theory of nonlinear pressure-induced magnetic island formation using a boundary layer analysis is presented. This theory extends previous work by including the effects of finite parallel heat transport and is applicable to general three dimensional magnetic configurations. In this work, particular attention is paid to the role of finite parallel heat conduction in the context of pressure-induced island physics. It is found that localized currents that require self-consistent deformation of the pressure profile, such as resistive interchange and bootstrap currents, are attenuated by finite parallel heat conduction when the magnetic islands are sufficiently small. However, these anisotropic effects do not change saturated island widths caused by Pfirsch-Schlüter current effects. Implications for finite pressure-induced island healing are discussed.

A neural network based reputation bootstrapping approach for service selection

NASA Astrophysics Data System (ADS)

Wu, Quanwang; Zhu, Qingsheng; Li, Peng

2015-10-01

With the concept of service-oriented computing becoming widely accepted in enterprise application integration, more and more computing resources are encapsulated as services and published online. Reputation mechanism has been studied to establish trust on prior unknown services. One of the limitations of current reputation mechanisms is that they cannot assess the reputation of newly deployed services as no record of their previous behaviours exists. Most of the current bootstrapping approaches merely assign default reputation values to newcomers. However, by this kind of methods, either newcomers or existing services will be favoured. In this paper, we present a novel reputation bootstrapping approach, where correlations between features and performance of existing services are learned through an artificial neural network (ANN) and they are then generalised to establish a tentative reputation when evaluating new and unknown services. Reputations of services published previously by the same provider are also incorporated for reputation bootstrapping if available. The proposed reputation bootstrapping approach is seamlessly embedded into an existing reputation model and implemented in the extended service-oriented architecture. Empirical studies of the proposed approach are shown at last.

Validation of neoclassical bootstrap current models in the edge of an H-mode plasma.

PubMed

Wade, M R; Murakami, M; Politzer, P A

2004-06-11

Analysis of the parallel electric field E(parallel) evolution following an L-H transition in the DIII-D tokamak indicates the generation of a large negative pulse near the edge which propagates inward, indicative of the generation of a noninductive edge current. Modeling indicates that the observed E(parallel) evolution is consistent with a narrow current density peak generated in the plasma edge. Very good quantitative agreement is found between the measured E(parallel) evolution and that expected from neoclassical theory predictions of the bootstrap current.

Optimization of Kink Stability in High-Beta Quasi-axisymmetric Stellarators

NASA Astrophysics Data System (ADS)

Fu, G. Y.; Ku, L.-P.; Manickam, J.; Cooper, W. A.

1998-11-01

A key issue for design of Quasi-axisymmetric stellarators( A. Reiman et al, this conference.) (QAS) is the stability of external kink modes driven by pressure-induced bootstrap current. In this work, the 3D MHD stability code TERPSICHORE(W.A. Cooper, Phys. Plasmas 3), 275(1996). is used to calculate the stability of low-n external kink modes in a high-beta QAS. The kink stability is optimized by adjusting plasma boundary shape (i.e., external coil configuration) as well as plasma pressure and current profiles. For this purpose, the TERPSICHORE code has been implemented successfully in an optimizer which maximizes kink stability as well as quasi-symmetry. A key factor for kink stability is rotational transform profile. It is found that the edge magnetic shear is strongly stabilizing. The amount of the shear needed for complete stabilization increases with edge transform. It is also found that the plasma boundary shape plays an important role in the kink stability besides transform profile. The physics mechanisms for the kink stability are being studied by examining the contributions of individual terms in δ W of the energy principle: the field line bending term, the current-driven term, the pressure-driven term, and the vacuum term. Detailed results will be reported.

High-beta, steady-state hybrid scenario on DIII-D

DOE PAGES

Petty, C. C.; Kinsey, J. E.; Holcomb, C. T.; ...

2015-12-17

Here, the potential of the hybrid scenario (first developed as an advanced inductive scenario for high fluence) as a regime for high-beta, steady-state plasmas is demonstrated on the DIII-D tokamak. These experiments show that the beneficial characteristics of hybrids, namely safety factor ≥1 with low central magnetic shear, high stability limits and excellent confinement, are maintained when strong central current drive (electron cyclotron and neutral beam) is applied to increase the calculated non-inductive fraction to ≈100% (≈50% bootstrap current). The best discharges achieve normalized beta of 3.4, IPB98(y,2) confinement factor of 1.4, surface loop voltage of 0.01 V, and nearlymore » equal electron and ion temperatures at low collisionality. A zero-dimensional physics model shows that steady-state hybrid operation with Q fus ~ 5 is feasible in FDF and ITER. The advantage of the hybrid scenario as an Advanced Tokamak regime is that the external current drive can be deposited near the plasma axis where the efficiency is high; additionally, good alignment between the current drive and plasma current profiles is not necessary as the poloidal magnetic flux pumping self-organizes the current density profile in hybrids with an m/n=3/2 tearing mode.« less

The Relationships Between ELM Suppression, Pedestal Profiles, and Lithium Wall Coatings in NSTX

DOE Office of Scientific and Technical Information (OSTI.GOV)

D.P. Boyle, R. Maingi, P.B. Snyder, J. Manickam, T.H. Osborne, R.E. Bell, B.P. LeBlanc, and the NSTX Team

2012-08-17

Recently in the National Spherical Torus Experiment (NSTX), increasing lithium wall coatings suppressed edge localized modes (ELMs), gradually but not quite monotonically. This work details profile and stability analysis as ELMs disappeared throughout the lithium scan. While the quantity of lithium deposited between discharges did not uniquely determine the presence of ELMs, profile analysis demonstrated that lithium was correlated to wider density and pressure pedestals with peak gradients farther from the separatrix. Moreover, the ELMy and ELM-free discharges were cleanly separated by their density and pedestal widths and peak gradient locations. Ultimately, ELMs were only suppressed when lithium caused themore » density pedestal to widen and shift inward. These changes in the density gradient were directly reflected in the pressure gradient and calculated bootstrap current. This supports the theory that ELMs in NSTX are caused by peeling and/or ballooning modes, as kink/peeling modes are stabilized when the edge current and pressure gradient shift away from the separatrix. Edge stability analysis using ELITE corroborated this picture, as reconstructed equilibria from ELM-free discharges were generally farther from their kink/peeling stability boundaries than ELMy discharges. We conclude that density profile control provided by lithium is the key first step to ELM suppression in NSTX« less

The relationships between edge localized modes suppression, pedestal profiles and lithium wall coatings in NSTX

DOE Office of Scientific and Technical Information (OSTI.GOV)

Boyle, D. P.; Maingi, R.; Snyder, P. B.

2011-01-01

Recently in the National Spherical Torus Experiment (NSTX), increasing lithium wall coatings suppressed edge localized modes (ELMs), gradually but not quite monotonically. This work details profile and stability analysis as ELMs disappeared throughout the lithium scan. While the quantity of lithium deposited between discharges did not uniquely determine the presence of ELMs, profile analysis demonstrated that lithium was correlated with wider density and pressure pedestals with peak gradients farther from the separatrix. Moreover, the ELMy and ELM-free discharges were cleanly separated by their density and pedestal widths and peak gradient locations. Ultimately, ELMs were only suppressed when lithium caused themore » density pedestal to widen and shift inward. These changes in the density gradient were directly reflected in the pressure gradient and calculated bootstrap current. This supports the theory that ELMs in NSTX are caused by peeling and/or ballooning modes, as kink/peeling modes are stabilized when the edge current and pressure gradient shift away from the separatrix. Edge stability analysis using ELITE corroborated this picture, as reconstructed equilibria from ELM-free discharges were generally farther from their kink/peeling stability boundaries than ELMy discharges. We conclude that density profile control provided by lithium is the key first step to ELM suppression in NSTX.« less

Advanced tokamak investigations in full-tungsten ASDEX Upgrade

NASA Astrophysics Data System (ADS)

Bock, A.; Doerk, H.; Fischer, R.; Rittich, D.; Stober, J.; Burckhart, A.; Fable, E.; Geiger, B.; Mlynek, A.; Reich, M.; Zohm, H.; ASDEX Upgrade Team

2018-05-01

The appropriate tailoring of the q-profile is the key to accessing Advanced Tokamak (AT) scenarios, which are of great benefit to future all-metal fusion power plants. Such scenarios depend on low collisionality ν* which permits efficient external current drive and high amounts of intrinsic bootstrap current. At constant pressure, lowering of the electron density ne leads to a strong decrease in the collisionality with increasing electron temperature ν* ˜ Te-3 . Simultaneously, the conditions for low ne also benefit impurity accumulation. This paper reports on how radiative collapses due to central W accumulation were overcome by improved understanding of the changes to recycling and pumping, substantially expanded ECRH capacities for both heating and current drive, and a new solid W divertor capable of withstanding the power loads at low ne. Furthermore, it reports on various improvements to the reliability of the q-profile reconstruction. A candidate steady state scenario for ITER/DEMO (q95 = 5.3, βN = 2.7, fbs > 40%) is presented. The ion temperature profiles are steeper than predicted by TGLF, but nonlinear electromagnetic gyro-kinetic analyses with GENE including fast particle effects matched the experimental heat fluxes. A fully non-inductive scenario at higher q95 = 7.1 for current drive model validation is also discussed. The results show that non-inductive operation is principally compatible with full-metal machines.

Multi-baseline bootstrapping at the Navy precision optical interferometer

NASA Astrophysics Data System (ADS)

Armstrong, J. T.; Schmitt, H. R.; Mozurkewich, D.; Jorgensen, A. M.; Muterspaugh, M. W.; Baines, E. K.; Benson, J. A.; Zavala, Robert T.; Hutter, D. J.

2014-07-01

The Navy Precision Optical Interferometer (NPOI) was designed from the beginning to support baseline boot- strapping with equally-spaced array elements. The motivation was the desire to image the surfaces of resolved stars with the maximum resolution possible with a six-element array. Bootstrapping two baselines together to track fringes on a third baseline has been used at the NPOI for many years, but the capabilities of the fringe tracking software did not permit us to bootstrap three or more baselines together. Recently, both a new backend (VISION; Tennessee State Univ.) and new hardware and firmware (AZ Embedded Systems and New Mexico Tech, respectively) for the current hybrid backend have made multi-baseline bootstrapping possible.

Transport simulation of EAST long-pulse H-mode discharge with integrated modeling

NASA Astrophysics Data System (ADS)

Wu, M. Q.; Li, G. Q.; Chen, J. L.; Du, H. F.; Gao, X.; Ren, Q. L.; Li, K.; Chan, Vincent; Pan, C. K.; Ding, S. Y.; Jian, X.; Zhu, X.; Lian, H.; Qian, J. P.; Gong, X. Z.; Zang, Q.; Duan, Y. M.; Liu, H. Q.; Lyu, B.

2018-04-01

In the 2017 EAST experimental campaign, a steady-state long-pulse H-mode discharge lasting longer than 100 s has been obtained using only radio frequency heating and current drive, and the confinement quality is slightly better than standard H-mode, H98y2 ~ 1.1, with stationary peaked electron temperature profiles. Integrated modeling of one long-pulse H-mode discharge in the 2016 EAST experimental campaign has been performed with equilibrium code EFIT, and transport codes TGYRO and ONETWO under integrated modeling framework OMFIT. The plasma current is fully-noninductively driven with a combination of ~2.2 MW LHW, ~0.3 MW ECH and ~1.1 MW ICRF. Time evolution of the predicted electron and ion temperature profiles through integrated modeling agree closely with that from measurements. The plasma current (I p ~ 0.45 MA) and electron density are kept constantly. A steady-state is achieved using integrated modeling, and the bootstrap current fraction is ~28%, the RF drive current fraction is ~72%. The predicted current density profile matches the experimental one well. Analysis shows that electron cyclotron heating (ECH) makes large contribution to the plasma confinement when heating in the core region while heating in large radius does smaller improvement, also a more peaked LHW driven current profile is got when heating in the core. Linear analysis shows that the high-k modes instability (electron temperature gradient driven modes) is suppressed in the core region where exists weak electron internal transport barriers. The trapped electron modes dominates in the low-k region, which is mainly responsible for driving the electron energy flux. It is found that the ECH heating effect is very local and not the main cause to sustained the good confinement, the peaked current density profile has the most important effect on plasma confinement improvement. Transport analysis of the long-pulse H-mode experiments on EAST will be helpful to build future experiments.

Bootstrap Current for the Edge Pedestal Plasma in a Diverted Tokamak Geometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koh, S.; Chang, C. S.; Ku, S.

The edge bootstrap current plays a critical role in the equilibrium and stability of the steep edge pedestal plasma. The pedestal plasma has an unconventional and difficult neoclassical property, as compared with the core plasma. It has a narrow passing particle region in velocity space that can be easily modified or destroyed by Coulomb collisions. At the same time, the edge pedestal plasma has steep pressure and electrostatic potential gradients whose scale-lengths are comparable with the ion banana width, and includes a magnetic separatrix surface, across which the topological properties of the magnetic field and particle orbits change abruptly. Amore » driftkinetic particle code XGC0, equipped with a mass-momentum-energy conserving collision operator, is used to study the edge bootstrap current in a realistic diverted magnetic field geometry with a self-consistent radial electric field. When the edge electrons are in the weakly collisional banana regime, surprisingly, the present kinetic simulation confirms that the existing analytic expressions [represented by O. Sauter et al. , Phys. Plasmas 6 , 2834 (1999)] are still valid in this unconventional region, except in a thin radial layer in contact with the magnetic separatrix. The agreement arises from the dominance of the electron contribution to the bootstrap current compared with ion contribution and from a reasonable separation of the trapped-passing dynamics without a strong collisional mixing. However, when the pedestal electrons are in plateau-collisional regime, there is significant deviation of numerical results from the existing analytic formulas, mainly due to large effective collisionality of the passing and the boundary layer trapped particles in edge region. In a conventional aspect ratio tokamak, the edge bootstrap current from kinetic simulation can be significantly less than that from the Sauter formula if the electron collisionality is high. On the other hand, when the aspect ratio is close to unity, the collisional edge bootstrap current can be significantly greater than that from the Sauter formula. Rapid toroidal rotation of the magnetic field lines at the high field side of a tight aspect-ratio tokamak is believed to be the cause of the different behavior. A new analytic fitting formula, as a simple modification to the Sauter formula, is obtained to bring the analytic expression to a better agreement with the edge kinetic simulation results« less

Bootstrap current for the edge pedestal plasma in a diverted tokamak geometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koh, S.; Choe, W.; Chang, C. S.

The edge bootstrap current plays a critical role in the equilibrium and stability of the steep edge pedestal plasma. The pedestal plasma has an unconventional and difficult neoclassical property, as compared with the core plasma. It has a narrow passing particle region in velocity space that can be easily modified or destroyed by Coulomb collisions. At the same time, the edge pedestal plasma has steep pressure and electrostatic potential gradients whose scale-lengths are comparable with the ion banana width, and includes a magnetic separatrix surface, across which the topological properties of the magnetic field and particle orbits change abruptly. Amore » drift-kinetic particle code XGC0, equipped with a mass-momentum-energy conserving collision operator, is used to study the edge bootstrap current in a realistic diverted magnetic field geometry with a self-consistent radial electric field. When the edge electrons are in the weakly collisional banana regime, surprisingly, the present kinetic simulation confirms that the existing analytic expressions [represented by O. Sauter et al., Phys. Plasmas 6, 2834 (1999)] are still valid in this unconventional region, except in a thin radial layer in contact with the magnetic separatrix. The agreement arises from the dominance of the electron contribution to the bootstrap current compared with ion contribution and from a reasonable separation of the trapped-passing dynamics without a strong collisional mixing. However, when the pedestal electrons are in plateau-collisional regime, there is significant deviation of numerical results from the existing analytic formulas, mainly due to large effective collisionality of the passing and the boundary layer trapped particles in edge region. In a conventional aspect ratio tokamak, the edge bootstrap current from kinetic simulation can be significantly less than that from the Sauter formula if the electron collisionality is high. On the other hand, when the aspect ratio is close to unity, the collisional edge bootstrap current can be significantly greater than that from the Sauter formula. Rapid toroidal rotation of the magnetic field lines at the high field side of a tight aspect-ratio tokamak is believed to be the cause of the different behavior. A new analytic fitting formula, as a simple modification to the Sauter formula, is obtained to bring the analytic expression to a better agreement with the edge kinetic simulation results.« less

Edge Stability and Performance of the ELM-Free Quiescent H-Mode and the Quiescent Double Barrier Mode on DIII-D

DOE Office of Scientific and Technical Information (OSTI.GOV)

West, W P; Burrell, K H; Casper, T A

2004-12-03

The quiescent H (QH) mode, an edge localized mode (ELM)-free, high-confinement mode, combines well with an internal transport barrier to form quiescent double barrier (QDB) stationary state, high performance plasmas. The QH-mode edge pedestal pressure is similar to that seen in ELMing phases of the same discharge, with similar global energy confinement. The pedestal density in early ELMing phases of strongly pumped counter injection discharges drops and a transition to QH-mode occurs, leading to lower calculated edge bootstrap current. Plasmas current ramp experiment and ELITE code modeling of edge stability suggest that QH-modes lie near an edge current stability boundary.more » At high triangularity, QH-mode discharges operate at higher pedestal density and pressure, and have achieved ITER level values of {beta}{sub PED} and {nu}*. The QDB achieves performance of {alpha}{sub N}H{sub 89} {approx} 7 in quasi-stationary conditions for a duration of 10 tE, limited by hardware. Recently we demonstrated stationary state QDB discharges with little change in kinetic and q profiles (q{sub 0} > 1) for 2 s, comparable to ELMing ''hybrid scenarios'', yet without the debilitating effects of ELMs. Plasma profile control tools, including electron cyclotron heating and current drive and neutral beam heating, have been demonstrated to control simultaneously the q profile development, the density peaking, impurity accumulation and plasma beta.« less

More accurate, calibrated bootstrap confidence intervals for correlating two autocorrelated climate time series

NASA Astrophysics Data System (ADS)

Olafsdottir, Kristin B.; Mudelsee, Manfred

2013-04-01

Estimation of the Pearson's correlation coefficient between two time series to evaluate the influences of one time depended variable on another is one of the most often used statistical method in climate sciences. Various methods are used to estimate confidence interval to support the correlation point estimate. Many of them make strong mathematical assumptions regarding distributional shape and serial correlation, which are rarely met. More robust statistical methods are needed to increase the accuracy of the confidence intervals. Bootstrap confidence intervals are estimated in the Fortran 90 program PearsonT (Mudelsee, 2003), where the main intention was to get an accurate confidence interval for correlation coefficient between two time series by taking the serial dependence of the process that generated the data into account. However, Monte Carlo experiments show that the coverage accuracy for smaller data sizes can be improved. Here we adapt the PearsonT program into a new version called PearsonT3, by calibrating the confidence interval to increase the coverage accuracy. Calibration is a bootstrap resampling technique, which basically performs a second bootstrap loop or resamples from the bootstrap resamples. It offers, like the non-calibrated bootstrap confidence intervals, robustness against the data distribution. Pairwise moving block bootstrap is used to preserve the serial correlation of both time series. The calibration is applied to standard error based bootstrap Student's t confidence intervals. The performances of the calibrated confidence intervals are examined with Monte Carlo simulations, and compared with the performances of confidence intervals without calibration, that is, PearsonT. The coverage accuracy is evidently better for the calibrated confidence intervals where the coverage error is acceptably small (i.e., within a few percentage points) already for data sizes as small as 20. One form of climate time series is output from numerical models which simulate the climate system. The method is applied to model data from the high resolution ocean model, INALT01 where the relationship between the Agulhas Leakage and the North Brazil Current is evaluated. Preliminary results show significant correlation between the two variables when there is 10 year lag between them, which is more or less the time that takes the Agulhas Leakage water to reach the North Brazil Current. Mudelsee, M., 2003. Estimating Pearson's correlation coefficient with bootstrap confidence interval from serially dependent time series. Mathematical Geology 35, 651-665.

Active core profile and transport modification by application of ion Bernstein wave power in the Princeton Beta Experiment-Modification

NASA Astrophysics Data System (ADS)

LeBlanc, B.; Batha, S.; Bell, R.; Bernabei, S.; Blush, L.; de la Luna, E.; Doerner, R.; Dunlap, J.; England, A.; Garcia, I.; Ignat, D.; Isler, R.; Jones, S.; Kaita, R.; Kaye, S.; Kugel, H.; Levinton, F.; Luckhardt, S.; Mutoh, T.; Okabayashi, M.; Ono, M.; Paoletti, F.; Paul, S.; Petravich, G.; Post-Zwicker, A.; Sauthoff, N.; Schmitz, L.; Sesnic, S.; Takahashi, H.; Talvard, M.; Tighe, W.; Tynan, G.; von Goeler, S.; Woskov, P.; Zolfaghari, A.

1995-03-01

Application of Ion Bernstein Wave Heating (IBWH) into the Princeton Beta Experiment-Modification (PBX-M) [Phys. Fluids B 2, 1271 (1990)] tokamak stabilizes sawtooth oscillations and generates peaked density profiles. A transport barrier, spatially correlated with the IBWH power deposition profile, is observed in the core of IBWH-assisted neutral beam injection (NBI) discharges. A precursor to the fully developed barrier is seen in the soft x-ray data during edge localized mode (ELM) activity. Sustained IBWH operation is conducive to a regime where the barrier supports large ∇ne, ∇Te, ∇νφ, and ∇Ti, delimiting the confinement zone. This regime is reminiscent of the H(high) mode, but with a confinement zone moved inward. The core region has better than H-mode confinement while the peripheral region is L(low)-mode-like. The peaked profile enhances NBI core deposition and increases nuclear reactivity. An increase in central Ti results from χi reduction (compared to the H mode) and better beam penetration. Bootstrap current fractions of up to 0.32-0.35 locally and 0.28 overall were obtained when an additional NBI burst is applied to this plasma.

Investigation of the n  =  1 resistive wall modes in the ITER high-mode confinement

NASA Astrophysics Data System (ADS)

Zheng, L. J.; Kotschenreuther, M. T.; Valanju, P.

2017-06-01

The n  =  1 resistive wall mode (RWM) stability of ITER high-mode confinement is investigated with bootstrap current included for equilibrium, together with the rotation and diamagnetic drift effects for stability. Here, n is the toroidal mode number. We use the CORSICA code for computing the free boundary equilibrium and AEGIS code for stability. We find that the inclusion of bootstrap current for equilibrium is critical. It can reduce the local magnetic shear in the pedestal, so that the infernal mode branches can develop. Consequently, the n  =  1 modes become unstable without a stabilizing wall at a considerably lower beta limit, driven by the steep pressure gradient in the pedestal. Typical values of the wall position stabilize the ideal mode, but give rise to the ‘pedestal’ resistive wall modes. We find that the rotation can contribute a stabilizing effect on RWMs and the diamagnetic drift effects can further improve the stability in the co-current rotation case. But, generally speaking, the rotation stabilization effects are not as effective as the case without including the bootstrap current effects on equilibrium. We also find that the diamagnetic drift effects are actually destabilizing when there is a counter-current rotation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shaing, K. C.; Peng, Yueng Kay Martin

Transport theory for potato orbits in the region near the magnetic axis in an axisymmetric torus such as tokamaks and spherical tori is extended to the situation where the toroidal flow speed is of the order of the sonic speed as observed in National Spherical Torus Experiment [E. J. Synakowski, M. G. Bell, R. E. Bell et al., Nucl. Fusion 43, 1653 (2003)]. It is found that transport fluxes such as ion radial heat flux, and bootstrap current density are modified by a factor of the order of the square of the toroidal Mach number. The consequences of the orbitmore » squeezing are also presented. The theory is developed for parabolic (in radius r) plasma profiles. A method to apply the results of the theory for the transport modeling is discussed.« less

A condition for small bootstrap current in three-dimensional toroidal configurations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mikhailov, M. I., E-mail: mikhaylov-mi@nrcki.ru; Nührenberg, J.; Zille, R.

2016-11-15

It is shown that, if the maximum of the magnetic field strength on a magnetic surface in a threedimensional magnetic confinement configuration with stellarator symmetry constitutes a line that is orthogonal to the field lines and crosses the symmetry line, then the bootstrap current density is smaller compared to that in quasi-axisymmetric (qa) [J. Nührenberg et al., in Proc. of Joint Varenna−Lausanne Int. Workshop on Theory of Fusion Plasmas, Varenna, 1994, p. 3] and quasi-helically (qh) symmetric [J. Nührenberg and R. Zille, Phys. Lett. A 129, 113 (1988)] configurations.

Carving out the end of the world or (superconformal bootstrap in six dimensions)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chang, Chi-Ming; Lin, Ying-Hsuan

We bootstrap N=(1,0) superconformal field theories in six dimensions, by analyzing the four-point function of flavor current multiplets. By assuming E 8 flavor group, we present universal bounds on the central charge C T and the flavor central charge C J. Based on the numerical data, we conjecture that the rank-one E-string theory saturates the universal lower bound on C J , and numerically determine the spectrum of long multiplets in the rank-one E-string theory. We comment on the possibility of solving the higher-rank E-string theories by bootstrap and thereby probing M-theory on AdS 7×S 4/Z 2 .

Carving out the end of the world or (superconformal bootstrap in six dimensions)

DOE PAGES

Chang, Chi-Ming; Lin, Ying-Hsuan

2017-08-29

We bootstrap N=(1,0) superconformal field theories in six dimensions, by analyzing the four-point function of flavor current multiplets. By assuming E 8 flavor group, we present universal bounds on the central charge C T and the flavor central charge C J. Based on the numerical data, we conjecture that the rank-one E-string theory saturates the universal lower bound on C J , and numerically determine the spectrum of long multiplets in the rank-one E-string theory. We comment on the possibility of solving the higher-rank E-string theories by bootstrap and thereby probing M-theory on AdS 7×S 4/Z 2 .

Innovation cascades: artefacts, organization and attributions

PubMed Central

2016-01-01

Innovation cascades inextricably link the introduction of new artefacts, transformations in social organization, and the emergence of new functionalities and new needs. This paper describes a positive feedback dynamic, exaptive bootstrapping, through which these cascades proceed, and the characteristics of the relationships in which the new attributions that drive this dynamic are generated. It concludes by arguing that the exaptive bootstrapping dynamic is the principal driver of our current Innovation Society. PMID:26926284

Progress Toward Steady State Tokamak Operation Exploiting the high bootstrap current fraction regime

NASA Astrophysics Data System (ADS)

Ren, Q.

2015-11-01

Recent DIII-D experiments have advanced the normalized fusion performance of the high bootstrap current fraction tokamak regime toward reactor-relevant steady state operation. The experiments, conducted by a joint team of researchers from the DIII-D and EAST tokamaks, developed a fully noninductive scenario that could be extended on EAST to a demonstration of long pulse steady-state tokamak operation. Fully noninductive plasmas with extremely high values of the poloidal beta, βp >= 4 , have been sustained at βT >= 2 % for long durations with excellent energy confinement quality (H98y,2 >= 1 . 5) and internal transport barriers (ITBs) generated at large minor radius (>= 0 . 6) in all channels (Te, Ti, ne, VTf). Large bootstrap fraction (fBS ~ 80 %) has been obtained with high βp. ITBs have been shown to be compatible with steady state operation. Because of the unusually large ITB radius, normalized pressure is not limited to low βN values by internal ITB-driven modes. βN up to ~4.3 has been obtained by optimizing the plasma-wall distance. The scenario is robust against several variations, including replacing some on-axis with off-axis neutral beam injection (NBI), adding electron cyclotron (EC) heating, and reducing the NBI torque by a factor of 2. This latter observation is particularly promising for extension of the scenario to EAST, where maximum power is obtained with balanced NBI injection, and to a reactor, expected to have low rotation. However, modeling of this regime has provided new challenges to state-of-the-art modeling capabilities: quasilinear models can dramatically underpredict the electron transport, and the Sauter bootstrap current can be insufficient. The analysis shows first-principle NEO is in good agreement with experiments for the bootstrap current calculation and ETG modes with a larger saturated amplitude or EM modes may provide the missing electron transport. Work supported in part by the US DOE under DE-FC02-04ER54698, DE-AC52-07NA27344, DE-AC02-09CH11466, and the NMCFP of China under 2015GB110000 and 2015GB102000.

Validation of a coupled core-transport, pedestal-structure, current-profile and equilibrium model

NASA Astrophysics Data System (ADS)

Meneghini, O.

2015-11-01

The first workflow capable of predicting the self-consistent solution to the coupled core-transport, pedestal structure, and equilibrium problems from first-principles and its experimental tests are presented. Validation with DIII-D discharges in high confinement regimes shows that the workflow is capable of robustly predicting the kinetic profiles from on axis to the separatrix and matching the experimental measurements to within their uncertainty, with no prior knowledge of the pedestal height nor of any measurement of the temperature or pressure. Self-consistent coupling has proven to be essential to match the experimental results, and capture the non-linear physics that governs the core and pedestal solutions. In particular, clear stabilization of the pedestal peeling ballooning instabilities by the global Shafranov shift and destabilization by additional edge bootstrap current, and subsequent effect on the core plasma profiles, have been clearly observed and documented. In our model, self-consistency is achieved by iterating between the TGYRO core transport solver (with NEO and TGLF for neoclassical and turbulent flux), and the pedestal structure predicted by the EPED model. A self-consistent equilibrium is calculated by EFIT, while the ONETWO transport package evolves the current profile and calculates the particle and energy sources. The capabilities of such workflow are shown to be critical for the design of future experiments such as ITER and FNSF, which operate in a regime where the equilibrium, the pedestal, and the core transport problems are strongly coupled, and for which none of these quantities can be assumed to be known. Self-consistent core-pedestal predictions for ITER, as well as initial optimizations, will be presented. Supported by the US Department of Energy under DE-FC02-04ER54698, DE-SC0012652.

Overview of physics research on the TCV tokamak

NASA Astrophysics Data System (ADS)

Fasoli, A.; TCV Team

2009-10-01

The Tokamak à Configuration Variable (TCV) tokamak is equipped with high-power (4.5 MW), real-time-controllable EC systems and flexible shaping, and plays an important role in fusion research by broadening the parameter range of reactor relevant regimes, by investigating tokamak physics questions and by developing new control tools. Steady-state discharges are achieved, in which the current is entirely self-generated through the bootstrap mechanism, a fundamental ingredient for ITER steady-state operation. The discharge remains quiescent over several current redistribution times, demonstrating that a self-consistent, 'bootstrap-aligned' equilibrium state is possible. Electron internal transport barrier regimes sustained by EC current drive have also been explored. MHD activity is shown to be crucial in scenarios characterized by large and slow oscillations in plasma confinement, which in turn can be modified by small Ohmic current perturbations altering the barrier strength. In studies of the relation between anomalous transport and plasma shape, the observed dependences of the electron thermal diffusivity on triangularity (direct) and collisionality (inverse) are qualitatively reproduced by non-linear gyro-kinetic simulations and shown to be governed by TEM turbulence. Parallel SOL flows are studied for their importance for material migration. Flow profiles are measured using a reciprocating Mach probe by changing from lower to upper single-null diverted equilibria and shifting the plasmas vertically. The dominant, field-direction-dependent Pfirsch-Schlüter component is found to be in good agreement with theoretical predictions. A field-direction-independent component is identified and is consistent with flows generated by transient over-pressure due to ballooning-like interchange turbulence. Initial high-resolution infrared images confirm that ELMs have a filamentary structure, while fast, localized radiation measurements reveal that ELM activity first appears in the X-point region. Real time control techniques are currently being applied to EC multiple independent power supplies and beam launchers, e.g. to control the plasma current in fully non-inductive conditions, and the plasma elongation through current broadening by far-off-axis heating at constant shaping field.

Refining search terms for nanotechnology

NASA Astrophysics Data System (ADS)

Porter, Alan L.; Youtie, Jan; Shapira, Philip; Schoeneck, David J.

2008-05-01

The ability to delineate the boundaries of an emerging technology is central to obtaining an understanding of the technology's research paths and commercialization prospects. Nowhere is this more relevant than in the case of nanotechnology (hereafter identified as "nano") given its current rapid growth and multidisciplinary nature. (Under the rubric of nanotechnology, we also include nanoscience and nanoengineering.) Past efforts have utilized several strategies, including simple term search for the prefix nano, complex lexical and citation-based approaches, and bootstrapping techniques. This research introduces a modularized Boolean approach to defining nanotechnology which has been applied to several research and patenting databases. We explain our approach to downloading and cleaning data, and report initial results. Comparisons of this approach with other nanotechnology search formulations are presented. Implications for search strategy development and profiling of the nanotechnology field are discussed.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Medvedev, S. Yu., E-mail: medvedev@a5.kiam.ru; Ivanov, A. A., E-mail: aai@a5.kiam.ru; Martynov, A. A., E-mail: martynov@a5.kiam.ru

The influence of current density and pressure gradient profiles in the pedestal on the access to the regimes free from edge localized modes (ELMs) like quiescent H-mode in ITER is investigated. Using the simulator of MHD modes localized near plasma boundary based on the KINX code, calculations of the ELM stability were performed for the ITER plasma in scenarios 2 and 4 under variations of density and temperature profiles with the self-consistent bootstrap current in the pedestal. Low pressure gradient values at the separatrix, the same position of the density and temperature pedestals and high poloidal beta values facilitate reachingmore » high current density in the pedestal and a potential transition into the regime with saturated large scale kink modes. New version of the localized MHD mode simulator allows one to compute the growth rates of ideal peeling-ballooning modes with different toroidal mode numbers and to determine the stability region taking into account diamagnetic stabilization. The edge stability diagrams computations and sensitivity studies of the stability limits to the value of diamagnetic frequency show that diamagnetic stabilization of the modes with high toroidal mode numbers can help to access the quiescent H-mode even with high plasma density but only with low pressure gradient values at the separatrix. The limiting pressure at the top of the pedestal increases for higher plasma density. With flat density profile the access to the quiescent H-mode is closed even with diamagnetic stabilization taken into account, while toroidal mode numbers of the most unstable peeling-ballooning mode decrease from n = 10−40 to n = 3−20.« less

Identical Profiles, Different Paths: Addressing Self-Selection Bias in Learning Community Cohorts

ERIC Educational Resources Information Center

Zobac, Stephanie; Spears, Julia; Barker, Gregory

2014-01-01

This article presents a method for addressing the self-selection bias of students who participate in learning communities (LCs). More specifically, this research utilizes equivalent comparison groups based on selected incoming characteristics of students, known as bootstraps, to account for self-selection bias. To address the differences in…

Exploration of high harmonic fast wave heating on the National Spherical Torus Experiment

NASA Astrophysics Data System (ADS)

Wilson, J. R.; Bell, R. E.; Bernabei, S.; Bitter, M.; Bonoli, P.; Gates, D.; Hosea, J.; LeBlanc, B.; Mau, T. K.; Medley, S.; Menard, J.; Mueller, D.; Ono, M.; Phillips, C. K.; Pinsker, R. I.; Raman, R.; Rosenberg, A.; Ryan, P.; Sabbagh, S.; Stutman, D.; Swain, D.; Takase, Y.; Wilgen, J.

2003-05-01

High harmonic fast wave (HHFW) heating has been proposed as a particularly attractive means for plasma heating and current drive in the high beta plasmas that are achievable in spherical torus (ST) devices. The National Spherical Torus Experiment (NSTX) [M. Ono, S. M. Kaye, S. Neumeyer et al., in Proceedings of the 18th IEEE/NPSS Symposium on Fusion Engineering, Albuquerque, 1999 (IEEE, Piscataway, NJ, 1999), p. 53] is such a device. An rf heating system has been installed on the NSTX to explore the physics of HHFW heating, current drive via rf waves and for use as a tool to demonstrate the attractiveness of the ST concept as a fusion device. To date, experiments have demonstrated many of the theoretical predictions for HHFW. In particular, strong wave absorption on electrons over a wide range of plasma parameters and wave parallel phase velocities, wave acceleration of energetic ions, and indications of current drive for directed wave spectra have been observed. In addition HHFW heating has been used to explore the energy transport properties of NSTX plasmas, to create H-mode discharges with a large fraction of bootstrap current and to control the plasma current profile during the early stages of the discharge.

Suppressing magnetic island growth by resonant magnetic perturbation

NASA Astrophysics Data System (ADS)

Yu, Q.; Günter, S.; Lackner, K.

2018-05-01

The effect of externally applied resonant magnetic perturbations (RMPs) on the growth of magnetic islands is investigated based on two-fluid equations. It is found that if the local bi-normal electron fluid velocity at the resonant surface is sufficiently large, static RMPs of the same helicity and of moderate amplitude can suppress the growth of magnetic islands in high-temperature plasmas. These islands will otherwise grow, driven by an unfavorable plasma current density profile and bootstrap current perturbation. These results indicate that the error field can stabilize island growth, if the error field amplitude is not too large and the local bi-normal electron fluid velocity is not too low. They also indicate that applied rotating RMPs with an appropriate frequency can be utilized to suppress island growth in high-temperature plasmas, even for a low bi-normal electron fluid velocity. A significant change in the local equilibrium plasma current density gradient by small amplitude RMPs is found for realistic plasma parameters, which are important for the island stability and are expected to be more important for fusion reactors with low plasma resistivity.

HSX as an example of a resilient non-resonant divertor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bader, A.; Boozer, A. H.; Hegna, C. C.

This study describes an initial description of the resilient divertor properties of quasi-symmetric (QS) stellarators using the HSX (Helically Symmetric eXperiment) configuration as a test-case. Divertors in high-performance QS stellarators will need to be resilient to changes in plasma configuration that arise due to evolution of plasma pressure profiles and bootstrap currents for divertor design. Resiliency is tested by examining the changes in strike point patterns from the field line following, which arise due to configurational changes. A low strike point variation with high configuration changes corresponds to high resiliency. The HSX edge displays resilient properties with configuration changes arisingmore » from the (1) wall position, (2) plasma current, and (3) external coils. The resilient behavior is lost if large edge islands intersect the wall structure. The resilient edge properties are corroborated by heat flux calculations from the fully 3-D plasma simulations using EMC3-EIRENE. Additionally, the strike point patterns are found to correspond to high curvature regions of magnetic flux surfaces.« less

HSX as an example of a resilient non-resonant divertor

DOE PAGES

Bader, A.; Boozer, A. H.; Hegna, C. C.; ...

2017-03-16

This study describes an initial description of the resilient divertor properties of quasi-symmetric (QS) stellarators using the HSX (Helically Symmetric eXperiment) configuration as a test-case. Divertors in high-performance QS stellarators will need to be resilient to changes in plasma configuration that arise due to evolution of plasma pressure profiles and bootstrap currents for divertor design. Resiliency is tested by examining the changes in strike point patterns from the field line following, which arise due to configurational changes. A low strike point variation with high configuration changes corresponds to high resiliency. The HSX edge displays resilient properties with configuration changes arisingmore » from the (1) wall position, (2) plasma current, and (3) external coils. The resilient behavior is lost if large edge islands intersect the wall structure. The resilient edge properties are corroborated by heat flux calculations from the fully 3-D plasma simulations using EMC3-EIRENE. Additionally, the strike point patterns are found to correspond to high curvature regions of magnetic flux surfaces.« less

Impurities in a non-axisymmetric plasma. Transport and effect on bootstrap current

DOE PAGES

Mollén, A.; Landreman, M.; Smith, H. M.; ...

2015-11-20

Impurities cause radiation losses and plasma dilution, and in stellarator plasmas the neoclassical ambipolar radial electric field is often unfavorable for avoiding strong impurity peaking. In this work we use a new continuum drift-kinetic solver, the SFINCS code (the Stellarator Fokker-Planck Iterative Neoclassical Conservative Solver) [M. Landreman et al., Phys. Plasmas 21 (2014) 042503] which employs the full linearized Fokker-Planck-Landau operator, to calculate neoclassical impurity transport coefficients for a Wendelstein 7-X (W7-X) magnetic configuration. We compare SFINCS calculations with theoretical asymptotes in the high collisionality limit. We observe and explain a 1/nu-scaling of the inter-species radial transport coefficient at lowmore » collisionality, arising due to the field term in the inter-species collision operator, and which is not found with simplified collision models even when momentum correction is applied. However, this type of scaling disappears if a radial electric field is present. We use SFINCS to analyze how the impurity content affects the neoclassical impurity dynamics and the bootstrap current. We show that a change in plasma effective charge Z eff of order unity can affect the bootstrap current enough to cause a deviation in the divertor strike point locations.« less

The prospects for magnetohydrodynamic stability in advanced tokamak regimes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Manickam, J.; Chance, M.S.; Jardin, S.C.

1994-05-01

Stability analysis of advanced regime tokamaks is presented. Here advanced regimes are defined to include configurations where the ratio of the bootstrap current, [ital I][sub BS], to the total plasma current, [ital I][sub [ital p

Incorporating external evidence in trial-based cost-effectiveness analyses: the use of resampling methods

PubMed Central

2014-01-01

Background Cost-effectiveness analyses (CEAs) that use patient-specific data from a randomized controlled trial (RCT) are popular, yet such CEAs are criticized because they neglect to incorporate evidence external to the trial. A popular method for quantifying uncertainty in a RCT-based CEA is the bootstrap. The objective of the present study was to further expand the bootstrap method of RCT-based CEA for the incorporation of external evidence. Methods We utilize the Bayesian interpretation of the bootstrap and derive the distribution for the cost and effectiveness outcomes after observing the current RCT data and the external evidence. We propose simple modifications of the bootstrap for sampling from such posterior distributions. Results In a proof-of-concept case study, we use data from a clinical trial and incorporate external evidence on the effect size of treatments to illustrate the method in action. Compared to the parametric models of evidence synthesis, the proposed approach requires fewer distributional assumptions, does not require explicit modeling of the relation between external evidence and outcomes of interest, and is generally easier to implement. A drawback of this approach is potential computational inefficiency compared to the parametric Bayesian methods. Conclusions The bootstrap method of RCT-based CEA can be extended to incorporate external evidence, while preserving its appealing features such as no requirement for parametric modeling of cost and effectiveness outcomes. PMID:24888356

Incorporating external evidence in trial-based cost-effectiveness analyses: the use of resampling methods.

PubMed

Sadatsafavi, Mohsen; Marra, Carlo; Aaron, Shawn; Bryan, Stirling

2014-06-03

Cost-effectiveness analyses (CEAs) that use patient-specific data from a randomized controlled trial (RCT) are popular, yet such CEAs are criticized because they neglect to incorporate evidence external to the trial. A popular method for quantifying uncertainty in a RCT-based CEA is the bootstrap. The objective of the present study was to further expand the bootstrap method of RCT-based CEA for the incorporation of external evidence. We utilize the Bayesian interpretation of the bootstrap and derive the distribution for the cost and effectiveness outcomes after observing the current RCT data and the external evidence. We propose simple modifications of the bootstrap for sampling from such posterior distributions. In a proof-of-concept case study, we use data from a clinical trial and incorporate external evidence on the effect size of treatments to illustrate the method in action. Compared to the parametric models of evidence synthesis, the proposed approach requires fewer distributional assumptions, does not require explicit modeling of the relation between external evidence and outcomes of interest, and is generally easier to implement. A drawback of this approach is potential computational inefficiency compared to the parametric Bayesian methods. The bootstrap method of RCT-based CEA can be extended to incorporate external evidence, while preserving its appealing features such as no requirement for parametric modeling of cost and effectiveness outcomes.

The Impact of Time Perspective Latent Profiles on College Drinking: A Multidimensional Approach

PubMed Central

Braitman, Abby L.; Henson, James M.

2015-01-01

Background Zimbardo and Boyd’s1 time perspective, or the temporal framework individuals use to process information, has been shown to predict health behaviors such as alcohol use. Previous studies supported the predictive validity of individual dimensions of time perspective, with some dimensions acting as protective factors and others as risk factors. However, some studies produced findings contrary to the general body of literature. In addition, time perspective is a multidimensional construct, and the combination of perspectives may be more predictive than individual dimensions in isolation; consequently, multidimensional profiles are a more accurate measure of individual differences and more appropriate for predicting health behaviors. Objectives The current study identified naturally occurring profiles of time perspective and examined their association with risky alcohol use. Methods Data were collected from a college student sample (n = 431, mean age = 20.41 years) using an online survey. Time perspective profiles were identified using latent profile analysis. Results Bootstrapped regression models identified a protective class that engaged in significantly less overall drinking (β = −0.254) as well as engaging in significantly less episodic high risk drinking (β = −0.274). There was also emerging evidence of a high risk time perspective profile that was linked to more overall drinking (β = 0.198) and engaging in more high risk drinking (β = 0.245), though these differences were not significant. Conclusions/Importance These findings support examining time perspective in a multidimensional framework rather than individual dimensions in isolation. Implications include identifying students most in need of interventions, and tailoring interventions to target temporal framing in decision-making. PMID:25607806

The impact of time perspective latent profiles on college drinking: a multidimensional approach.

PubMed

Braitman, Abby L; Henson, James M

2015-04-01

Zimbardo and Boyd's(1) time perspective, or the temporal framework individuals use to process information, has been shown to predict health behaviors such as alcohol use. Previous studies supported the predictive validity of individual dimensions of time perspective, with some dimensions acting as protective factors and others as risk factors. However, some studies produced findings contrary to the general body of literature. In addition, time perspective is a multidimensional construct, and the combination of perspectives may be more predictive than individual dimensions in isolation; consequently, multidimensional profiles are a more accurate measure of individual differences and more appropriate for predicting health behaviors. The current study identified naturally occurring profiles of time perspective and examined their association with risky alcohol use. Data were collected from a college student sample (n = 431, mean age = 20.41 years) using an online survey. Time perspective profiles were identified using latent profile analysis. Bootstrapped regression models identified a protective class that engaged in significantly less overall drinking (β = -0.254) as well as engaging in significantly less episodic high risk drinking (β = -0.274). There was also emerging evidence of a high risk time perspective profile that was linked to more overall drinking (β = 0.198) and engaging in more high risk drinking (β = 0.245), though these differences were not significant. CONCLUSIONS/IMPORTANCE: These findings support examining time perspective in a multidimensional framework rather than individual dimensions in isolation. Implications include identifying students most in need of interventions, and tailoring interventions to target temporal framing in decision-making.

Causality constraints in conformal field theory

DOE PAGES

Hartman, Thomas; Jain, Sachin; Kundu, Sandipan

2016-05-17

Causality places nontrivial constraints on QFT in Lorentzian signature, for example fixing the signs of certain terms in the low energy Lagrangian. In d dimensional conformal field theory, we show how such constraints are encoded in crossing symmetry of Euclidean correlators, and derive analogous constraints directly from the conformal bootstrap (analytically). The bootstrap setup is a Lorentzian four-point function corresponding to propagation through a shockwave. Crossing symmetry fixes the signs of certain log terms that appear in the conformal block expansion, which constrains the interactions of low-lying operators. As an application, we use the bootstrap to rederive the well knownmore » sign constraint on the (Φ) 4 coupling in effective field theory, from a dual CFT. We also find constraints on theories with higher spin conserved currents. As a result, our analysis is restricted to scalar correlators, but we argue that similar methods should also impose nontrivial constraints on the interactions of spinning operators« less

Conformal Bootstrap in Mellin Space

NASA Astrophysics Data System (ADS)

Gopakumar, Rajesh; Kaviraj, Apratim; Sen, Kallol; Sinha, Aninda

2017-02-01

We propose a new approach towards analytically solving for the dynamical content of conformal field theories (CFTs) using the bootstrap philosophy. This combines the original bootstrap idea of Polyakov with the modern technology of the Mellin representation of CFT amplitudes. We employ exchange Witten diagrams with built-in crossing symmetry as our basic building blocks rather than the conventional conformal blocks in a particular channel. Demanding consistency with the operator product expansion (OPE) implies an infinite set of constraints on operator dimensions and OPE coefficients. We illustrate the power of this method in the ɛ expansion of the Wilson-Fisher fixed point by reproducing anomalous dimensions and, strikingly, obtaining OPE coefficients to higher orders in ɛ than currently available using other analytic techniques (including Feynman diagram calculations). Our results enable us to get a somewhat better agreement between certain observables in the 3D Ising model and the precise numerical values that have been recently obtained.

Comparison of fusion alpha performance in JET advanced scenario and H-mode plasmas

NASA Astrophysics Data System (ADS)

Asunta, O.; Kurki-Suonio, T.; Tala, T.; Sipilä, S.; Salomaa, R.; contributors, JET-EFDA

2008-12-01

Currently, plasmas with internal transport barriers (ITBs) appear the most likely candidates for steady-state scenarios for future fusion reactors. In such plasmas, the broad hot and dense region in the plasma core leads to high fusion gain, while the cool edge protects the integrity of the first wall. Economically desirable large bootstrap current fraction and low inductive current drive may, however, lead to degraded fast ion confinement. In this work the confinement and heating profile of fusion alphas were compared between H-mode and ITB plasmas in realistic JET geometry. The work was carried out using the Monte Carlo-based guiding-center-following code ASCOT. For the same plasma current, the ITB discharges were found to produce four to eight times more fusion power than a comparable ELMy H-mode discharge. Unfortunately, also the alpha particle losses were larger (~16%) compared with the H-mode discharge (7%). In the H-mode discharges, alpha power was deposited to the plasma symmetrically around the magnetic axis, whereas in the current-hole discharge, the power was spread out to a larger volume in the plasma center. This was due to wider particle orbits, and the magnetic structure allowing for a broader hot region in the centre.

Exploration of High Harmonic Fast Wave Heating on the National Spherical Torus Experiment

DOE Office of Scientific and Technical Information (OSTI.GOV)

J.R. Wilson; R.E. Bell; S. Bernabei

2003-02-11

High Harmonic Fast Wave (HHFW) heating has been proposed as a particularly attractive means for plasma heating and current drive in the high-beta plasmas that are achievable in spherical torus (ST) devices. The National Spherical Torus Experiment (NSTX) [Ono, M., Kaye, S.M., Neumeyer, S., et al., Proceedings, 18th IEEE/NPSS Symposium on Fusion Engineering, Albuquerque, 1999, (IEEE, Piscataway, NJ (1999), p. 53.)] is such a device. An radio-frequency (rf) heating system has been installed on NSTX to explore the physics of HHFW heating, current drive via rf waves and for use as a tool to demonstrate the attractiveness of the STmore » concept as a fusion device. To date, experiments have demonstrated many of the theoretical predictions for HHFW. In particular, strong wave absorption on electrons over a wide range of plasma parameters and wave parallel phase velocities, wave acceleration of energetic ions, and indications of current drive for directed wave spectra have been observed. In addition HHFW heating has been used to explore the energy transport properties of NSTX plasmas, to create H-mode (high-confinement mode) discharges with a large fraction of bootstrap current and to control the plasma current profile during the early stages of the discharge.« less

Heating and current drive requirements towards steady state operation in ITER

NASA Astrophysics Data System (ADS)

Poli, F. M.; Bonoli, P. T.; Kessel, C. E.; Batchelor, D. B.; Gorelenkova, M.; Harvey, B.; Petrov, Y.

2014-02-01

Steady state scenarios envisaged for ITER aim at optimizing the bootstrap current, while maintaining sufficient confinement and stability to provide the necessary fusion yield. Non-inductive scenarios will need to operate with Internal Transport Barriers (ITBs) in order to reach adequate fusion gain at typical currents of 9 MA. However, the large pressure gradients associated with ITBs in regions of weak or negative magnetic shear can be conducive to ideal MHD instabilities, reducing the no-wall limit. The E × B flow shear from toroidal plasma rotation is expected to be low in ITER, with a major role in the ITB dynamics being played by magnetic geometry. Combinations of H/CD sources that maintain weakly reversed magnetic shear profiles throughout the discharge are the focus of this work. Time-dependent transport simulations indicate that, with a trade-off of the EC equatorial and upper launcher, the formation and sustainment of quasi-steady state ITBs could be demonstrated in ITER with the baseline heating configuration. However, with proper constraints from peeling-ballooning theory on the pedestal width and height, the fusion gain and the maximum non-inductive current are below the ITER target. Upgrades of the heating and current drive system in ITER, like the use of Lower Hybrid current drive, could overcome these limitations, sustaining higher non-inductive current and confinement, more expanded ITBs which are ideal MHD stable.

Advanced Tokamak Investigations in Full-Tungsten ASDEX Upgrade

NASA Astrophysics Data System (ADS)

Bock, Alexander

2017-10-01

The tailoring of the q-profile is the foundation of Advanced Tokamak (AT) scenarios. It depends on low collisionality ν* which permits efficient external current drive and high amounts of intrinsic bootstrap current. At constant pressure, lowering ne leads to a strong decrease of ν* Te - 3 . After the conversion of ASDEX Upgrade to fully W-coated plasma facing components, radiative collapses of H-modes with little gas puffing due to central W accumulation could only be avoided partially with central ECRH. Also, operation at high β with low ne presented a challenge for the divertor. Together, these issues prevented meaningful AT investigations. To overcome this, several major feats have been accomplished: Access to lower ne was achieved through a better understanding of the changes to recycling and pumping, and optionally the density pump-out phenomenon due to RMPs. ECRH capacities were substantially expanded for both heating and current drive, and a solid W divertor capable of withstanding the power loads was installed. A major overhaul improved the reliability of the current profile diagnostics. This contribution will detail the efforts needed to re-access AT scenarios and report on the development of candidate steady state scenarios for ITER/DEMO. Starting from the `hybrid scenario,' a non-inductive scenario (q95 = 5.3 , βN = 2.7 , fbs > 40 %) was developed. It can be sustained for many τE, limited only by technical boundaries, and is also independent of the ramp-up scenario. The β-limit is set by ideal modes that convert into NTMs. The Ti-profiles are steeper than predicted by TGLF, but nonlinear electromagnetic gyro-kinetic analyses with GENE including fast particle effects matched the experimental heat fluxes. We will also report on scenarios at higher q95, similar to the EAST/DIII-D steady state scenario. The extrapolation of these scenarios to ITER/DEMO will be discussed.

Integrated modelling of steady-state scenarios and heating and current drive mixes for ITER

DOE Office of Scientific and Technical Information (OSTI.GOV)

Murakami, Masanori; Park, Jin Myung; Giruzzi, G.

2011-01-01

Recent progress on ITER steady-state (SS) scenario modelling by the ITPA-IOS group is reviewed. Code-to-code benchmarks as the IOS group's common activities for the two SS scenarios (weak shear scenario and internal transport barrier scenario) are discussed in terms of transport, kinetic profiles, and heating and current drive (CD) sources using various transport codes. Weak magnetic shear scenarios integrate the plasma core and edge by combining a theory-based transport model (GLF23) with scaled experimental boundary profiles. The edge profiles (at normalized radius rho = 0.8-1.0) are adopted from an edge-localized mode-averaged analysis of a DIII-D ITER demonstration discharge. A fullymore » noninductive SS scenario is achieved with fusion gain Q = 4.3, noninductive fraction f(NI) = 100%, bootstrap current fraction f(BS) = 63% and normalized beta beta(N) = 2.7 at plasma current I(p) = 8MA and toroidal field B(T) = 5.3 T using ITER day-1 heating and CD capability. Substantial uncertainties come from outside the radius of setting the boundary conditions (rho = 0.8). The present simulation assumed that beta(N)(rho) at the top of the pedestal (rho = 0.91) is about 25% above the peeling-ballooning threshold. ITER will have a challenge to achieve the boundary, considering different operating conditions (T(e)/T(i) approximate to 1 and density peaking). Overall, the experimentally scaled edge is an optimistic side of the prediction. A number of SS scenarios with different heating and CD mixes in a wide range of conditions were explored by exploiting the weak-shear steady-state solution procedure with the GLF23 transport model and the scaled experimental edge. The results are also presented in the operation space for DT neutron power versus stationary burn pulse duration with assumed poloidal flux availability at the beginning of stationary burn, indicating that the long pulse operation goal (3000s) at I(p) = 9 MA is possible. Source calculations in these simulations have been revised for electron cyclotron current drive including parallel momentum conservation effects and for neutral beam current drive with finite orbit and magnetic pitch effects.« less

Heating and current drive requirements towards steady state operation in ITER

NASA Astrophysics Data System (ADS)

Poli, Francesca; Kessel, Charles; Bonoli, Paul; Batchelor, Donald; Harvey, Bob

2013-10-01

Steady state scenarios envisaged for ITER aim at optimizing the bootstrap current, while maintaining sufficient confinement and stability. Non-inductive scenarios will need to operate with Internal Transport Barriers (ITBs) to reach adequate fusion gain at typical currents of 9 MA. Scenarios are established as relaxed flattop states with time-dependent transport simulations with TSC. The E × B flow shear from toroidal plasma rotation is expected to be low in ITER, with a major role in the ITB dynamics being played by magnetic geometry. Combinations of external sources that maintain weakly reversed shear profiles and ρ (qmin >= 0 . 5 are the focus of this work. Simulations indicate that, with a trade-off of the EC equatorial and upper launcher, the formation and sustainment of ITBs could be demonstrated with the baseline configuration. However, with proper constraints from peeling-ballooning theory on the pedestal width and height, the fusion gain and the maximum non-inductive current (6.2MA) are below the target. Upgrades of the heating and current drive system, like the use of Lower Hybrid current drive, could overcome these limitations. With 30MW of coupled LH in the flattop and operating at the Greenwald density, plasmas can sustain ~ 9 MA and achieve Q ~ 4 . Work supported by the US Department of Energy under DE-AC02-CH0911466.

A comparison of bootstrap methods and an adjusted bootstrap approach for estimating the prediction error in microarray classification.

PubMed

Jiang, Wenyu; Simon, Richard

2007-12-20

This paper first provides a critical review on some existing methods for estimating the prediction error in classifying microarray data where the number of genes greatly exceeds the number of specimens. Special attention is given to the bootstrap-related methods. When the sample size n is small, we find that all the reviewed methods suffer from either substantial bias or variability. We introduce a repeated leave-one-out bootstrap (RLOOB) method that predicts for each specimen in the sample using bootstrap learning sets of size ln. We then propose an adjusted bootstrap (ABS) method that fits a learning curve to the RLOOB estimates calculated with different bootstrap learning set sizes. The ABS method is robust across the situations we investigate and provides a slightly conservative estimate for the prediction error. Even with small samples, it does not suffer from large upward bias as the leave-one-out bootstrap and the 0.632+ bootstrap, and it does not suffer from large variability as the leave-one-out cross-validation in microarray applications. Copyright (c) 2007 John Wiley & Sons, Ltd.

Associations between dietary and lifestyle risk factors and colorectal cancer in the Scottish population.

PubMed

Theodoratou, Evropi; Farrington, Susan M; Tenesa, Albert; McNeill, Geraldine; Cetnarskyj, Roseanne; Korakakis, Emmanouil; Din, Farhat V N; Porteous, Mary E; Dunlop, Malcolm G; Campbell, Harry

2014-01-01

Colorectal cancer (CRC) accounts for 9.7% of all cancer cases and for 8% of all cancer-related deaths. Established risk factors include personal or family history of CRC as well as lifestyle and dietary factors. We investigated the relationship between CRC and demographic, lifestyle, food and nutrient risk factors through a case-control study that included 2062 patients and 2776 controls from Scotland. Forward and backward stepwise regression was applied and the stability of the models was assessed in 1000 bootstrap samples. The variables that were automatically selected to be included by the forward or backward stepwise regression and whose selection was verified by bootstrap sampling in the current study were family history, dietary energy, 'high-energy snack foods', eggs, juice, sugar-sweetened beverages and white fish (associated with an increased CRC risk) and NSAIDs, coffee and magnesium (associated with a decreased CRC risk). Application of forward and backward stepwise regression in this CRC study identified some already established as well as some novel potential risk factors. Bootstrap findings suggest that examination of the stability of regression models by bootstrap sampling is useful in the interpretation of study findings. 'High-energy snack foods' and high-energy drinks (including sugar-sweetened beverages and fruit juices) as risk factors for CRC have not been reported previously and merit further investigation as such snacks and beverages are important contributors in European and North American diets.

Using the Bootstrap Concept to Build an Adaptable and Compact Subversion Artifice

DTIC Science & Technology

2003-06-01

however, and the current “second generation” of microkernel implementations has resulted in significantly better performance. Of note is the L4 micro...63 c. GEMSOS Kernel .....................................................................63 d. L4 ... Microkernel ........................................................................64 VI. CONCLUSIONS

Fast, Exact Bootstrap Principal Component Analysis for p > 1 million

PubMed Central

Fisher, Aaron; Caffo, Brian; Schwartz, Brian; Zipunnikov, Vadim

2015-01-01

Many have suggested a bootstrap procedure for estimating the sampling variability of principal component analysis (PCA) results. However, when the number of measurements per subject (p) is much larger than the number of subjects (n), calculating and storing the leading principal components from each bootstrap sample can be computationally infeasible. To address this, we outline methods for fast, exact calculation of bootstrap principal components, eigenvalues, and scores. Our methods leverage the fact that all bootstrap samples occupy the same n-dimensional subspace as the original sample. As a result, all bootstrap principal components are limited to the same n-dimensional subspace and can be efficiently represented by their low dimensional coordinates in that subspace. Several uncertainty metrics can be computed solely based on the bootstrap distribution of these low dimensional coordinates, without calculating or storing the p-dimensional bootstrap components. Fast bootstrap PCA is applied to a dataset of sleep electroencephalogram recordings (p = 900, n = 392), and to a dataset of brain magnetic resonance images (MRIs) (p ≈ 3 million, n = 352). For the MRI dataset, our method allows for standard errors for the first 3 principal components based on 1000 bootstrap samples to be calculated on a standard laptop in 47 minutes, as opposed to approximately 4 days with standard methods. PMID:27616801

L-H transition and pedestal studies on MAST

NASA Astrophysics Data System (ADS)

Meyer, H.; De Bock, M. F. M.; Conway, N. J.; Freethy, S. J.; Gibson, K.; Hiratsuka, J.; Kirk, A.; Michael, C. A.; Morgan, T.; Scannell, R.; Naylor, G.; Saarelma, S.; Saveliev, A. N.; Shevchenko, V. F.; Suttrop, W.; Temple, D.; Vann, R. G. L.; MAST, the; NBI Teams

2011-11-01

On MAST studies of the profile evolution of the electron temperature (Te), electron density (ne), radial electric field (Er) as well as novel measurements of the ion temperature (Ti) and toroidal current density (jphi) in the pedestal region allow further insight into the processes forming and defining the pedestal such as the H-mode access conditions and MHD stability. This includes studies of fast evolution of Te, ne and Er with Δt = 0.2 ms time resolution and the evolution of pe and jphi through an edge-localized mode (ELM) cycle. Measurements of the H-mode power threshold, PL-H revealed that about 40% more power is required to access H-mode in 4He than in D and that a change in the Z-position of the X-point can change PL-H significantly in single and double null configurations. The profile measurements in the L-mode phase prior to H-mode suggest that neither the gradient nor the value of the mean Te or Er at the plasma edge play a major role in triggering the L-H transition. After the transitions, first the fluctuations are suppressed, then the Er shear layer and the ne pedestal develops followed by the Te pedestal. In the banana regime at low collisionality (νsstarf) ∇Ti ≈ 0 leading to Ti > Te in the pedestal region with Ti ~ 0.3 keV close to the separatrix. A clear correlation of ∇Ti with νsstarf is observed. The measured jphi (using the motional Stark effect) Te and ne are in broad agreement with the common peeling-ballooning stability picture for ELMs and neoclassical calculations of the bootstrap current. The jphi and ∇pe evolution Δt ≈ 2 ms as well as profiles in discharges with counter current neutral beam injection raise questions with respect to this edge stability picture.

Speeding Up Non-Parametric Bootstrap Computations for Statistics Based on Sample Moments in Small/Moderate Sample Size Applications

PubMed Central

Chaibub Neto, Elias

2015-01-01

In this paper we propose a vectorized implementation of the non-parametric bootstrap for statistics based on sample moments. Basically, we adopt the multinomial sampling formulation of the non-parametric bootstrap, and compute bootstrap replications of sample moment statistics by simply weighting the observed data according to multinomial counts instead of evaluating the statistic on a resampled version of the observed data. Using this formulation we can generate a matrix of bootstrap weights and compute the entire vector of bootstrap replications with a few matrix multiplications. Vectorization is particularly important for matrix-oriented programming languages such as R, where matrix/vector calculations tend to be faster than scalar operations implemented in a loop. We illustrate the application of the vectorized implementation in real and simulated data sets, when bootstrapping Pearson’s sample correlation coefficient, and compared its performance against two state-of-the-art R implementations of the non-parametric bootstrap, as well as a straightforward one based on a for loop. Our investigations spanned varying sample sizes and number of bootstrap replications. The vectorized bootstrap compared favorably against the state-of-the-art implementations in all cases tested, and was remarkably/considerably faster for small/moderate sample sizes. The same results were observed in the comparison with the straightforward implementation, except for large sample sizes, where the vectorized bootstrap was slightly slower than the straightforward implementation due to increased time expenditures in the generation of weight matrices via multinomial sampling. PMID:26125965

Overcoming confounded controls in the analysis of gene expression data from microarray experiments.

PubMed

Bhattacharya, Soumyaroop; Long, Dang; Lyons-Weiler, James

2003-01-01

A potential limitation of data from microarray experiments exists when improper control samples are used. In cancer research, comparisons of tumour expression profiles to those from normal samples is challenging due to tissue heterogeneity (mixed cell populations). A specific example exists in a published colon cancer dataset, in which tissue heterogeneity was reported among the normal samples. In this paper, we show how to overcome or avoid the problem of using normal samples that do not derive from the same tissue of origin as the tumour. We advocate an exploratory unsupervised bootstrap analysis that can reveal unexpected and undesired, but strongly supported, clusters of samples that reflect tissue differences instead of tumour versus normal differences. All of the algorithms used in the analysis, including the maximum difference subset algorithm, unsupervised bootstrap analysis, pooled variance t-test for finding differentially expressed genes and the jackknife to reduce false positives, are incorporated into our online Gene Expression Data Analyzer ( http:// bioinformatics.upmc.edu/GE2/GEDA.html ).

Bootstrapping the O(N) archipelago

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kos, Filip; Poland, David; Simmons-Duffin, David

2015-11-17

We study 3d CFTs with an O(N) global symmetry using the conformal bootstrap for a system of mixed correlators. Specifically, we consider all nonvanishing scalar four-point functions containing the lowest dimension O(N) vector Φ i and the lowest dimension O(N) singlet s, assumed to be the only relevant operators in their symmetry representations. The constraints of crossing symmetry and unitarity for these four-point functions force the scaling dimensions (Δ Φ , Δ s ) to lie inside small islands. Here, we also make rigorous determinations of current two-point functions in the O(2) and O(3) models, with applications to transport inmore » condensed matter systems.« less

Coefficient Omega Bootstrap Confidence Intervals: Nonnormal Distributions

ERIC Educational Resources Information Center

Padilla, Miguel A.; Divers, Jasmin

2013-01-01

The performance of the normal theory bootstrap (NTB), the percentile bootstrap (PB), and the bias-corrected and accelerated (BCa) bootstrap confidence intervals (CIs) for coefficient omega was assessed through a Monte Carlo simulation under conditions not previously investigated. Of particular interests were nonnormal Likert-type and binary items.…

Tests of Independence for Ordinal Data Using Bootstrap.

ERIC Educational Resources Information Center

Chan, Wai; Yung, Yiu-Fai; Bentler, Peter M.; Tang, Man-Lai

1998-01-01

Two bootstrap tests are proposed to test the independence hypothesis in a two-way cross table. Monte Carlo studies are used to compare the traditional asymptotic test with these bootstrap methods, and the bootstrap methods are found superior in two ways: control of Type I error and statistical power. (SLD)

Modeling of Steady-state Scenarios for the Fusion Nuclear Science Facility, Advanced Tokamak Approach

NASA Astrophysics Data System (ADS)

Garofalo, A. M.; Chan, V. S.; Prater, R.; Smith, S. P.; St. John, H. E.; Meneghini, O.

2013-10-01

A Fusion National Science Facility (FNSF) would complement ITER in addressing the community identified science and technology gaps to a commercially attractive DEMO, including breeding tritium and completing the fuel cycle, qualifying nuclear materials for high fluence, developing suitable materials for the plasma-boundary interface, and demonstrating power extraction. Steady-state plasma operation is highly desirable to address the requirements for fusion nuclear technology testing [1]. The Advanced Tokamak (AT) is a strong candidate for an FNSF as a consequence of its mature physics base, capability to address the key issues with a more compact device, and the direct relevance to an attractive target power plant. Key features of AT are fully noninductive current drive, strong plasma cross section shaping, internal profiles consistent with high bootstrap fraction, and operation at high beta, typically above the free boundary limit, βN > 3 . Work supported by GA IR&D funding, DE-FC02-04ER54698, and DE-FG02-95ER43309.

Recent results from the electron cyclotron heated plasmas in Tokamak à Configuration Variable (TCV)

NASA Astrophysics Data System (ADS)

Henderson, M. A.; Alberti, S.; Angioni, C.; Arnoux, G.; Behn, R.; Blanchard, P.; Bosshard, P.; Camenen, Y.; Coda, S.; Condrea, I.; Goodman, T. P.; Hofmann, F.; Hogge, J.-Ph.; Karpushov, A.; Manini, A.; Martynov, An.; Moret, J.-M.; Nikkola, P.; Nelson-Melby, E.; Pochelon, A.; Porte, L.; Sauter, O.; Ahmed, S. M.; Andrèbe, Y.; Appert, K.; Chavan, R.; Degeling, A.; Duval, B. P.; Etienne, P.; Fasel, D.; Fasoli, A.; Favez, J.-Y.; Furno, I.; Horacek, J.; Isoz, P.; Joye, B.; Klimanov, I.; Lavanchy, P.; Lister, J. B.; Llobet, X.; Magnin, J.-C.; Marlétaz, B.; Marmillod, P.; Martin, Y.; Mayor, J.-M.; Mylnar, J.; Paris, P. J.; Perez, A.; Peysson, Y.; Pitts, R. A.; Raju, D.; Reimerdes, H.; Scarabosio, A.; Scavino, E.; Seo, S. H.; Siravo, U.; Sushkov, A.; Tonetti, G.; Tran, M. Q.; Weisen, H.; Wischmeier, M.; Zabolotsky, A.; Yhuang, G.

2003-05-01

In noninductively driven discharges, 0.9 MW second harmonic (X2) off-axis co-electron cyclotron current drive deposition is combined with 0.45 MW X2 central heating to create an electron internal transport barrier (eITB) in steady plasma conditions resulting in a 1.6-fold increase of the confinement time (τEe) over ITER-98L-mode scaling. The eITB is associated with a reversed shear current profile enhanced by a large bootstrap current fraction (up to 80%) and is sustained for up to 10 current redistribution times. A linear dependence of the confinement improvement on the product of the global shear reversal factor (q0/qmin) and the reversed shear volume (ρq-min2) is shown. In other discharges heated with X2 the sawteeth are destabilized (respectively stabilized) when heating just inside (respectively outside) the q=1 surface. Control of the sawteeth may allow the avoidance of neoclassical tearing modes that can be seeded by the sawtooth instability. Results on H-mode and highly elongated plasmas using the newly completed third harmonic (X3) system and achieving up to 100% absorption are also discussed, along with comparison of experimental results with the TORAY-GA ray tracing code [K. Matsuda, IEEE Trans. Plasma Sci. PS-17, 6 (1989); R. H. Cohen, Phys. Fluids 30, 2442 (1987)].

Extending the validation of multi-mode model for anomalous transport to high beta poloidal tokamak scenario in DIII-D

NASA Astrophysics Data System (ADS)

Pankin, A. Y.; Kritz, A. H.; Rafiq, T.; Garofalo, A. M.; Holod, I.; Weiland, J.

2018-05-01

The Multi-Mode Model (MMM7.1) for anomalous transport is tested in predictive modeling of temperature profiles of a high beta poloidal DIII-D discharge. This new H-mode plasma regime, with high beta poloidal and high bootstrap currents, has been studied in DIII-D tokamak discharges [A. Garofalo et al., Nucl. Fusion 55, 123025 (2015)]. The role of instabilities that can drive the anomalous transport described by MMM7.1 is investigated. The temperature profiles for a high beta poloidal DIII-D discharge are computed using the NCLASS model for the neoclassical transport and the Weiland and Electron Temperature Gradient (ETG) components of the MMM7.1 model for the anomalous transport. The neoclassical transport is found to be the main contributor to the ion thermal transport in the plasma core. The contributions from the ion temperature gradient driven modes are found to be important only outside of the internal transport barrier. The magnitudes of the predicted temperature profiles are found to be in a reasonable agreement with experimental profiles. The simulation results approximately reproduce the internal transport barrier in the ion temperature profile but not in the electron temperature profile due to a weak dependence of the ETG driven transport on the Shafranov shift in the ETG component of MMM7.1. Possible effects that can contribute to stabilization of these modes, for example, effects associated with the large beta poloidal such as the Shafranov shift stabilization in the MMM7.1 model, are discussed. It is demonstrated that the E × B flow shear has a relatively small effect in the formation of the internal transport barrier in the high beta poloidal DIII-D discharge 154406. The Shafranov shift (alpha stabilization) and small or reversed magnetic shear profiles are found to be the primary reasons for quenched anomalous transport in this discharge.

Does Bootstrap Procedure Provide Biased Estimates? An Empirical Examination for a Case of Multiple Regression.

ERIC Educational Resources Information Center

Fan, Xitao

This paper empirically and systematically assessed the performance of bootstrap resampling procedure as it was applied to a regression model. Parameter estimates from Monte Carlo experiments (repeated sampling from population) and bootstrap experiments (repeated resampling from one original bootstrap sample) were generated and compared. Sample…

Using the Descriptive Bootstrap to Evaluate Result Replicability (Because Statistical Significance Doesn't)

ERIC Educational Resources Information Center

Spinella, Sarah

2011-01-01

As result replicability is essential to science and difficult to achieve through external replicability, the present paper notes the insufficiency of null hypothesis statistical significance testing (NHSST) and explains the bootstrap as a plausible alternative, with a heuristic example to illustrate the bootstrap method. The bootstrap relies on…

Projecting High Beta Steady-State Scenarios from DIII-D Advanced Tokamk Discharges

NASA Astrophysics Data System (ADS)

Park, J. M.

2013-10-01

Fusion power plant studies based on steady-state tokamak operation suggest that normalized beta in the range of 4-6 is needed for economic viability. DIII-D is exploring a range of candidate high beta scenarios guided by FASTRAN modeling in a repeated cycle of experiment and modeling validation. FASTRAN is a new iterative numerical procedure coupled to the Integrated Plasma Simulator (IPS) that integrates models of core transport, heating and current drive, equilibrium and stability self-consistently to find steady state (d / dt = 0) solutions, and reproduces most features of DIII-D high beta discharges with a stationary current profile. Separately, modeling components such as core transport (TGLF) and off-axis neutral beam current drive (NUBEAM) show reasonable agreement with experiment. Projecting forward to scenarios possible on DIII-D with future upgrades, two self-consistent noninductive scenarios at βN > 4 are found: high qmin and high internal inductance li. Both have bootstrap current fraction fBS > 0 . 5 and rely on the planned addition of a second off-axis neutral beamline and increased electron cyclotron heating. The high qmin > 2 scenario achieves stable operation at βN as high as 5 by a very broad current density profile to improve the ideal-wall stabilization of low-n instabilities along with confinement enhancement from low magnetic shear. The li near 1 scenario does not depend on ideal-wall stabilization. Improved confinement from strong magnetic shear makes up for the lower pedestal needed to maintain li high. The tradeoff between increasing li and reduced edge pedestal determines the achievable βN (near 4) and fBS (near 0.5). This modeling identifies the necessary upgrades to achieve target scenarios and clarifies the pros and cons of particular scenarios to better inform the development of steady-state fusion. Supported by the US Department of Energy under DE-AC05-00OR22725 & DE-FC02-04ER54698.

Performance of Bootstrapping Approaches To Model Test Statistics and Parameter Standard Error Estimation in Structural Equation Modeling.

ERIC Educational Resources Information Center

Nevitt, Jonathan; Hancock, Gregory R.

2001-01-01

Evaluated the bootstrap method under varying conditions of nonnormality, sample size, model specification, and number of bootstrap samples drawn from the resampling space. Results for the bootstrap suggest the resampling-based method may be conservative in its control over model rejections, thus having an impact on the statistical power associated…

Nonparametric bootstrap analysis with applications to demographic effects in demand functions.

PubMed

Gozalo, P L

1997-12-01

"A new bootstrap proposal, labeled smooth conditional moment (SCM) bootstrap, is introduced for independent but not necessarily identically distributed data, where the classical bootstrap procedure fails.... A good example of the benefits of using nonparametric and bootstrap methods is the area of empirical demand analysis. In particular, we will be concerned with their application to the study of two important topics: what are the most relevant effects of household demographic variables on demand behavior, and to what extent present parametric specifications capture these effects." excerpt

Resilient Diffusive Clouds

DTIC Science & Technology

2017-02-01

scale blade servers (Dell PowerEdge) [20]. It must be recognized however, that the findings are distributed over this collection of architectures not...current operating system designs run into millions of lines of code. Moreover, they compound the opportunity for compromise by granting device drivers...properties (e.g. IP & MAC address) so as to invalidate an adversary’s surveillance data. The current running and bootstrapping instances of the micro

Quasi-Axially Symmetric Stellarators with 3 Field Periods

NASA Astrophysics Data System (ADS)

Garabedian, Paul; Ku, Long-Poe

1998-11-01

Compact hybrid configurations with 2 field periods have been studied recently as candidates for a proof of principle experiment at PPPL, cf. A. Reiman et al., Physics design of a high beta quasi-axially symmetric stellarator, J. Plas. Fus. Res. SERIES 1, 429(1998). This enterprise has led us to the discovery of a family of quasi-axially symmetric stellarators with 3 field periods that seem to have significant advantages, although their aspect ratios are a little larger. They have reversed shear and perform better in a local analysis of ballooning modes. Nonlinear equilibrium and stability calculations predict that the average beta limit may be as high as 6% if the bootstrap current turns out to be as big as that expected in comparable tokamaks. The concept relies on a combination of helical fields and bootstrap current to achieve adequate rotational transform at low aspect ratio. A detailed manuscript describing some of this work will be published soon, cf. P.R. Garabedian, Quasi-axially symmetric stellarators, Proc. Natl. Acad. Sci. USA 95 (1998).

The Success of Linear Bootstrapping Models: Decision Domain-, Expertise-, and Criterion-Specific Meta-Analysis

PubMed Central

Kaufmann, Esther; Wittmann, Werner W.

2016-01-01

The success of bootstrapping or replacing a human judge with a model (e.g., an equation) has been demonstrated in Paul Meehl’s (1954) seminal work and bolstered by the results of several meta-analyses. To date, however, analyses considering different types of meta-analyses as well as the potential dependence of bootstrapping success on the decision domain, the level of expertise of the human judge, and the criterion for what constitutes an accurate decision have been missing from the literature. In this study, we addressed these research gaps by conducting a meta-analysis of lens model studies. We compared the results of a traditional (bare-bones) meta-analysis with findings of a meta-analysis of the success of bootstrap models corrected for various methodological artifacts. In line with previous studies, we found that bootstrapping was more successful than human judgment. Furthermore, bootstrapping was more successful in studies with an objective decision criterion than in studies with subjective or test score criteria. We did not find clear evidence that the success of bootstrapping depended on the decision domain (e.g., education or medicine) or on the judge’s level of expertise (novice or expert). Correction of methodological artifacts increased the estimated success of bootstrapping, suggesting that previous analyses without artifact correction (i.e., traditional meta-analyses) may have underestimated the value of bootstrapping models. PMID:27327085

Efficient bootstrap estimates for tail statistics

NASA Astrophysics Data System (ADS)

Breivik, Øyvind; Aarnes, Ole Johan

2017-03-01

Bootstrap resamples can be used to investigate the tail of empirical distributions as well as return value estimates from the extremal behaviour of the sample. Specifically, the confidence intervals on return value estimates or bounds on in-sample tail statistics can be obtained using bootstrap techniques. However, non-parametric bootstrapping from the entire sample is expensive. It is shown here that it suffices to bootstrap from a small subset consisting of the highest entries in the sequence to make estimates that are essentially identical to bootstraps from the entire sample. Similarly, bootstrap estimates of confidence intervals of threshold return estimates are found to be well approximated by using a subset consisting of the highest entries. This has practical consequences in fields such as meteorology, oceanography and hydrology where return values are calculated from very large gridded model integrations spanning decades at high temporal resolution or from large ensembles of independent and identically distributed model fields. In such cases the computational savings are substantial.

What Teachers Should Know About the Bootstrap: Resampling in the Undergraduate Statistics Curriculum

PubMed Central

Hesterberg, Tim C.

2015-01-01

Bootstrapping has enormous potential in statistics education and practice, but there are subtle issues and ways to go wrong. For example, the common combination of nonparametric bootstrapping and bootstrap percentile confidence intervals is less accurate than using t-intervals for small samples, though more accurate for larger samples. My goals in this article are to provide a deeper understanding of bootstrap methods—how they work, when they work or not, and which methods work better—and to highlight pedagogical issues. Supplementary materials for this article are available online. [Received December 2014. Revised August 2015] PMID:27019512

The PIT-trap-A "model-free" bootstrap procedure for inference about regression models with discrete, multivariate responses.

PubMed

Warton, David I; Thibaut, Loïc; Wang, Yi Alice

2017-01-01

Bootstrap methods are widely used in statistics, and bootstrapping of residuals can be especially useful in the regression context. However, difficulties are encountered extending residual resampling to regression settings where residuals are not identically distributed (thus not amenable to bootstrapping)-common examples including logistic or Poisson regression and generalizations to handle clustered or multivariate data, such as generalised estimating equations. We propose a bootstrap method based on probability integral transform (PIT-) residuals, which we call the PIT-trap, which assumes data come from some marginal distribution F of known parametric form. This method can be understood as a type of "model-free bootstrap", adapted to the problem of discrete and highly multivariate data. PIT-residuals have the key property that they are (asymptotically) pivotal. The PIT-trap thus inherits the key property, not afforded by any other residual resampling approach, that the marginal distribution of data can be preserved under PIT-trapping. This in turn enables the derivation of some standard bootstrap properties, including second-order correctness of pivotal PIT-trap test statistics. In multivariate data, bootstrapping rows of PIT-residuals affords the property that it preserves correlation in data without the need for it to be modelled, a key point of difference as compared to a parametric bootstrap. The proposed method is illustrated on an example involving multivariate abundance data in ecology, and demonstrated via simulation to have improved properties as compared to competing resampling methods.

Bootstrap Percolation on Homogeneous Trees Has 2 Phase Transitions

NASA Astrophysics Data System (ADS)

Fontes, L. R. G.; Schonmann, R. H.

2008-09-01

We study the threshold θ bootstrap percolation model on the homogeneous tree with degree b+1, 2≤ θ≤ b, and initial density p. It is known that there exists a nontrivial critical value for p, which we call p f , such that a) for p> p f , the final bootstrapped configuration is fully occupied for almost every initial configuration, and b) if p< p f , then for almost every initial configuration, the final bootstrapped configuration has density of occupied vertices less than 1. In this paper, we establish the existence of a distinct critical value for p, p c , such that 0< p c < p f , with the following properties: 1) if p≤ p c , then for almost every initial configuration there is no infinite cluster of occupied vertices in the final bootstrapped configuration; 2) if p> p c , then for almost every initial configuration there are infinite clusters of occupied vertices in the final bootstrapped configuration. Moreover, we show that 3) for p< p c , the distribution of the occupied cluster size in the final bootstrapped configuration has an exponential tail; 4) at p= p c , the expected occupied cluster size in the final bootstrapped configuration is infinite; 5) the probability of percolation of occupied vertices in the final bootstrapped configuration is continuous on [0, p f ] and analytic on ( p c , p f ), admitting an analytic continuation from the right at p c and, only in the case θ= b, also from the left at p f .

Bootstrap-based methods for estimating standard errors in Cox's regression analyses of clustered event times.

PubMed

Xiao, Yongling; Abrahamowicz, Michal

2010-03-30

We propose two bootstrap-based methods to correct the standard errors (SEs) from Cox's model for within-cluster correlation of right-censored event times. The cluster-bootstrap method resamples, with replacement, only the clusters, whereas the two-step bootstrap method resamples (i) the clusters, and (ii) individuals within each selected cluster, with replacement. In simulations, we evaluate both methods and compare them with the existing robust variance estimator and the shared gamma frailty model, which are available in statistical software packages. We simulate clustered event time data, with latent cluster-level random effects, which are ignored in the conventional Cox's model. For cluster-level covariates, both proposed bootstrap methods yield accurate SEs, and type I error rates, and acceptable coverage rates, regardless of the true random effects distribution, and avoid serious variance under-estimation by conventional Cox-based standard errors. However, the two-step bootstrap method over-estimates the variance for individual-level covariates. We also apply the proposed bootstrap methods to obtain confidence bands around flexible estimates of time-dependent effects in a real-life analysis of cluster event times.

Visuospatial bootstrapping: implicit binding of verbal working memory to visuospatial representations in children and adults.

PubMed

Darling, Stephen; Parker, Mary-Jane; Goodall, Karen E; Havelka, Jelena; Allen, Richard J

2014-03-01

When participants carry out visually presented digit serial recall, their performance is better if they are given the opportunity to encode extra visuospatial information at encoding-a phenomenon that has been termed visuospatial bootstrapping. This bootstrapping is the result of integration of information from different modality-specific short-term memory systems and visuospatial knowledge in long term memory, and it can be understood in the context of recent models of working memory that address multimodal binding (e.g., models incorporating an episodic buffer). Here we report a cross-sectional developmental study that demonstrated visuospatial bootstrapping in adults (n=18) and 9-year-old children (n=15) but not in 6-year-old children (n=18). This is the first developmental study addressing visuospatial bootstrapping, and results demonstrate that the developmental trajectory of bootstrapping is different from that of basic verbal and visuospatial working memory. This pattern suggests that bootstrapping (and hence integrative functions such as those associated with the episodic buffer) emerge independent of the development of basic working memory slave systems during childhood. Copyright © 2013 Elsevier Inc. All rights reserved.

A bootstrap based space-time surveillance model with an application to crime occurrences

NASA Astrophysics Data System (ADS)

Kim, Youngho; O'Kelly, Morton

2008-06-01

This study proposes a bootstrap-based space-time surveillance model. Designed to find emerging hotspots in near-real time, the bootstrap based model is characterized by its use of past occurrence information and bootstrap permutations. Many existing space-time surveillance methods, using population at risk data to generate expected values, have resulting hotspots bounded by administrative area units and are of limited use for near-real time applications because of the population data needed. However, this study generates expected values for local hotspots from past occurrences rather than population at risk. Also, bootstrap permutations of previous occurrences are used for significant tests. Consequently, the bootstrap-based model, without the requirement of population at risk data, (1) is free from administrative area restriction, (2) enables more frequent surveillance for continuously updated registry database, and (3) is readily applicable to criminology and epidemiology surveillance. The bootstrap-based model performs better for space-time surveillance than the space-time scan statistic. This is shown by means of simulations and an application to residential crime occurrences in Columbus, OH, year 2000.

Augmenting Literacy: The Role of Expertise in Digital Writing

ERIC Educational Resources Information Center

Van Ittersum, Derek

2011-01-01

This essay presents a model of reflective use of writing technologies, one that provides a means of more fully exploiting the possibilities of these tools for transforming writing activity. Derived from the work of computer designer Douglas Engelbart, the "bootstrapping" model of reflective use extends current arguments in the field…

Variance Estimation Using Replication Methods in Structural Equation Modeling with Complex Sample Data

ERIC Educational Resources Information Center

Stapleton, Laura M.

2008-01-01

This article discusses replication sampling variance estimation techniques that are often applied in analyses using data from complex sampling designs: jackknife repeated replication, balanced repeated replication, and bootstrapping. These techniques are used with traditional analyses such as regression, but are currently not used with structural…

What You See Is What You Get!

ERIC Educational Resources Information Center

Harrison, David

1979-01-01

The issue of observability and the relative roles of the senses and reason in understanding the world is reviewed. Eastern "mystical" philosophy serves as a focus in which interpretations of quantum mechanics, as well as the current bootstrap-quark controversy are seen in some slightly different contexts. (Author/GA)

An SAS Macro for Implementing the Modified Bollen-Stine Bootstrap for Missing Data: Implementing the Bootstrap Using Existing Structural Equation Modeling Software

ERIC Educational Resources Information Center

Enders, Craig K.

2005-01-01

The Bollen-Stine bootstrap can be used to correct for standard error and fit statistic bias that occurs in structural equation modeling (SEM) applications due to nonnormal data. The purpose of this article is to demonstrate the use of a custom SAS macro program that can be used to implement the Bollen-Stine bootstrap with existing SEM software.…

Comparison of Sample Size by Bootstrap and by Formulas Based on Normal Distribution Assumption.

PubMed

Wang, Zuozhen

2018-01-01

Bootstrapping technique is distribution-independent, which provides an indirect way to estimate the sample size for a clinical trial based on a relatively smaller sample. In this paper, sample size estimation to compare two parallel-design arms for continuous data by bootstrap procedure are presented for various test types (inequality, non-inferiority, superiority, and equivalence), respectively. Meanwhile, sample size calculation by mathematical formulas (normal distribution assumption) for the identical data are also carried out. Consequently, power difference between the two calculation methods is acceptably small for all the test types. It shows that the bootstrap procedure is a credible technique for sample size estimation. After that, we compared the powers determined using the two methods based on data that violate the normal distribution assumption. To accommodate the feature of the data, the nonparametric statistical method of Wilcoxon test was applied to compare the two groups in the data during the process of bootstrap power estimation. As a result, the power estimated by normal distribution-based formula is far larger than that by bootstrap for each specific sample size per group. Hence, for this type of data, it is preferable that the bootstrap method be applied for sample size calculation at the beginning, and that the same statistical method as used in the subsequent statistical analysis is employed for each bootstrap sample during the course of bootstrap sample size estimation, provided there is historical true data available that can be well representative of the population to which the proposed trial is planning to extrapolate.

Application of the Bootstrap Methods in Factor Analysis.

ERIC Educational Resources Information Center

Ichikawa, Masanori; Konishi, Sadanori

1995-01-01

A Monte Carlo experiment was conducted to investigate the performance of bootstrap methods in normal theory maximum likelihood factor analysis when the distributional assumption was satisfied or unsatisfied. Problems arising with the use of bootstrap methods are highlighted. (SLD)

Equilibrium drives of the low and high field side n = 2 plasma response and impact on global confinement

DOE Office of Scientific and Technical Information (OSTI.GOV)

Paz-Soldan, C.; Logan, N. C.; Haskey, S. R.

The nature of the multi-modal n=2 plasma response and its impact on global confinement is studied as a function of the axisymmetric equilibrium pressure, edge safety factor, collisionality, and L-versus H-mode conditions. Varying the relative phase (ΔΦ UL) between upper and lower in-vessel coils demonstrates that different n=2 poloidal spectra preferentially excite different plasma responses. These different plasma response modes are preferentially detected on the tokamak high-field side (HFS) or low-field side (LFS) midplanes, have different radial extents, couple differently to the resonant surfaces, and have variable impacts on edge stability and global confinement. In all equilibrium conditions studied, themore » observed confinement degradation shares the same ΔΦ UL dependence as the coupling to the resonant surfaces given by both ideal (IPEC) and resistive (MARS-F) MHD computation. Varying the edge safety factor shifts the equilibrium field-line pitch and thus the ΔΦ UL dependence of both the global confinement and the n=2 magnetic response. As edge safety factor is varied, modeling finds that the HFS response (but not the LFS response), the resonant surface coupling, and the edge displacements near the X-point all share the same ΔΦ UL dependence. The LFS response magnitude is strongly sensitive to the core pressure and is insensitive to the collisionality and edge safety factor. This indicates that the LFS measurements are primarily sensitive to a pressure-driven kink-ballooning mode that couples to the core plasma. MHD modeling accurately reproduces these (and indeed all) LFS experimental trends and supports this interpretation. In contrast to the LFS, the HFS magnetic response and correlated global confinement impact is unchanged with plasma pressure, but is strongly reduced in high collisionality conditions in both H- and L-mode. This experimentally suggests the bootstrap current drives the HFS response through the kink-peeling mode drive, though surprisingly weak or no dependence on the bootstrap current is seen in modeling. Instead, modeling is revealed to be very sensitive to the details of the edge current profile and equilibrium truncation. Furthermore, holding truncation fixed, most HFS experimental trends are not captured, thus demonstrating a stark contrast between the robustness of the HFS experimental results and the sensitivity of its computation.« less

Equilibrium drives of the low and high field side n  =  2 plasma response and impact on global confinement

NASA Astrophysics Data System (ADS)

Paz-Soldan, C.; Logan, N. C.; Haskey, S. R.; Nazikian, R.; Strait, E. J.; Chen, X.; Ferraro, N. M.; King, J. D.; Lyons, B. C.; Park, J.-K.

2016-05-01

The nature of the multi-modal n  =  2 plasma response and its impact on global confinement is studied as a function of the axisymmetric equilibrium pressure, edge safety factor, collisionality, and L-versus H-mode conditions. Varying the relative phase (Δ {φ\\text{UL}} ) between upper and lower in-vessel coils demonstrates that different n  =  2 poloidal spectra preferentially excite different plasma responses. These different plasma response modes are preferentially detected on the tokamak high-field side (HFS) or low-field side (LFS) midplanes, have different radial extents, couple differently to the resonant surfaces, and have variable impacts on edge stability and global confinement. In all equilibrium conditions studied, the observed confinement degradation shares the same Δ {φ\\text{UL}} dependence as the coupling to the resonant surfaces given by both ideal (IPEC) and resistive (MARS-F) MHD computation. Varying the edge safety factor shifts the equilibrium field-line pitch and thus the Δ {φ\\text{UL}} dependence of both the global confinement and the n  =  2 magnetic response. As edge safety factor is varied, modeling finds that the HFS response (but not the LFS response), the resonant surface coupling, and the edge displacements near the X-point all share the same Δ {φ\\text{UL}} dependence. The LFS response magnitude is strongly sensitive to the core pressure and is insensitive to the collisionality and edge safety factor. This indicates that the LFS measurements are primarily sensitive to a pressure-driven kink-ballooning mode that couples to the core plasma. MHD modeling accurately reproduces these (and indeed all) LFS experimental trends and supports this interpretation. In contrast to the LFS, the HFS magnetic response and correlated global confinement impact is unchanged with plasma pressure, but is strongly reduced in high collisionality conditions in both H- and L-mode. This experimentally suggests the bootstrap current drives the HFS response through the kink-peeling mode drive, though surprisingly weak or no dependence on the bootstrap current is seen in modeling. Instead, modeling is revealed to be very sensitive to the details of the edge current profile and equilibrium truncation. Holding truncation fixed, most HFS experimental trends are not captured, thus demonstrating a stark contrast between the robustness of the HFS experimental results and the sensitivity of its computation.

Equilibrium drives of the low and high field side n = 2 plasma response and impact on global confinement

DOE PAGES

Paz-Soldan, C.; Logan, N. C.; Haskey, S. R.; ...

2016-03-31

The nature of the multi-modal n=2 plasma response and its impact on global confinement is studied as a function of the axisymmetric equilibrium pressure, edge safety factor, collisionality, and L-versus H-mode conditions. Varying the relative phase (ΔΦ UL) between upper and lower in-vessel coils demonstrates that different n=2 poloidal spectra preferentially excite different plasma responses. These different plasma response modes are preferentially detected on the tokamak high-field side (HFS) or low-field side (LFS) midplanes, have different radial extents, couple differently to the resonant surfaces, and have variable impacts on edge stability and global confinement. In all equilibrium conditions studied, themore » observed confinement degradation shares the same ΔΦ UL dependence as the coupling to the resonant surfaces given by both ideal (IPEC) and resistive (MARS-F) MHD computation. Varying the edge safety factor shifts the equilibrium field-line pitch and thus the ΔΦ UL dependence of both the global confinement and the n=2 magnetic response. As edge safety factor is varied, modeling finds that the HFS response (but not the LFS response), the resonant surface coupling, and the edge displacements near the X-point all share the same ΔΦ UL dependence. The LFS response magnitude is strongly sensitive to the core pressure and is insensitive to the collisionality and edge safety factor. This indicates that the LFS measurements are primarily sensitive to a pressure-driven kink-ballooning mode that couples to the core plasma. MHD modeling accurately reproduces these (and indeed all) LFS experimental trends and supports this interpretation. In contrast to the LFS, the HFS magnetic response and correlated global confinement impact is unchanged with plasma pressure, but is strongly reduced in high collisionality conditions in both H- and L-mode. This experimentally suggests the bootstrap current drives the HFS response through the kink-peeling mode drive, though surprisingly weak or no dependence on the bootstrap current is seen in modeling. Instead, modeling is revealed to be very sensitive to the details of the edge current profile and equilibrium truncation. Furthermore, holding truncation fixed, most HFS experimental trends are not captured, thus demonstrating a stark contrast between the robustness of the HFS experimental results and the sensitivity of its computation.« less

Comparison of Dissolution Similarity Assessment Methods for Products with Large Variations: f2 Statistics and Model-Independent Multivariate Confidence Region Procedure for Dissolution Profiles of Multiple Oral Products.

PubMed

Yoshida, Hiroyuki; Shibata, Hiroko; Izutsu, Ken-Ichi; Goda, Yukihiro

2017-01-01

The current Japanese Ministry of Health Labour and Welfare (MHLW)'s Guideline for Bioequivalence Studies of Generic Products uses averaged dissolution rates for the assessment of dissolution similarity between test and reference formulations. This study clarifies how the application of model-independent multivariate confidence region procedure (Method B), described in the European Medical Agency and U.S. Food and Drug Administration guidelines, affects similarity outcomes obtained empirically from dissolution profiles with large variations in individual dissolution rates. Sixty-one datasets of dissolution profiles for immediate release, oral generic, and corresponding innovator products that showed large variation in individual dissolution rates in generic products were assessed on their similarity by using the f 2 statistics defined in the MHLW guidelines (MHLW f 2 method) and two different Method B procedures, including a bootstrap method applied with f 2 statistics (BS method) and a multivariate analysis method using the Mahalanobis distance (MV method). The MHLW f 2 and BS methods provided similar dissolution similarities between reference and generic products. Although a small difference in the similarity assessment may be due to the decrease in the lower confidence interval for expected f 2 values derived from the large variation in individual dissolution rates, the MV method provided results different from those obtained through MHLW f 2 and BS methods. Analysis of actual dissolution data for products with large individual variations would provide valuable information towards an enhanced understanding of these methods and their possible incorporation in the MHLW guidelines.

Small sample mediation testing: misplaced confidence in bootstrapped confidence intervals.

PubMed

Koopman, Joel; Howe, Michael; Hollenbeck, John R; Sin, Hock-Peng

2015-01-01

Bootstrapping is an analytical tool commonly used in psychology to test the statistical significance of the indirect effect in mediation models. Bootstrapping proponents have particularly advocated for its use for samples of 20-80 cases. This advocacy has been heeded, especially in the Journal of Applied Psychology, as researchers are increasingly utilizing bootstrapping to test mediation with samples in this range. We discuss reasons to be concerned with this escalation, and in a simulation study focused specifically on this range of sample sizes, we demonstrate not only that bootstrapping has insufficient statistical power to provide a rigorous hypothesis test in most conditions but also that bootstrapping has a tendency to exhibit an inflated Type I error rate. We then extend our simulations to investigate an alternative empirical resampling method as well as a Bayesian approach and demonstrate that they exhibit comparable statistical power to bootstrapping in small samples without the associated inflated Type I error. Implications for researchers testing mediation hypotheses in small samples are presented. For researchers wishing to use these methods in their own research, we have provided R syntax in the online supplemental materials. (c) 2015 APA, all rights reserved.

Forensic surface metrology: tool mark evidence.

PubMed

Gambino, Carol; McLaughlin, Patrick; Kuo, Loretta; Kammerman, Frani; Shenkin, Peter; Diaczuk, Peter; Petraco, Nicholas; Hamby, James; Petraco, Nicholas D K

2011-01-01

Over the last several decades, forensic examiners of impression evidence have come under scrutiny in the courtroom due to analysis methods that rely heavily on subjective morphological comparisons. Currently, there is no universally accepted system that generates numerical data to independently corroborate visual comparisons. Our research attempts to develop such a system for tool mark evidence, proposing a methodology that objectively evaluates the association of striated tool marks with the tools that generated them. In our study, 58 primer shear marks on 9 mm cartridge cases, fired from four Glock model 19 pistols, were collected using high-resolution white light confocal microscopy. The resulting three-dimensional surface topographies were filtered to extract all "waviness surfaces"-the essential "line" information that firearm and tool mark examiners view under a microscope. Extracted waviness profiles were processed with principal component analysis (PCA) for dimension reduction. Support vector machines (SVM) were used to make the profile-gun associations, and conformal prediction theory (CPT) for establishing confidence levels. At the 95% confidence level, CPT coupled with PCA-SVM yielded an empirical error rate of 3.5%. Complementary, bootstrap-based computations for estimated error rates were 0%, indicating that the error rate for the algorithmic procedure is likely to remain low on larger data sets. Finally, suggestions are made for practical courtroom application of CPT for assigning levels of confidence to SVM identifications of tool marks recorded with confocal microscopy. Copyright © 2011 Wiley Periodicals, Inc.

Bootstrap confidence levels for phylogenetic trees.

PubMed

Efron, B; Halloran, E; Holmes, S

1996-07-09

Evolutionary trees are often estimated from DNA or RNA sequence data. How much confidence should we have in the estimated trees? In 1985, Felsenstein [Felsenstein, J. (1985) Evolution 39, 783-791] suggested the use of the bootstrap to answer this question. Felsenstein's method, which in concept is a straightforward application of the bootstrap, is widely used, but has been criticized as biased in the genetics literature. This paper concerns the use of the bootstrap in the tree problem. We show that Felsenstein's method is not biased, but that it can be corrected to better agree with standard ideas of confidence levels and hypothesis testing. These corrections can be made by using the more elaborate bootstrap method presented here, at the expense of considerably more computation.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Batchelor, D.B.; Carreras, B.A.; Hirshman, S.P.

Significant progress has been made in the development of new modest-size compact stellarator devices that could test optimization principles for the design of a more attractive reactor. These are 3 and 4 field period low-aspect-ratio quasi-omnigenous (QO) stellarators based on an optimization method that targets improved confinement, stability, ease of coil design, low-aspect-ratio, and low bootstrap current.

Working Memory Deficits and Social Problems in Children with ADHD

ERIC Educational Resources Information Center

Kofler, Michael J.; Rapport, Mark D.; Bolden, Jennifer; Sarver, Dustin E.; Raiker, Joseph S.; Alderson, R. Matt

2011-01-01

Social problems are a prevalent feature of ADHD and reflect a major source of functional impairment for these children. The current study examined the impact of working memory deficits on parent- and teacher-reported social problems in a sample of children with ADHD and typically developing boys (N = 39). Bootstrapped, bias-corrected mediation…

An algebraic approach to the analytic bootstrap

DOE PAGES

Alday, Luis F.; Zhiboedov, Alexander

2017-04-27

We develop an algebraic approach to the analytic bootstrap in CFTs. By acting with the Casimir operator on the crossing equation we map the problem of doing large spin sums to any desired order to the problem of solving a set of recursion relations. We compute corrections to the anomalous dimension of large spin operators due to the exchange of a primary and its descendants in the crossed channel and show that this leads to a Borel-summable expansion. Here, we analyse higher order corrections to the microscopic CFT data in the direct channel and its matching to infinite towers ofmore » operators in the crossed channel. We apply this method to the critical O(N ) model. At large N we reproduce the first few terms in the large spin expansion of the known two-loop anomalous dimensions of higher spin currents in the traceless symmetric representation of O(N ) and make further predictions. At small N we present the results for the truncated large spin expansion series of anomalous dimensions of higher spin currents.« less

Progress toward steady-state tokamak operation exploiting the high bootstrap current fraction regime

DOE PAGES

Ren, Q. L.; Garofalo, A. M.; Gong, X. Z.; ...

2016-06-20

Recent DIII-D experiments have increased the normalized fusion performance of the high bootstrap current fraction tokamak regime toward reactor-relevant steady state operation. The experiments, conducted by a joint team of researchers from the DIII-D and EAST tokamaks, developed a fully noninductive scenario that could be extended on EAST to a demonstration of long pulse steady-state tokamak operation. Improved understanding of scenario stability has led to the achievement of very high values of β p and β N despite strong ITBs. Good confinement has been achieved with reduced toroidal rotation. These high β p plasmas challenge the energy transport understanding, especiallymore » in the electron energy channel. A new turbulent transport model, named 2 TGLF-SAT1, has been developed which improves the transport prediction. Experiments extending results to long pulse on EAST, based on the physics basis developed at DIII-D, have been conducted. Finally, more investigations will be carried out on EAST with more additional auxiliary power to come online in the near term.« less

Coefficient Alpha Bootstrap Confidence Interval under Nonnormality

ERIC Educational Resources Information Center

Padilla, Miguel A.; Divers, Jasmin; Newton, Matthew

2012-01-01

Three different bootstrap methods for estimating confidence intervals (CIs) for coefficient alpha were investigated. In addition, the bootstrap methods were compared with the most promising coefficient alpha CI estimation methods reported in the literature. The CI methods were assessed through a Monte Carlo simulation utilizing conditions…

Pearson-type goodness-of-fit test with bootstrap maximum likelihood estimation.

PubMed

Yin, Guosheng; Ma, Yanyuan

2013-01-01

The Pearson test statistic is constructed by partitioning the data into bins and computing the difference between the observed and expected counts in these bins. If the maximum likelihood estimator (MLE) of the original data is used, the statistic generally does not follow a chi-squared distribution or any explicit distribution. We propose a bootstrap-based modification of the Pearson test statistic to recover the chi-squared distribution. We compute the observed and expected counts in the partitioned bins by using the MLE obtained from a bootstrap sample. This bootstrap-sample MLE adjusts exactly the right amount of randomness to the test statistic, and recovers the chi-squared distribution. The bootstrap chi-squared test is easy to implement, as it only requires fitting exactly the same model to the bootstrap data to obtain the corresponding MLE, and then constructs the bin counts based on the original data. We examine the test size and power of the new model diagnostic procedure using simulation studies and illustrate it with a real data set.

Development of a repetitive compact torus injector

NASA Astrophysics Data System (ADS)

Onchi, Takumi; McColl, David; Dreval, Mykola; Rohollahi, Akbar; Xiao, Chijin; Hirose, Akira; Zushi, Hideki

2013-10-01

A system for Repetitive Compact Torus Injection (RCTI) has been developed at the University of Saskatchewan. CTI is a promising fuelling technology to directly fuel the core region of tokamak reactors. In addition to fuelling, CTI has also the potential for (a) optimization of density profile and thus bootstrap current and (b) momentum injection. For steady-state reactor operation, RCTI is necessary. The approach to RCTI is to charge a storage capacitor bank with a large capacitance and quickly charge the CT capacitor bank through a stack of integrated-gate bipolar transistors (IGBTs). When the CT bank is fully charged, the IGBT stack will be turned off to isolate banks, and CT formation/acceleration sequence will start. After formation of each CT, the fast bank will be replenished and a new CT will be formed and accelerated. Circuits for the formation and the acceleration in University of Saskatchewan CT Injector (USCTI) have been modified. Three CT shots at 10 Hz or eight shots at 1.7 Hz have been achieved. This work has been sponsored by the CRC and NSERC, Canada.

Neoclassical tearing mode seeding by coupling with infernal modes in low-shear tokamaks

NASA Astrophysics Data System (ADS)

Kleiner, A.; Graves, J. P.; Brunetti, D.; Cooper, W. A.; Halpern, F. D.; Luciani, J.-F.; Lütjens, H.

2016-09-01

A numerical and an analytical study of the triggering of resistive MHD modes in tokamak plasmas with low magnetic shear core is presented. Flat q profiles give rise to fast growing pressure driven MHD modes, such as infernal modes. It has been shown that infernal modes drive fast growing islands on neighbouring rational surfaces. Numerical simulations of such instabilities in a MAST-like configuration are performed with the initial value stability code XTOR-2F in the resistive frame. The evolution of magnetic islands are computed from XTOR-2F simulations and an analytical model is developed based on Rutherford’s theory in combination with a model of resistive infernal modes. The parameter {{Δ }\\prime} is extended from the linear phase to the non-linear phase. Additionally, the destabilising contribution due to a helically perturbed bootstrap current is considered. Comparing the numerical XTOR-2F simulations to the model, we find that coupling has a strong destabilising effect on (neoclassical) tearing modes and is able to seed 2/1 magnetic islands in situations when the standard NTM theory predicts stability.

The PIT-trap—A “model-free” bootstrap procedure for inference about regression models with discrete, multivariate responses

PubMed Central

Thibaut, Loïc; Wang, Yi Alice

2017-01-01

Bootstrap methods are widely used in statistics, and bootstrapping of residuals can be especially useful in the regression context. However, difficulties are encountered extending residual resampling to regression settings where residuals are not identically distributed (thus not amenable to bootstrapping)—common examples including logistic or Poisson regression and generalizations to handle clustered or multivariate data, such as generalised estimating equations. We propose a bootstrap method based on probability integral transform (PIT-) residuals, which we call the PIT-trap, which assumes data come from some marginal distribution F of known parametric form. This method can be understood as a type of “model-free bootstrap”, adapted to the problem of discrete and highly multivariate data. PIT-residuals have the key property that they are (asymptotically) pivotal. The PIT-trap thus inherits the key property, not afforded by any other residual resampling approach, that the marginal distribution of data can be preserved under PIT-trapping. This in turn enables the derivation of some standard bootstrap properties, including second-order correctness of pivotal PIT-trap test statistics. In multivariate data, bootstrapping rows of PIT-residuals affords the property that it preserves correlation in data without the need for it to be modelled, a key point of difference as compared to a parametric bootstrap. The proposed method is illustrated on an example involving multivariate abundance data in ecology, and demonstrated via simulation to have improved properties as compared to competing resampling methods. PMID:28738071

Bootstrap Estimates of Standard Errors in Generalizability Theory

ERIC Educational Resources Information Center

Tong, Ye; Brennan, Robert L.

2007-01-01

Estimating standard errors of estimated variance components has long been a challenging task in generalizability theory. Researchers have speculated about the potential applicability of the bootstrap for obtaining such estimates, but they have identified problems (especially bias) in using the bootstrap. Using Brennan's bias-correcting procedures…

Problems with Multivariate Normality: Can the Multivariate Bootstrap Help?

ERIC Educational Resources Information Center

Thompson, Bruce

Multivariate normality is required for some statistical tests. This paper explores the implications of violating the assumption of multivariate normality and illustrates a graphical procedure for evaluating multivariate normality. The logic for using the multivariate bootstrap is presented. The multivariate bootstrap can be used when distribution…

Lung cancer signature biomarkers: tissue specific semantic similarity based clustering of digital differential display (DDD) data.

PubMed

Srivastava, Mousami; Khurana, Pankaj; Sugadev, Ragumani

2012-11-02

The tissue-specific Unigene Sets derived from more than one million expressed sequence tags (ESTs) in the NCBI, GenBank database offers a platform for identifying significantly and differentially expressed tissue-specific genes by in-silico methods. Digital differential display (DDD) rapidly creates transcription profiles based on EST comparisons and numerically calculates, as a fraction of the pool of ESTs, the relative sequence abundance of known and novel genes. However, the process of identifying the most likely tissue for a specific disease in which to search for candidate genes from the pool of differentially expressed genes remains difficult. Therefore, we have used 'Gene Ontology semantic similarity score' to measure the GO similarity between gene products of lung tissue-specific candidate genes from control (normal) and disease (cancer) sets. This semantic similarity score matrix based on hierarchical clustering represents in the form of a dendrogram. The dendrogram cluster stability was assessed by multiple bootstrapping. Multiple bootstrapping also computes a p-value for each cluster and corrects the bias of the bootstrap probability. Subsequent hierarchical clustering by the multiple bootstrapping method (α = 0.95) identified seven clusters. The comparative, as well as subtractive, approach revealed a set of 38 biomarkers comprising four distinct lung cancer signature biomarker clusters (panel 1-4). Further gene enrichment analysis of the four panels revealed that each panel represents a set of lung cancer linked metastasis diagnostic biomarkers (panel 1), chemotherapy/drug resistance biomarkers (panel 2), hypoxia regulated biomarkers (panel 3) and lung extra cellular matrix biomarkers (panel 4). Expression analysis reveals that hypoxia induced lung cancer related biomarkers (panel 3), HIF and its modulating proteins (TGM2, CSNK1A1, CTNNA1, NAMPT/Visfatin, TNFRSF1A, ETS1, SRC-1, FN1, APLP2, DMBT1/SAG, AIB1 and AZIN1) are significantly down regulated. All down regulated genes in this panel were highly up regulated in most other types of cancers. These panels of proteins may represent signature biomarkers for lung cancer and will aid in lung cancer diagnosis and disease monitoring as well as in the prediction of responses to therapeutics.

Investigation of geomagnetic induced current at high latitude during the storm-time variation

NASA Astrophysics Data System (ADS)

Falayi, E. O.; Ogunmodimu, O.; Bolaji, O. S.; Ayanda, J. D.; Ojoniyi, O. S.

2017-06-01

During the geomagnetic disturbances, the geomagnetically induced current (GIC) are influenced by the geoelectric field flowing in conductive Earth. In this paper, we studied the variability of GICs, the time derivatives of the geomagnetic field (dB/dt), geomagnetic indices: Symmetric disturbance field in H (SYM-H) index, AU (eastward electrojet) and AL (westward electrojet) indices, Interplanetary parameters such as solar wind speed (v), and interplanetary magnetic field (Bz) during the geomagnetic storms on 31 March 2001, 21 October 2001, 6 November 2001, 29 October 2003, 31 October 2003 and 9 November 2004 with high solar wind speed due to a coronal mass ejection. Wavelet spectrum based approach was employed to analyze the GIC time series in a sequence of time scales of one to twenty four hours. It was observed that there are more concentration of power between the 14-24 h on 31 March 2001, 17-24 h on 21 October 2001, 1-7 h on 6 November 2001, two peaks were observed between 5-8 h and 21-24 h on 29 October 2003, 1-3 h on 31 October 2003 and 18-22 h on 9 November 2004. Bootstrap method was used to obtain regression correlations between the time derivative of the geomagnetic field (dB/dt) and the observed values of the geomagnetic induced current on 31 March 2001, 21 October 2001, 6 November 2001, 29 October 2003, 31 October 2003 and 9 November 2004 which shows a distributed cluster of correlation coefficients at around r = -0.567, -0.717, -0.477, -0.419, -0.210 and r = -0.488 respectively. We observed that high energy wavelet coefficient correlated well with bootstrap correlation, while low energy wavelet coefficient gives low bootstrap correlation. It was noticed that the geomagnetic storm has a influence on GIC and geomagnetic field derivatives (dB/dt). This might be ascribed to the coronal mass ejection with solar wind due to particle acceleration processes in the solar atmosphere.

Transport in the plateau regime in a tokamak pedestal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Seol, J.; Shaing, K. C.

In a tokamak H-mode, a strong E Multiplication-Sign B flow shear is generated during the L-H transition. Turbulence in a pedestal is suppressed significantly by this E Multiplication-Sign B flow shear. In this case, neoclassical transport may become important. The neoclassical fluxes are calculated in the plateau regime with the parallel plasma flow using their kinetic definitions. In an axisymmetric tokamak, the neoclassical particles fluxes can be decomposed into the banana-plateau flux and the Pfirsch-Schlueter flux. The banana-plateau particle flux is driven by the parallel viscous force and the Pfirsch-Schlueter flux by the poloidal variation of the friction force. Themore » combined quantity of the radial electric field and the parallel flow is determined by the flux surface averaged parallel momentum balance equation rather than requiring the ambipolarity of the total particle fluxes. In this process, the Pfirsch-Schlueter flux does not appear in the flux surface averaged parallel momentum equation. Only the banana-plateau flux is used to determine the parallel flow in the form of the flux surface averaged parallel viscosity. The heat flux, obtained using the solution of the parallel momentum balance equation, decreases exponentially in the presence of sonic M{sub p} without any enhancement over that in the standard neoclassical theory. Here, M{sub p} is a combination of the poloidal E Multiplication-Sign B flow and the parallel mass flow. The neoclassical bootstrap current in the plateau regime is presented. It indicates that the neoclassical bootstrap current also is related only to the banana-plateau fluxes. Finally, transport fluxes are calculated when M{sub p} is large enough to make the parallel electron viscosity comparable with the parallel ion viscosity. It is found that the bootstrap current has a finite value regardless of the magnitude of M{sub p}.« less

Impact of Sampling Density on the Extent of HIV Clustering

PubMed Central

Novitsky, Vlad; Moyo, Sikhulile; Lei, Quanhong; DeGruttola, Victor

2014-01-01

Abstract Identifying and monitoring HIV clusters could be useful in tracking the leading edge of HIV transmission in epidemics. Currently, greater specificity in the definition of HIV clusters is needed to reduce confusion in the interpretation of HIV clustering results. We address sampling density as one of the key aspects of HIV cluster analysis. The proportion of viral sequences in clusters was estimated at sampling densities from 1.0% to 70%. A set of 1,248 HIV-1C env gp120 V1C5 sequences from a single community in Botswana was utilized in simulation studies. Matching numbers of HIV-1C V1C5 sequences from the LANL HIV Database were used as comparators. HIV clusters were identified by phylogenetic inference under bootstrapped maximum likelihood and pairwise distance cut-offs. Sampling density below 10% was associated with stochastic HIV clustering with broad confidence intervals. HIV clustering increased linearly at sampling density >10%, and was accompanied by narrowing confidence intervals. Patterns of HIV clustering were similar at bootstrap thresholds 0.7 to 1.0, but the extent of HIV clustering decreased with higher bootstrap thresholds. The origin of sampling (local concentrated vs. scattered global) had a substantial impact on HIV clustering at sampling densities ≥10%. Pairwise distances at 10% were estimated as a threshold for cluster analysis of HIV-1 V1C5 sequences. The node bootstrap support distribution provided additional evidence for 10% sampling density as the threshold for HIV cluster analysis. The detectability of HIV clusters is substantially affected by sampling density. A minimal genotyping density of 10% and sampling density of 50–70% are suggested for HIV-1 V1C5 cluster analysis. PMID:25275430

Visceral sensitivity, anxiety, and smoking among treatment-seeking smokers.

PubMed

Zvolensky, Michael J; Bakhshaie, Jafar; Norton, Peter J; Smits, Jasper A J; Buckner, Julia D; Garey, Lorra; Manning, Kara

2017-12-01

It is widely recognized that smoking is related to abdominal pain and discomfort, as well as gastrointestinal disorders. Research has shown that visceral sensitivity, experiencing anxiety around gastrointestinal sensations, is associated with poorer gastrointestinal health and related health outcomes. Visceral sensitivity also increases anxiety symptoms and mediates the relation with other risk factors, including gastrointestinal distress. No work to date, however, has evaluated visceral sensitivity in the context of smoking despite the strong association between smoking and poor physical and mental health. The current study sought to examine visceral sensitivity as a unique predictor of cigarette dependence, threat-related smoking abstinence expectancies (somatic symptoms and harmful consequences), and perceived barriers for cessation via anxiety symptoms. Eighty-four treatment seeking adult daily smokers (M age =45.1years [SD=10.4]; 71.6% male) participated in this study. There was a statistically significant indirect effect of visceral sensitivity via general anxiety symptoms on cigarette dependence (b=0.02, SE=0.01, Bootstrapped 95% CI [0.006, 0.05]), smoking abstinence somatic expectancies (b=0.10, SE=0.03, Bootstrapped 95% CI [0.03, 0.19]), smoking abstinence harmful experiences (b=0.13, SE=0.05, Bootstrapped 95% CI [0.03, 0.25]), and barriers to cessation (b=0.05, SE=0.06, Bootstrapped 95% CI [0.01, 0.13]). Overall, the present study serves as an initial investigation into the nature of the associations between visceral sensitivity, anxiety symptoms, and clinically significant smoking processes among treatment-seeking smokers. Future work is needed to explore the extent to which anxiety accounts for relations between visceral sensitivity and other smoking processes (e.g., withdrawal, cessation outcome). Copyright © 2017 Elsevier Ltd. All rights reserved.

Unbiased Estimates of Variance Components with Bootstrap Procedures

ERIC Educational Resources Information Center

Brennan, Robert L.

2007-01-01

This article provides general procedures for obtaining unbiased estimates of variance components for any random-model balanced design under any bootstrap sampling plan, with the focus on designs of the type typically used in generalizability theory. The results reported here are particularly helpful when the bootstrap is used to estimate standard…

Explorations in Statistics: the Bootstrap

ERIC Educational Resources Information Center

Curran-Everett, Douglas

2009-01-01

Learning about statistics is a lot like learning about science: the learning is more meaningful if you can actively explore. This fourth installment of Explorations in Statistics explores the bootstrap. The bootstrap gives us an empirical approach to estimate the theoretical variability among possible values of a sample statistic such as the…

Bootstrapping Confidence Intervals for Robust Measures of Association.

ERIC Educational Resources Information Center

King, Jason E.

A Monte Carlo simulation study was conducted to determine the bootstrap correction formula yielding the most accurate confidence intervals for robust measures of association. Confidence intervals were generated via the percentile, adjusted, BC, and BC(a) bootstrap procedures and applied to the Winsorized, percentage bend, and Pearson correlation…

Bootstrap Prediction Intervals in Non-Parametric Regression with Applications to Anomaly Detection

NASA Technical Reports Server (NTRS)

Kumar, Sricharan; Srivistava, Ashok N.

2012-01-01

Prediction intervals provide a measure of the probable interval in which the outputs of a regression model can be expected to occur. Subsequently, these prediction intervals can be used to determine if the observed output is anomalous or not, conditioned on the input. In this paper, a procedure for determining prediction intervals for outputs of nonparametric regression models using bootstrap methods is proposed. Bootstrap methods allow for a non-parametric approach to computing prediction intervals with no specific assumptions about the sampling distribution of the noise or the data. The asymptotic fidelity of the proposed prediction intervals is theoretically proved. Subsequently, the validity of the bootstrap based prediction intervals is illustrated via simulations. Finally, the bootstrap prediction intervals are applied to the problem of anomaly detection on aviation data.

HEXT, a software supporting tree-based screens for hybrid taxa in multilocus data sets, and an evaluation of the homoplasy excess test.

PubMed

Schneider, Kevin; Koblmüller, Stephan; Sefc, Kristina M

2015-11-11

The homoplasy excess test (HET) is a tree-based screen for hybrid taxa in multilocus nuclear phylogenies. Homoplasy between a hybrid taxon and the clades containing the parental taxa reduces bootstrap support in the tree. The HET is based on the expectation that excluding the hybrid taxon from the data set increases the bootstrap support for the parental clades, whereas excluding non-hybrid taxa has little effect on statistical node support. To carry out a HET, bootstrap trees are calculated with taxon-jackknife data sets, that is excluding one taxon (species, population) at a time. Excess increase in bootstrap support for certain nodes upon exclusion of a particular taxon indicates the hybrid (the excluded taxon) and its parents (the clades with increased support).We introduce a new software program, hext, which generates the taxon-jackknife data sets, runs the bootstrap tree calculations, and identifies excess bootstrap increases as outlier values in boxplot graphs. hext is written in r language and accepts binary data (0/1; e.g. AFLP) as well as co-dominant SNP and genotype data.We demonstrate the usefulness of hext in large SNP data sets containing putative hybrids and their parents. For instance, using published data of the genus Vitis (~6,000 SNP loci), hext output supports V. × champinii as a hybrid between V. rupestris and V. mustangensis .With simulated SNP and AFLP data sets, excess increases in bootstrap support were not always connected with the hybrid taxon (false positives), whereas the expected bootstrap signal failed to appear on several occasions (false negatives). Potential causes for both types of spurious results are discussed.With both empirical and simulated data sets, the taxon-jackknife output generated by hext provided additional signatures of hybrid taxa, including changes in tree topology across trees, consistent effects of exclusions of the hybrid and the parent taxa, and moderate (rather than excessive) increases in bootstrap support. hext significantly facilitates the taxon-jackknife approach to hybrid taxon detection, even though the simple test for excess bootstrap increase may not reliably identify hybrid taxa in all applications.

NATbox: a network analysis toolbox in R.

PubMed

Chavan, Shweta S; Bauer, Michael A; Scutari, Marco; Nagarajan, Radhakrishnan

2009-10-08

There has been recent interest in capturing the functional relationships (FRs) from high-throughput assays using suitable computational techniques. FRs elucidate the working of genes in concert as a system as opposed to independent entities hence may provide preliminary insights into biological pathways and signalling mechanisms. Bayesian structure learning (BSL) techniques and its extensions have been used successfully for modelling FRs from expression profiles. Such techniques are especially useful in discovering undocumented FRs, investigating non-canonical signalling mechanisms and cross-talk between pathways. The objective of the present study is to develop a graphical user interface (GUI), NATbox: Network Analysis Toolbox in the language R that houses a battery of BSL algorithms in conjunction with suitable statistical tools for modelling FRs in the form of acyclic networks from gene expression profiles and their subsequent analysis. NATbox is a menu-driven open-source GUI implemented in the R statistical language for modelling and analysis of FRs from gene expression profiles. It provides options to (i) impute missing observations in the given data (ii) model FRs and network structure from gene expression profiles using a battery of BSL algorithms and identify robust dependencies using a bootstrap procedure, (iii) present the FRs in the form of acyclic graphs for visualization and investigate its topological properties using network analysis metrics, (iv) retrieve FRs of interest from published literature. Subsequently, use these FRs as structural priors in BSL (v) enhance scalability of BSL across high-dimensional data by parallelizing the bootstrap routines. NATbox provides a menu-driven GUI for modelling and analysis of FRs from gene expression profiles. By incorporating readily available functions from existing R-packages, it minimizes redundancy and improves reproducibility, transparency and sustainability, characteristic of open-source environments. NATbox is especially suited for interdisciplinary researchers and biologists with minimal programming experience and would like to use systems biology approaches without delving into the algorithmic aspects. The GUI provides appropriate parameter recommendations for the various menu options including default parameter choices for the user. NATbox can also prove to be a useful demonstration and teaching tool in graduate and undergraduate course in systems biology. It has been tested successfully under Windows and Linux operating systems. The source code along with installation instructions and accompanying tutorial can be found at http://bioinformatics.ualr.edu/natboxWiki/index.php/Main_Page.

Modeling T-cell activation using gene expression profiling and state-space models.

PubMed

Rangel, Claudia; Angus, John; Ghahramani, Zoubin; Lioumi, Maria; Sotheran, Elizabeth; Gaiba, Alessia; Wild, David L; Falciani, Francesco

2004-06-12

We have used state-space models to reverse engineer transcriptional networks from highly replicated gene expression profiling time series data obtained from a well-established model of T-cell activation. State space models are a class of dynamic Bayesian networks that assume that the observed measurements depend on some hidden state variables that evolve according to Markovian dynamics. These hidden variables can capture effects that cannot be measured in a gene expression profiling experiment, e.g. genes that have not been included in the microarray, levels of regulatory proteins, the effects of messenger RNA and protein degradation, etc. Bootstrap confidence intervals are developed for parameters representing 'gene-gene' interactions over time. Our models represent the dynamics of T-cell activation and provide a methodology for the development of rational and experimentally testable hypotheses. Supplementary data and Matlab computer source code will be made available on the web at the URL given below. http://public.kgi.edu/~wild/LDS/index.htm

Bootstrap Estimation of Sample Statistic Bias in Structural Equation Modeling.

ERIC Educational Resources Information Center

Thompson, Bruce; Fan, Xitao

This study empirically investigated bootstrap bias estimation in the area of structural equation modeling (SEM). Three correctly specified SEM models were used under four different sample size conditions. Monte Carlo experiments were carried out to generate the criteria against which bootstrap bias estimation should be judged. For SEM fit indices,…

A Bootstrap Generalization of Modified Parallel Analysis for IRT Dimensionality Assessment

ERIC Educational Resources Information Center

Finch, Holmes; Monahan, Patrick

2008-01-01

This article introduces a bootstrap generalization to the Modified Parallel Analysis (MPA) method of test dimensionality assessment using factor analysis. This methodology, based on the use of Marginal Maximum Likelihood nonlinear factor analysis, provides for the calculation of a test statistic based on a parametric bootstrap using the MPA…

Long multiplet bootstrap

NASA Astrophysics Data System (ADS)

Cornagliotto, Martina; Lemos, Madalena; Schomerus, Volker

2017-10-01

Applications of the bootstrap program to superconformal field theories promise unique new insights into their landscape and could even lead to the discovery of new models. Most existing results of the superconformal bootstrap were obtained form correlation functions of very special fields in short (BPS) representations of the superconformal algebra. Our main goal is to initiate a superconformal bootstrap for long multiplets, one that exploits all constraints from superprimaries and their descendants. To this end, we work out the Casimir equations for four-point correlators of long multiplets of the two-dimensional global N=2 superconformal algebra. After constructing the full set of conformal blocks we discuss two different applications. The first one concerns two-dimensional (2,0) theories. The numerical bootstrap analysis we perform serves a twofold purpose, as a feasibility study of our long multiplet bootstrap and also as an exploration of (2,0) theories. A second line of applications is directed towards four-dimensional N=3 SCFTs. In this context, our results imply a new bound c≥ 13/24 for the central charge of such models, which we argue cannot be saturated by an interacting SCFT.

Unconventional Expressions: Productive Syntax in the L2 Acquisition of Formulaic Language

ERIC Educational Resources Information Center

Bardovi-Harlig, Kathleen; Stringer, David

2017-01-01

This article presents a generative analysis of the acquisition of formulaic language as an alternative to current usage-based proposals. One influential view of the role of formulaic expressions in second language (L2) development is that they are a bootstrapping mechanism into the L2 grammar; an initial repertoire of constructions allows for…

Epistemic uncertainty in the location and magnitude of earthquakes in Italy from Macroseismic data

USGS Publications Warehouse

Bakun, W.H.; Gomez, Capera A.; Stucchi, M.

2011-01-01

Three independent techniques (Bakun and Wentworth, 1997; Boxer from Gasperini et al., 1999; and Macroseismic Estimation of Earthquake Parameters [MEEP; see Data and Resources section, deliverable D3] from R.M.W. Musson and M.J. Jimenez) have been proposed for estimating an earthquake location and magnitude from intensity data alone. The locations and magnitudes obtained for a given set of intensity data are almost always different, and no one technique is consistently best at matching instrumental locations and magnitudes of recent well-recorded earthquakes in Italy. Rather than attempting to select one of the three solutions as best, we use all three techniques to estimate the location and the magnitude and the epistemic uncertainties among them. The estimates are calculated using bootstrap resampled data sets with Monte Carlo sampling of a decision tree. The decision-tree branch weights are based on goodness-of-fit measures of location and magnitude for recent earthquakes. The location estimates are based on the spatial distribution of locations calculated from the bootstrap resampled data. The preferred source location is the locus of the maximum bootstrap location spatial density. The location uncertainty is obtained from contours of the bootstrap spatial density: 68% of the bootstrap locations are within the 68% confidence region, and so on. For large earthquakes, our preferred location is not associated with the epicenter but with a location on the extended rupture surface. For small earthquakes, the epicenters are generally consistent with the location uncertainties inferred from the intensity data if an epicenter inaccuracy of 2-3 km is allowed. The preferred magnitude is the median of the distribution of bootstrap magnitudes. As with location uncertainties, the uncertainties in magnitude are obtained from the distribution of bootstrap magnitudes: the bounds of the 68% uncertainty range enclose 68% of the bootstrap magnitudes, and so on. The instrumental magnitudes for large and small earthquakes are generally consistent with the confidence intervals inferred from the distribution of bootstrap resampled magnitudes.

Latent class profile of psychiatric symptoms and treatment utilization in a sample of patients with co-occurring disorders.

PubMed

Villalobos-Gallegos, Luis; Marín-Navarrete, Rodrigo; Roncero, Calos; González-Cantú, Hugo

2017-01-01

To identify symptom-based subgroups within a sample of patients with co-occurring disorders (CODs) and to analyze intersubgroup differences in mental health services utilization. Two hundred and fifteen patients with COD from an addiction clinic completed the Symptom Checklist 90-Revised. Subgroups were determined using latent class profile analysis. Services utilization data were collected from electronic records during a 3-year span. The five-class model obtained the best fit (Bayesian information criteria [BIC] = 3,546.95; adjusted BIC = 3,363.14; bootstrapped likelihood ratio test p < 0.0001). Differences between classes were quantitative, and groups were labeled according to severity: mild (26%), mild-moderate (28.8%), moderate (18.6%), moderate-severe (17.2%), and severe (9.3%). A significant time by class interaction was obtained (chi-square [χ2[15

Confidence Intervals for the Mean: To Bootstrap or Not to Bootstrap

ERIC Educational Resources Information Center

Calzada, Maria E.; Gardner, Holly

2011-01-01

The results of a simulation conducted by a research team involving undergraduate and high school students indicate that when data is symmetric the student's "t" confidence interval for a mean is superior to the studied non-parametric bootstrap confidence intervals. When data is skewed and for sample sizes n greater than or equal to 10,…

The Beginner's Guide to the Bootstrap Method of Resampling.

ERIC Educational Resources Information Center

Lane, Ginny G.

The bootstrap method of resampling can be useful in estimating the replicability of study results. The bootstrap procedure creates a mock population from a given sample of data from which multiple samples are then drawn. The method extends the usefulness of the jackknife procedure as it allows for computation of a given statistic across a maximal…

Application of a New Resampling Method to SEM: A Comparison of S-SMART with the Bootstrap

ERIC Educational Resources Information Center

Bai, Haiyan; Sivo, Stephen A.; Pan, Wei; Fan, Xitao

2016-01-01

Among the commonly used resampling methods of dealing with small-sample problems, the bootstrap enjoys the widest applications because it often outperforms its counterparts. However, the bootstrap still has limitations when its operations are contemplated. Therefore, the purpose of this study is to examine an alternative, new resampling method…

A Primer on Bootstrap Factor Analysis as Applied to Health Studies Research

ERIC Educational Resources Information Center

Lu, Wenhua; Miao, Jingang; McKyer, E. Lisako J.

2014-01-01

Objectives: To demonstrate how the bootstrap method could be conducted in exploratory factor analysis (EFA) with a syntax written in SPSS. Methods: The data obtained from the Texas Childhood Obesity Prevention Policy Evaluation project (T-COPPE project) were used for illustration. A 5-step procedure to conduct bootstrap factor analysis (BFA) was…

Forecasting drought risks for a water supply storage system using bootstrap position analysis

USGS Publications Warehouse

Tasker, Gary; Dunne, Paul

1997-01-01

Forecasting the likelihood of drought conditions is an integral part of managing a water supply storage and delivery system. Position analysis uses a large number of possible flow sequences as inputs to a simulation of a water supply storage and delivery system. For a given set of operating rules and water use requirements, water managers can use such a model to forecast the likelihood of specified outcomes such as reservoir levels falling below a specified level or streamflows falling below statutory passing flows a few months ahead conditioned on the current reservoir levels and streamflows. The large number of possible flow sequences are generated using a stochastic streamflow model with a random resampling of innovations. The advantages of this resampling scheme, called bootstrap position analysis, are that it does not rely on the unverifiable assumption of normality and it allows incorporation of long-range weather forecasts into the analysis.

Bootstrap position analysis for forecasting low flow frequency

USGS Publications Warehouse

Tasker, Gary D.; Dunne, P.

1997-01-01

A method of random resampling of residuals from stochastic models is used to generate a large number of 12-month-long traces of natural monthly runoff to be used in a position analysis model for a water-supply storage and delivery system. Position analysis uses the traces to forecast the likelihood of specified outcomes such as reservoir levels falling below a specified level or streamflows falling below statutory passing flows conditioned on the current reservoir levels and streamflows. The advantages of this resampling scheme, called bootstrap position analysis, are that it does not rely on the unverifiable assumption of normality, fewer parameters need to be estimated directly from the data, and accounting for parameter uncertainty is easily done. For a given set of operating rules and water-use requirements for a system, water managers can use such a model as a decision-making tool to evaluate different operating rules. ?? ASCE,.

Analysis of small sample size studies using nonparametric bootstrap test with pooled resampling method.

PubMed

Dwivedi, Alok Kumar; Mallawaarachchi, Indika; Alvarado, Luis A

2017-06-30

Experimental studies in biomedical research frequently pose analytical problems related to small sample size. In such studies, there are conflicting findings regarding the choice of parametric and nonparametric analysis, especially with non-normal data. In such instances, some methodologists questioned the validity of parametric tests and suggested nonparametric tests. In contrast, other methodologists found nonparametric tests to be too conservative and less powerful and thus preferred using parametric tests. Some researchers have recommended using a bootstrap test; however, this method also has small sample size limitation. We used a pooled method in nonparametric bootstrap test that may overcome the problem related with small samples in hypothesis testing. The present study compared nonparametric bootstrap test with pooled resampling method corresponding to parametric, nonparametric, and permutation tests through extensive simulations under various conditions and using real data examples. The nonparametric pooled bootstrap t-test provided equal or greater power for comparing two means as compared with unpaired t-test, Welch t-test, Wilcoxon rank sum test, and permutation test while maintaining type I error probability for any conditions except for Cauchy and extreme variable lognormal distributions. In such cases, we suggest using an exact Wilcoxon rank sum test. Nonparametric bootstrap paired t-test also provided better performance than other alternatives. Nonparametric bootstrap test provided benefit over exact Kruskal-Wallis test. We suggest using nonparametric bootstrap test with pooled resampling method for comparing paired or unpaired means and for validating the one way analysis of variance test results for non-normal data in small sample size studies. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Comparison of Parametric and Nonparametric Bootstrap Methods for Estimating Random Error in Equipercentile Equating

ERIC Educational Resources Information Center

Cui, Zhongmin; Kolen, Michael J.

2008-01-01

This article considers two methods of estimating standard errors of equipercentile equating: the parametric bootstrap method and the nonparametric bootstrap method. Using a simulation study, these two methods are compared under three sample sizes (300, 1,000, and 3,000), for two test content areas (the Iowa Tests of Basic Skills Maps and Diagrams…

swot: Super W Of Theta

NASA Astrophysics Data System (ADS)

Coupon, Jean; Leauthaud, Alexie; Kilbinger, Martin; Medezinski, Elinor

2017-07-01

SWOT (Super W Of Theta) computes two-point statistics for very large data sets, based on “divide and conquer” algorithms, mainly, but not limited to data storage in binary trees, approximation at large scale, parellelization (open MPI), and bootstrap and jackknife resampling methods “on the fly”. It currently supports projected and 3D galaxy auto and cross correlations, galaxy-galaxy lensing, and weighted histograms.

DOE Office of Scientific and Technical Information (OSTI.GOV)

A. Brooks; A.H. Reiman; G.H. Neilson

High-beta, low-aspect-ratio (compact) stellarators are promising solutions to the problem of developing a magnetic plasma configuration for magnetic fusion power plants that can be sustained in steady-state without disrupting. These concepts combine features of stellarators and advanced tokamaks and have aspect ratios similar to those of tokamaks (2-4). They are based on computed plasma configurations that are shaped in three dimensions to provide desired stability and transport properties. Experiments are planned as part of a program to develop this concept. A beta = 4% quasi-axisymmetric plasma configuration has been evaluated for the National Compact Stellarator Experiment (NCSX). It has amore » substantial bootstrap current and is shaped to stabilize ballooning, external kink, vertical, and neoclassical tearing modes without feedback or close-fitting conductors. Quasi-omnigeneous plasma configurations stable to ballooning modes at beta = 4% have been evaluated for the Quasi-Omnigeneous Stellarator (QOS) experiment. These equilibria have relatively low bootstrap currents and are insensitive to changes in beta. Coil configurations have been calculated that reconstruct these plasma configurations, preserving their important physics properties. Theory- and experiment-based confinement analyses are used to evaluate the technical capabilities needed to reach target plasma conditions. The physics basis for these complementary experiments is described.« less

Population pharmacokinetics and safety of eptifibatide in healthy Chinese volunteers and simulations on the dose regimens approved for a Western population.

PubMed

Wang, Xi-Pei; Zhou, Zhi-Ling; Yang, Min; Mai, Li-Ping; Zheng, Zhi-Jie; He, Guo-Dong; Wu, Yue-Heng; Lin, Qiu-Xiong; Shan, Zhi-Xin; Yu, Xi-Yong

2015-08-01

This study was designed to evaluate the pharmacokinetics (PK) and safety of eptifibatide in healthy Chinese volunteers and provide information for the further study in the Chinese population. 30 healthy volunteers (15 male) were enrolled in the study and divided into three dose groups (45 µg x kg⁻¹, 90 µg x kg⁻¹, and 180 µg x kg⁻¹). Plasma and urine samples were drawn after one single-bolus administration and measured by LC-MS/MS. The plasma and urine data were analyzed simultaneously by the population approach using the NONMEM software and evaluated by the visual predicted check (VPC) and bootstraping. The PK profiles of dose regimens approved for a Western population in the Chinese population were simulated. A two-compartment model adequately described the PK profiles of eptifibatide. The clearance (CL) and the distribution volume (V₁) of the central compartment were 0.128 L x h⁻¹ x kg⁻¹ and 0.175 L x kg⁻¹, respectively. The clearance (Q) and V₂of the peripheral compartment were 0.0988 L x h⁻¹ x kg⁻¹ and 0.147 L x kg⁻¹, respectively. The elimination fraction from plasma to urine (F₀) was 17.2%. No covariates were found to have a significant effect. Inter-individual variabilites were all within 33.9%. The VPC plots and bootstrap results indicated good precision and prediction of the model. The simulations of the approved regimens in the Chinese population showed much lower steady-state concentrations than the target concentration obtained from the Western clinical trials. No severe safety events were found in this study. The PK model of eptifibatide was established and could provide PK information for further studies in the Chinese population.

Semantic Drift in Espresso-style Bootstrapping: Graph-theoretic Analysis and Evaluation in Word Sense Disambiguation

NASA Astrophysics Data System (ADS)

Komachi, Mamoru; Kudo, Taku; Shimbo, Masashi; Matsumoto, Yuji

Bootstrapping has a tendency, called semantic drift, to select instances unrelated to the seed instances as the iteration proceeds. We demonstrate the semantic drift of Espresso-style bootstrapping has the same root as the topic drift of Kleinberg's HITS, using a simplified graph-based reformulation of bootstrapping. We confirm that two graph-based algorithms, the von Neumann kernels and the regularized Laplacian, can reduce the effect of semantic drift in the task of word sense disambiguation (WSD) on Senseval-3 English Lexical Sample Task. Proposed algorithms achieve superior performance to Espresso and previous graph-based WSD methods, even though the proposed algorithms have less parameters and are easy to calibrate.

Confidence limit calculation for antidotal potency ratio derived from lethal dose 50

PubMed Central

Manage, Ananda; Petrikovics, Ilona

2013-01-01

AIM: To describe confidence interval calculation for antidotal potency ratios using bootstrap method. METHODS: We can easily adapt the nonparametric bootstrap method which was invented by Efron to construct confidence intervals in such situations like this. The bootstrap method is a resampling method in which the bootstrap samples are obtained by resampling from the original sample. RESULTS: The described confidence interval calculation using bootstrap method does not require the sampling distribution antidotal potency ratio. This can serve as a substantial help for toxicologists, who are directed to employ the Dixon up-and-down method with the application of lower number of animals to determine lethal dose 50 values for characterizing the investigated toxic molecules and eventually for characterizing the antidotal protections by the test antidotal systems. CONCLUSION: The described method can serve as a useful tool in various other applications. Simplicity of the method makes it easier to do the calculation using most of the programming software packages. PMID:25237618

Topics in Statistical Calibration

DTIC Science & Technology

2014-03-27

on a parametric bootstrap where, instead of sampling directly from the residuals , samples are drawn from a normal distribution. This procedure will...addition to centering them (Davison and Hinkley, 1997). When there are outliers in the residuals , the bootstrap distribution of x̂0 can become skewed or...based and inversion methods using the linear mixed-effects model. Then, a simple parametric bootstrap algorithm is proposed that can be used to either

Variable selection under multiple imputation using the bootstrap in a prognostic study

PubMed Central

Heymans, Martijn W; van Buuren, Stef; Knol, Dirk L; van Mechelen, Willem; de Vet, Henrica CW

2007-01-01

Background Missing data is a challenging problem in many prognostic studies. Multiple imputation (MI) accounts for imputation uncertainty that allows for adequate statistical testing. We developed and tested a methodology combining MI with bootstrapping techniques for studying prognostic variable selection. Method In our prospective cohort study we merged data from three different randomized controlled trials (RCTs) to assess prognostic variables for chronicity of low back pain. Among the outcome and prognostic variables data were missing in the range of 0 and 48.1%. We used four methods to investigate the influence of respectively sampling and imputation variation: MI only, bootstrap only, and two methods that combine MI and bootstrapping. Variables were selected based on the inclusion frequency of each prognostic variable, i.e. the proportion of times that the variable appeared in the model. The discriminative and calibrative abilities of prognostic models developed by the four methods were assessed at different inclusion levels. Results We found that the effect of imputation variation on the inclusion frequency was larger than the effect of sampling variation. When MI and bootstrapping were combined at the range of 0% (full model) to 90% of variable selection, bootstrap corrected c-index values of 0.70 to 0.71 and slope values of 0.64 to 0.86 were found. Conclusion We recommend to account for both imputation and sampling variation in sets of missing data. The new procedure of combining MI with bootstrapping for variable selection, results in multivariable prognostic models with good performance and is therefore attractive to apply on data sets with missing values. PMID:17629912

Assessing uncertainties in superficial water provision by different bootstrap-based techniques

NASA Astrophysics Data System (ADS)

Rodrigues, Dulce B. B.; Gupta, Hoshin V.; Mendiondo, Eduardo Mario

2014-05-01

An assessment of water security can incorporate several water-related concepts, characterizing the interactions between societal needs, ecosystem functioning, and hydro-climatic conditions. The superficial freshwater provision level depends on the methods chosen for 'Environmental Flow Requirement' estimations, which integrate the sources of uncertainty in the understanding of how water-related threats to aquatic ecosystem security arise. Here, we develop an uncertainty assessment of superficial freshwater provision based on different bootstrap techniques (non-parametric resampling with replacement). To illustrate this approach, we use an agricultural basin (291 km2) within the Cantareira water supply system in Brazil monitored by one daily streamflow gage (24-year period). The original streamflow time series has been randomly resampled for different times or sample sizes (N = 500; ...; 1000), then applied to the conventional bootstrap approach and variations of this method, such as: 'nearest neighbor bootstrap'; and 'moving blocks bootstrap'. We have analyzed the impact of the sampling uncertainty on five Environmental Flow Requirement methods, based on: flow duration curves or probability of exceedance (Q90%, Q75% and Q50%); 7-day 10-year low-flow statistic (Q7,10); and presumptive standard (80% of the natural monthly mean ?ow). The bootstrap technique has been also used to compare those 'Environmental Flow Requirement' (EFR) methods among themselves, considering the difference between the bootstrap estimates and the "true" EFR characteristic, which has been computed averaging the EFR values of the five methods and using the entire streamflow record at monitoring station. This study evaluates the bootstrapping strategies, the representativeness of streamflow series for EFR estimates and their confidence intervals, in addition to overview of the performance differences between the EFR methods. The uncertainties arisen during EFR methods assessment will be propagated through water security indicators referring to water scarcity and vulnerability, seeking to provide meaningful support to end-users and water managers facing the incorporation of uncertainties in the decision making process.

A Pre-Screening Questionnaire to Predict Non-24-Hour Sleep-Wake Rhythm Disorder (N24HSWD) among the Blind

PubMed Central

Flynn-Evans, Erin E.; Lockley, Steven W.

2016-01-01

Study Objectives: There is currently no questionnaire-based pre-screening tool available to detect non-24-hour sleep-wake rhythm disorder (N24HSWD) among blind patients. Our goal was to develop such a tool, derived from gold standard, objective hormonal measures of circadian entrainment status, for the detection of N24HSWD among those with visual impairment. Methods: We evaluated the contribution of 40 variables in their ability to predict N24HSWD among 127 blind women, classified using urinary 6-sulfatoxymelatonin period, an objective marker of circadian entrainment status in this population. We subjected the 40 candidate predictors to 1,000 bootstrapped iterations of a logistic regression forward selection model to predict N24HSWD, with model inclusion set at the p < 0.05 level. We removed any predictors that were not selected at least 1% of the time in the 1,000 bootstrapped models and applied a second round of 1,000 bootstrapped logistic regression forward selection models to the remaining 23 candidate predictors. We included all questions that were selected at least 10% of the time in the final model. We subjected the selected predictors to a final logistic regression model to predict N24SWD over 1,000 bootstrapped models to calculate the concordance statistic and adjusted optimism of the final model. We used this information to generate a predictive model and determined the sensitivity and specificity of the model. Finally, we applied the model to a cohort of 1,262 blind women who completed the survey, but did not collect urine samples. Results: The final model consisted of eight questions. The concordance statistic, adjusted for bootstrapping, was 0.85. The positive predictive value was 88%, the negative predictive value was 79%. Applying this model to our larger dataset of women, we found that 61% of those without light perception, and 27% with some degree of light perception, would be referred for further screening for N24HSWD. Conclusions: Our model has predictive utility sufficient to serve as a pre-screening questionnaire for N24HSWD among the blind. Citation: Flynn-Evans EE, Lockley SW. A pre-screening questionnaire to predict non-24-hour sleep-wake rhythm disorder (N24HSWD) among the blind. J Clin Sleep Med 2016;12(5):703–710. PMID:26951421

Counting conformal correlators

NASA Astrophysics Data System (ADS)

Kravchuk, Petr; Simmons-Duffin, David

2018-02-01

We introduce simple group-theoretic techniques for classifying conformallyinvariant tensor structures. With them, we classify tensor structures of general n-point functions of non-conserved operators, and n ≥ 4-point functions of general conserved currents, with or without permutation symmetries, and in any spacetime dimension d. Our techniques are useful for bootstrap applications. The rules we derive simultaneously count tensor structures for flat-space scattering amplitudes in d + 1 dimensions.

Differentiating Dark Triad Traits Within and Across Interpersonal Circumplex Surfaces.

PubMed

Dowgwillo, Emily A; Pincus, Aaron L

2017-01-01

Recent discussions surrounding the Dark Triad (narcissism, psychopathy, and Machiavellianism) have centered on areas of distinctiveness and overlap. Given that interpersonal dysfunction is a core feature of Dark Triad traits, the current study uses self-report data from 562 undergraduate students to examine the interpersonal characteristics associated with narcissism, psychopathy, and Machiavellianism on four interpersonal circumplex (IPC) surfaces. The distinctiveness of these characteristics was examined using a novel bootstrapping methodology for computing confidence intervals around circumplex structural summary method parameters. Results suggest that Dark Triad traits exhibit distinct structural summary method parameters with narcissism characterized by high dominance, psychopathy characterized by a blend of high dominance and low affiliation, and Machiavellianism characterized by low affiliation on the problems, values, and efficacies IPC surfaces. Additionally, there was some heterogeneity in findings for different measures of psychopathy. Gender differences in structural summary parameters were examined, finding similar parameter values despite mean-level differences in Dark Triad traits. Finally, interpersonal information was integrated across different IPC surfaces to create profiles associated with each Dark Triad trait and to provide a more in-depth portrait of associated interpersonal dynamics. © The Author(s) 2016.

Simulation of the hybrid and steady state advanced operating modes in ITER

NASA Astrophysics Data System (ADS)

Kessel, C. E.; Giruzzi, G.; Sips, A. C. C.; Budny, R. V.; Artaud, J. F.; Basiuk, V.; Imbeaux, F.; Joffrin, E.; Schneider, M.; Murakami, M.; Luce, T.; St. John, Holger; Oikawa, T.; Hayashi, N.; Takizuka, T.; Ozeki, T.; Na, Y.-S.; Park, J. M.; Garcia, J.; Tucillo, A. A.

2007-09-01

Integrated simulations are performed to establish a physics basis, in conjunction with present tokamak experiments, for the operating modes in the International Thermonuclear Experimental Reactor (ITER). Simulations of the hybrid mode are done using both fixed and free-boundary 1.5D transport evolution codes including CRONOS, ONETWO, TSC/TRANSP, TOPICS and ASTRA. The hybrid operating mode is simulated using the GLF23 and CDBM05 energy transport models. The injected powers are limited to the negative ion neutral beam, ion cyclotron and electron cyclotron heating systems. Several plasma parameters and source parameters are specified for the hybrid cases to provide a comparison of 1.5D core transport modelling assumptions, source physics modelling assumptions, as well as numerous peripheral physics modelling. Initial results indicate that very strict guidelines will need to be imposed on the application of GLF23, for example, to make useful comparisons. Some of the variations among the simulations are due to source models which vary widely among the codes used. In addition, there are a number of peripheral physics models that should be examined, some of which include fusion power production, bootstrap current, treatment of fast particles and treatment of impurities. The hybrid simulations project to fusion gains of 5.6-8.3, βN values of 2.1-2.6 and fusion powers ranging from 350 to 500 MW, under the assumptions outlined in section 3. Simulations of the steady state operating mode are done with the same 1.5D transport evolution codes cited above, except the ASTRA code. In these cases the energy transport model is more difficult to prescribe, so that energy confinement models will range from theory based to empirically based. The injected powers include the same sources as used for the hybrid with the possible addition of lower hybrid. The simulations of the steady state mode project to fusion gains of 3.5-7, βN values of 2.3-3.0 and fusion powers of 290 to 415 MW, under the assumptions described in section 4. These simulations will be presented and compared with particular focus on the resulting temperature profiles, source profiles and peripheral physics profiles. The steady state simulations are at an early stage and are focused on developing a range of safety factor profiles with 100% non-inductive current.

Learning predictive models that use pattern discovery--a bootstrap evaluative approach applied in organ functioning sequences.

PubMed

Toma, Tudor; Bosman, Robert-Jan; Siebes, Arno; Peek, Niels; Abu-Hanna, Ameen

2010-08-01

An important problem in the Intensive Care is how to predict on a given day of stay the eventual hospital mortality for a specific patient. A recent approach to solve this problem suggested the use of frequent temporal sequences (FTSs) as predictors. Methods following this approach were evaluated in the past by inducing a model from a training set and validating the prognostic performance on an independent test set. Although this evaluative approach addresses the validity of the specific models induced in an experiment, it falls short of evaluating the inductive method itself. To achieve this, one must account for the inherent sources of variation in the experimental design. The main aim of this work is to demonstrate a procedure based on bootstrapping, specifically the .632 bootstrap procedure, for evaluating inductive methods that discover patterns, such as FTSs. A second aim is to apply this approach to find out whether a recently suggested inductive method that discovers FTSs of organ functioning status is superior over a traditional method that does not use temporal sequences when compared on each successive day of stay at the Intensive Care Unit. The use of bootstrapping with logistic regression using pre-specified covariates is known in the statistical literature. Using inductive methods of prognostic models based on temporal sequence discovery within the bootstrap procedure is however novel at least in predictive models in the Intensive Care. Our results of applying the bootstrap-based evaluative procedure demonstrate the superiority of the FTS-based inductive method over the traditional method in terms of discrimination as well as accuracy. In addition we illustrate the insights gained by the analyst into the discovered FTSs from the bootstrap samples. Copyright 2010 Elsevier Inc. All rights reserved.

Topical ketoprofen nanogel: artificial neural network optimization, clustered bootstrap validation, and in vivo activity evaluation based on longitudinal dose response modeling.

PubMed

Elkomy, Mohammed H; Elmenshawe, Shahira F; Eid, Hussein M; Ali, Ahmed M A

2016-11-01

This work aimed at investigating the potential of solid lipid nanoparticles (SLN) as carriers for topical delivery of Ketoprofen (KP); evaluating a novel technique incorporating Artificial Neural Network (ANN) and clustered bootstrap for optimization of KP-loaded SLN (KP-SLN); and demonstrating a longitudinal dose response (LDR) modeling-based approach to compare the activity of topical non-steroidal anti-inflammatory drug formulations. KP-SLN was fabricated by a modified emulsion/solvent evaporation method. Box-Behnken design was implemented to study the influence of glycerylpalmitostearate-to-KP ratio, Tween 80, and lecithin concentrations on particle size, entrapment efficiency, and amount of drug permeated through rat skin in 24 hours. Following clustered bootstrap ANN optimization, the optimized KP-SLN was incorporated into an aqueous gel and evaluated for rheology, in vitro release, permeability, skin irritation and in vivo activity using carrageenan-induced rat paw edema model and LDR mathematical model to analyze the time course of anti-inflammatory effect at various application durations. Lipid-to-drug ratio of 7.85 [bootstrap 95%CI: 7.63-8.51], Tween 80 of 1.27% [bootstrap 95%CI: 0.601-2.40%], and Lecithin of 0.263% [bootstrap 95%CI: 0.263-0.328%] were predicted to produce optimal characteristics. Compared with profenid® gel, the optimized KP-SLN gel exhibited slower release, faster permeability, better texture properties, greater efficacy, and similar potency. SLNs are safe and effective permeation enhancers. ANN coupled with clustered bootstrap is a useful method for finding optimal solutions and estimating uncertainty associated with them. LDR models allow mechanistic understanding of comparative in vivo performances of different topical formulations, and help design efficient dermatological bioequivalence assessment methods.

Lightweight CoAP-Based Bootstrapping Service for the Internet of Things.

PubMed

Garcia-Carrillo, Dan; Marin-Lopez, Rafael

2016-03-11

The Internet of Things (IoT) is becoming increasingly important in several fields of industrial applications and personal applications, such as medical e-health, smart cities, etc. The research into protocols and security aspects related to this area is continuously advancing in making these networks more reliable and secure, taking into account these aspects by design. Bootstrapping is a procedure by which a user obtains key material and configuration information, among other parameters, to operate as an authenticated party in a security domain. Until now solutions have focused on re-using security protocols that were not developed for IoT constraints. For this reason, in this work we propose a design and implementation of a lightweight bootstrapping service for IoT networks that leverages one of the application protocols used in IoT : Constrained Application Protocol (CoAP). Additionally, in order to provide flexibility, scalability, support for large scale deployment, accountability and identity federation, our design uses technologies such as the Extensible Authentication Protocol (EAP) and Authentication Authorization and Accounting (AAA). We have named this service CoAP-EAP. First, we review the state of the art in the field of bootstrapping and specifically for IoT. Second, we detail the bootstrapping service: the architecture with entities and interfaces and the flow operation. Third, we obtain performance measurements of CoAP-EAP (bootstrapping time, memory footprint, message processing time, message length and energy consumption) and compare them with PANATIKI. The most significant and constrained representative of the bootstrapping solutions related with CoAP-EAP. As we will show, our solution provides significant improvements, mainly due to an important reduction of the message length.

Lightweight CoAP-Based Bootstrapping Service for the Internet of Things

PubMed Central

Garcia-Carrillo, Dan; Marin-Lopez, Rafael

2016-01-01

The Internet of Things (IoT) is becoming increasingly important in several fields of industrial applications and personal applications, such as medical e-health, smart cities, etc. The research into protocols and security aspects related to this area is continuously advancing in making these networks more reliable and secure, taking into account these aspects by design. Bootstrapping is a procedure by which a user obtains key material and configuration information, among other parameters, to operate as an authenticated party in a security domain. Until now solutions have focused on re-using security protocols that were not developed for IoT constraints. For this reason, in this work we propose a design and implementation of a lightweight bootstrapping service for IoT networks that leverages one of the application protocols used in IoT : Constrained Application Protocol (CoAP). Additionally, in order to provide flexibility, scalability, support for large scale deployment, accountability and identity federation, our design uses technologies such as the Extensible Authentication Protocol (EAP) and Authentication Authorization and Accounting (AAA). We have named this service CoAP-EAP. First, we review the state of the art in the field of bootstrapping and specifically for IoT. Second, we detail the bootstrapping service: the architecture with entities and interfaces and the flow operation. Third, we obtain performance measurements of CoAP-EAP (bootstrapping time, memory footprint, message processing time, message length and energy consumption) and compare them with PANATIKI. The most significant and constrained representative of the bootstrapping solutions related with CoAP-EAP. As we will show, our solution provides significant improvements, mainly due to an important reduction of the message length. PMID:26978362

Recent Heating and Current Drive results on JET

NASA Astrophysics Data System (ADS)

Tuccillo, A. A.; Baranov, Y.; Barbato, E.; Bibet, Ph.; Castaldo, C.; Cesario, R.; Cocilovo, V.; Crisanti, F.; De Angelis, R.; Ekedahl, A. C.; Figueiredo, A.; Graham, M.; Granucci, G.; Hartmann, D.; Heikkinen, J.; Hellsten, T.; Imbeaux, F.; Jones, T. T. H.; Johnson, T.; Kirov, K. V.; Lamalle, P.; Laxaback, M.; Leuterer, F.; Litaudon, X.; Maget, P.; Mailloux, J.; Mantsinen, M. J.; Mayoral, M. L.; Meo, F.; Monakhov, I.; Nguyen, F.; Noterdaeme, J.-M.; Pericoli-Ridolfini, V.; Podda, S.; Panaccione, L.; Righi, E.; Rimini, F.; Sarazin, Y.; Sibley, A.; Staebler, A.; Tala, T.; Van Eester, D.

2001-10-01

An overview is presented of the results obtained on JET by the Heating and Current Drive Task Force (TF-H) in the period May 2000—March 2001. A strongly improved Lower Hybrid (LH) coupling was achieved by optimizing the plasma shape and by controlling the local edge density via the injection of CD4. Up to 4 MW have been coupled in type III ELMy H-mode and/or on Internal Transport Barrier (ITB) plasmas with reflection coefficients as low as 4%. Long lasting quasi steady-state ITBs have been obtained by adding the LH current to the bootstrap and beam driven components. Furthermore the use of LH in the pre-heat phase results in electron temperature in excess of 10 keV, deep negative magnetic shear and strongly reduced power threshold for ITB formation. Preliminary results on ICRF coupling are reported including the effect of CD4 injection and the commissioning of the wide band matching system on ELMy plasmas. IC CD scenarios have been studied in H and 3He minority and used to modify the stability of the sawtooth to influence the formation of seed islands for the appearance of NTM. Up to 3 MW of IC power was coupled in the high magnetic field fast wave CD scenario. Preliminary MSE measurements indicate differences in the current profiles between -90° and +90° phasing. Careful measurements of the toroidal rotation, in plasmas heated by ICRF only show some dependence on the position of the resonance layer. Finally the use of ICRF minority heating under real-time control, in response to measured plasma parameters to simulate the effect of alpha particles, is presented. ICRF heating results in ITER non-activated scenarios are reported in a companion paper.

Using Cluster Bootstrapping to Analyze Nested Data With a Few Clusters.

PubMed

Huang, Francis L

2018-04-01

Cluster randomized trials involving participants nested within intact treatment and control groups are commonly performed in various educational, psychological, and biomedical studies. However, recruiting and retaining intact groups present various practical, financial, and logistical challenges to evaluators and often, cluster randomized trials are performed with a low number of clusters (~20 groups). Although multilevel models are often used to analyze nested data, researchers may be concerned of potentially biased results due to having only a few groups under study. Cluster bootstrapping has been suggested as an alternative procedure when analyzing clustered data though it has seen very little use in educational and psychological studies. Using a Monte Carlo simulation that varied the number of clusters, average cluster size, and intraclass correlations, we compared standard errors using cluster bootstrapping with those derived using ordinary least squares regression and multilevel models. Results indicate that cluster bootstrapping, though more computationally demanding, can be used as an alternative procedure for the analysis of clustered data when treatment effects at the group level are of primary interest. Supplementary material showing how to perform cluster bootstrapped regressions using R is also provided.

Prospects for steady-state scenarios on JET

NASA Astrophysics Data System (ADS)

Litaudon, X.; Bizarro, J. P. S.; Challis, C. D.; Crisanti, F.; DeVries, P. C.; Lomas, P.; Rimini, F. G.; Tala, T. J. J.; Akers, R.; Andrew, Y.; Arnoux, G.; Artaud, J. F.; Baranov, Yu F.; Beurskens, M.; Brix, M.; Cesario, R.; DeLa Luna, E.; Fundamenski, W.; Giroud, C.; Hawkes, N. C.; Huber, A.; Joffrin, E.; Pitts, R. A.; Rachlew, E.; Reyes-Cortes, S. D. A.; Sharapov, S. E.; Zastrow, K. D.; Zimmermann, O.; JET EFDA contributors, the

2007-09-01

In the 2006 experimental campaign, progress has been made on JET to operate non-inductive scenarios at higher applied powers (31 MW) and density (nl ~ 4 × 1019 m-3), with ITER-relevant safety factor (q95 ~ 5) and plasma shaping, taking advantage of the new divertor capabilities. The extrapolation of the performance using transport modelling benchmarked on the experimental database indicates that the foreseen power upgrade (~45 MW) will allow the development of non-inductive scenarios where the bootstrap current is maximized together with the fusion yield and not, as in present-day experiments, at its expense. The tools for the long-term JET programme are the new ITER-like ICRH antenna (~15 MW), an upgrade of the NB power (35 MW/20 s or 17.5 MW/40 s), a new ITER-like first wall, a new pellet injector for edge localized mode control together with improved diagnostic and control capability. Operation with the new wall will set new constraints on non-inductive scenarios that are already addressed experimentally and in the modelling. The fusion performance and driven current that could be reached at high density and power have been estimated using either 0D or 1-1/2D validated transport models. In the high power case (45 MW), the calculations indicate the potential for the operational space of the non-inductive regime to be extended in terms of current (~2.5 MA) and density (nl > 5 × 1019 m-3), with high βN (βN > 3.0) and a fraction of the bootstrap current within 60-70% at high toroidal field (~3.5 T).

Bootstrapping Least Squares Estimates in Biochemical Reaction Networks

PubMed Central

Linder, Daniel F.

2015-01-01

The paper proposes new computational methods of computing confidence bounds for the least squares estimates (LSEs) of rate constants in mass-action biochemical reaction network and stochastic epidemic models. Such LSEs are obtained by fitting the set of deterministic ordinary differential equations (ODEs), corresponding to the large volume limit of a reaction network, to network’s partially observed trajectory treated as a continuous-time, pure jump Markov process. In the large volume limit the LSEs are asymptotically Gaussian, but their limiting covariance structure is complicated since it is described by a set of nonlinear ODEs which are often ill-conditioned and numerically unstable. The current paper considers two bootstrap Monte-Carlo procedures, based on the diffusion and linear noise approximations for pure jump processes, which allow one to avoid solving the limiting covariance ODEs. The results are illustrated with both in-silico and real data examples from the LINE 1 gene retrotranscription model and compared with those obtained using other methods. PMID:25898769

Percolation in education and application in the 21st century

NASA Astrophysics Data System (ADS)

Adler, Joan; Elfenbaum, Shaked; Sharir, Liran

2017-03-01

Percolation, "so simple you could teach it to your wife" (Chuck Newman, last century) is an ideal system to introduce young students to phase transitions. Two recent projects in the Computational Physics group at the Technion make this easy. One is a set of analog models to be mounted on our walls and enable visitors to switch between samples to see which mixtures of glass and metal objects have a percolating current. The second is a website enabling the creation of stereo samples of two and three dimensional clusters (suited for viewing with Oculus rift) on desktops, tablets and smartphones. Although there have been many physical applications for regular percolation in the past, for Bootstrap Percolation, where only sites with sufficient occupied neighbours remain active, there have not been a surfeit of condensed matter applications. We have found that the creation of diamond membranes for quantum computers can be modeled with a bootstrap process of graphitization in diamond, enabling prediction of optimal processing procedures.

The synchronous neural interactions test as a functional neuromarker for post-traumatic stress disorder (PTSD): a robust classification method based on the bootstrap

NASA Astrophysics Data System (ADS)

Georgopoulos, A. P.; Tan, H.-R. M.; Lewis, S. M.; Leuthold, A. C.; Winskowski, A. M.; Lynch, J. K.; Engdahl, B.

2010-02-01

Traumatic experiences can produce post-traumatic stress disorder (PTSD) which is a debilitating condition and for which no biomarker currently exists (Institute of Medicine (US) 2006 Posttraumatic Stress Disorder: Diagnosis and Assessment (Washington, DC: National Academies)). Here we show that the synchronous neural interactions (SNI) test which assesses the functional interactions among neural populations derived from magnetoencephalographic (MEG) recordings (Georgopoulos A P et al 2007 J. Neural Eng. 4 349-55) can successfully differentiate PTSD patients from healthy control subjects. Externally cross-validated, bootstrap-based analyses yielded >90% overall accuracy of classification. In addition, all but one of 18 patients who were not receiving medications for their disease were correctly classified. Altogether, these findings document robust differences in brain function between the PTSD and control groups that can be used for differential diagnosis and which possess the potential for assessing and monitoring disease progression and effects of therapy.

Service Mediation and Negotiation Bootstrapping as First Achievements Towards Self-adaptable Cloud Services

NASA Astrophysics Data System (ADS)

Brandic, Ivona; Music, Dejan; Dustdar, Schahram

Nowadays, novel computing paradigms as for example Cloud Computing are gaining more and more on importance. In case of Cloud Computing users pay for the usage of the computing power provided as a service. Beforehand they can negotiate specific functional and non-functional requirements relevant for the application execution. However, providing computing power as a service bears different research challenges. On one hand dynamic, versatile, and adaptable services are required, which can cope with system failures and environmental changes. On the other hand, human interaction with the system should be minimized. In this chapter we present the first results in establishing adaptable, versatile, and dynamic services considering negotiation bootstrapping and service mediation achieved in context of the Foundations of Self-Governing ICT Infrastructures (FoSII) project. We discuss novel meta-negotiation and SLA mapping solutions for Cloud services bridging the gap between current QoS models and Cloud middleware and representing important prerequisites for the establishment of autonomic Cloud services.

Phylogenetic relationships among arecoid palms (Arecaceae: Arecoideae)

PubMed Central

Baker, William J.; Norup, Maria V.; Clarkson, James J.; Couvreur, Thomas L. P.; Dowe, John L.; Lewis, Carl E.; Pintaud, Jean-Christophe; Savolainen, Vincent; Wilmot, Tomas; Chase, Mark W.

2011-01-01

Background and Aims The Arecoideae is the largest and most diverse of the five subfamilies of palms (Arecaceae/Palmae), containing >50 % of the species in the family. Despite its importance, phylogenetic relationships among Arecoideae are poorly understood. Here the most densely sampled phylogenetic analysis of Arecoideae available to date is presented. The results are used to test the current classification of the subfamily and to identify priority areas for future research. Methods DNA sequence data for the low-copy nuclear genes PRK and RPB2 were collected from 190 palm species, covering 103 (96 %) genera of Arecoideae. The data were analysed using the parsimony ratchet, maximum likelihood, and both likelihood and parsimony bootstrapping. Key Results and Conclusions Despite the recovery of paralogues and pseudogenes in a small number of taxa, PRK and RPB2 were both highly informative, producing well-resolved phylogenetic trees with many nodes well supported by bootstrap analyses. Simultaneous analyses of the combined data sets provided additional resolution and support. Two areas of incongruence between PRK and RPB2 were strongly supported by the bootstrap relating to the placement of tribes Chamaedoreeae, Iriarteeae and Reinhardtieae; the causes of this incongruence remain uncertain. The current classification within Arecoideae was strongly supported by the present data. Of the 14 tribes and 14 sub-tribes in the classification, only five sub-tribes from tribe Areceae (Basseliniinae, Linospadicinae, Oncospermatinae, Rhopalostylidinae and Verschaffeltiinae) failed to receive support. Three major higher level clades were strongly supported: (1) the RRC clade (Roystoneeae, Reinhardtieae and Cocoseae), (2) the POS clade (Podococceae, Oranieae and Sclerospermeae) and (3) the core arecoid clade (Areceae, Euterpeae, Geonomateae, Leopoldinieae, Manicarieae and Pelagodoxeae). However, new data sources are required to elucidate ambiguities that remain in phylogenetic relationships among and within the major groups of Arecoideae, as well as within the Areceae, the largest tribe in the palm family. PMID:21325340

Comparison of parametric and bootstrap method in bioequivalence test.

PubMed

Ahn, Byung-Jin; Yim, Dong-Seok

2009-10-01

The estimation of 90% parametric confidence intervals (CIs) of mean AUC and Cmax ratios in bioequivalence (BE) tests are based upon the assumption that formulation effects in log-transformed data are normally distributed. To compare the parametric CIs with those obtained from nonparametric methods we performed repeated estimation of bootstrap-resampled datasets. The AUC and Cmax values from 3 archived datasets were used. BE tests on 1,000 resampled datasets from each archived dataset were performed using SAS (Enterprise Guide Ver.3). Bootstrap nonparametric 90% CIs of formulation effects were then compared with the parametric 90% CIs of the original datasets. The 90% CIs of formulation effects estimated from the 3 archived datasets were slightly different from nonparametric 90% CIs obtained from BE tests on resampled datasets. Histograms and density curves of formulation effects obtained from resampled datasets were similar to those of normal distribution. However, in 2 of 3 resampled log (AUC) datasets, the estimates of formulation effects did not follow the Gaussian distribution. Bias-corrected and accelerated (BCa) CIs, one of the nonparametric CIs of formulation effects, shifted outside the parametric 90% CIs of the archived datasets in these 2 non-normally distributed resampled log (AUC) datasets. Currently, the 80~125% rule based upon the parametric 90% CIs is widely accepted under the assumption of normally distributed formulation effects in log-transformed data. However, nonparametric CIs may be a better choice when data do not follow this assumption.

Comparison of Parametric and Bootstrap Method in Bioequivalence Test

PubMed Central

Ahn, Byung-Jin

2009-01-01

The estimation of 90% parametric confidence intervals (CIs) of mean AUC and Cmax ratios in bioequivalence (BE) tests are based upon the assumption that formulation effects in log-transformed data are normally distributed. To compare the parametric CIs with those obtained from nonparametric methods we performed repeated estimation of bootstrap-resampled datasets. The AUC and Cmax values from 3 archived datasets were used. BE tests on 1,000 resampled datasets from each archived dataset were performed using SAS (Enterprise Guide Ver.3). Bootstrap nonparametric 90% CIs of formulation effects were then compared with the parametric 90% CIs of the original datasets. The 90% CIs of formulation effects estimated from the 3 archived datasets were slightly different from nonparametric 90% CIs obtained from BE tests on resampled datasets. Histograms and density curves of formulation effects obtained from resampled datasets were similar to those of normal distribution. However, in 2 of 3 resampled log (AUC) datasets, the estimates of formulation effects did not follow the Gaussian distribution. Bias-corrected and accelerated (BCa) CIs, one of the nonparametric CIs of formulation effects, shifted outside the parametric 90% CIs of the archived datasets in these 2 non-normally distributed resampled log (AUC) datasets. Currently, the 80~125% rule based upon the parametric 90% CIs is widely accepted under the assumption of normally distributed formulation effects in log-transformed data. However, nonparametric CIs may be a better choice when data do not follow this assumption. PMID:19915699

Prenatal Drug Exposure and Adolescent Cortisol Reactivity: Association with Behavioral Concerns.

PubMed

Buckingham-Howes, Stacy; Mazza, Dayna; Wang, Yan; Granger, Douglas A; Black, Maureen M

2016-09-01

To examine stress reactivity in a sample of adolescents with prenatal drug exposure (PDE) by examining the consequences of PDE on stress-related adrenocortical reactivity, behavioral problems, and drug experimentation during adolescence. Participants (76 PDE, 61 non-drug exposed [NE]; 99% African-American; 50% male; mean age = 14.17 yr, SD = 1.17) provided a urine sample, completed a drug use questionnaire, and provided saliva samples (later assayed for cortisol) before and after a mild laboratory stress task. Caregivers completed the Behavior Assessment System for Children, Second Edition (BASC II) and reported their relationship to the adolescent. The NE group was more likely to exhibit task-related cortisol reactivity compared to the PDE group. Overall behavior problems and drug experimentation were comparable across groups with no differences between PDE and NE groups. In unadjusted mediation analyses, cortisol reactivity mediated the association between PDE and BASC II aggression scores (95% bootstrap confidence interval [CI], 0.04-4.28), externalizing problems scores (95% bootstrap CI, 0.03-4.50), and drug experimentation (95% bootstrap CI, 0.001-0.54). The associations remain with the inclusion of gender as a covariate but not when age is included. Findings support and expand current research in cortisol reactivity and PDE by demonstrating that cortisol reactivity attenuates the association between PDE and behavioral problems (aggression) and drug experimentation. If replicated, PDE may have long-lasting effects on stress-sensitive physiological mechanisms associated with behavioral problems (aggression) and drug experimentation in adolescence.

Bootstrap investigation of the stability of a Cox regression model.

PubMed

Altman, D G; Andersen, P K

1989-07-01

We describe a bootstrap investigation of the stability of a Cox proportional hazards regression model resulting from the analysis of a clinical trial of azathioprine versus placebo in patients with primary biliary cirrhosis. We have considered stability to refer both to the choice of variables included in the model and, more importantly, to the predictive ability of the model. In stepwise Cox regression analyses of 100 bootstrap samples using 17 candidate variables, the most frequently selected variables were those selected in the original analysis, and no other important variable was identified. Thus there was no reason to doubt the model obtained in the original analysis. For each patient in the trial, bootstrap confidence intervals were constructed for the estimated probability of surviving two years. It is shown graphically that these intervals are markedly wider than those obtained from the original model.

Bootstrap and Counter-Bootstrap approaches for formation of the cortege of Informative indicators by Results of Measurements

NASA Astrophysics Data System (ADS)

Artemenko, M. V.; Chernetskaia, I. E.; Kalugina, N. M.; Shchekina, E. N.

2018-04-01

This article describes the solution of the actual problem of the productive formation of a cortege of informative measured features of the object of observation and / or control using author's algorithms for the use of bootstraps and counter-bootstraps technologies for processing the results of measurements of various states of the object on the basis of different volumes of the training sample. The work that is presented in this paper considers aggregation by specific indicators of informative capacity by linear, majority, logical and “greedy” methods, applied both individually and integrally. The results of the computational experiment are discussed, and in conclusion is drawn that the application of the proposed methods contributes to an increase in the efficiency of classification of the states of the object from the results of measurements.

How bootstrap can help in forecasting time series with more than one seasonal pattern

NASA Astrophysics Data System (ADS)

Cordeiro, Clara; Neves, M. Manuela

2012-09-01

The search for the future is an appealing challenge in time series analysis. The diversity of forecasting methodologies is inevitable and is still in expansion. Exponential smoothing methods are the launch platform for modelling and forecasting in time series analysis. Recently this methodology has been combined with bootstrapping revealing a good performance. The algorithm (Boot. EXPOS) using exponential smoothing and bootstrap methodologies, has showed promising results for forecasting time series with one seasonal pattern. In case of more than one seasonal pattern, the double seasonal Holt-Winters methods and the exponential smoothing methods were developed. A new challenge was now to combine these seasonal methods with bootstrap and carry over a similar resampling scheme used in Boot. EXPOS procedure. The performance of such partnership will be illustrated for some well-know data sets existing in software.

How Many Subjects are Needed for a Visual Field Normative Database? A Comparison of Ground Truth and Bootstrapped Statistics.

PubMed

Phu, Jack; Bui, Bang V; Kalloniatis, Michael; Khuu, Sieu K

2018-03-01

The number of subjects needed to establish the normative limits for visual field (VF) testing is not known. Using bootstrap resampling, we determined whether the ground truth mean, distribution limits, and standard deviation (SD) could be approximated using different set size ( x ) levels, in order to provide guidance for the number of healthy subjects required to obtain robust VF normative data. We analyzed the 500 Humphrey Field Analyzer (HFA) SITA-Standard results of 116 healthy subjects and 100 HFA full threshold results of 100 psychophysically experienced healthy subjects. These VFs were resampled (bootstrapped) to determine mean sensitivity, distribution limits (5th and 95th percentiles), and SD for different ' x ' and numbers of resamples. We also used the VF results of 122 glaucoma patients to determine the performance of ground truth and bootstrapped results in identifying and quantifying VF defects. An x of 150 (for SITA-Standard) and 60 (for full threshold) produced bootstrapped descriptive statistics that were no longer different to the original distribution limits and SD. Removing outliers produced similar results. Differences between original and bootstrapped limits in detecting glaucomatous defects were minimized at x = 250. Ground truth statistics of VF sensitivities could be approximated using set sizes that are significantly smaller than the original cohort. Outlier removal facilitates the use of Gaussian statistics and does not significantly affect the distribution limits. We provide guidance for choosing the cohort size for different levels of error when performing normative comparisons with glaucoma patients.

A bootstrap estimation scheme for chemical compositional data with nondetects

USGS Publications Warehouse

Palarea-Albaladejo, J; Martín-Fernández, J.A; Olea, Ricardo A.

2014-01-01

The bootstrap method is commonly used to estimate the distribution of estimators and their associated uncertainty when explicit analytic expressions are not available or are difficult to obtain. It has been widely applied in environmental and geochemical studies, where the data generated often represent parts of whole, typically chemical concentrations. This kind of constrained data is generically called compositional data, and they require specialised statistical methods to properly account for their particular covariance structure. On the other hand, it is not unusual in practice that those data contain labels denoting nondetects, that is, concentrations falling below detection limits. Nondetects impede the implementation of the bootstrap and represent an additional source of uncertainty that must be taken into account. In this work, a bootstrap scheme is devised that handles nondetects by adding an imputation step within the resampling process and conveniently propagates their associated uncertainly. In doing so, it considers the constrained relationships between chemical concentrations originated from their compositional nature. Bootstrap estimates using a range of imputation methods, including new stochastic proposals, are compared across scenarios of increasing difficulty. They are formulated to meet compositional principles following the log-ratio approach, and an adjustment is introduced in the multivariate case to deal with nonclosed samples. Results suggest that nondetect bootstrap based on model-based imputation is generally preferable. A robust approach based on isometric log-ratio transformations appears to be particularly suited in this context. Computer routines in the R statistical programming language are provided. 

Evaluating sufficient similarity for drinking-water disinfection by-product (DBP) mixtures with bootstrap hypothesis test procedures.

PubMed

Feder, Paul I; Ma, Zhenxu J; Bull, Richard J; Teuschler, Linda K; Rice, Glenn

2009-01-01

In chemical mixtures risk assessment, the use of dose-response data developed for one mixture to estimate risk posed by a second mixture depends on whether the two mixtures are sufficiently similar. While evaluations of similarity may be made using qualitative judgments, this article uses nonparametric statistical methods based on the "bootstrap" resampling technique to address the question of similarity among mixtures of chemical disinfectant by-products (DBP) in drinking water. The bootstrap resampling technique is a general-purpose, computer-intensive approach to statistical inference that substitutes empirical sampling for theoretically based parametric mathematical modeling. Nonparametric, bootstrap-based inference involves fewer assumptions than parametric normal theory based inference. The bootstrap procedure is appropriate, at least in an asymptotic sense, whether or not the parametric, distributional assumptions hold, even approximately. The statistical analysis procedures in this article are initially illustrated with data from 5 water treatment plants (Schenck et al., 2009), and then extended using data developed from a study of 35 drinking-water utilities (U.S. EPA/AMWA, 1989), which permits inclusion of a greater number of water constituents and increased structure in the statistical models.

Using the Bootstrap Method to Evaluate the Critical Range of Misfit for Polytomous Rasch Fit Statistics.

PubMed

Seol, Hyunsoo

2016-06-01

The purpose of this study was to apply the bootstrap procedure to evaluate how the bootstrapped confidence intervals (CIs) for polytomous Rasch fit statistics might differ according to sample sizes and test lengths in comparison with the rule-of-thumb critical value of misfit. A total of 25 simulated data sets were generated to fit the Rasch measurement and then a total of 1,000 replications were conducted to compute the bootstrapped CIs under each of 25 testing conditions. The results showed that rule-of-thumb critical values for assessing the magnitude of misfit were not applicable because the infit and outfit mean square error statistics showed different magnitudes of variability over testing conditions and the standardized fit statistics did not exactly follow the standard normal distribution. Further, they also do not share the same critical range for the item and person misfit. Based on the results of the study, the bootstrapped CIs can be used to identify misfitting items or persons as they offer a reasonable alternative solution, especially when the distributions of the infit and outfit statistics are not well known and depend on sample size. © The Author(s) 2016.

Characterization of Escherichia coli isolates from different fecal sources by means of classification tree analysis of fatty acid methyl ester (FAME) profiles.

PubMed

Seurinck, Sylvie; Deschepper, Ellen; Deboch, Bishaw; Verstraete, Willy; Siciliano, Steven

2006-03-01

Microbial source tracking (MST) methods need to be rapid, inexpensive and accurate. Unfortunately, many MST methods provide a wealth of information that is difficult to interpret by the regulators who use this information to make decisions. This paper describes the use of classification tree analysis to interpret the results of a MST method based on fatty acid methyl ester (FAME) profiles of Escherichia coli isolates, and to present results in a format readily interpretable by water quality managers. Raw sewage E. coli isolates and animal E. coli isolates from cow, dog, gull, and horse were isolated and their FAME profiles collected. Correct classification rates determined with leaveone-out cross-validation resulted in an overall low correct classification rate of 61%. A higher overall correct classification rate of 85% was obtained when the animal isolates were pooled together and compared to the raw sewage isolates. Bootstrap aggregation or adaptive resampling and combining of the FAME profile data increased correct classification rates substantially. Other MST methods may be better suited to differentiate between different fecal sources but classification tree analysis has enabled us to distinguish raw sewage from animal E. coli isolates, which previously had not been possible with other multivariate methods such as principal component analysis and cluster analysis.

Poor sleep as a pathophysiological pathway underlying the association between stressful experiences and the diurnal cortisol profile among children and adolescents

PubMed Central

Ly, Jinshia; McGrath, Jennifer J.; Gouin, Jean-Philippe

2017-01-01

Summary Recent evidence suggests that poor sleep is a potential pathway underlying the association between stressful experiences and the diurnal cortisol profile. However, existing findings are largely limited to adults. The present study examines whether poor sleep (duration, quality) mediates the relation between stressful experiences and the diurnal cortisol profile in children and adolescents. Children and adolescents (N = 220, Mage = 12.62) provided six saliva samples over two days to derive cortisol indices (bedtime, AUCAG, AUCTG, slopeMAX). Perceived stress, stressful life events, self-reported sleep duration, and sleep quality were measured. Using bootstrapping analyses, sleep quality mediated the relation between perceived stress and AUCTG (R2 = 0.10, F(7, 212) = 3.55, p = .001; 95% BCI[0.09, 1.15]), as well as the relation between stressful life events and AUCTG (R2 = 0.11, F(7, 212) = 3.69, p = .001; 95% BCI[0.40, 3.82]). These mediation models remained significant after adjusting for sleep duration, suggesting that poor sleep quality underlies the association between stressful experiences and the diurnal cortisol profile in children and adolescents. Longitudinal data combined with objectively-measured sleep is essential to further disentangle the complex association between sleep and stress. PMID:25889840

The Novaya Zemlya Event of 31 December 1992 and Seismic Identification Issues: Annual Seismic Research Symposium (15th) Held in Vail, Colorado on 8-10 September 1993

DTIC Science & Technology

1993-09-10

1993). A bootstrap generalizedlikelihood ratio test in discriminant analysis, Proc. 15th Annual Seismic Research Symposium, in press. I Hedlin, M., J... ratio indicate that the event does not belong to the first class. The bootstrap technique is used here as well to set the critical value of the test ...Methodist University. Baek, J., H. L. Gray, W. A. Woodward and M.D. Fisk (1993). A Bootstrap Generalized Likelihood Ratio Test in Discriminant

Combining Nordtest method and bootstrap resampling for measurement uncertainty estimation of hematology analytes in a medical laboratory.

PubMed

Cui, Ming; Xu, Lili; Wang, Huimin; Ju, Shaoqing; Xu, Shuizhu; Jing, Rongrong

2017-12-01

Measurement uncertainty (MU) is a metrological concept, which can be used for objectively estimating the quality of test results in medical laboratories. The Nordtest guide recommends an approach that uses both internal quality control (IQC) and external quality assessment (EQA) data to evaluate the MU. Bootstrap resampling is employed to simulate the unknown distribution based on the mathematical statistics method using an existing small sample of data, where the aim is to transform the small sample into a large sample. However, there have been no reports of the utilization of this method in medical laboratories. Thus, this study applied the Nordtest guide approach based on bootstrap resampling for estimating the MU. We estimated the MU for the white blood cell (WBC) count, red blood cell (RBC) count, hemoglobin (Hb), and platelets (Plt). First, we used 6months of IQC data and 12months of EQA data to calculate the MU according to the Nordtest method. Second, we combined the Nordtest method and bootstrap resampling with the quality control data and calculated the MU using MATLAB software. We then compared the MU results obtained using the two approaches. The expanded uncertainty results determined for WBC, RBC, Hb, and Plt using the bootstrap resampling method were 4.39%, 2.43%, 3.04%, and 5.92%, respectively, and 4.38%, 2.42%, 3.02%, and 6.00% with the existing quality control data (U [k=2]). For WBC, RBC, Hb, and Plt, the differences between the results obtained using the two methods were lower than 1.33%. The expanded uncertainty values were all less than the target uncertainties. The bootstrap resampling method allows the statistical analysis of the MU. Combining the Nordtest method and bootstrap resampling is considered a suitable alternative method for estimating the MU. Copyright © 2017 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Comparison between numerical and analytical results on the required rf current for stabilizing neoclassical tearing modes

NASA Astrophysics Data System (ADS)

Wang, Xiaojing; Yu, Qingquan; Zhang, Xiaodong; Zhang, Yang; Zhu, Sizheng; Wang, Xiaoguang; Wu, Bin

2018-04-01

Numerical studies on the stabilization of neoclassical tearing modes (NTMs) by electron cyclotron current drive (ECCD) have been carried out based on reduced MHD equations, focusing on the amount of the required driven current for mode stabilization and the comparison with analytical results. The dependence of the minimum driven current required for NTM stabilization on some parameters, including the bootstrap current density, radial width of the driven current, radial deviation of the driven current from the resonant surface, and the island width when applying ECCD, are studied. By fitting the numerical results, simple expressions for these dependences are obtained. Analysis based on the modified Rutherford equation (MRE) has also been carried out, and the corresponding results have the same trend as numerical ones, while a quantitative difference between them exists. This difference becomes smaller when the applied radio frequency (rf) current is smaller.

Exploring the Replicability of a Study's Results: Bootstrap Statistics for the Multivariate Case.

ERIC Educational Resources Information Center

Thompson, Bruce

1995-01-01

Use of the bootstrap method in a canonical correlation analysis to evaluate the replicability of a study's results is illustrated. More confidence may be vested in research results that replicate. (SLD)

The Role of GRAIL Orbit Determination in Preprocessing of Gravity Science Measurements

NASA Technical Reports Server (NTRS)

Kruizinga, Gerhard; Asmar, Sami; Fahnestock, Eugene; Harvey, Nate; Kahan, Daniel; Konopliv, Alex; Oudrhiri, Kamal; Paik, Meegyeong; Park, Ryan; Strekalov, Dmitry;

The economics of bootstrapping space industries - Development of an analytic computer model

NASA Technical Reports Server (NTRS)

Goldberg, A. H.; Criswell, D. R.

1982-01-01

A simple economic model of 'bootstrapping' industrial growth in space and on the Moon is presented. An initial space manufacturing facility (SMF) is assumed to consume lunar materials to enlarge the productive capacity in space. After reaching a predetermined throughput, the enlarged SMF is devoted to products which generate revenue continuously in proportion to the accumulated output mass (such as space solar power stations). Present discounted value and physical estimates for the general factors of production (transport, capital efficiency, labor, etc.) are combined to explore optimum growth in terms of maximized discounted revenues. It is found that 'bootstrapping' reduces the fractional cost to a space industry of transport off-Earth, permits more efficient use of a given transport fleet. It is concluded that more attention should be given to structuring 'bootstrapping' scenarios in which 'learning while doing' can be more fully incorporated in program analysis.

Towards a bootstrap approach to higher orders of epsilon expansion

NASA Astrophysics Data System (ADS)

Dey, Parijat; Kaviraj, Apratim

2018-02-01

We employ a hybrid approach in determining the anomalous dimension and OPE coefficient of higher spin operators in the Wilson-Fisher theory. First we do a large spin analysis for CFT data where we use results obtained from the usual and the Mellin bootstrap and also from Feynman diagram literature. This gives new predictions at O( ɛ 4) and O( ɛ 5) for anomalous dimensions and OPE coefficients, and also provides a cross-check for the results from Mellin bootstrap. These higher orders get contributions from all higher spin operators in the crossed channel. We also use the bootstrap in Mellin space method for ϕ 3 in d = 6 - ɛ CFT where we calculate general higher spin OPE data. We demonstrate a higher loop order calculation in this approach by summing over contributions from higher spin operators of the crossed channel in the same spirit as before.

Point Set Denoising Using Bootstrap-Based Radial Basis Function.

PubMed

Liew, Khang Jie; Ramli, Ahmad; Abd Majid, Ahmad

2016-01-01

This paper examines the application of a bootstrap test error estimation of radial basis functions, specifically thin-plate spline fitting, in surface smoothing. The presence of noisy data is a common issue of the point set model that is generated from 3D scanning devices, and hence, point set denoising is one of the main concerns in point set modelling. Bootstrap test error estimation, which is applied when searching for the smoothing parameters of radial basis functions, is revisited. The main contribution of this paper is a smoothing algorithm that relies on a bootstrap-based radial basis function. The proposed method incorporates a k-nearest neighbour search and then projects the point set to the approximated thin-plate spline surface. Therefore, the denoising process is achieved, and the features are well preserved. A comparison of the proposed method with other smoothing methods is also carried out in this study.

Abstract: Inference and Interval Estimation for Indirect Effects With Latent Variable Models.

PubMed

Falk, Carl F; Biesanz, Jeremy C

2011-11-30

Models specifying indirect effects (or mediation) and structural equation modeling are both popular in the social sciences. Yet relatively little research has compared methods that test for indirect effects among latent variables and provided precise estimates of the effectiveness of different methods. This simulation study provides an extensive comparison of methods for constructing confidence intervals and for making inferences about indirect effects with latent variables. We compared the percentile (PC) bootstrap, bias-corrected (BC) bootstrap, bias-corrected accelerated (BC a ) bootstrap, likelihood-based confidence intervals (Neale & Miller, 1997), partial posterior predictive (Biesanz, Falk, and Savalei, 2010), and joint significance tests based on Wald tests or likelihood ratio tests. All models included three reflective latent variables representing the independent, dependent, and mediating variables. The design included the following fully crossed conditions: (a) sample size: 100, 200, and 500; (b) number of indicators per latent variable: 3 versus 5; (c) reliability per set of indicators: .7 versus .9; (d) and 16 different path combinations for the indirect effect (α = 0, .14, .39, or .59; and β = 0, .14, .39, or .59). Simulations were performed using a WestGrid cluster of 1680 3.06GHz Intel Xeon processors running R and OpenMx. Results based on 1,000 replications per cell and 2,000 resamples per bootstrap method indicated that the BC and BC a bootstrap methods have inflated Type I error rates. Likelihood-based confidence intervals and the PC bootstrap emerged as methods that adequately control Type I error and have good coverage rates.

SYBR Green-based Real-Time PCR targeting kinetoplast DNA can be used to discriminate between the main etiologic agents of Brazilian cutaneous and visceral leishmaniases

PubMed Central

2012-01-01

Background Leishmaniases control has been hampered by the unavailability of rapid detection methods and the lack of suitable therapeutic and prophylactic measures. Accurate diagnosis, which can distinguish between Leishmania isolates, is essential for conducting appropriate prognosis, therapy and epidemiology. Molecular methods are currently being employed to detect Leishmania infection and categorize the parasites up to genus, complex or species level. Real-time PCR offers several advantages over traditional PCR, including faster processing time, higher sensitivity and decreased contamination risk. Results A SYBR Green real-time PCR targeting the conserved region of kinetoplast DNA minicircles was able to differentiate between Leishmania subgenera. A panel of reference strains representing subgenera Leishmania and Viannia was evaluated by the derivative dissociation curve analyses of the amplified fragment. Distinct values for the average melting temperature were observed, being 78.95°C ± 0.01 and 77.36°C ± 0.02 for Leishmania and Viannia, respectively (p < 0.05). Using the Neighbor-Joining method and Kimura 2-parameters, the alignment of 12 sequences from the amplified conserved minicircles segment grouped together L. (V.) braziliensis and L. (V.) shawii with a bootstrap value of 100%; while for L. (L.) infantum and L. (L.) amazonensis, two groups were formed with bootstrap values of 100% and 62%, respectively. The lower dissociation temperature observed for the subgenus Viannia amplicons could be due to a lower proportion of guanine/cytosine sites (43.6%) when compared to species from subgenus Leishmania (average of 48.4%). The method was validated with 30 clinical specimens from visceral or cutaneous leishmaniases patients living in Brazil and also with DNA samples from naturally infected Lutzomyia spp. captured in two Brazilian localities. Conclusions For all tested samples, a characteristic amplicon melting profile was evidenced for each Leishmania subgenus, corroborating the data from reference strains. Therefore, the analysis of thermal dissociation curves targeting the conserved kinetoplast DNA minicircles region is able to provide a rapid and reliable method to identify the main etiologic agents of cutaneous and visceral leishmaniases in endemic regions of Brazil. PMID:22240199

An attenuation of the 'normal' category effect in patients with Alzheimer's disease: a review and bootstrap analysis.

PubMed

Moreno-Martínez, F Javier; Laws, Keith R

2007-03-01

There is a consensus that Alzheimer's disease (AD) impairs semantic information, with one of the first markers being anomia i.e. an impaired ability to name items. Doubts remain, however, about whether this naming impairment differentially affects items from the living and nonliving knowledge domains. Most studies have reported an impairment for naming living things (e.g. animals or plants), a minority have found an impairment for nonliving things (e.g. tools or vehicles), and some have found no category-specific effect. A survey of the literature reveals that this lack of agreement may reflect a failure to control for intrinsic variables (such as familiarity) and the problems associated with ceiling effects in the control data. Investigating picture naming in 32 AD patients and 34 elderly controls, we used bootstrap techniques to deal with the abnormal distributions in both groups. Our analyses revealed the previously reported impairment for naming living things in AD patients and that this persisted even when intrinsic variables were covaried; however, covarying control performance eliminated the significant category effect. Indeed, the within-group comparison of living and nonliving naming revealed a larger effect size for controls than patients. We conclude that the category effect in Alzheimer's disease is no larger than is expected in the healthy brain and may even represent a small diminution of the normal profile.

Combining test statistics and models in bootstrapped model rejection: it is a balancing act

PubMed Central

2014-01-01

Background Model rejections lie at the heart of systems biology, since they provide conclusive statements: that the corresponding mechanistic assumptions do not serve as valid explanations for the experimental data. Rejections are usually done using e.g. the chi-square test (χ2) or the Durbin-Watson test (DW). Analytical formulas for the corresponding distributions rely on assumptions that typically are not fulfilled. This problem is partly alleviated by the usage of bootstrapping, a computationally heavy approach to calculate an empirical distribution. Bootstrapping also allows for a natural extension to estimation of joint distributions, but this feature has so far been little exploited. Results We herein show that simplistic combinations of bootstrapped tests, like the max or min of the individual p-values, give inconsistent, i.e. overly conservative or liberal, results. A new two-dimensional (2D) approach based on parametric bootstrapping, on the other hand, is found both consistent and with a higher power than the individual tests, when tested on static and dynamic examples where the truth is known. In the same examples, the most superior test is a 2D χ2vsχ2, where the second χ2-value comes from an additional help model, and its ability to describe bootstraps from the tested model. This superiority is lost if the help model is too simple, or too flexible. If a useful help model is found, the most powerful approach is the bootstrapped log-likelihood ratio (LHR). We show that this is because the LHR is one-dimensional, because the second dimension comes at a cost, and because LHR has retained most of the crucial information in the 2D distribution. These approaches statistically resolve a previously published rejection example for the first time. Conclusions We have shown how to, and how not to, combine tests in a bootstrap setting, when the combination is advantageous, and when it is advantageous to include a second model. These results also provide a deeper insight into the original motivation for formulating the LHR, for the more general setting of nonlinear and non-nested models. These insights are valuable in cases when accuracy and power, rather than computational speed, are prioritized. PMID:24742065

Trends and Correlation Estimation in Climate Sciences: Effects of Timescale Errors

NASA Astrophysics Data System (ADS)

Mudelsee, M.; Bermejo, M. A.; Bickert, T.; Chirila, D.; Fohlmeister, J.; Köhler, P.; Lohmann, G.; Olafsdottir, K.; Scholz, D.

2012-12-01

Trend describes time-dependence in the first moment of a stochastic process, and correlation measures the linear relation between two random variables. Accurately estimating the trend and correlation, including uncertainties, from climate time series data in the uni- and bivariate domain, respectively, allows first-order insights into the geophysical process that generated the data. Timescale errors, ubiquitious in paleoclimatology, where archives are sampled for proxy measurements and dated, poses a problem to the estimation. Statistical science and the various applied research fields, including geophysics, have almost completely ignored this problem due to its theoretical almost-intractability. However, computational adaptations or replacements of traditional error formulas have become technically feasible. This contribution gives a short overview of such an adaptation package, bootstrap resampling combined with parametric timescale simulation. We study linear regression, parametric change-point models and nonparametric smoothing for trend estimation. We introduce pairwise-moving block bootstrap resampling for correlation estimation. Both methods share robustness against autocorrelation and non-Gaussian distributional shape. We shortly touch computing-intensive calibration of bootstrap confidence intervals and consider options to parallelize the related computer code. Following examples serve not only to illustrate the methods but tell own climate stories: (1) the search for climate drivers of the Agulhas Current on recent timescales, (2) the comparison of three stalagmite-based proxy series of regional, western German climate over the later part of the Holocene, and (3) trends and transitions in benthic oxygen isotope time series from the Cenozoic. Financial support by Deutsche Forschungsgemeinschaft (FOR 668, FOR 1070, MU 1595/4-1) and the European Commission (MC ITN 238512, MC ITN 289447) is acknowledged.

A Critical Meta-Analysis of Lens Model Studies in Human Judgment and Decision-Making

PubMed Central

Kaufmann, Esther; Reips, Ulf-Dietrich; Wittmann, Werner W.

2013-01-01

Achieving accurate judgment (‘judgmental achievement’) is of utmost importance in daily life across multiple domains. The lens model and the lens model equation provide useful frameworks for modeling components of judgmental achievement and for creating tools to help decision makers (e.g., physicians, teachers) reach better judgments (e.g., a correct diagnosis, an accurate estimation of intelligence). Previous meta-analyses of judgment and decision-making studies have attempted to evaluate overall judgmental achievement and have provided the basis for evaluating the success of bootstrapping (i.e., replacing judges by linear models that guide decision making). However, previous meta-analyses have failed to appropriately correct for a number of study design artifacts (e.g., measurement error, dichotomization), which may have potentially biased estimations (e.g., of the variability between studies) and led to erroneous interpretations (e.g., with regards to moderator variables). In the current study we therefore conduct the first psychometric meta-analysis of judgmental achievement studies that corrects for a number of study design artifacts. We identified 31 lens model studies (N = 1,151, k = 49) that met our inclusion criteria. We evaluated overall judgmental achievement as well as whether judgmental achievement depended on decision domain (e.g., medicine, education) and/or the level of expertise (expert vs. novice). We also evaluated whether using corrected estimates affected conclusions with regards to the success of bootstrapping with psychometrically-corrected models. Further, we introduce a new psychometric trim-and-fill method to estimate the effect sizes of potentially missing studies correct psychometric meta-analyses for effects of publication bias. Comparison of the results of the psychometric meta-analysis with the results of a traditional meta-analysis (which only corrected for sampling error) indicated that artifact correction leads to a) an increase in values of the lens model components, b) reduced heterogeneity between studies, and c) increases the success of bootstrapping. We argue that psychometric meta-analysis is useful for accurately evaluating human judgment and show the success of bootstrapping. PMID:24391781

A critical meta-analysis of lens model studies in human judgment and decision-making.

PubMed

Kaufmann, Esther; Reips, Ulf-Dietrich; Wittmann, Werner W

2013-01-01

Achieving accurate judgment ('judgmental achievement') is of utmost importance in daily life across multiple domains. The lens model and the lens model equation provide useful frameworks for modeling components of judgmental achievement and for creating tools to help decision makers (e.g., physicians, teachers) reach better judgments (e.g., a correct diagnosis, an accurate estimation of intelligence). Previous meta-analyses of judgment and decision-making studies have attempted to evaluate overall judgmental achievement and have provided the basis for evaluating the success of bootstrapping (i.e., replacing judges by linear models that guide decision making). However, previous meta-analyses have failed to appropriately correct for a number of study design artifacts (e.g., measurement error, dichotomization), which may have potentially biased estimations (e.g., of the variability between studies) and led to erroneous interpretations (e.g., with regards to moderator variables). In the current study we therefore conduct the first psychometric meta-analysis of judgmental achievement studies that corrects for a number of study design artifacts. We identified 31 lens model studies (N = 1,151, k = 49) that met our inclusion criteria. We evaluated overall judgmental achievement as well as whether judgmental achievement depended on decision domain (e.g., medicine, education) and/or the level of expertise (expert vs. novice). We also evaluated whether using corrected estimates affected conclusions with regards to the success of bootstrapping with psychometrically-corrected models. Further, we introduce a new psychometric trim-and-fill method to estimate the effect sizes of potentially missing studies correct psychometric meta-analyses for effects of publication bias. Comparison of the results of the psychometric meta-analysis with the results of a traditional meta-analysis (which only corrected for sampling error) indicated that artifact correction leads to a) an increase in values of the lens model components, b) reduced heterogeneity between studies, and c) increases the success of bootstrapping. We argue that psychometric meta-analysis is useful for accurately evaluating human judgment and show the success of bootstrapping.

Simulating realistic predator signatures in quantitative fatty acid signature analysis

USGS Publications Warehouse

Bromaghin, Jeffrey F.

2015-01-01

Diet estimation is an important field within quantitative ecology, providing critical insights into many aspects of ecology and community dynamics. Quantitative fatty acid signature analysis (QFASA) is a prominent method of diet estimation, particularly for marine mammal and bird species. Investigators using QFASA commonly use computer simulation to evaluate statistical characteristics of diet estimators for the populations they study. Similar computer simulations have been used to explore and compare the performance of different variations of the original QFASA diet estimator. In both cases, computer simulations involve bootstrap sampling prey signature data to construct pseudo-predator signatures with known properties. However, bootstrap sample sizes have been selected arbitrarily and pseudo-predator signatures therefore may not have realistic properties. I develop an algorithm to objectively establish bootstrap sample sizes that generates pseudo-predator signatures with realistic properties, thereby enhancing the utility of computer simulation for assessing QFASA estimator performance. The algorithm also appears to be computationally efficient, resulting in bootstrap sample sizes that are smaller than those commonly used. I illustrate the algorithm with an example using data from Chukchi Sea polar bears (Ursus maritimus) and their marine mammal prey. The concepts underlying the approach may have value in other areas of quantitative ecology in which bootstrap samples are post-processed prior to their use.

Fusion Plasma Performance and Confinement Studies on JT-60 and JT-60U

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kamada, Y.; Fujita, T.; Ishida, S.

2002-09-15

Fusion plasma performance and confinement studies on JT-60 and JT-60U are reviewed. With the main aim of providing a physics basis for ITER and the steady-state tokamak reactors, JT-60/JT-60U has been developing and optimizing the operational concepts, and extending the discharge regimes toward sustainment of high integrated performance in the reactor relevant parameter regime. In addition to achievement of high fusion plasma performances such as the equivalent breakeven condition (Q{sub DT}{sup eq} up to 1.25) and a high fusion triple product n{sub D}(0){tau}{sub E}T{sub i}(0) = 1.5 x 10{sup 21} m{sup -3}skeV, JT-60U has demonstrated the integrated performance of highmore » confinement, high {beta}{sub N}, full non-inductive current drive with a large fraction of bootstrap current. These favorable performances have been achieved in the two advanced operation regimes, the reversed magnetic shear (RS) and the weak magnetic shear (high-{beta}{sub p}) ELMy H modes characterized by both internal transport barriers (ITB) and edge transport barriers (ETB). The key factors in optimizing these plasmas towards high integrated performance are control of profiles of current, pressure, rotation, etc. utilizing a variety of heating, current drive, torque input, and particle control capabilities and high triangularity operation. As represented by discovery of ITBs (density ITB in the central pellet mode, ion temperature ITB in the high-{beta}{sub p} mode, and electron temperature ITB in the reversed shear mode), confinement studies in JT-60/JT-60U have been emphasizing freedom and also restriction of radial profiles of temperature and density. In addition to characterization of confinement and analyses of transport properties of the OH, the L-mode, the H-mode, the pellet mode, the high-{beta}{sub p} mode, and the RS mode, JT-60U has clarified formation conditions, spatial structures and dynamics of edge and internal transport barriers, and evaluated effects of repetitive MHD events on confinement such as sawteeth and ELMs. Through these studies, JT-60U has demonstrated applicability of the high confinement modes to ITER and the steady-state tokamak reactors.« less

Migration of the ATLAS Metadata Interface (AMI) to Web 2.0 and cloud

NASA Astrophysics Data System (ADS)

Odier, J.; Albrand, S.; Fulachier, J.; Lambert, F.

2015-12-01

The ATLAS Metadata Interface (AMI), a mature application of more than 10 years of existence, is currently under adaptation to some recently available technologies. The web interfaces, which previously manipulated XML documents using XSL transformations, are being migrated to Asynchronous JavaScript (AJAX). Web development is considerably simplified by the introduction of a framework based on JQuery and Twitter Bootstrap. Finally, the AMI services are being migrated to an OpenStack cloud infrastructure.

On heat loading, novel divertors, and fusion reactors

NASA Astrophysics Data System (ADS)

Kotschenreuther, M.; Valanju, P. M.; Mahajan, S. M.; Wiley, J. C.

2007-07-01

The limited thermal power handling capacity of the standard divertors (used in current as well as projected tokamaks) is likely to force extremely high (˜90%) radiation fractions frad in tokamak fusion reactors that have heating powers considerably larger than ITER [D. J. Campbell, Phys. Plasmas 8, 2041 (2001)]. Such enormous values of necessary frad could have serious and debilitating consequences on the core confinement, stability, and dependability for a fusion power reactor, especially in reactors with Internal Transport Barriers. A new class of divertors, called X-divertors (XD), which considerably enhance the divertor thermal capacity through a flaring of the field lines only near the divertor plates, may be necessary and sufficient to overcome these problems and lead to a dependable fusion power reactor with acceptable economics. X-divertors will lower the bar on the necessary confinement to bring it in the range of the present experimental results. Its ability to reduce the radiative burden imparts the X-divertor with a key advantage. Lower radiation demands allow sharply peaked density profiles that enhance the bootstrap fraction creating the possibility for a highly increased beta for the same beta normal discharges. The X-divertor emerges as a beta-enhancer capable of raising it by up to roughly a factor of 2.

Finite Beta Boundary Magnetic Fields of NCSX

NASA Astrophysics Data System (ADS)

Grossman, A.; Kaiser, T.; Mioduszewski, P.

2004-11-01

The magnetic field between the plasma surface and wall of the National Compact Stellarator (NCSX), which uses quasi-symmetry to combine the best features of the tokamak and stellarator in a configuration of low aspect ratio is mapped via field line tracing in a range of finite beta in which part of the rotational transform is generated by the bootstrap current. We adopt the methodology developed for W7-X, in which an equilibrium solution is computed by an inverse equilibrium solver based on an energy minimizing variational moments code, VMEC2000[1], which solves directly for the shape of the flux surfaces given the external coils and their currents as well as a bootstrap current provided by a separate transport calculation. The VMEC solution and the Biot-Savart vacuum fields are coupled to the magnetic field solver for finite-beta equilibrium (MFBE2001)[2] code to determine the magnetic field on a 3D grid over a computational domain. It is found that the edge plasma is more stellarator-like, with a complex 3D structure, and less like the ordered 2D symmetric structure of a tokamak. The field lines make a transition from ergodically covering a surface to ergodically covering a volume, as the distance from the last closed magnetic surface is increased. The results are compared with the PIES[3] calculations. [1] S.P. Hirshman et al. Comput. Phys. Commun. 43 (1986) 143. [2] E. Strumberger, et al. Nucl. Fusion 42 (2002) 827. [3] A.H. Reiman and H.S. Greenside, Comput. Phys. Commun. 43, 157 (1986).

Bootstrap Methods: A Very Leisurely Look.

ERIC Educational Resources Information Center

Hinkle, Dennis E.; Winstead, Wayland H.

The Bootstrap method, a computer-intensive statistical method of estimation, is illustrated using a simple and efficient Statistical Analysis System (SAS) routine. The utility of the method for generating unknown parameters, including standard errors for simple statistics, regression coefficients, discriminant function coefficients, and factor…

Bootstrapping Student Understanding of What Is Going on in Econometrics.

ERIC Educational Resources Information Center

Kennedy, Peter E.

2001-01-01

Explains that econometrics is an intellectual game played by rules based on the sampling distribution concept. Contains explanations for why many students are uncomfortable with econometrics. Encourages instructors to use explain-how-to-bootstrap exercises to promote student understanding. (RLH)

Using the bootstrap to establish statistical significance for relative validity comparisons among patient-reported outcome measures

PubMed Central

2013-01-01

Background Relative validity (RV), a ratio of ANOVA F-statistics, is often used to compare the validity of patient-reported outcome (PRO) measures. We used the bootstrap to establish the statistical significance of the RV and to identify key factors affecting its significance. Methods Based on responses from 453 chronic kidney disease (CKD) patients to 16 CKD-specific and generic PRO measures, RVs were computed to determine how well each measure discriminated across clinically-defined groups of patients compared to the most discriminating (reference) measure. Statistical significance of RV was quantified by the 95% bootstrap confidence interval. Simulations examined the effects of sample size, denominator F-statistic, correlation between comparator and reference measures, and number of bootstrap replicates. Results The statistical significance of the RV increased as the magnitude of denominator F-statistic increased or as the correlation between comparator and reference measures increased. A denominator F-statistic of 57 conveyed sufficient power (80%) to detect an RV of 0.6 for two measures correlated at r = 0.7. Larger denominator F-statistics or higher correlations provided greater power. Larger sample size with a fixed denominator F-statistic or more bootstrap replicates (beyond 500) had minimal impact. Conclusions The bootstrap is valuable for establishing the statistical significance of RV estimates. A reasonably large denominator F-statistic (F > 57) is required for adequate power when using the RV to compare the validity of measures with small or moderate correlations (r < 0.7). Substantially greater power can be achieved when comparing measures of a very high correlation (r > 0.9). PMID:23721463

Four Bootstrap Confidence Intervals for the Binomial-Error Model.

ERIC Educational Resources Information Center

Lin, Miao-Hsiang; Hsiung, Chao A.

1992-01-01

Four bootstrap methods are identified for constructing confidence intervals for the binomial-error model. The extent to which similar results are obtained and the theoretical foundation of each method and its relevance and ranges of modeling the true score uncertainty are discussed. (SLD)

Nonparametric Regression and the Parametric Bootstrap for Local Dependence Assessment.

ERIC Educational Resources Information Center

Habing, Brian

2001-01-01

Discusses ideas underlying nonparametric regression and the parametric bootstrap with an overview of their application to item response theory and the assessment of local dependence. Illustrates the use of the method in assessing local dependence that varies with examinee trait levels. (SLD)

Application of the Bootstrap Statistical Method in Deriving Vibroacoustic Specifications

NASA Technical Reports Server (NTRS)

Hughes, William O.; Paez, Thomas L.

2006-01-01

This paper discusses the Bootstrap Method for specification of vibroacoustic test specifications. Vibroacoustic test specifications are necessary to properly accept or qualify a spacecraft and its components for the expected acoustic, random vibration and shock environments seen on an expendable launch vehicle. Traditionally, NASA and the U.S. Air Force have employed methods of Normal Tolerance Limits to derive these test levels based upon the amount of data available, and the probability and confidence levels desired. The Normal Tolerance Limit method contains inherent assumptions about the distribution of the data. The Bootstrap is a distribution-free statistical subsampling method which uses the measured data themselves to establish estimates of statistical measures of random sources. This is achieved through the computation of large numbers of Bootstrap replicates of a data measure of interest and the use of these replicates to derive test levels consistent with the probability and confidence desired. The comparison of the results of these two methods is illustrated via an example utilizing actual spacecraft vibroacoustic data.

The Reliability and Stability of an Inferred Phylogenetic Tree from Empirical Data.

PubMed

Katsura, Yukako; Stanley, Craig E; Kumar, Sudhir; Nei, Masatoshi

2017-03-01

The reliability of a phylogenetic tree obtained from empirical data is usually measured by the bootstrap probability (Pb) of interior branches of the tree. If the bootstrap probability is high for most branches, the tree is considered to be reliable. If some interior branches show relatively low bootstrap probabilities, we are not sure that the inferred tree is really reliable. Here, we propose another quantity measuring the reliability of the tree called the stability of a subtree. This quantity refers to the probability of obtaining a subtree (Ps) of an inferred tree obtained. We then show that if the tree is to be reliable, both Pb and Ps must be high. We also show that Ps is given by a bootstrap probability of the subtree with the closest outgroup sequence, and computer program RESTA for computing the Pb and Ps values will be presented. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Closure of the operator product expansion in the non-unitary bootstrap

DOE Office of Scientific and Technical Information (OSTI.GOV)

Esterlis, Ilya; Fitzpatrick, A. Liam; Ramirez, David M.

We use the numerical conformal bootstrap in two dimensions to search for finite, closed sub-algebras of the operator product expansion (OPE), without assuming unitarity. We find the minimal models as special cases, as well as additional lines of solutions that can be understood in the Coulomb gas formalism. All the solutions we find that contain the vacuum in the operator algebra are cases where the external operators of the bootstrap equation are degenerate operators, and we argue that this follows analytically from the expressions in arXiv:1202.4698 for the crossing matrices of Virasoro conformal blocks. Our numerical analysis is a specialmore » case of the “Gliozzi” bootstrap method, and provides a simpler setting in which to study technical challenges with the method. In the supplementary material, we provide a Mathematica notebook that automates the calculation of the crossing matrices and OPE coefficients for degenerate operators using the formulae of Dotsenko and Fateev.« less

A revisit to contingency table and tests of independence: bootstrap is preferred to Chi-square approximations as well as Fisher's exact test.

PubMed

Lin, Jyh-Jiuan; Chang, Ching-Hui; Pal, Nabendu

2015-01-01

To test the mutual independence of two qualitative variables (or attributes), it is a common practice to follow the Chi-square tests (Pearson's as well as likelihood ratio test) based on data in the form of a contingency table. However, it should be noted that these popular Chi-square tests are asymptotic in nature and are useful when the cell frequencies are "not too small." In this article, we explore the accuracy of the Chi-square tests through an extensive simulation study and then propose their bootstrap versions that appear to work better than the asymptotic Chi-square tests. The bootstrap tests are useful even for small-cell frequencies as they maintain the nominal level quite accurately. Also, the proposed bootstrap tests are more convenient than the Fisher's exact test which is often criticized for being too conservative. Finally, all test methods are applied to a few real-life datasets for demonstration purposes.

Closure of the operator product expansion in the non-unitary bootstrap

DOE PAGES

Esterlis, Ilya; Fitzpatrick, A. Liam; Ramirez, David M.

2016-11-07

We use the numerical conformal bootstrap in two dimensions to search for finite, closed sub-algebras of the operator product expansion (OPE), without assuming unitarity. We find the minimal models as special cases, as well as additional lines of solutions that can be understood in the Coulomb gas formalism. All the solutions we find that contain the vacuum in the operator algebra are cases where the external operators of the bootstrap equation are degenerate operators, and we argue that this follows analytically from the expressions in arXiv:1202.4698 for the crossing matrices of Virasoro conformal blocks. Our numerical analysis is a specialmore » case of the “Gliozzi” bootstrap method, and provides a simpler setting in which to study technical challenges with the method. In the supplementary material, we provide a Mathematica notebook that automates the calculation of the crossing matrices and OPE coefficients for degenerate operators using the formulae of Dotsenko and Fateev.« less

Edge Currents and Stability in DIII-D

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thomas, D M; Fenstermacher, M E; Finkenthal, D K

2004-12-01

Understanding the stability physics of the H-mode pedestal in tokamak devices requires an accurate measurement of plasma current in the pedestal region with good spatial resolution. Theoretically, the high pressure gradients achieved in the edge of H-mode plasmas should lead to generation of a significant edge current density peak through bootstrap and Pfirsh-Schl{umlt u}ter effects. This edge current is important for the achievement of second stability in the context of coupled magneto hydrodynamic (MHD) modes which are both pressure (ballooning) and current (peeling) driven. Many aspects of edge localized mode (ELM) behavior can be accounted for in terms of anmore » edge current density peak, with the identification of Type 1 ELMs as intermediate-n toroidal mode number MHD modes being a natural feature of this model. The development of a edge localized instabilities in tokamak experiments code (ELITE) based on this model allows one to efficiently calculate the stability and growth of the relevant modes for a broad range of plasma parameters and thus provides a framework for understanding the limits on pedestal height. This however requires an accurate assessment of the edge current. While estimates of j{sub edge} can be made based on specific bootstrap models, their validity may be limited in the edge (gradient scalelengths comparable to orbit size, large changes in collisionality, etc.). Therefore it is highly desirable to have an actual measurement. Such measurements have been made on the DIII-D tokamak using combined polarimetry and spectroscopy of an injected lithium beam. By analyzing one of the Zeeman-split 2S-2P lithium resonance line components, one can obtain direct information on the local magnetic field components. These values allow one to infer details of the edge current density. Because of the negligible Stark mixing of the relevant atomic levels in lithium, this method of determining j(r) is insensitive to the large local electric fields typically found in enhanced confinement (H-mode) edges, and thus avoids an ambiguity common to MSE measurements of B{sub pol}.« less

Edge Currents and Stability in DIII-D

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thomas, D M; Fenstermacher, M E; Finkenthal, D K

2005-05-05

Understanding the stability physics of the H-mode pedestal in tokamak devices requires an accurate measurement of plasma current in the pedestal region with good spatial resolution. Theoretically, the high pressure gradients achieved in the edge of H-mode plasmas should lead to generation of a significant edge current density peak through bootstrap and Pfirsh-Schlueter effects. This edge current is important for the achievement of second stability in the context of coupled magneto hydrodynamic (MHD) modes which are both pressure (ballooning) and current (peeling) driven [1]. Many aspects of edge localized mode (ELM) behavior can be accounted for in terms of anmore » edge current density peak, with the identification of Type 1 ELMs as intermediate-n toroidal mode number MHD modes being a natural feature of this model [2]. The development of a edge localized instabilities in tokamak experiments code (ELITE) based on this model allows one to efficiently calculate the stability and growth of the relevant modes for a broad range of plasma parameters [3,4] and thus provides a framework for understanding the limits on pedestal height. This however requires an accurate assessment of the edge current. While estimates of j{sub edge} can be made based on specific bootstrap models, their validity may be limited in the edge (gradient scale lengths comparable to orbit size, large changes in collisionality, etc.). Therefore it is highly desirable to have an actual measurement. Such measurements have been made on the DIII-D tokamak using combined polarimetry and spectroscopy of an injected lithium beam. [5,6]. By analyzing one of the Zeeman-split 2S-2P lithium resonance line components, one can obtain direct information on the local magnetic field components. These values allow one to infer details of the edge current density. Because of the negligible Stark mixing of the relevant atomic levels in lithium, this method of determining j(r) is insensitive to the large local electric fields typically found in enhanced confinement (H-mode) edges, and thus avoids an ambiguity common to MSE measurements of B{sub pol}.« less

Confidence Interval Coverage for Cohen's Effect Size Statistic

ERIC Educational Resources Information Center

Algina, James; Keselman, H. J.; Penfield, Randall D.

2006-01-01

Kelley compared three methods for setting a confidence interval (CI) around Cohen's standardized mean difference statistic: the noncentral-"t"-based, percentile (PERC) bootstrap, and biased-corrected and accelerated (BCA) bootstrap methods under three conditions of nonnormality, eight cases of sample size, and six cases of population…

A Bootstrap Procedure of Propensity Score Estimation

ERIC Educational Resources Information Center

Bai, Haiyan

2013-01-01

Propensity score estimation plays a fundamental role in propensity score matching for reducing group selection bias in observational data. To increase the accuracy of propensity score estimation, the author developed a bootstrap propensity score. The commonly used propensity score matching methods: nearest neighbor matching, caliper matching, and…

Software Supportability Risk Assessment in OT&E (Operational Test and Evaluation): Literature Review, Current Research Review, and Data Base Assemblage.

DTIC Science & Technology

1984-09-28

variables before simula- tion of model - Search for reality checks a, - Express uncertainty as a probability density distribution. a. H2 a, H-22 TWIF... probability that the software con- tains errors. This prior is updated as test failure data are accumulated. Only a p of 1 (software known to contain...discusssed; both parametric and nonparametric versions are presented. It is shown by the author that the bootstrap underlies the jackknife method and

Bootstrapping Methods Applied for Simulating Laboratory Works

ERIC Educational Resources Information Center

Prodan, Augustin; Campean, Remus

2005-01-01

Purpose: The aim of this work is to implement bootstrapping methods into software tools, based on Java. Design/methodology/approach: This paper presents a category of software e-tools aimed at simulating laboratory works and experiments. Findings: Both students and teaching staff use traditional statistical methods to infer the truth from sample…

Bootstrap Confidence Intervals for Ordinary Least Squares Factor Loadings and Correlations in Exploratory Factor Analysis

ERIC Educational Resources Information Center

Zhang, Guangjian; Preacher, Kristopher J.; Luo, Shanhong

2010-01-01

This article is concerned with using the bootstrap to assign confidence intervals for rotated factor loadings and factor correlations in ordinary least squares exploratory factor analysis. Coverage performances of "SE"-based intervals, percentile intervals, bias-corrected percentile intervals, bias-corrected accelerated percentile…

Bootstrap Estimation and Testing for Variance Equality.

ERIC Educational Resources Information Center

Olejnik, Stephen; Algina, James

The purpose of this study was to develop a single procedure for comparing population variances which could be used for distribution forms. Bootstrap methodology was used to estimate the variability of the sample variance statistic when the population distribution was normal, platykurtic and leptokurtic. The data for the study were generated and…

Bootstrapping the Syntactic Bootstrapper: Probabilistic Labeling of Prosodic Phrases

ERIC Educational Resources Information Center

Gutman, Ariel; Dautriche, Isabelle; Crabbé, Benoît; Christophe, Anne

2015-01-01

The "syntactic bootstrapping" hypothesis proposes that syntactic structure provides children with cues for learning the meaning of novel words. In this article, we address the question of how children might start acquiring some aspects of syntax before they possess a sizeable lexicon. The study presents two models of early syntax…

Evaluating the Use of Random Distribution Theory to Introduce Statistical Inference Concepts to Business Students

ERIC Educational Resources Information Center

Larwin, Karen H.; Larwin, David A.

2011-01-01

Bootstrapping methods and random distribution methods are increasingly recommended as better approaches for teaching students about statistical inference in introductory-level statistics courses. The authors examined the effect of teaching undergraduate business statistics students using random distribution and bootstrapping simulations. It is the…

Rapid and accurate taxonomic classification of insect (class Insecta) cytochrome c oxidase subunit 1 (COI) DNA barcode sequences using a naïve Bayesian classifier

PubMed Central

Porter, Teresita M; Gibson, Joel F; Shokralla, Shadi; Baird, Donald J; Golding, G Brian; Hajibabaei, Mehrdad

2014-01-01

Current methods to identify unknown insect (class Insecta) cytochrome c oxidase (COI barcode) sequences often rely on thresholds of distances that can be difficult to define, sequence similarity cut-offs, or monophyly. Some of the most commonly used metagenomic classification methods do not provide a measure of confidence for the taxonomic assignments they provide. The aim of this study was to use a naïve Bayesian classifier (Wang et al. Applied and Environmental Microbiology, 2007; 73: 5261) to automate taxonomic assignments for large batches of insect COI sequences such as data obtained from high-throughput environmental sequencing. This method provides rank-flexible taxonomic assignments with an associated bootstrap support value, and it is faster than the blast-based methods commonly used in environmental sequence surveys. We have developed and rigorously tested the performance of three different training sets using leave-one-out cross-validation, two field data sets, and targeted testing of Lepidoptera, Diptera and Mantodea sequences obtained from the Barcode of Life Data system. We found that type I error rates, incorrect taxonomic assignments with a high bootstrap support, were already relatively low but could be lowered further by ensuring that all query taxa are actually present in the reference database. Choosing bootstrap support cut-offs according to query length and summarizing taxonomic assignments to more inclusive ranks can also help to reduce error while retaining the maximum number of assignments. Additionally, we highlight gaps in the taxonomic and geographic representation of insects in public sequence databases that will require further work by taxonomists to improve the quality of assignments generated using any method.

A SYSTEMATIC RETRIEVAL ANALYSIS OF SECONDARY ECLIPSE SPECTRA. I. A COMPARISON OF ATMOSPHERIC RETRIEVAL TECHNIQUES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Line, Michael R.; Wolf, Aaron S.; Zhang, Xi

Exoplanet atmosphere spectroscopy enables us to improve our understanding of exoplanets just as remote sensing in our own solar system has increased our understanding of the solar system bodies. The challenge is to quantitatively determine the range of temperatures and molecular abundances allowed by the data, which is often difficult given the low information content of most exoplanet spectra that commonly leads to degeneracies in the interpretation. A variety of spectral retrieval approaches have been applied to exoplanet spectra, but no previous investigations have sought to compare these approaches. We compare three different retrieval methods: optimal estimation, differential evolution Markovmore » chain Monte Carlo, and bootstrap Monte Carlo on a synthetic water-dominated hot Jupiter. We discuss expectations of uncertainties in abundances and temperatures given current and potential future observations. In general, we find that the three approaches agree for high spectral resolution, high signal-to-noise data expected to come from potential future spaceborne missions, but disagree for low-resolution, low signal-to-noise spectra representative of current observations. We also compare the results from a parameterized temperature profile versus a full classical Level-by-Level approach and discriminate in which situations each of these approaches is applicable. Furthermore, we discuss the implications of our models for the inferred C-to-O ratios of exoplanetary atmospheres. Specifically, we show that in the observational limit of a few photometric points, the retrieved C/O is biased toward values near solar and near one simply due to the assumption of uninformative priors.« less

Impact of E × B shear flow on low-n MHD instabilities.

PubMed

Chen, J G; Xu, X Q; Ma, C H; Xi, P W; Kong, D F; Lei, Y A

2017-05-01

Recently, the stationary high confinement operations with improved pedestal conditions have been achieved in DIII-D [K. H. Burrell et al. , Phys. Plasmas 23 , 056103 (2016)], accompanying the spontaneous transition from the coherent edge harmonic oscillation (EHO) to the broadband MHD turbulence state by reducing the neutral beam injection torque to zero. It is highly significant for the burning plasma devices such as ITER. Simulations about the effects of E  ×  B shear flow on the quiescent H-mode (QH-mode) are carried out using the three-field two-fluid model in the field-aligned coordinate under the BOUT++ framework. Using the shifted circular cross-section equilibriums including bootstrap current, the results demonstrate that the E  ×  B shear flow strongly destabilizes low-n peeling modes, which are mainly driven by the gradient of parallel current in peeling-dominant cases and are sensitive to the E r shear. Adopting the much more general shape of E  ×  B shear ([Formula: see text]) profiles, the linear and nonlinear BOUT++ simulations show qualitative consistence with the experiments. The stronger shear flow shifts the most unstable mode to lower-n and narrows the mode spectrum. At the meantime, the nonlinear simulations of the QH-mode indicate that the shear flow in both co- and counter directions of diamagnetic flow has some similar effects. The nonlinear mode interaction is enhanced during the mode amplitude saturation phase. These results reveal that the fundamental physics mechanism of the QH-mode may be shear flow and are significant for understanding the mechanism of EHO and QH-mode.

Impact of E × B shear flow on low-n MHD instabilities

NASA Astrophysics Data System (ADS)

Chen, J. G.; Xu, X. Q.; Ma, C. H.; Xi, P. W.; Kong, D. F.; Lei, Y. A.

2017-05-01

Recently, the stationary high confinement operations with improved pedestal conditions have been achieved in DIII-D [K. H. Burrell et al., Phys. Plasmas 23, 056103 (2016)], accompanying the spontaneous transition from the coherent edge harmonic oscillation (EHO) to the broadband MHD turbulence state by reducing the neutral beam injection torque to zero. It is highly significant for the burning plasma devices such as ITER. Simulations about the effects of E × B shear flow on the quiescent H-mode (QH-mode) are carried out using the three-field two-fluid model in the field-aligned coordinate under the BOUT++ framework. Using the shifted circular cross-section equilibriums including bootstrap current, the results demonstrate that the E × B shear flow strongly destabilizes low-n peeling modes, which are mainly driven by the gradient of parallel current in peeling-dominant cases and are sensitive to the Er shear. Adopting the much more general shape of E × B shear ( ω E = E r / R B θ ) profiles, the linear and nonlinear BOUT++ simulations show qualitative consistence with the experiments. The stronger shear flow shifts the most unstable mode to lower-n and narrows the mode spectrum. At the meantime, the nonlinear simulations of the QH-mode indicate that the shear flow in both co- and counter directions of diamagnetic flow has some similar effects. The nonlinear mode interaction is enhanced during the mode amplitude saturation phase. These results reveal that the fundamental physics mechanism of the QH-mode may be shear flow and are significant for understanding the mechanism of EHO and QH-mode.

Impact of E × B shear flow on low-n MHD instabilities

PubMed Central

Chen, J. G.; Ma, C. H.; Xi, P. W.; Lei, Y. A.

2017-01-01

Recently, the stationary high confinement operations with improved pedestal conditions have been achieved in DIII-D [K. H. Burrell et al., Phys. Plasmas 23, 056103 (2016)], accompanying the spontaneous transition from the coherent edge harmonic oscillation (EHO) to the broadband MHD turbulence state by reducing the neutral beam injection torque to zero. It is highly significant for the burning plasma devices such as ITER. Simulations about the effects of E × B shear flow on the quiescent H-mode (QH-mode) are carried out using the three-field two-fluid model in the field-aligned coordinate under the BOUT++ framework. Using the shifted circular cross-section equilibriums including bootstrap current, the results demonstrate that the E × B shear flow strongly destabilizes low-n peeling modes, which are mainly driven by the gradient of parallel current in peeling-dominant cases and are sensitive to the Er shear. Adopting the much more general shape of E × B shear (ωE=Er/RBθ) profiles, the linear and nonlinear BOUT++ simulations show qualitative consistence with the experiments. The stronger shear flow shifts the most unstable mode to lower-n and narrows the mode spectrum. At the meantime, the nonlinear simulations of the QH-mode indicate that the shear flow in both co- and counter directions of diamagnetic flow has some similar effects. The nonlinear mode interaction is enhanced during the mode amplitude saturation phase. These results reveal that the fundamental physics mechanism of the QH-mode may be shear flow and are significant for understanding the mechanism of EHO and QH-mode. PMID:28579732

Antimicrobial Resistance Profiles and Diversity in Salmonella from Humans and Cattle, 2004-2011.

PubMed

Afema, J A; Mather, A E; Sischo, W M

2015-11-01

Analysis of long-term anti-microbial resistance (AMR) data is useful to understand source and transmission dynamics of AMR. We analysed 5124 human clinical isolates from Washington State Department of Health, 391 cattle clinical isolates from the Washington Animal Disease Diagnostic Laboratory and 1864 non-clinical isolates from foodborne disease research on dairies in the Pacific Northwest. Isolates were assigned profiles based on phenotypic resistance to 11 anti-microbials belonging to eight classes. Salmonella Typhimurium (ST), Salmonella Newport (SN) and Salmonella Montevideo (SM) were the most common serovars in both humans and cattle. Multinomial logistic regression showed ST and SN from cattle had greater probability of resistance to multiple classes of anti-microbials than ST and SN from humans (P < 0.0001). While these findings could be consistent with the belief that cattle are a source of resistant ST and SN for people, occurrence of profiles unique to cattle and not observed in temporally related human isolates indicates these profiles are circulating in cattle only. We used various measures to assess AMR diversity, conditional on the weighting of rare versus abundant profiles. AMR profile richness was greater in the common serovars from humans, although both source data sets were dominated by relatively few profiles. The greater profile richness in human Salmonella may be due to greater diversity of sources entering the human population compared to cattle or due to continuous evolution in the human environment. Also, AMR diversity was greater in clinical compared to non-clinical cattle Salmonella, and this could be due to anti-microbial selection pressure in diseased cattle that received treatment. The use of bootstrapping techniques showed that although there were shared profiles between humans and cattle, the expected and observed number of profiles was different, suggesting Salmonella and associated resistance from humans and cattle may not be wholly derived from a common population. © 2014 The Authors. Zoonoses and Public Health Published by Blackwell Verlag GmbH.

Bootstrapping N=2 chiral correlators

NASA Astrophysics Data System (ADS)

Lemos, Madalena; Liendo, Pedro

2016-01-01

We apply the numerical bootstrap program to chiral operators in four-dimensional N=2 SCFTs. In the first part of this work we study four-point functions in which all fields have the same conformal dimension. We give special emphasis to bootstrapping a specific theory: the simplest Argyres-Douglas fixed point with no flavor symmetry. In the second part we generalize our setup and consider correlators of fields with unequal dimension. This is an example of a mixed correlator and allows us to probe new regions in the parameter space of N=2 SCFTs. In particular, our results put constraints on relations in the Coulomb branch chiral ring and on the curvature of the Zamolodchikov metric.

Exploring the Replicability of a Study's Results: Bootstrap Statistics for the Multivariate Case.

ERIC Educational Resources Information Center

Thompson, Bruce

Conventional statistical significance tests do not inform the researcher regarding the likelihood that results will replicate. One strategy for evaluating result replication is to use a "bootstrap" resampling of a study's data so that the stability of results across numerous configurations of the subjects can be explored. This paper…

Introducing Statistical Inference to Biology Students through Bootstrapping and Randomization

ERIC Educational Resources Information Center

Lock, Robin H.; Lock, Patti Frazer

2008-01-01

Bootstrap methods and randomization tests are increasingly being used as alternatives to standard statistical procedures in biology. They also serve as an effective introduction to the key ideas of statistical inference in introductory courses for biology students. We discuss the use of such simulation based procedures in an integrated curriculum…

Computing Robust, Bootstrap-Adjusted Fit Indices for Use with Nonnormal Data

ERIC Educational Resources Information Center

Walker, David A.; Smith, Thomas J.

2017-01-01

Nonnormality of data presents unique challenges for researchers who wish to carry out structural equation modeling. The subsequent SPSS syntax program computes bootstrap-adjusted fit indices (comparative fit index, Tucker-Lewis index, incremental fit index, and root mean square error of approximation) that adjust for nonnormality, along with the…

Forgetski Vygotsky: Or, a Plea for Bootstrapping Accounts of Learning

ERIC Educational Resources Information Center

Luntley, Michael

2017-01-01

This paper argues that sociocultural accounts of learning fail to answer the key question about learning--how is it possible? Accordingly, we should adopt an individualist bootstrapping methodology in providing a theory of learning. Such a methodology takes seriously the idea that learning is staged and distinguishes between a non-comprehending…

Higher curvature gravities, unlike GR, cannot be bootstrapped from their (usual) linearizations

NASA Astrophysics Data System (ADS)

Deser, S.

2017-12-01

We show that higher curvature order gravities, in particular the propagating quadratic curvature models, cannot be derived by self-coupling from their linear, flat space, forms, except through an unphysical version of linearization; only GR can. Separately, we comment on an early version of the self-coupling bootstrap.

Methods for Estimating Uncertainty in PMF Solutions: Examples with Ambient Air and Water Quality Data and Guidance on Reporting PMF Results

EPA Science Inventory

The new version of EPA’s positive matrix factorization (EPA PMF) software, 5.0, includes three error estimation (EE) methods for analyzing factor analytic solutions: classical bootstrap (BS), displacement of factor elements (DISP), and bootstrap enhanced by displacement (BS-DISP)...

Bootsie: estimation of coefficient of variation of AFLP data by bootstrap analysis

USDA-ARS?s Scientific Manuscript database

Bootsie is an English-native replacement for ASG Coelho’s “DBOOT” utility for estimating coefficient of variation of a population of AFLP marker data using bootstrapping. Bootsie improves on DBOOT by supporting batch processing, time-to-completion estimation, built-in graphs, and a suite of export t...

How to Bootstrap a Human Communication System

ERIC Educational Resources Information Center

Fay, Nicolas; Arbib, Michael; Garrod, Simon

2013-01-01

How might a human communication system be bootstrapped in the absence of conventional language? We argue that motivated signs play an important role (i.e., signs that are linked to meaning by structural resemblance or by natural association). An experimental study is then reported in which participants try to communicate a range of pre-specified…

Measuring and Benchmarking Technical Efficiency of Public Hospitals in Tianjin, China: A Bootstrap-Data Envelopment Analysis Approach.

PubMed

Li, Hao; Dong, Siping

2015-01-01

China has long been stuck in applying traditional data envelopment analysis (DEA) models to measure technical efficiency of public hospitals without bias correction of efficiency scores. In this article, we have introduced the Bootstrap-DEA approach from the international literature to analyze the technical efficiency of public hospitals in Tianjin (China) and tried to improve the application of this method for benchmarking and inter-organizational learning. It is found that the bias corrected efficiency scores of Bootstrap-DEA differ significantly from those of the traditional Banker, Charnes, and Cooper (BCC) model, which means that Chinese researchers need to update their DEA models for more scientific calculation of hospital efficiency scores. Our research has helped shorten the gap between China and the international world in relative efficiency measurement and improvement of hospitals. It is suggested that Bootstrap-DEA be widely applied into afterward research to measure relative efficiency and productivity of Chinese hospitals so as to better serve for efficiency improvement and related decision making. © The Author(s) 2015.

Weak percolation on multiplex networks

NASA Astrophysics Data System (ADS)

Baxter, Gareth J.; Dorogovtsev, Sergey N.; Mendes, José F. F.; Cellai, Davide

2014-04-01

Bootstrap percolation is a simple but nontrivial model. It has applications in many areas of science and has been explored on random networks for several decades. In single-layer (simplex) networks, it has been recently observed that bootstrap percolation, which is defined as an incremental process, can be seen as the opposite of pruning percolation, where nodes are removed according to a connectivity rule. Here we propose models of both bootstrap and pruning percolation for multiplex networks. We collectively refer to these two models with the concept of "weak" percolation, to distinguish them from the somewhat classical concept of ordinary ("strong") percolation. While the two models coincide in simplex networks, we show that they decouple when considering multiplexes, giving rise to a wealth of critical phenomena. Our bootstrap model constitutes the simplest example of a contagion process on a multiplex network and has potential applications in critical infrastructure recovery and information security. Moreover, we show that our pruning percolation model may provide a way to diagnose missing layers in a multiplex network. Finally, our analytical approach allows us to calculate critical behavior and characterize critical clusters.

Visuospatial bootstrapping: Binding useful visuospatial information during verbal working memory encoding does not require set-shifting executive resources.

PubMed

Calia, Clara; Darling, Stephen; Havelka, Jelena; Allen, Richard J

2018-05-01

Immediate serial recall of digits is better when the digits are shown by highlighting them in a familiar array, such as a phone keypad, compared with presenting them serially in a single location, a pattern referred to as "visuospatial bootstrapping." This pattern implies the establishment of temporary links between verbal and spatial working memory, alongside access to information in long-term memory. However, the role of working memory control processes like those implied by the "Central Executive" in bootstrapping has not been directly investigated. Here, we report a study addressing this issue, focusing on executive processes of attentional shifting. Tasks in which information has to be sequenced are thought to be heavily dependent on shifting. Memory for digits presented in keypads versus single locations was assessed under two secondary task load conditions, one with and one without a sequencing requirement, and hence differing in the degree to which they invoke shifting. Results provided clear evidence that multimodal binding (visuospatial bootstrapping) can operate independently of this form of executive control process.

Understanding roles of E  ×  B flow and magnetic shear on the formation of internal and edge transport barriers using two-field bifurcation concept

NASA Astrophysics Data System (ADS)

Chatthong, B.; Onjun, T.

2016-01-01

A set of heat and particle transport equations with the inclusion of E  ×  B flow and magnetic shear is used to understand the formation and behaviors of edge transport barriers (ETBs) and internal transport barriers (ITBs) in tokamak plasmas based on two-field bifurcation concept. A simple model that can describe the E  ×  B flow shear and magnetic shear effect in tokamak plasma is used for anomalous transport suppression with the effect of bootstrap current included. Consequently, conditions and formations of ETB and ITB can be visualized and studied. It can be seen that the ETB formation depends sensitively on the E  ×  B flow shear suppression with small dependence on the magnetic shear suppression. However, the ITB formation depends sensitively on the magnetic shear suppression with a small dependence on the E  ×  B flow shear suppression. Once the H-mode is achieved, the s-curve bifurcation diagram is modified due to an increase of bootstrap current at the plasma edge, resulting in reductions of both L-H and H-L transition thresholds with stronger hysteresis effects. It is also found that both ITB and ETB widths appear to be governed by heat or particle sources and the location of the current peaking. In addition, at a marginal flux just below the L-H threshold, a small perturbation in terms of heat or density fluctuation can result in a transition, which can remain after the perturbation is removed due to the hysteresis effect.

Diamagnetic drift effects on the low-n magnetohydrodynamic modes at the high mode pedestal with plasma rotation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zheng, L. J.; Kotschenreuther, M. T.; Valanju, P.

2014-06-15

The diamagnetic drift effects on the low-n magnetohydrodynamic instabilities at the high-mode (H-mode) pedestal are investigated in this paper with the inclusion of bootstrap current for equilibrium and rotation effects for stability, where n is the toroidal mode number. The AEGIS (Adaptive EiGenfunction Independent Solutions) code [L. J. Zheng and M. T. Kotschenreuther, J. Comp. Phys. 211 (2006)] is extended to include the diamagnetic drift effects. This can be viewed as the lowest order approximation of the finite Larmor radius effects in consideration of the pressure gradient steepness at the pedestal. The H-mode discharges at Jointed European Torus is reconstructedmore » numerically using the VMEC code [P. Hirshman and J. C. Whitson, Phys. Fluids 26, 3553 (1983)], with bootstrap current taken into account. Generally speaking, the diamagnetic drift effects are stabilizing. Our results show that the effectiveness of diamagnetic stabilization depends sensitively on the safe factor value (q{sub s}) at the safety-factor reversal or plateau region. The diamagnetic stabilization are weaker, when q{sub s} is larger than an integer; while stronger, when q{sub s} is smaller or less larger than an integer. We also find that the diamagnetic drift effects also depend sensitively on the rotation direction. The diamagnetic stabilization in the co-rotation case is stronger than in the counter rotation case with respect to the ion diamagnetic drift direction.« less

Generalized Bootstrap Method for Assessment of Uncertainty in Semivariogram Inference

USGS Publications Warehouse

Olea, R.A.; Pardo-Iguzquiza, E.

2011-01-01

The semivariogram and its related function, the covariance, play a central role in classical geostatistics for modeling the average continuity of spatially correlated attributes. Whereas all methods are formulated in terms of the true semivariogram, in practice what can be used are estimated semivariograms and models based on samples. A generalized form of the bootstrap method to properly model spatially correlated data is used to advance knowledge about the reliability of empirical semivariograms and semivariogram models based on a single sample. Among several methods available to generate spatially correlated resamples, we selected a method based on the LU decomposition and used several examples to illustrate the approach. The first one is a synthetic, isotropic, exhaustive sample following a normal distribution, the second example is also a synthetic but following a non-Gaussian random field, and a third empirical sample consists of actual raingauge measurements. Results show wider confidence intervals than those found previously by others with inadequate application of the bootstrap. Also, even for the Gaussian example, distributions for estimated semivariogram values and model parameters are positively skewed. In this sense, bootstrap percentile confidence intervals, which are not centered around the empirical semivariogram and do not require distributional assumptions for its construction, provide an achieved coverage similar to the nominal coverage. The latter cannot be achieved by symmetrical confidence intervals based on the standard error, regardless if the standard error is estimated from a parametric equation or from bootstrap. ?? 2010 International Association for Mathematical Geosciences.

Classification of bacteria by simultaneous methylation-solid phase microextraction and gas chromatography/mass spectrometry analysis of fatty acid methyl esters.

PubMed

Lu, Yao; Harrington, Peter B

2010-08-01

Direct methylation and solid-phase microextraction (SPME) were used as a sample preparation technique for classification of bacteria based on fatty acid methyl ester (FAME) profiles. Methanolic tetramethylammonium hydroxide was applied as a dual-function reagent to saponify and derivatize whole-cell bacterial fatty acids into FAMEs in one step, and SPME was used to extract the bacterial FAMEs from the headspace. Compared with traditional alkaline saponification and sample preparation using liquid-liquid extraction, the method presented in this work avoids using comparatively large amounts of inorganic and organic solvents and greatly decreases the sample preparation time as well. Characteristic gas chromatography/mass spectrometry (GC/MS) of FAME profiles was achieved for six bacterial species. The difference between Gram-positive and Gram-negative bacteria was clearly visualized with the application of principal component analysis of the GC/MS data of bacterial FAMEs. A cross-validation study using ten bootstrap Latin partitions and the fuzzy rule building expert system demonstrated 87 +/- 3% correct classification efficiency.

Predicting Postsurgical Satisfaction in Adolescents With Idiopathic Scoliosis: The Role of Presurgical Functioning and Expectations.

PubMed

Sieberg, Christine B; Manganella, Juliana; Manalo, Gem; Simons, Laura E; Hresko, M Timothy

2017-12-01

There is a need to better assess patient satisfaction and surgical outcomes. The purpose of the current study is to identify how preoperative expectations can impact postsurgical satisfaction among youth with adolescent idiopathic scoliosis undergoing spinal fusion surgery. The present study includes patients with adolescent idiopathic scoliosis undergoing spinal fusion surgery enrolled in a prospective, multicentered registry examining postsurgical outcomes. The Scoliosis Research Society Questionnaire-Version 30, which assesses pain, self-image, mental health, and satisfaction with management, along with the Spinal Appearance Questionnaire, which measures surgical expectations was administered to 190 patients before surgery and 1 and 2 years postoperatively. Regression analyses with bootstrapping (with n=5000 bootstrap samples) were conducted with 99% bias-corrected confidence intervals to examine the extent to which preoperative expectations for spinal appearance mediated the relationship between presurgical mental health and pain and 2-year postsurgical satisfaction. Results indicate that preoperative mental health, pain, and expectations are predictive of postsurgical satisfaction. With the shifting health care system, physicians may want to consider patient mental health, pain, and expectations before surgery to optimize satisfaction and ultimately improve clinical care and patient outcomes. Level I-prognostic study.

Standard errors and confidence intervals for variable importance in random forest regression, classification, and survival.

PubMed

Ishwaran, Hemant; Lu, Min

2018-06-04

Random forests are a popular nonparametric tree ensemble procedure with broad applications to data analysis. While its widespread popularity stems from its prediction performance, an equally important feature is that it provides a fully nonparametric measure of variable importance (VIMP). A current limitation of VIMP, however, is that no systematic method exists for estimating its variance. As a solution, we propose a subsampling approach that can be used to estimate the variance of VIMP and for constructing confidence intervals. The method is general enough that it can be applied to many useful settings, including regression, classification, and survival problems. Using extensive simulations, we demonstrate the effectiveness of the subsampling estimator and in particular find that the delete-d jackknife variance estimator, a close cousin, is especially effective under low subsampling rates due to its bias correction properties. These 2 estimators are highly competitive when compared with the .164 bootstrap estimator, a modified bootstrap procedure designed to deal with ties in out-of-sample data. Most importantly, subsampling is computationally fast, thus making it especially attractive for big data settings. Copyright © 2018 John Wiley & Sons, Ltd.

Correcting the Standard Errors of 2-Stage Residual Inclusion Estimators for Mendelian Randomization Studies

PubMed Central

Palmer, Tom M; Holmes, Michael V; Keating, Brendan J; Sheehan, Nuala A

2017-01-01

Abstract Mendelian randomization studies use genotypes as instrumental variables to test for and estimate the causal effects of modifiable risk factors on outcomes. Two-stage residual inclusion (TSRI) estimators have been used when researchers are willing to make parametric assumptions. However, researchers are currently reporting uncorrected or heteroscedasticity-robust standard errors for these estimates. We compared several different forms of the standard error for linear and logistic TSRI estimates in simulations and in real-data examples. Among others, we consider standard errors modified from the approach of Newey (1987), Terza (2016), and bootstrapping. In our simulations Newey, Terza, bootstrap, and corrected 2-stage least squares (in the linear case) standard errors gave the best results in terms of coverage and type I error. In the real-data examples, the Newey standard errors were 0.5% and 2% larger than the unadjusted standard errors for the linear and logistic TSRI estimators, respectively. We show that TSRI estimators with modified standard errors have correct type I error under the null. Researchers should report TSRI estimates with modified standard errors instead of reporting unadjusted or heteroscedasticity-robust standard errors. PMID:29106476

Peace of Mind, Academic Motivation, and Academic Achievement in Filipino High School Students.

PubMed

Datu, Jesus Alfonso D

2017-04-09

Recent literature has recognized the advantageous role of low-arousal positive affect such as feelings of peacefulness and internal harmony in collectivist cultures. However, limited research has explored the benefits of low-arousal affective states in the educational setting. The current study examined the link of peace of mind (PoM) to academic motivation (i.e., amotivation, controlled motivation, and autonomous motivation) and academic achievement among 525 Filipino high school students. Findings revealed that PoM was positively associated with academic achievement β = .16, p < .05, autonomous motivation β = .48, p < .001, and controlled motivation β = .25, p < .01. As expected, PoM was negatively related to amotivation β = -.19, p < .05, and autonomous motivation was positively associated with academic achievement β = .52, p < .01. Furthermore, the results of bias-corrected bootstrap analyses at 95% confidence interval based on 5,000 bootstrapped resamples demonstrated that peace of mind had an indirect influence on academic achievement through the mediating effects of autonomous motivation. In terms of the effect sizes, the findings showed that PoM explained about 1% to 18% of the variance in academic achievement and motivation. The theoretical and practical implications of the results are elucidated.

Performance of an SOI Boot-Strapped Full-Bridge MOSFET Driver, Type CHT-FBDR, under Extreme Temperatures

NASA Technical Reports Server (NTRS)

Patterson, Richard; Hammoud, Ahmad

2009-01-01

Electronic systems designed for use in deep space and planetary exploration missions are expected to encounter extreme temperatures and wide thermal swings. Silicon-based devices are limited in their wide-temperature capability and usually require extra measures, such as cooling or heating mechanisms, to provide adequate ambient temperature for proper operation. Silicon-On-Insulator (SOI) technology, on the other hand, lately has been gaining wide spread use in applications where high temperatures are encountered. Due to their inherent design, SOI-based integrated circuit chips are able to operate at temperatures higher than those of the silicon devices by virtue of reducing leakage currents, eliminating parasitic junctions, and limiting internal heating. In addition, SOI devices provide faster switching, consume less power, and offer improved radiation-tolerance. Very little data, however, exist on the performance of such devices and circuits under cryogenic temperatures. In this work, the performance of an SOI bootstrapped, full-bridge driver integrated circuit was evaluated under extreme temperatures and thermal cycling. The investigations were carried out to establish a baseline on the functionality and to determine suitability of this device for use in space exploration missions under extreme temperature conditions.

Pulling Econometrics Students up by Their Bootstraps

ERIC Educational Resources Information Center

O'Hara, Michael E.

2014-01-01

Although the concept of the sampling distribution is at the core of much of what we do in econometrics, it is a concept that is often difficult for students to grasp. The thought process behind bootstrapping provides a way for students to conceptualize the sampling distribution in a way that is intuitive and visual. However, teaching students to…

Accuracy assessment of percent canopy cover, cover type, and size class

Treesearch

H. T. Schreuder; S. Bain; R. C. Czaplewski

2003-01-01

Truth for vegetation cover percent and type is obtained from very large-scale photography (VLSP), stand structure as measured by size classes, and vegetation types from a combination of VLSP and ground sampling. We recommend using the Kappa statistic with bootstrap confidence intervals for overall accuracy, and similarly bootstrap confidence intervals for percent...

Finding One's Meaning: A Test of the Relation between Quantifiers and Integers in Language Development

ERIC Educational Resources Information Center

Barner, David; Chow, Katherine; Yang, Shu-Ju

2009-01-01

We explored children's early interpretation of numerals and linguistic number marking, in order to test the hypothesis (e.g., Carey (2004). Bootstrapping and the origin of concepts. "Daedalus", 59-68) that children's initial distinction between "one" and other numerals (i.e., "two," "three," etc.) is bootstrapped from a prior distinction between…

A Class of Population Covariance Matrices in the Bootstrap Approach to Covariance Structure Analysis

ERIC Educational Resources Information Center

Yuan, Ke-Hai; Hayashi, Kentaro; Yanagihara, Hirokazu

2007-01-01

Model evaluation in covariance structure analysis is critical before the results can be trusted. Due to finite sample sizes and unknown distributions of real data, existing conclusions regarding a particular statistic may not be applicable in practice. The bootstrap procedure automatically takes care of the unknown distribution and, for a given…

A Resampling Analysis of Federal Family Assistance Program Quality Control Data: An Application of the Bootstrap.

ERIC Educational Resources Information Center

Hand, Michael L.

1990-01-01

Use of the bootstrap resampling technique (BRT) is assessed in its application to resampling analysis associated with measurement of payment allocation errors by federally funded Family Assistance Programs. The BRT is applied to a food stamp quality control database in Oregon. This analysis highlights the outlier-sensitivity of the…

Calculating Confidence Intervals for Regional Economic Impacts of Recreastion by Bootstrapping Visitor Expenditures

Treesearch

Donald B.K. English

2000-01-01

In this paper I use bootstrap procedures to develop confidence intervals for estimates of total industrial output generated per thousand tourist visits. Mean expenditures from replicated visitor expenditure data included weights to correct for response bias. Impacts were estimated with IMPLAN. Ninety percent interval endpoints were 6 to 16 percent above or below the...

Comparison of Methods for Estimating Low Flow Characteristics of Streams

USGS Publications Warehouse

Tasker, Gary D.

1987-01-01

Four methods for estimating the 7-day, 10-year and 7-day, 20-year low flows for streams are compared by the bootstrap method. The bootstrap method is a Monte Carlo technique in which random samples are drawn from an unspecified sampling distribution defined from observed data. The nonparametric nature of the bootstrap makes it suitable for comparing methods based on a flow series for which the true distribution is unknown. Results show that the two methods based on hypothetical distribution (Log-Pearson III and Weibull) had lower mean square errors than did the G. E. P. Box-D. R. Cox transformation method or the Log-W. C. Boughton method which is based on a fit of plotting positions.

The exposure history of Jilin and production rates of cosmogenic nuclides

NASA Technical Reports Server (NTRS)

Heusser, G.

1986-01-01

Jilin, the largest known story meteorite, is a very suitable object for studying the systematics of cosmic ray produced nuclides in stony meteorites. Its well established two stage exposure history even permits to gain information about two different irradiation geometries (2pi and 4pi). All stable and long-lived cosmogenic nuclides measured in Jilin so far correlate well with each other. An example is shown where the Al-26 activities are plotted vs. the spallogenic Ne-21 concentration. These records of cosmic-ray interaction in Jilin can be used both to determine the history of the target and to study the nature of production rate profiles. This is unavoidably a bootstrap process, involving studying one with assumption about the other. Production rate equations are presented and discussed.

Self-consistent modeling of the dynamic evolution of magnetic island growth in the presence of stabilizing electron-cyclotron current drive

NASA Astrophysics Data System (ADS)

Chatziantonaki, Ioanna; Tsironis, Christos; Isliker, Heinz; Vlahos, Loukas

2013-11-01

The most promising technique for the control of neoclassical tearing modes in tokamak experiments is the compensation of the missing bootstrap current with an electron-cyclotron current drive (ECCD). In this frame, the dynamics of magnetic islands has been studied extensively in terms of the modified Rutherford equation (MRE), including the presence of a current drive, either analytically described or computed by numerical methods. In this article, a self-consistent model for the dynamic evolution of the magnetic island and the driven current is derived, which takes into account the island's magnetic topology and its effect on the current drive. The model combines the MRE with a ray-tracing approach to electron-cyclotron wave-propagation and absorption. Numerical results exhibit a decrease in the time required for complete stabilization with respect to the conventional computation (not taking into account the island geometry), which increases by increasing the initial island size and radial misalignment of the deposition.

Numerical Analysis of the Effects of Normalized Plasma Pressure on RMP ELM Suppression in DIII-D

DOE Office of Scientific and Technical Information (OSTI.GOV)

Orlov, D. M.; Moyer, R.A.; Evans, T. E.

2010-01-01

The effect of normalized plasma pressure as characterized by normalized pressure parameter (beta(N)) on the suppression of edge localized modes (ELMs) using resonant magnetic perturbations (RMPs) is studied in low-collisionality (nu* <= 0.2) H-mode plasmas with low-triangularity ( = 0.25) and ITER similar shapes ( = 0.51). Experimental results have suggested that ELM suppression by RMPs requires a minimum threshold in plasma pressure as characterized by beta(N). The variations in the vacuum field topology with beta(N) due to safety factor profile and island overlap changes caused by variation of the Shafranov shift and pedestal bootstrap current are examined numerically withmore » the field line integration code TRIP3D. The results show very small differences in the vacuum field structure in terms of the Chirikov (magnetic island overlap) parameter, Poincare sections and field line loss fractions. These differences do not appear to explain the observed threshold in beta(N) for ELM suppression. Linear peeling-ballooning stability analysis with the ELITE code suggests that the ELMs which persist during the RMPs when beta(N) is below the observed threshold are not type I ELMs, because the pedestal conditions are deep within the stable regime for peeling-ballooning modes. These ELMs have similarities to type III ELMs or low density ELMs.« less

Exact Mass-Coupling Relation for the Homogeneous Sine-Gordon Model.

PubMed

Bajnok, Zoltán; Balog, János; Ito, Katsushi; Satoh, Yuji; Tóth, Gábor Zsolt

2016-05-06

We derive the exact mass-coupling relation of the simplest multiscale quantum integrable model, i.e., the homogeneous sine-Gordon model with two mass scales. The relation is obtained by comparing the perturbed conformal field theory description of the model valid at short distances to the large distance bootstrap description based on the model's integrability. In particular, we find a differential equation for the relation by constructing conserved tensor currents, which satisfy a generalization of the Θ sum rule Ward identity. The mass-coupling relation is written in terms of hypergeometric functions.

Technical and scale efficiency in public and private Irish nursing homes - a bootstrap DEA approach.

PubMed

Ni Luasa, Shiovan; Dineen, Declan; Zieba, Marta

2016-10-27

This article provides methodological and empirical insights into the estimation of technical efficiency in the nursing home sector. Focusing on long-stay care and using primary data, we examine technical and scale efficiency in 39 public and 73 private Irish nursing homes by applying an input-oriented data envelopment analysis (DEA). We employ robust bootstrap methods to validate our nonparametric DEA scores and to integrate the effects of potential determinants in estimating the efficiencies. Both the homogenous and two-stage double bootstrap procedures are used to obtain confidence intervals for the bias-corrected DEA scores. Importantly, the application of the double bootstrap approach affords true DEA technical efficiency scores after adjusting for the effects of ownership, size, case-mix, and other determinants such as location, and quality. Based on our DEA results for variable returns to scale technology, the average technical efficiency score is 62 %, and the mean scale efficiency is 88 %, with nearly all units operating on the increasing returns to scale part of the production frontier. Moreover, based on the double bootstrap results, Irish nursing homes are less technically efficient, and more scale efficient than the conventional DEA estimates suggest. Regarding the efficiency determinants, in terms of ownership, we find that private facilities are less efficient than the public units. Furthermore, the size of the nursing home has a positive effect, and this reinforces our finding that Irish homes produce at increasing returns to scale. Also, notably, we find that a tendency towards quality improvements can lead to poorer technical efficiency performance.

Empirical single sample quantification of bias and variance in Q-ball imaging.

PubMed

Hainline, Allison E; Nath, Vishwesh; Parvathaneni, Prasanna; Blaber, Justin A; Schilling, Kurt G; Anderson, Adam W; Kang, Hakmook; Landman, Bennett A

2018-02-06

The bias and variance of high angular resolution diffusion imaging methods have not been thoroughly explored in the literature and may benefit from the simulation extrapolation (SIMEX) and bootstrap techniques to estimate bias and variance of high angular resolution diffusion imaging metrics. The SIMEX approach is well established in the statistics literature and uses simulation of increasingly noisy data to extrapolate back to a hypothetical case with no noise. The bias of calculated metrics can then be computed by subtracting the SIMEX estimate from the original pointwise measurement. The SIMEX technique has been studied in the context of diffusion imaging to accurately capture the bias in fractional anisotropy measurements in DTI. Herein, we extend the application of SIMEX and bootstrap approaches to characterize bias and variance in metrics obtained from a Q-ball imaging reconstruction of high angular resolution diffusion imaging data. The results demonstrate that SIMEX and bootstrap approaches provide consistent estimates of the bias and variance of generalized fractional anisotropy, respectively. The RMSE for the generalized fractional anisotropy estimates shows a 7% decrease in white matter and an 8% decrease in gray matter when compared with the observed generalized fractional anisotropy estimates. On average, the bootstrap technique results in SD estimates that are approximately 97% of the true variation in white matter, and 86% in gray matter. Both SIMEX and bootstrap methods are flexible, estimate population characteristics based on single scans, and may be extended for bias and variance estimation on a variety of high angular resolution diffusion imaging metrics. © 2018 International Society for Magnetic Resonance in Medicine.

Uncertainty Estimation using Bootstrapped Kriging Predictions for Precipitation Isoscapes

NASA Astrophysics Data System (ADS)

Ma, C.; Bowen, G. J.; Vander Zanden, H.; Wunder, M.

2017-12-01

Isoscapes are spatial models representing the distribution of stable isotope values across landscapes. Isoscapes of hydrogen and oxygen in precipitation are now widely used in a diversity of fields, including geology, biology, hydrology, and atmospheric science. To generate isoscapes, geostatistical methods are typically applied to extend predictions from limited data measurements. Kriging is a popular method in isoscape modeling, but quantifying the uncertainty associated with the resulting isoscapes is challenging. Applications that use precipitation isoscapes to determine sample origin require estimation of uncertainty. Here we present a simple bootstrap method (SBM) to estimate the mean and uncertainty of the krigged isoscape and compare these results with a generalized bootstrap method (GBM) applied in previous studies. We used hydrogen isotopic data from IsoMAP to explore these two approaches for estimating uncertainty. We conducted 10 simulations for each bootstrap method and found that SBM results in more kriging predictions (9/10) compared to GBM (4/10). Prediction from SBM was closer to the original prediction generated without bootstrapping and had less variance than GBM. SBM was tested on different datasets from IsoMAP with different numbers of observation sites. We determined that predictions from the datasets with fewer than 40 observation sites using SBM were more variable than the original prediction. The approaches we used for estimating uncertainty will be compiled in an R package that is under development. We expect that these robust estimates of precipitation isoscape uncertainty can be applied in diagnosing the origin of samples ranging from various type of waters to migratory animals, food products, and humans.

Bootstrapping rapidity anomalous dimensions for transverse-momentum resummation

DOE PAGES

Li, Ye; Zhu, Hua Xing

2017-01-11

Soft function relevant for transverse-momentum resummation for Drell-Yan or Higgs production at hadron colliders are computed through to three loops in the expansion of strong coupling, with the help of bootstrap technique and supersymmetric decomposition. The corresponding rapidity anomalous dimension is extracted. Furthermore, an intriguing relation between anomalous dimensions for transverse-momentum resummation and threshold resummation is found.

Reliability of confidence intervals calculated by bootstrap and classical methods using the FIA 1-ha plot design

Treesearch

H. T. Schreuder; M. S. Williams

2000-01-01

In simulation sampling from forest populations using sample sizes of 20, 40, and 60 plots respectively, confidence intervals based on the bootstrap (accelerated, percentile, and t-distribution based) were calculated and compared with those based on the classical t confidence intervals for mapped populations and subdomains within those populations. A 68.1 ha mapped...

Morphological Cues vs. Number of Nominals in Learning Verb Types in Turkish: The Syntactic Bootstrapping Mechanism Revisited

ERIC Educational Resources Information Center

Ural, A. Engin; Yuret, Deniz; Ketrez, F. Nihan; Kocbas, Dilara; Kuntay, Aylin C.

2009-01-01

The syntactic bootstrapping mechanism of verb learning was evaluated against child-directed speech in Turkish, a language with rich morphology, nominal ellipsis and free word order. Machine-learning algorithms were run on transcribed caregiver speech directed to two Turkish learners (one hour every two weeks between 0;9 to 1;10) of different…

A Comparison of the Bootstrap-F, Improved General Approximation, and Brown-Forsythe Multivariate Approaches in a Mixed Repeated Measures Design

ERIC Educational Resources Information Center

Seco, Guillermo Vallejo; Izquierdo, Marcelino Cuesta; Garcia, M. Paula Fernandez; Diez, F. Javier Herrero

2006-01-01

The authors compare the operating characteristics of the bootstrap-F approach, a direct extension of the work of Berkovits, Hancock, and Nevitt, with Huynh's improved general approximation (IGA) and the Brown-Forsythe (BF) multivariate approach in a mixed repeated measures design when normality and multisample sphericity assumptions do not hold.…

Sample-based estimation of tree species richness in a wet tropical forest compartment

Treesearch

Steen Magnussen; Raphael Pelissier

2007-01-01

Petersen's capture-recapture ratio estimator and the well-known bootstrap estimator are compared across a range of simulated low-intensity simple random sampling with fixed-area plots of 100 m? in a rich wet tropical forest compartment with 93 tree species in the Western Ghats of India. Petersen's ratio estimator was uniformly superior to the bootstrap...

Common Ground between Form and Content: The Pragmatic Solution to the Bootstrapping Problem

ERIC Educational Resources Information Center

Oller, John W.

2005-01-01

The frame of reference for this article is second or foreign language (L2 or FL) acquisition, but the pragmatic bootstrapping hypothesis applies to language processing and acquisition in any context or modality. It is relevant to teaching children to read. It shows how connections between target language surface forms and their content can be made…

The Bacterial Gene IfpA Influences the Potent Induction of Calcitonin Receptor and Osteoclast-Related Genes in Burkholderia Pseudomallei-Induced TRAP-Positive Multinucleated Giant Cells

DTIC Science & Technology

2006-06-13

with arithmetic mean ( UPGMA ) using random tie breaking and uncorrected pairwise distances in MacVector 7.0 (Oxford Molecular). Numbers on branches...denote the UPGMA bootstrap percentage using a highly stringent number (1000) of replications (Felsenstein, 1985). All bootstrap values are 50%, as shown

A Comparison of Single Sample and Bootstrap Methods to Assess Mediation in Cluster Randomized Trials

ERIC Educational Resources Information Center

Pituch, Keenan A.; Stapleton, Laura M.; Kang, Joo Youn

2006-01-01

A Monte Carlo study examined the statistical performance of single sample and bootstrap methods that can be used to test and form confidence interval estimates of indirect effects in two cluster randomized experimental designs. The designs were similar in that they featured random assignment of clusters to one of two treatment conditions and…

Multilingual Phoneme Models for Rapid Speech Processing System Development

DTIC Science & Technology

2006-09-01

processes are used to develop an Arabic speech recognition system starting from monolingual English models, In- ternational Phonetic Association (IPA...clusters. It was found that multilingual bootstrapping methods out- perform monolingual English bootstrapping methods on the Arabic evaluation data initially...International Phonetic Alphabet . . . . . . . . . 7 2.3.2 Multilingual vs. Monolingual Speech Recognition 7 2.3.3 Data-Driven Approaches

An inferential study of the phenotype for the chromosome 15q24 microdeletion syndrome: a bootstrap analysis

PubMed Central

Ramírez-Prado, Dolores; Cortés, Ernesto; Aguilar-Segura, María Soledad; Gil-Guillén, Vicente Francisco

2016-01-01

In January 2012, a review of the cases of chromosome 15q24 microdeletion syndrome was published. However, this study did not include inferential statistics. The aims of the present study were to update the literature search and calculate confidence intervals for the prevalence of each phenotype using bootstrap methodology. Published case reports of patients with the syndrome that included detailed information about breakpoints and phenotype were sought and 36 were included. Deletions in megabase (Mb) pairs were determined to calculate the size of the interstitial deletion of the phenotypes studied in 2012. To determine confidence intervals for the prevalence of the phenotype and the interstitial loss, we used bootstrap methodology. Using the bootstrap percentiles method, we found wide variability in the prevalence of the different phenotypes (3–100%). The mean interstitial deletion size was 2.72 Mb (95% CI [2.35–3.10 Mb]). In comparison with our work, which expanded the literature search by 45 months, there were differences in the prevalence of 17% of the phenotypes, indicating that more studies are needed to analyze this rare disease. PMID:26925314

Bootstrap imputation with a disease probability model minimized bias from misclassification due to administrative database codes.

PubMed

van Walraven, Carl

2017-04-01

Diagnostic codes used in administrative databases cause bias due to misclassification of patient disease status. It is unclear which methods minimize this bias. Serum creatinine measures were used to determine severe renal failure status in 50,074 hospitalized patients. The true prevalence of severe renal failure and its association with covariates were measured. These were compared to results for which renal failure status was determined using surrogate measures including the following: (1) diagnostic codes; (2) categorization of probability estimates of renal failure determined from a previously validated model; or (3) bootstrap methods imputation of disease status using model-derived probability estimates. Bias in estimates of severe renal failure prevalence and its association with covariates were minimal when bootstrap methods were used to impute renal failure status from model-based probability estimates. In contrast, biases were extensive when renal failure status was determined using codes or methods in which model-based condition probability was categorized. Bias due to misclassification from inaccurate diagnostic codes can be minimized using bootstrap methods to impute condition status using multivariable model-derived probability estimates. Copyright © 2017 Elsevier Inc. All rights reserved.

Reference interval computation: which method (not) to choose?

PubMed

Pavlov, Igor Y; Wilson, Andrew R; Delgado, Julio C

2012-07-11

When different methods are applied to reference interval (RI) calculation the results can sometimes be substantially different, especially for small reference groups. If there are no reliable RI data available, there is no way to confirm which method generates results closest to the true RI. We randomly drawn samples obtained from a public database for 33 markers. For each sample, RIs were calculated by bootstrapping, parametric, and Box-Cox transformed parametric methods. Results were compared to the values of the population RI. For approximately half of the 33 markers, results of all 3 methods were within 3% of the true reference value. For other markers, parametric results were either unavailable or deviated considerably from the true values. The transformed parametric method was more accurate than bootstrapping for sample size of 60, very close to bootstrapping for sample size 120, but in some cases unavailable. We recommend against using parametric calculations to determine RIs. The transformed parametric method utilizing Box-Cox transformation would be preferable way of RI calculation, if it satisfies normality test. If not, the bootstrapping is always available, and is almost as accurate and precise as the transformed parametric method. Copyright © 2012 Elsevier B.V. All rights reserved.

The sound symbolism bootstrapping hypothesis for language acquisition and language evolution

PubMed Central

Imai, Mutsumi; Kita, Sotaro

2014-01-01

Sound symbolism is a non-arbitrary relationship between speech sounds and meaning. We review evidence that, contrary to the traditional view in linguistics, sound symbolism is an important design feature of language, which affects online processing of language, and most importantly, language acquisition. We propose the sound symbolism bootstrapping hypothesis, claiming that (i) pre-verbal infants are sensitive to sound symbolism, due to a biologically endowed ability to map and integrate multi-modal input, (ii) sound symbolism helps infants gain referential insight for speech sounds, (iii) sound symbolism helps infants and toddlers associate speech sounds with their referents to establish a lexical representation and (iv) sound symbolism helps toddlers learn words by allowing them to focus on referents embedded in a complex scene, alleviating Quine's problem. We further explore the possibility that sound symbolism is deeply related to language evolution, drawing the parallel between historical development of language across generations and ontogenetic development within individuals. Finally, we suggest that sound symbolism bootstrapping is a part of a more general phenomenon of bootstrapping by means of iconic representations, drawing on similarities and close behavioural links between sound symbolism and speech-accompanying iconic gesture. PMID:25092666

Estimating uncertainty in respondent-driven sampling using a tree bootstrap method.

PubMed

Baraff, Aaron J; McCormick, Tyler H; Raftery, Adrian E

2016-12-20

Respondent-driven sampling (RDS) is a network-based form of chain-referral sampling used to estimate attributes of populations that are difficult to access using standard survey tools. Although it has grown quickly in popularity since its introduction, the statistical properties of RDS estimates remain elusive. In particular, the sampling variability of these estimates has been shown to be much higher than previously acknowledged, and even methods designed to account for RDS result in misleadingly narrow confidence intervals. In this paper, we introduce a tree bootstrap method for estimating uncertainty in RDS estimates based on resampling recruitment trees. We use simulations from known social networks to show that the tree bootstrap method not only outperforms existing methods but also captures the high variability of RDS, even in extreme cases with high design effects. We also apply the method to data from injecting drug users in Ukraine. Unlike other methods, the tree bootstrap depends only on the structure of the sampled recruitment trees, not on the attributes being measured on the respondents, so correlations between attributes can be estimated as well as variability. Our results suggest that it is possible to accurately assess the high level of uncertainty inherent in RDS.

A bootstrap lunar base: Preliminary design review 2

NASA Technical Reports Server (NTRS)

1987-01-01

A bootstrap lunar base is the gateway to manned solar system exploration and requires new ideas and new designs on the cutting edge of technology. A preliminary design for a Bootstrap Lunar Base, the second provided by this contractor, is presented. An overview of the work completed is discussed as well as the technical, management, and cost strategies to complete the program requirements. The lunar base design stresses the transforming capabilities of its lander vehicles to aid in base construction. The design also emphasizes modularity and expandability in the base configuration to support the long-term goals of scientific research and profitable lunar resource exploitation. To successfully construct, develop, and inhabit a permanent lunar base, however, several technological advancements must first be realized. Some of these technological advancements are also discussed.

Spheres, charges, instantons, and bootstrap: A five-dimensional odyssey

NASA Astrophysics Data System (ADS)

Chang, Chi-Ming; Fluder, Martin; Lin, Ying-Hsuan; Wang, Yifan

2018-03-01

We combine supersymmetric localization and the conformal bootstrap to study five-dimensional superconformal field theories. To begin, we classify the admissible counter-terms and derive a general relation between the five-sphere partition function and the conformal and flavor central charges. Along the way, we discover a new superconformal anomaly in five dimensions. We then propose a precise triple factorization formula for the five-sphere partition function, that incorporates instantons and is consistent with flavor symmetry enhancement. We numerically evaluate the central charges for the rank-one Seiberg and Morrison-Seiberg theories, and find strong evidence for their saturation of bootstrap bounds, thereby determining the spectra of long multiplets in these theories. Lastly, our results provide new evidence for the F-theorem and possibly a C-theorem in five-dimensional superconformal theories.

Fast Ion Transport Studies in DIII-D High βN Steady-State Scenarios

NASA Astrophysics Data System (ADS)

Holcomb, C. T.

2014-10-01

DIII-D research is identifying paths to optimize energetic particle (EP) transport in high βN steady-state tokamak scenarios. Operation with qmin > 2 is predicted to achieve high βN, confinement, and bootstrap fraction. However DIII-D experiments have shown that Alfvén eigenmodes (AE) and correlated EP transport can limit the performance of some qmin > 2 plasmas. Enhanced EP transport occurs in plasmas with qmin = 2-2.5, q95 = 5-7, and relatively long slowing down time. Strong AEs are present, the confinement factor H89 = 1.6-1.8 and βN is limited to ~3 by the available power. These observations are consistent with EP transport models having a critical gradient in βf. However, adjusting the parameters can recover classical EP confinement or improve thermal confinement so that H89 > 2 . One example is a scenario with βP and βN ~ 3 . 2 , qmin > 3 and q95 ~ 11 developed to test control of long pulse, high heat flux operation on devices like EAST. This has an internal transport barrier at ρ ~ 0 . 7 , bootstrap fraction >75%, density limit fraction ~1, and H89 >= 2 . In these cases AE activity and EP transport is very dynamic - it varies between classical and anomalous from shot to shot and within shots. Thus these plasmas are close to a threshold for enhanced EP transport. This may be governed by a combination of a relatively low ∇βfast due to good thermal confinement and lower beam power, short slowing down time, and possibly changes to the q-profile. Another example is scenarios with qmin ~ 1.1. These typically have classical EP confinement and good thermal confinement. Thus by using its flexible parameters and profile control tools DIII-D is comparing a wide range of steady-state scenarios to identify the key physics setting EP transport. Work supported by the US Department of Energy under DE-AC52-07NA27344, SC-G903402, DE-FC02-04ER54698, and DE-AC02-09CH11466.

Using a Nonparametric Bootstrap to Obtain a Confidence Interval for Pearson's "r" with Cluster Randomized Data: A Case Study

ERIC Educational Resources Information Center

Wagstaff, David A.; Elek, Elvira; Kulis, Stephen; Marsiglia, Flavio

2009-01-01

A nonparametric bootstrap was used to obtain an interval estimate of Pearson's "r," and test the null hypothesis that there was no association between 5th grade students' positive substance use expectancies and their intentions to not use substances. The students were participating in a substance use prevention program in which the unit of…

Bootstrapping a five-loop amplitude using Steinmann relations

DOE PAGES

Caron-Huot, Simon; Dixon, Lance J.; McLeod, Andrew; ...

2016-12-05

Here, the analytic structure of scattering amplitudes is restricted by Steinmann relations, which enforce the vanishing of certain discontinuities of discontinuities. We show that these relations dramatically simplify the function space for the hexagon function bootstrap in planar maximally supersymmetric Yang-Mills theory. Armed with this simplification, along with the constraints of dual conformal symmetry and Regge exponentiation, we obtain the complete five-loop six-particle amplitude.

A Bootstrap Algorithm for Mixture Models and Interval Data in Inter-Comparisons

DTIC Science & Technology

2001-07-01

parametric bootstrap. The present algorithm will be applied to a thermometric inter-comparison, where data cannot be assumed to be normally distributed. 2 Data...experimental methods, used in each laboratory) often imply that the statistical assumptions are not satisfied, as for example in several thermometric ...triangular). Indeed, in thermometric experiments these three probabilistic models can represent several common stochastic variabilities for

On the Model-Based Bootstrap with Missing Data: Obtaining a "P"-Value for a Test of Exact Fit

ERIC Educational Resources Information Center

Savalei, Victoria; Yuan, Ke-Hai

2009-01-01

Evaluating the fit of a structural equation model via bootstrap requires a transformation of the data so that the null hypothesis holds exactly in the sample. For complete data, such a transformation was proposed by Beran and Srivastava (1985) for general covariance structure models and applied to structural equation modeling by Bollen and Stine…

A Comparison of Kernel Equating and Traditional Equipercentile Equating Methods and the Parametric Bootstrap Methods for Estimating Standard Errors in Equipercentile Equating

ERIC Educational Resources Information Center

Choi, Sae Il

2009-01-01

This study used simulation (a) to compare the kernel equating method to traditional equipercentile equating methods under the equivalent-groups (EG) design and the nonequivalent-groups with anchor test (NEAT) design and (b) to apply the parametric bootstrap method for estimating standard errors of equating. A two-parameter logistic item response…

Measuring Efficiency of Tunisian Schools in the Presence of Quasi-Fixed Inputs: A Bootstrap Data Envelopment Analysis Approach

ERIC Educational Resources Information Center

Essid, Hedi; Ouellette, Pierre; Vigeant, Stephane

2010-01-01

The objective of this paper is to measure the efficiency of high schools in Tunisia. We use a statistical data envelopment analysis (DEA)-bootstrap approach with quasi-fixed inputs to estimate the precision of our measure. To do so, we developed a statistical model serving as the foundation of the data generation process (DGP). The DGP is…

BootGraph: probabilistic fiber tractography using bootstrap algorithms and graph theory.

PubMed

Vorburger, Robert S; Reischauer, Carolin; Boesiger, Peter

2013-02-01

Bootstrap methods have recently been introduced to diffusion-weighted magnetic resonance imaging to estimate the measurement uncertainty of ensuing diffusion parameters directly from the acquired data without the necessity to assume a noise model. These methods have been previously combined with deterministic streamline tractography algorithms to allow for the assessment of connection probabilities in the human brain. Thereby, the local noise induced disturbance in the diffusion data is accumulated additively due to the incremental progression of streamline tractography algorithms. Graph based approaches have been proposed to overcome this drawback of streamline techniques. For this reason, the bootstrap method is in the present work incorporated into a graph setup to derive a new probabilistic fiber tractography method, called BootGraph. The acquired data set is thereby converted into a weighted, undirected graph by defining a vertex in each voxel and edges between adjacent vertices. By means of the cone of uncertainty, which is derived using the wild bootstrap, a weight is thereafter assigned to each edge. Two path finding algorithms are subsequently applied to derive connection probabilities. While the first algorithm is based on the shortest path approach, the second algorithm takes all existing paths between two vertices into consideration. Tracking results are compared to an established algorithm based on the bootstrap method in combination with streamline fiber tractography and to another graph based algorithm. The BootGraph shows a very good performance in crossing situations with respect to false negatives and permits incorporating additional constraints, such as a curvature threshold. By inheriting the advantages of the bootstrap method and graph theory, the BootGraph method provides a computationally efficient and flexible probabilistic tractography setup to compute connection probability maps and virtual fiber pathways without the drawbacks of streamline tractography algorithms or the assumption of a noise distribution. Moreover, the BootGraph can be applied to common DTI data sets without further modifications and shows a high repeatability. Thus, it is very well suited for longitudinal studies and meta-studies based on DTI. Copyright © 2012 Elsevier Inc. All rights reserved.

Comparison of Bootstrapping and Markov Chain Monte Carlo for Copula Analysis of Hydrological Droughts

NASA Astrophysics Data System (ADS)

Yang, P.; Ng, T. L.; Yang, W.

2015-12-01

Effective water resources management depends on the reliable estimation of the uncertainty of drought events. Confidence intervals (CIs) are commonly applied to quantify this uncertainty. A CI seeks to be at the minimal length necessary to cover the true value of the estimated variable with the desired probability. In drought analysis where two or more variables (e.g., duration and severity) are often used to describe a drought, copulas have been found suitable for representing the joint probability behavior of these variables. However, the comprehensive assessment of the parameter uncertainties of copulas of droughts has been largely ignored, and the few studies that have recognized this issue have not explicitly compared the various methods to produce the best CIs. Thus, the objective of this study to compare the CIs generated using two widely applied uncertainty estimation methods, bootstrapping and Markov Chain Monte Carlo (MCMC). To achieve this objective, (1) the marginal distributions lognormal, Gamma, and Generalized Extreme Value, and the copula functions Clayton, Frank, and Plackett are selected to construct joint probability functions of two drought related variables. (2) The resulting joint functions are then fitted to 200 sets of simulated realizations of drought events with known distribution and extreme parameters and (3) from there, using bootstrapping and MCMC, CIs of the parameters are generated and compared. The effect of an informative prior on the CIs generated by MCMC is also evaluated. CIs are produced for different sample sizes (50, 100, and 200) of the simulated drought events for fitting the joint probability functions. Preliminary results assuming lognormal marginal distributions and the Clayton copula function suggest that for cases with small or medium sample sizes (~50-100), MCMC to be superior method if an informative prior exists. Where an informative prior is unavailable, for small sample sizes (~50), both bootstrapping and MCMC yield the same level of performance, and for medium sample sizes (~100), bootstrapping is better. For cases with a large sample size (~200), there is little difference between the CIs generated using bootstrapping and MCMC regardless of whether or not an informative prior exists.

Predicting pathway cross-talks in ankylosing spondylitis through investigating the interactions among pathways.

PubMed

Gu, Xiang; Liu, Cong-Jian; Wei, Jian-Jie

2017-11-13

Given that the pathogenesis of ankylosing spondylitis (AS) remains unclear, the aim of this study was to detect the potentially functional pathway cross-talk in AS to further reveal the pathogenesis of this disease. Using microarray profile of AS and biological pathways as study objects, Monte Carlo cross-validation method was used to identify the significant pathway cross-talks. In the process of Monte Carlo cross-validation, all steps were iterated 50 times. For each run, detection of differentially expressed genes (DEGs) between two groups was conducted. The extraction of the potential disrupted pathways enriched by DEGs was then implemented. Subsequently, we established a discriminating score (DS) for each pathway pair according to the distribution of gene expression levels. After that, we utilized random forest (RF) classification model to screen out the top 10 paired pathways with the highest area under the curve (AUCs), which was computed using 10-fold cross-validation approach. After 50 bootstrap, the best pairs of pathways were identified. According to their AUC values, the pair of pathways, antigen presentation pathway and fMLP signaling in neutrophils, achieved the best AUC value of 1.000, which indicated that this pathway cross-talk could distinguish AS patients from normal subjects. Moreover, the paired pathways of SAPK/JNK signaling and mitochondrial dysfunction were involved in 5 bootstraps. Two paired pathways (antigen presentation pathway and fMLP signaling in neutrophil, as well as SAPK/JNK signaling and mitochondrial dysfunction) can accurately distinguish AS and control samples. These paired pathways may be helpful to identify patients with AS for early intervention.

Numerical Calculation of Neoclassical Distribution Functions and Current Profiles in Low Collisionality, Axisymmetric Plasmas

DOE Office of Scientific and Technical Information (OSTI.GOV)

B.C. Lyons, S.C. Jardin, and J.J. Ramos

2012-06-28

A new code, the Neoclassical Ion-Electron Solver (NIES), has been written to solve for stationary, axisymmetric distribution functions (f ) in the conventional banana regime for both ions and elec trons using a set of drift-kinetic equations (DKEs) with linearized Fokker-Planck-Landau collision operators. Solvability conditions on the DKEs determine the relevant non-adiabatic pieces of f (called h ). We work in a 4D phase space in which Ψ defines a flux surface, θ is the poloidal angle, v is the total velocity referenced to the mean flow velocity, and λ is the dimensionless magnetic moment parameter. We expand h inmore » finite elements in both v and λ . The Rosenbluth potentials, φ and ψ, which define the integral part of the collision operator, are expanded in Legendre series in cos χ , where χ is the pitch angle, Fourier series in cos θ , and finite elements in v . At each ψ , we solve a block tridiagonal system for hi (independent of fe ), then solve another block tridiagonal system for he (dependent on fi ). We demonstrate that such a formulation can be accurately and efficiently solved. NIES is coupled to the MHD equilibrium code JSOLVER [J. DeLucia, et al., J. Comput. Phys. 37 , pp 183-204 (1980).] allowing us to work with realistic magnetic geometries. The bootstrap current is calculated as a simple moment of the distribution function. Results are benchmarked against the Sauter analytic formulas and can be used as a kinetic closure for an MHD code (e.g., M3D-C1 [S.C. Jardin, et al ., Computational Science & Discovery, 4 (2012).]).« less

Reliability of dose volume constraint inference from clinical data.

PubMed

Lutz, C M; Møller, D S; Hoffmann, L; Knap, M M; Alber, M

2017-04-21

Dose volume histogram points (DVHPs) frequently serve as dose constraints in radiotherapy treatment planning. An experiment was designed to investigate the reliability of DVHP inference from clinical data for multiple cohort sizes and complication incidence rates. The experimental background was radiation pneumonitis in non-small cell lung cancer and the DVHP inference method was based on logistic regression. From 102 NSCLC real-life dose distributions and a postulated DVHP model, an 'ideal' cohort was generated where the most predictive model was equal to the postulated model. A bootstrap and a Cohort Replication Monte Carlo (CoRepMC) approach were applied to create 1000 equally sized populations each. The cohorts were then analyzed to establish inference frequency distributions. This was applied to nine scenarios for cohort sizes of 102 (1), 500 (2) to 2000 (3) patients (by sampling with replacement) and three postulated DVHP models. The Bootstrap was repeated for a 'non-ideal' cohort, where the most predictive model did not coincide with the postulated model. The Bootstrap produced chaotic results for all models of cohort size 1 for both the ideal and non-ideal cohorts. For cohort size 2 and 3, the distributions for all populations were more concentrated around the postulated DVHP. For the CoRepMC, the inference frequency increased with cohort size and incidence rate. Correct inference rates  >[Formula: see text] were only achieved by cohorts with more than 500 patients. Both Bootstrap and CoRepMC indicate that inference of the correct or approximate DVHP for typical cohort sizes is highly uncertain. CoRepMC results were less spurious than Bootstrap results, demonstrating the large influence that randomness in dose-response has on the statistical analysis.

Reliability of dose volume constraint inference from clinical data

NASA Astrophysics Data System (ADS)

Lutz, C. M.; Møller, D. S.; Hoffmann, L.; Knap, M. M.; Alber, M.

2017-04-01

Dose volume histogram points (DVHPs) frequently serve as dose constraints in radiotherapy treatment planning. An experiment was designed to investigate the reliability of DVHP inference from clinical data for multiple cohort sizes and complication incidence rates. The experimental background was radiation pneumonitis in non-small cell lung cancer and the DVHP inference method was based on logistic regression. From 102 NSCLC real-life dose distributions and a postulated DVHP model, an ‘ideal’ cohort was generated where the most predictive model was equal to the postulated model. A bootstrap and a Cohort Replication Monte Carlo (CoRepMC) approach were applied to create 1000 equally sized populations each. The cohorts were then analyzed to establish inference frequency distributions. This was applied to nine scenarios for cohort sizes of 102 (1), 500 (2) to 2000 (3) patients (by sampling with replacement) and three postulated DVHP models. The Bootstrap was repeated for a ‘non-ideal’ cohort, where the most predictive model did not coincide with the postulated model. The Bootstrap produced chaotic results for all models of cohort size 1 for both the ideal and non-ideal cohorts. For cohort size 2 and 3, the distributions for all populations were more concentrated around the postulated DVHP. For the CoRepMC, the inference frequency increased with cohort size and incidence rate. Correct inference rates  >85 % were only achieved by cohorts with more than 500 patients. Both Bootstrap and CoRepMC indicate that inference of the correct or approximate DVHP for typical cohort sizes is highly uncertain. CoRepMC results were less spurious than Bootstrap results, demonstrating the large influence that randomness in dose-response has on the statistical analysis.

Statistical inference based on the nonparametric maximum likelihood estimator under double-truncation.

PubMed

Emura, Takeshi; Konno, Yoshihiko; Michimae, Hirofumi

2015-07-01

Doubly truncated data consist of samples whose observed values fall between the right- and left- truncation limits. With such samples, the distribution function of interest is estimated using the nonparametric maximum likelihood estimator (NPMLE) that is obtained through a self-consistency algorithm. Owing to the complicated asymptotic distribution of the NPMLE, the bootstrap method has been suggested for statistical inference. This paper proposes a closed-form estimator for the asymptotic covariance function of the NPMLE, which is computationally attractive alternative to bootstrapping. Furthermore, we develop various statistical inference procedures, such as confidence interval, goodness-of-fit tests, and confidence bands to demonstrate the usefulness of the proposed covariance estimator. Simulations are performed to compare the proposed method with both the bootstrap and jackknife methods. The methods are illustrated using the childhood cancer dataset.

Model specification and bootstrapping for multiply imputed data: An application to count models for the frequency of alcohol use

PubMed Central

Comulada, W. Scott

2015-01-01

Stata’s mi commands provide powerful tools to conduct multiple imputation in the presence of ignorable missing data. In this article, I present Stata code to extend the capabilities of the mi commands to address two areas of statistical inference where results are not easily aggregated across imputed datasets. First, mi commands are restricted to covariate selection. I show how to address model fit to correctly specify a model. Second, the mi commands readily aggregate model-based standard errors. I show how standard errors can be bootstrapped for situations where model assumptions may not be met. I illustrate model specification and bootstrapping on frequency counts for the number of times that alcohol was consumed in data with missing observations from a behavioral intervention. PMID:26973439

Heptagons from the Steinmann cluster bootstrap

DOE PAGES

Dixon, Lance J.; Drummond, James; Harrington, Thomas; ...

2017-02-28

We reformulate the heptagon cluster bootstrap to take advantage of the Steinmann relations, which require certain double discontinuities of any amplitude to vanish. These constraints vastly reduce the number of functions needed to bootstrap seven-point amplitudes in planarmore » $$ \\mathcal{N} $$ = 4 supersymmetric Yang-Mills theory, making higher-loop contributions to these amplitudes more computationally accessible. In particular, dual superconformal symmetry and well-defined collinear limits suffice to determine uniquely the symbols of the three-loop NMHV and four-loop MHV seven-point amplitudes. We also show that at three loops, relaxing the dual superconformal $$\\bar{Q}$$ relations and imposing dihedral symmetry (and for NMHV the absence of spurious poles) leaves only a single ambiguity in the heptagon amplitudes. These results point to a strong tension between the collinear properties of the amplitudes and the Steinmann relations.« less

Kepler Planet Detection Metrics: Statistical Bootstrap Test

NASA Technical Reports Server (NTRS)

Jenkins, Jon M.; Burke, Christopher J.

2016-01-01

This document describes the data produced by the Statistical Bootstrap Test over the final three Threshold Crossing Event (TCE) deliveries to NExScI: SOC 9.1 (Q1Q16)1 (Tenenbaum et al. 2014), SOC 9.2 (Q1Q17) aka DR242 (Seader et al. 2015), and SOC 9.3 (Q1Q17) aka DR253 (Twicken et al. 2016). The last few years have seen significant improvements in the SOC science data processing pipeline, leading to higher quality light curves and more sensitive transit searches. The statistical bootstrap analysis results presented here and the numerical results archived at NASAs Exoplanet Science Institute (NExScI) bear witness to these software improvements. This document attempts to introduce and describe the main features and differences between these three data sets as a consequence of the software changes.

Imaging with New Classic and Vision at the NPOI

NASA Astrophysics Data System (ADS)

Jorgensen, Anders

2018-04-01

The Navy Precision Optical Interferometer (NPOI) is unique among interferometric observatories for its ability to position telescopes in an equally-spaced array configuration. This configuration is optimal for interferometric imaging because it allows the use of bootstrapping to track fringes on long baselines with signal-to-noise ratio less than one. When combined with coherent integration techniques this can produce visibilities with acceptable SNR on baselines long enough to resolve features on the surfaces of stars. The stellar surface imaging project at NPOI combines the bootstrapping array configuration of the NPOI array, real-time fringe tracking, baseline- and wavelength bootstrapping with Earth rotation to provide dense coverage in the UV plane at a wide range of spatial frequencies. In this presentation, we provide an overview of the project and an update of the latest status and results from the project.

Predicting fatty acid profiles in blood based on food intake and the FADS1 rs174546 SNP.

PubMed

Hallmann, Jacqueline; Kolossa, Silvia; Gedrich, Kurt; Celis-Morales, Carlos; Forster, Hannah; O'Donovan, Clare B; Woolhead, Clara; Macready, Anna L; Fallaize, Rosalind; Marsaux, Cyril F M; Lambrinou, Christina-Paulina; Mavrogianni, Christina; Moschonis, George; Navas-Carretero, Santiago; San-Cristobal, Rodrigo; Godlewska, Magdalena; Surwiłło, Agnieszka; Mathers, John C; Gibney, Eileen R; Brennan, Lorraine; Walsh, Marianne C; Lovegrove, Julie A; Saris, Wim H M; Manios, Yannis; Martinez, Jose Alfredo; Traczyk, Iwona; Gibney, Michael J; Daniel, Hannelore

2015-12-01

A high intake of n-3 PUFA provides health benefits via changes in the n-6/n-3 ratio in blood. In addition to such dietary PUFAs, variants in the fatty acid desaturase 1 (FADS1) gene are also associated with altered PUFA profiles. We used mathematical modeling to predict levels of PUFA in whole blood, based on multiple hypothesis testing and bootstrapped LASSO selected food items, anthropometric and lifestyle factors, and the rs174546 genotypes in FADS1 from 1607 participants (Food4Me Study). The models were developed using data from the first reported time point (training set) and their predictive power was evaluated using data from the last reported time point (test set). Among other food items, fish, pizza, chicken, and cereals were identified as being associated with the PUFA profiles. Using these food items and the rs174546 genotypes as predictors, models explained 26-43% of the variability in PUFA concentrations in the training set and 22-33% in the test set. Selecting food items using multiple hypothesis testing is a valuable contribution to determine predictors, as our models' predictive power is higher compared to analogue studies. As unique feature, we additionally confirmed our models' power based on a test set. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Bootstrapping and Maintaining Trust in the Cloud

DTIC Science & Technology

2016-12-01

proliferation and popularity of infrastructure-as-a- service (IaaS) cloud computing services such as Amazon Web Services and Google Compute Engine means...IaaS trusted computing system: • Secure Bootstrapping – the system should enable the tenant to securely install an initial root secret into each cloud ...elastically instantiated and terminated. Prior cloud trusted computing solutions address a subset of these features, but none achieve all. Excalibur [31] sup

Sample Reuse in Statistical Remodeling.

DTIC Science & Technology

1987-08-01

as the jackknife and bootstrap, is an expansion of the functional, T(Fn), or of its distribution function or both. Frangos and Schucany (1987a) used...accelerated bootstrap. In the same report Frangos and Schucany demonstrated the small sample superiority of that approach over the proposals that take...higher order terms of an Edgeworth expansion into account. In a second report Frangos and Schucany (1987b) examined the small sample performance of

Bootstrapping Development of a Cloud-Based Spoken Dialog System in the Educational Domain from Scratch Using Crowdsourced Data. Research Report. ETS RR-16-16

ERIC Educational Resources Information Center

Ramanarayanan, Vikram; Suendermann-Oeft, David; Lange, Patrick; Ivanov, Alexei V.; Evanini, Keelan; Yu, Zhou; Tsuprun, Eugene; Qian, Yao

2016-01-01

We propose a crowdsourcing-based framework to iteratively and rapidly bootstrap a dialog system from scratch for a new domain. We leverage the open-source modular HALEF dialog system to deploy dialog applications. We illustrate the usefulness of this framework using four different prototype dialog items with applications in the educational domain…

The sound symbolism bootstrapping hypothesis for language acquisition and language evolution.

PubMed

Imai, Mutsumi; Kita, Sotaro

2014-09-19

Sound symbolism is a non-arbitrary relationship between speech sounds and meaning. We review evidence that, contrary to the traditional view in linguistics, sound symbolism is an important design feature of language, which affects online processing of language, and most importantly, language acquisition. We propose the sound symbolism bootstrapping hypothesis, claiming that (i) pre-verbal infants are sensitive to sound symbolism, due to a biologically endowed ability to map and integrate multi-modal input, (ii) sound symbolism helps infants gain referential insight for speech sounds, (iii) sound symbolism helps infants and toddlers associate speech sounds with their referents to establish a lexical representation and (iv) sound symbolism helps toddlers learn words by allowing them to focus on referents embedded in a complex scene, alleviating Quine's problem. We further explore the possibility that sound symbolism is deeply related to language evolution, drawing the parallel between historical development of language across generations and ontogenetic development within individuals. Finally, we suggest that sound symbolism bootstrapping is a part of a more general phenomenon of bootstrapping by means of iconic representations, drawing on similarities and close behavioural links between sound symbolism and speech-accompanying iconic gesture. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Advancing theory development: exploring the leadership-climate relationship as a mechanism of the implementation of cultural competence.

PubMed

Guerrero, Erick G; Fenwick, Karissa; Kong, Yinfei

2017-11-14

Leadership style and specific organizational climates have emerged as critical mechanisms to implement targeted practices in organizations. Drawing from relevant theories, we propose that climate for implementation of cultural competence reflects how transformational leadership may enhance the organizational implementation of culturally responsive practices in health care organizations. Using multilevel data from 427 employees embedded in 112 addiction treatment programs collected in 2013, confirmatory factor analysis showed adequate fit statistics for our measure of climate for implementation of cultural competence (Cronbach's alpha = .88) and three outcomes: knowledge (Cronbach's alpha = .88), services (Cronbach's alpha = .86), and personnel (Cronbach's alpha = .86) practices. Results from multilevel path analyses indicate a positive relationship between employee perceptions of transformational leadership and climate for implementation of cultural competence (standardized indirect effect = .057, bootstrap p < .001). We also found a positive indirect effect between transformational leadership and each of the culturally competent practices: knowledge (standardized indirect effect = .006, bootstrap p = .004), services (standardized indirect effect = .019, bootstrap p < .001), and personnel (standardized indirect effect = .014, bootstrap p = .005). Findings contribute to implementation science. They build on leadership theory and offer evidence of the mediating role of climate in the implementation of cultural competence in addiction health service organizations.

Non-parametric methods for cost-effectiveness analysis: the central limit theorem and the bootstrap compared.

PubMed

Nixon, Richard M; Wonderling, David; Grieve, Richard D

2010-03-01

Cost-effectiveness analyses (CEA) alongside randomised controlled trials commonly estimate incremental net benefits (INB), with 95% confidence intervals, and compute cost-effectiveness acceptability curves and confidence ellipses. Two alternative non-parametric methods for estimating INB are to apply the central limit theorem (CLT) or to use the non-parametric bootstrap method, although it is unclear which method is preferable. This paper describes the statistical rationale underlying each of these methods and illustrates their application with a trial-based CEA. It compares the sampling uncertainty from using either technique in a Monte Carlo simulation. The experiments are repeated varying the sample size and the skewness of costs in the population. The results showed that, even when data were highly skewed, both methods accurately estimated the true standard errors (SEs) when sample sizes were moderate to large (n>50), and also gave good estimates for small data sets with low skewness. However, when sample sizes were relatively small and the data highly skewed, using the CLT rather than the bootstrap led to slightly more accurate SEs. We conclude that while in general using either method is appropriate, the CLT is easier to implement, and provides SEs that are at least as accurate as the bootstrap. (c) 2009 John Wiley & Sons, Ltd.

Smokers’ sensory beliefs mediate the relation between smoking a ‘light/low tar’ cigarette and perceptions of harm

PubMed Central

Elton-Marshall, Tara; Fong, Geoffrey T; Yong, Hua-Hie; Borland, Ron; Xu, Steve Shaowei; Quah, Anne C K; Feng, Guoze; Jiang, Yuan

2016-01-01

Background The sensory belief that ‘light/low tar’ cigarettes are smoother can also influence the belief that ‘light/low tar’ cigarettes are less harmful. However, the ‘light’ concept is one of several factors influencing beliefs. No studies have examined the impact of the sensory belief about one’s own brand of cigarettes on perceptions of harm. Objective The current study examines whether a smoker’s sensory belief that their brand is smoother is associated with the belief that their brand is less harmful and whether sensory beliefs mediate the relation between smoking a ‘light/low tar’ cigarette and relative perceptions of harm among smokers in China. Methods Data are from 5209 smokers who were recruited using a stratified multistage sampling design and participated in wave 3 of the International Tobacco Control (ITC) China Survey, a face-to-face survey of adult smokers and non-smokers in seven cities. Results Smokers who agreed that their brand of cigarettes was smoother were significantly more likely to say that their brand of cigarettes was less harmful (p<0.001, OR=6.86, 95% CI 5.64 to 8.33). Mediational analyses using the bootstrapping procedure indicated that both the direct effect of ‘light/low tar’ cigarette smokers on the belief that their cigarettes are less harmful (b=0.24, bootstrapped bias corrected 95% CI 0.13 to 0.34, p<0.001) and the indirect effect via their belief that their cigarettes are smoother were significant (b=0.32, bootstrapped bias-corrected 95% CI 0.28 to 0.37, p<0.001), suggesting that the mediation was partial. Conclusions These results demonstrate the importance of implementing tobacco control policies that address the impact that cigarette design and marketing can have in capitalising on the smoker’s natural associations between smoother sensations and lowered perceptions of harm. PMID:25370698

Smokers' sensory beliefs mediate the relation between smoking a light/low tar cigarette and perceptions of harm.

PubMed

Elton-Marshall, Tara; Fong, Geoffrey T; Yong, Hua-Hie; Borland, Ron; Xu, Steve Shaowei; Quah, Anne C K; Feng, Guoze; Jiang, Yuan

2015-11-01

The sensory belief that 'light/low tar' cigarettes are smoother can also influence the belief that 'light/low tar' cigarettes are less harmful. However, the 'light' concept is one of several factors influencing beliefs. No studies have examined the impact of the sensory belief about one's own brand of cigarettes on perceptions of harm. The current study examines whether a smoker's sensory belief that their brand is smoother is associated with the belief that their brand is less harmful and whether sensory beliefs mediate the relation between smoking a 'light/low tar' cigarette and relative perceptions of harm among smokers in China. Data are from 5209 smokers who were recruited using a stratified multistage sampling design and participated in Wave 3 of the International Tobacco Control (ITC) China Survey, a face-to-face survey of adult smokers and non-smokers in seven cities. Smokers who agreed that their brand of cigarettes was smoother were significantly more likely to say that their brand of cigarettes was less harmful (p<0.001, OR=6.86, 95% CI 5.64 to 8.33). Mediational analyses using the bootstrapping procedure indicated that both the direct effect of 'light/low tar' cigarette smokers on the belief that their cigarettes are less harmful (b=0.24, bootstrapped bias corrected 95% CI 0.13 to 0.34, p<0.001) and the indirect effect via their belief that their cigarettes are smoother were significant (b=0.32, bootstrapped bias-corrected 95% CI 0.28 to 0.37, p<0.001), suggesting that the mediation was partial. These results demonstrate the importance of implementing tobacco control policies that address the impact that cigarette design and marketing can have in capitalising on the smoker's natural associations between smoother sensations and lowered perceptions of harm. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://www.bmj.com/company/products-services/rights-and-licensing/

Maternal depression and trait anger as risk factors for escalated physical discipline.

PubMed

Shay, Nicole L; Knutson, John F

2008-02-01

To test the hypothesized anger-mediated relation between maternal depression and escalation of physical discipline, 122 economically disadvantaged mothers were assessed for current and lifetime diagnoses of depression using the Current Depressive Episode, Past Depression, and Dysthymia sections of the Structured Clinical Interview for DSM-IV (SCID) and a measure of current depressive symptoms, the Beck Depression Inventory-Second Edition (BDI-II). Escalation of physical discipline was assessed using a video analog parenting task; maternal anger not specific to discipline was assessed using the Spielberger Trait Anger Expression Inventory. Reports of anger were associated with the diagnosis of depression and depressive symptoms. Bootstrap analyses of indirect effects indicated that the link between depression and escalated discipline was mediated by anger. Parallel analyses based on BDI-II scores identified a marginally significant indirect effect of depression on discipline. Findings suggest that anger and irritability are central to the putative link between depression and harsh discipline.

BOOTSTRAPPING THE CORONAL MAGNETIC FIELD WITH STEREO: UNIPOLAR POTENTIAL FIELD MODELING

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aschwanden, Markus J.; Sandman, Anne W., E-mail: aschwanden@lmsal.co

We investigate the recently quantified misalignment of {alpha}{sub mis} {approx} 20{sup 0}-40{sup 0} between the three-dimensional geometry of stereoscopically triangulated coronal loops observed with STEREO/EUVI (in four active regions (ARs)) and theoretical (potential or nonlinear force-free) magnetic field models extrapolated from photospheric magnetograms. We develop an efficient method of bootstrapping the coronal magnetic field by forward fitting a parameterized potential field model to the STEREO-observed loops. The potential field model consists of a number of unipolar magnetic charges that are parameterized by decomposing a photospheric magnetogram from the Michelson Doppler Imager. The forward-fitting method yields a best-fit magnetic field modelmore » with a reduced misalignment of {alpha}{sub PF} {approx} 13{sup 0}-20{sup 0}. We also evaluate stereoscopic measurement errors and find a contribution of {alpha}{sub SE} {approx} 7{sup 0}-12{sup 0}, which constrains the residual misalignment to {alpha}{sub NP} {approx} 11{sup 0}-17{sup 0}, which is likely due to the nonpotentiality of the ARs. The residual misalignment angle, {alpha}{sub NP}, of the potential field due to nonpotentiality is found to correlate with the soft X-ray flux of the AR, which implies a relationship between electric currents and plasma heating.« less

Correcting the Standard Errors of 2-Stage Residual Inclusion Estimators for Mendelian Randomization Studies.

PubMed

Palmer, Tom M; Holmes, Michael V; Keating, Brendan J; Sheehan, Nuala A

2017-11-01

Mendelian randomization studies use genotypes as instrumental variables to test for and estimate the causal effects of modifiable risk factors on outcomes. Two-stage residual inclusion (TSRI) estimators have been used when researchers are willing to make parametric assumptions. However, researchers are currently reporting uncorrected or heteroscedasticity-robust standard errors for these estimates. We compared several different forms of the standard error for linear and logistic TSRI estimates in simulations and in real-data examples. Among others, we consider standard errors modified from the approach of Newey (1987), Terza (2016), and bootstrapping. In our simulations Newey, Terza, bootstrap, and corrected 2-stage least squares (in the linear case) standard errors gave the best results in terms of coverage and type I error. In the real-data examples, the Newey standard errors were 0.5% and 2% larger than the unadjusted standard errors for the linear and logistic TSRI estimators, respectively. We show that TSRI estimators with modified standard errors have correct type I error under the null. Researchers should report TSRI estimates with modified standard errors instead of reporting unadjusted or heteroscedasticity-robust standard errors. © The Author(s) 2017. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health.

Advances in the high bootstrap fraction regime on DIII-D towards the Q = 5 mission of ITER steady state

DOE PAGES

Qian, Jinping P.; Garofalo, Andrea M.; Gong, Xianzu Z.; ...

2017-03-20

Recent EAST/DIII-D joint experiments on the high poloidal betamore » $${{\\beta}_{\\text{P}}}$$ regime in DIII-D have extended operation with internal transport barriers (ITBs) and excellent energy confinement (H 98y2 ~ 1.6) to higher plasma current, for lower q 95 ≤ 7.0, and more balanced neutral beam injection (NBI) (torque injection < 2 Nm), for lower plasma rotation than previous results. Transport analysis and experimental measurements at low toroidal rotation suggest that the E × B shear effect is not key to the ITB formation in these high $${{\\beta}_{\\text{P}}}$$ discharges. Experiments and TGLF modeling show that the Shafranov shift has a key stabilizing effect on turbulence. Extrapolation of the DIII-D results using a 0D model shows that with the improved confinement, the high bootstrap fraction regime could achieve fusion gain Q = 5 in ITER at $${{\\beta}_{\\text{N}}}$$ ~ 2.9 and q 95 ~ 7. With the optimization of q(0), the required improved confinement is achievable when using 1.5D TGLF-SAT1 for transport simulations. Furthermore, results reported in this paper suggest that the DIII-D high $${{\\beta}_{\\text{P}}}$$ scenario could be a candidate for ITER steady state operation.« less

Parametric methods outperformed non-parametric methods in comparisons of discrete numerical variables.

PubMed

Fagerland, Morten W; Sandvik, Leiv; Mowinckel, Petter

2011-04-13

The number of events per individual is a widely reported variable in medical research papers. Such variables are the most common representation of the general variable type called discrete numerical. There is currently no consensus on how to compare and present such variables, and recommendations are lacking. The objective of this paper is to present recommendations for analysis and presentation of results for discrete numerical variables. Two simulation studies were used to investigate the performance of hypothesis tests and confidence interval methods for variables with outcomes {0, 1, 2}, {0, 1, 2, 3}, {0, 1, 2, 3, 4}, and {0, 1, 2, 3, 4, 5}, using the difference between the means as an effect measure. The Welch U test (the T test with adjustment for unequal variances) and its associated confidence interval performed well for almost all situations considered. The Brunner-Munzel test also performed well, except for small sample sizes (10 in each group). The ordinary T test, the Wilcoxon-Mann-Whitney test, the percentile bootstrap interval, and the bootstrap-t interval did not perform satisfactorily. The difference between the means is an appropriate effect measure for comparing two independent discrete numerical variables that has both lower and upper bounds. To analyze this problem, we encourage more frequent use of parametric hypothesis tests and confidence intervals.

The effect of sheared toroidal rotation on pressure driven magnetic islands in toroidal plasmas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hegna, C. C.

2016-05-15

The impact of sheared toroidal rotation on the evolution of pressure driven magnetic islands in tokamak plasmas is investigated using a resistive magnetohydrodynamics model augmented by a neoclassical Ohm's law. Particular attention is paid to the asymptotic matching data as the Mercier indices are altered in the presence of sheared flow. Analysis of the nonlinear island Grad-Shafranov equation shows that sheared flows tend to amplify the stabilizing pressure/curvature contribution to pressure driven islands in toroidal tokamaks relative to the island bootstrap current contribution. As such, sheared toroidal rotation tends to reduce saturated magnetic island widths.

Forensic discrimination of copper wire using trace element concentrations.

PubMed

Dettman, Joshua R; Cassabaum, Alyssa A; Saunders, Christopher P; Snyder, Deanna L; Buscaglia, JoAnn

2014-08-19

Copper may be recovered as evidence in high-profile cases such as thefts and improvised explosive device incidents; comparison of copper samples from the crime scene and those associated with the subject of an investigation can provide probative associative evidence and investigative support. A solution-based inductively coupled plasma mass spectrometry method for measuring trace element concentrations in high-purity copper was developed using standard reference materials. The method was evaluated for its ability to use trace element profiles to statistically discriminate between copper samples considering the precision of the measurement and manufacturing processes. The discriminating power was estimated by comparing samples chosen on the basis of the copper refining and production process to represent the within-source (samples expected to be similar) and between-source (samples expected to be different) variability using multivariate parametric- and empirical-based data simulation models with bootstrap resampling. If the false exclusion rate is set to 5%, >90% of the copper samples can be correctly determined to originate from different sources using a parametric-based model and >87% with an empirical-based approach. These results demonstrate the potential utility of the developed method for the comparison of copper samples encountered as forensic evidence.

Bootstrapping and Maintaining Trust in the Cloud

DTIC Science & Technology

2016-03-16

of infrastructure-as-a- service (IaaS) cloud computing services such as Ama- zon Web Services, Google Compute Engine, Rackspace, et. al. means that...Implementation We implemented keylime in ∼3.2k lines of Python in four components: registrar, node, CV, and tenant. The registrar offers a REST-based web ...bootstrap key K. It provides an unencrypted REST-based web service for these two functions. As described earlier, the pro- tocols for exchanging data

Reduced Power Laer Designation Systems

DTIC Science & Technology

2008-06-20

200KD, Ri = = 60Kfl, and R 2 = R4 = 2K yields an overall transimpedance gain of 200K x 30 x 30 = 180MV/A. Figure 3. Three stage photodiode amplifier ...transistor circuit for bootstrap buffering of the input stage, comparing the noise performance of the candidate amplifier designs, selecting the two...transistor bootstrap design as the circuit of choice, and comparing the performance of this circuit against that of a basic transconductance amplifier

Benchmarking the efficiency of the Chilean water and sewerage companies: a double-bootstrap approach.

PubMed

Molinos-Senante, María; Donoso, Guillermo; Sala-Garrido, Ramon; Villegas, Andrés

2018-03-01

Benchmarking the efficiency of water companies is essential to set water tariffs and to promote their sustainability. In doing so, most of the previous studies have applied conventional data envelopment analysis (DEA) models. However, it is a deterministic method that does not allow to identify environmental factors influencing efficiency scores. To overcome this limitation, this paper evaluates the efficiency of a sample of Chilean water and sewerage companies applying a double-bootstrap DEA model. Results evidenced that the ranking of water and sewerage companies changes notably whether efficiency scores are computed applying conventional or double-bootstrap DEA models. Moreover, it was found that the percentage of non-revenue water and customer density are factors influencing the efficiency of Chilean water and sewerage companies. This paper illustrates the importance of using a robust and reliable method to increase the relevance of benchmarking tools.

Probabilistic sensitivity analysis incorporating the bootstrap: an example comparing treatments for the eradication of Helicobacter pylori.

PubMed

Pasta, D J; Taylor, J L; Henning, J M

1999-01-01

Decision-analytic models are frequently used to evaluate the relative costs and benefits of alternative therapeutic strategies for health care. Various types of sensitivity analysis are used to evaluate the uncertainty inherent in the models. Although probabilistic sensitivity analysis is more difficult theoretically and computationally, the results can be much more powerful and useful than deterministic sensitivity analysis. The authors show how a Monte Carlo simulation can be implemented using standard software to perform a probabilistic sensitivity analysis incorporating the bootstrap. The method is applied to a decision-analytic model evaluating the cost-effectiveness of Helicobacter pylori eradication. The necessary steps are straightforward and are described in detail. The use of the bootstrap avoids certain difficulties encountered with theoretical distributions. The probabilistic sensitivity analysis provided insights into the decision-analytic model beyond the traditional base-case and deterministic sensitivity analyses and should become the standard method for assessing sensitivity.

Bootstrapping the energy flow in the beginning of life.

PubMed

Hengeveld, R; Fedonkin, M A

2007-01-01

This paper suggests that the energy flow on which all living structures depend only started up slowly, the low-energy, initial phase starting up a second, slightly more energetic phase, and so on. In this way, the build up of the energy flow follows a bootstrapping process similar to that found in the development of computers, the first generation making possible the calculations necessary for constructing the second one, etc. In the biogenetic upstart of an energy flow, non-metals in the lower periods of the Periodic Table of Elements would have constituted the most primitive systems, their operation being enhanced and later supplanted by elements in the higher periods that demand more energy. This bootstrapping process would put the development of the metabolisms based on the second period elements carbon, nitrogen and oxygen at the end of the evolutionary process rather than at, or even before, the biogenetic event.

Demonstration of Current Profile Shaping using Double Dog-Leg Emittance Exchange Beam Line at Argonne Wakefield Accelerator

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ha, Gwanghui; Cho, Moo-Hyun; Conde, Manoel

Emittance exchange (EEX) based longitudinal current profile shaping is the one of the promising current profile shaping technique. This method can generate high quality arbitrary current profiles under the ideal conditions. The double dog-leg EEX beam line was recently installed at the Argonne Wakefield Accelerator (AWA) to explore the shaping capability and confirm the quality of this method. To demonstrate the arbitrary current profile generation, several different transverse masks are applied to generate different final current profiles. The phase space slopes and the charge of incoming beam are varied to observe and suppress the aberrations on the ideal profile. Wemore » present current profile shaping results, aberrations on the shaped profile, and its suppression.« less

Seasonal comparisons of sea ice concentration estimates derived from SSM/I, OKEAN, and RADARSAT data

USGS Publications Warehouse

Belchansky, Gennady I.; Douglas, David C.

2002-01-01

The Special Sensor Microwave Imager (SSM/I) microwave satellite radiometer and its predecessor SMMR are primary sources of information for global sea ice and climate studies. However, comparisons of SSM/I, Landsat, AVHRR, and ERS-1 synthetic aperture radar (SAR) have shown substantial seasonal and regional differences in their estimates of sea ice concentration. To evaluate these differences, we compared SSM/I estimates of sea ice coverage derived with the NASA Team and Bootstrap algorithms to estimates made using RADARSAT, and OKEAN-01 satellite sensor data. The study area included the Barents Sea, Kara Sea, Laptev Sea, and adjacent parts of the Arctic Ocean, during October 1995 through October 1999. Ice concentration estimates from spatially and temporally near-coincident imagery were calculated using independent algorithms for each sensor type. The OKEAN algorithm implemented the satellite's two-channel active (radar) and passive microwave data in a linear mixture model based on the measured values of brightness temperature and radar backscatter. The RADARSAT algorithm utilized a segmentation approach of the measured radar backscatter, and the SSM/I ice concentrations were derived at National Snow and Ice Data Center (NSIDC) using the NASA Team and Bootstrap algorithms. Seasonal and monthly differences between SSM/I, OKEAN, and RADARSAT ice concentrations were calculated and compared. Overall, total sea ice concentration estimates derived independently from near-coincident RADARSAT, OKEAN-01, and SSM/I satellite imagery demonstrated mean differences of less than 5.5% (S.D.<9.5%) during the winter period. Differences between the SSM/I NASA Team and the SSM/I Bootstrap concentrations were no more than 3.1% (S.D.<5.4%) during this period. RADARSAT and OKEAN-01 data both yielded higher total ice concentrations than the NASA Team and the Bootstrap algorithms. The Bootstrap algorithm yielded higher total ice concentrations than the NASA Team algorithm. Total ice concentrations derived from OKEAN-01 and SSM/I satellite imagery were highly correlated during winter, spring, and fall, with mean differences of less than 8.1% (S.D.<15%) for the NASA Team algorithm, and less than 2.8% (S.D.<13.8%) for the Bootstrap algorithm. Respective differences between SSM/I NASA Team and SSM/I Bootstrap total concentrations were less than 5.3% (S.D.<6.9%). Monthly mean differences between SSM/I and OKEAN differed annually by less than 6%, with smaller differences primarily in winter. The NASA Team and Bootstrap algorithms underestimated the total sea ice concentrations relative to the RADARSAT ScanSAR no more than 3.0% (S.D.<9%) and 1.2% (S.D.<7.5%) during cold months, and no more than 12% and 7% during summer, respectively. ScanSAR tended to estimate higher ice concentrations for ice concentrations greater than 50%, when compared to SSM/I during all months. ScanSAR underestimated total sea ice concentration by 2% compared to the OKEAN-01 algorithm during cold months, and gave an overestimation by 2% during spring and summer months. Total NASA Team and Bootstrap sea ice concentration estimates derived from coincident SSM/I and OKEAN-01 data demonstrated mean differences of no more than 5.3% (S.D.<7%), 3.1% (S.D.<5.5%), 2.0% (S.D.<5.5%), and 7.3% (S.D.<10%) for fall, winter, spring, and summer periods, respectively. Large disagreements were observed between the OKEAN and NASA Team results in spring and summer for estimates of the first-year (FY) and multiyear (MY) age classes. The OKEAN-01 algorithm and data tended to estimate, on average, lower concentrations of young or FY ice and higher concentrations of total and MY ice for all months and seasons. Our results contribute to the growing body of documentation about the levels of disparity obtained when seasonal sea ice concentrations are estimated using various types of satellite data and algorithms.

Assessment of genetic diversity in indigenous turmeric (Curcuma longa) germplasm from India using molecular markers.

PubMed

Verma, Sushma; Singh, Shweta; Sharma, Suresh; Tewari, S K; Roy, R K; Goel, A K; Rana, T S

2015-04-01

Curcuma longa L., commonly known as turmeric, is one of the economically and medicinally important plant species. It is predominantly cultivated in the tropical and sub tropical countries. India is the largest producer, and exporter of turmeric in the world, followed by China, Indonesia, Bangladesh and Thailand. In the present study, Directed Amplification of Minisatellite DNA (DAMD) and Inter Simple Sequence Repeats (ISSR), methods were used to estimate the genetic variability in indigenous turmeric germplasm. Cumulative data analysis for DAMD (15) and ISSR (13) markers resulted into 478 fragments, out of which 392 fragments were polymorphic, revealing 82 % polymorphism across the turmeric genotypes. Wide range of pairwise genetic distances (0.03-0.59) across the genotypes revealed that these genotypes are genetically quite diverse. The UPGMA dendrogram generated using cumulative data showed significant relationships amongst the genotypes. All 29 genotypes studied grouped into two clusters irrespective of their geographical affiliations with 100 % bootstrap value except few genotypes, suggesting considerable diversity amongst the genotypes. These results suggested that the current collection of turmeric genotypes preserve the vast majority of natural variations. The results further demonstrate the efficiency and reliability of DAMD and ISSR markers in determining the genetic diversity and relationships among the indigenous turmeric germplasm. DAMD and ISSR profiling have identified diverse turmeric genotypes, which could be further utilized in various genetic improvement programmes including conventional as well as marker assisted breeding towards development of new and desirable turmeric genotypes.

A cluster bootstrap for two-loop MHV amplitudes

DOE PAGES

Golden, John; Spradlin, Marcus

2015-02-02

We apply a bootstrap procedure to two-loop MHV amplitudes in planar N=4 super-Yang-Mills theory. We argue that the mathematically most complicated part (the Λ 2 B 2 coproduct component) of the n-particle amplitude is uniquely determined by a simple cluster algebra property together with a few physical constraints (dihedral symmetry, analytic structure, supersymmetry, and well-defined collinear limits). Finally, we present a concise, closed-form expression which manifests these properties for all n.

Wrappers for Performance Enhancement and Oblivious Decision Graphs

DTIC Science & Technology

1995-09-01

always select all relevant features. We test di erent search engines to search the space of feature subsets and introduce compound operators to speed...distinct instances from the original dataset appearing in the test set is thus 0:632m. The 0i accuracy estimate is derived by using bootstrap sample...i for training and the rest of the instances for testing . Given a number b, the number of bootstrap samples, let 0i be the accuracy estimate for

CME Velocity and Acceleration Error Estimates Using the Bootstrap Method

NASA Technical Reports Server (NTRS)

Michalek, Grzegorz; Gopalswamy, Nat; Yashiro, Seiji

2017-01-01

The bootstrap method is used to determine errors of basic attributes of coronal mass ejections (CMEs) visually identified in images obtained by the Solar and Heliospheric Observatory (SOHO) mission's Large Angle and Spectrometric Coronagraph (LASCO) instruments. The basic parameters of CMEs are stored, among others, in a database known as the SOHO/LASCO CME catalog and are widely employed for many research studies. The basic attributes of CMEs (e.g. velocity and acceleration) are obtained from manually generated height-time plots. The subjective nature of manual measurements introduces random errors that are difficult to quantify. In many studies the impact of such measurement errors is overlooked. In this study we present a new possibility to estimate measurements errors in the basic attributes of CMEs. This approach is a computer-intensive method because it requires repeating the original data analysis procedure several times using replicate datasets. This is also commonly called the bootstrap method in the literature. We show that the bootstrap approach can be used to estimate the errors of the basic attributes of CMEs having moderately large numbers of height-time measurements. The velocity errors are in the vast majority small and depend mostly on the number of height-time points measured for a particular event. In the case of acceleration, the errors are significant, and for more than half of all CMEs, they are larger than the acceleration itself.

Simplified Estimation and Testing in Unbalanced Repeated Measures Designs.

PubMed

Spiess, Martin; Jordan, Pascal; Wendt, Mike

2018-05-07

In this paper we propose a simple estimator for unbalanced repeated measures design models where each unit is observed at least once in each cell of the experimental design. The estimator does not require a model of the error covariance structure. Thus, circularity of the error covariance matrix and estimation of correlation parameters and variances are not necessary. Together with a weak assumption about the reason for the varying number of observations, the proposed estimator and its variance estimator are unbiased. As an alternative to confidence intervals based on the normality assumption, a bias-corrected and accelerated bootstrap technique is considered. We also propose the naive percentile bootstrap for Wald-type tests where the standard Wald test may break down when the number of observations is small relative to the number of parameters to be estimated. In a simulation study we illustrate the properties of the estimator and the bootstrap techniques to calculate confidence intervals and conduct hypothesis tests in small and large samples under normality and non-normality of the errors. The results imply that the simple estimator is only slightly less efficient than an estimator that correctly assumes a block structure of the error correlation matrix, a special case of which is an equi-correlation matrix. Application of the estimator and the bootstrap technique is illustrated using data from a task switch experiment based on an experimental within design with 32 cells and 33 participants.

Using the Bootstrap Method for a Statistical Significance Test of Differences between Summary Histograms

NASA Technical Reports Server (NTRS)

Xu, Kuan-Man

2006-01-01

A new method is proposed to compare statistical differences between summary histograms, which are the histograms summed over a large ensemble of individual histograms. It consists of choosing a distance statistic for measuring the difference between summary histograms and using a bootstrap procedure to calculate the statistical significance level. Bootstrapping is an approach to statistical inference that makes few assumptions about the underlying probability distribution that describes the data. Three distance statistics are compared in this study. They are the Euclidean distance, the Jeffries-Matusita distance and the Kuiper distance. The data used in testing the bootstrap method are satellite measurements of cloud systems called cloud objects. Each cloud object is defined as a contiguous region/patch composed of individual footprints or fields of view. A histogram of measured values over footprints is generated for each parameter of each cloud object and then summary histograms are accumulated over all individual histograms in a given cloud-object size category. The results of statistical hypothesis tests using all three distances as test statistics are generally similar, indicating the validity of the proposed method. The Euclidean distance is determined to be most suitable after comparing the statistical tests of several parameters with distinct probability distributions among three cloud-object size categories. Impacts on the statistical significance levels resulting from differences in the total lengths of satellite footprint data between two size categories are also discussed.

Image analysis of representative food structures: application of the bootstrap method.

PubMed

Ramírez, Cristian; Germain, Juan C; Aguilera, José M

2009-08-01

Images (for example, photomicrographs) are routinely used as qualitative evidence of the microstructure of foods. In quantitative image analysis it is important to estimate the area (or volume) to be sampled, the field of view, and the resolution. The bootstrap method is proposed to estimate the size of the sampling area as a function of the coefficient of variation (CV(Bn)) and standard error (SE(Bn)) of the bootstrap taking sub-areas of different sizes. The bootstrap method was applied to simulated and real structures (apple tissue). For simulated structures, 10 computer-generated images were constructed containing 225 black circles (elements) and different coefficient of variation (CV(image)). For apple tissue, 8 images of apple tissue containing cellular cavities with different CV(image) were analyzed. Results confirmed that for simulated and real structures, increasing the size of the sampling area decreased the CV(Bn) and SE(Bn). Furthermore, there was a linear relationship between the CV(image) and CV(Bn) (.) For example, to obtain a CV(Bn) = 0.10 in an image with CV(image) = 0.60, a sampling area of 400 x 400 pixels (11% of whole image) was required, whereas if CV(image) = 1.46, a sampling area of 1000 x 100 pixels (69% of whole image) became necessary. This suggests that a large-size dispersion of element sizes in an image requires increasingly larger sampling areas or a larger number of images.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Oberije, Cary, E-mail: cary.oberije@maastro.nl; De Ruysscher, Dirk; Universitaire Ziekenhuizen Leuven, KU Leuven

Purpose: Although patients with stage III non-small cell lung cancer (NSCLC) are homogeneous according to the TNM staging system, they form a heterogeneous group, which is reflected in the survival outcome. The increasing amount of information for an individual patient and the growing number of treatment options facilitate personalized treatment, but they also complicate treatment decision making. Decision support systems (DSS), which provide individualized prognostic information, can overcome this but are currently lacking. A DSS for stage III NSCLC requires the development and integration of multiple models. The current study takes the first step in this process by developing andmore » validating a model that can provide physicians with a survival probability for an individual NSCLC patient. Methods and Materials: Data from 548 patients with stage III NSCLC were available to enable the development of a prediction model, using stratified Cox regression. Variables were selected by using a bootstrap procedure. Performance of the model was expressed as the c statistic, assessed internally and on 2 external data sets (n=174 and n=130). Results: The final multivariate model, stratified for treatment, consisted of age, gender, World Health Organization performance status, overall treatment time, equivalent radiation dose, number of positive lymph node stations, and gross tumor volume. The bootstrapped c statistic was 0.62. The model could identify risk groups in external data sets. Nomograms were constructed to predict an individual patient's survival probability ( (www.predictcancer.org)). The data set can be downloaded at (https://www.cancerdata.org/10.1016/j.ijrobp.2015.02.048). Conclusions: The prediction model for overall survival of patients with stage III NSCLC highlights the importance of combining patient, clinical, and treatment variables. Nomograms were developed and validated. This tool could be used as a first building block for a decision support system.« less

PROGRESS IN THE PEELING-BALLOONING MODEL OF ELMS: TOROIDAL ROTATION AND 3D NONLINEAR DYNAMICS

DOE Office of Scientific and Technical Information (OSTI.GOV)

SNYDER,P.B; WILSON,H.R; XU,X.Q

2004-06-01

Understanding the physics of the H-Mode pedestal and edge localized modes (ELMs) is very important to next-step fusion devices for two primary reasons: (1) The pressure at the top of the edge barrier (''pedestal height'') strongly impacts global confinement and fusion performance, and (2) large ELMs lead to localized transient heat loads on material surfaces that may constrain component lifetimes. The development of the peeling-ballooning model has shed light on these issues by positing a mechanism for ELM onset and constraints on the pedestal height. The mechanism involves instability of ideal coupled ''peeling-ballooning'' modes driven by the sharp pressure gradientmore » and consequent large bootstrap current in the H-mode edge. It was first investigated in the local, high-n limit [1], and later quantified for non-local, finite-n modes in general toroidal geometry [2,3]. Important aspects are that a range of wavelengths may potentially be unstable, with intermediate n's (n {approx} 3-30) generally limiting in high performance regimes, and that stability bounds are strongly sensitive to shape [Fig l(a)], and to collisionality (i.e. temperature and density) [4] through the bootstrap current. The development of efficient MHD stability codes such as ELITE [3,2] and MISHKA [5] has allowed detailed quantification of peeling-ballooning stability bounds (e.g. [6]) and extensive and largely successful comparisons with observation (e.g. [2,6-9]). These previous calculations are ideal, static, and linear. Here we extend this work to incorporate the impact of sheared toroidal rotation, and the non-ideal, nonlinear dynamics which must be studied to quantify ELM size and heat deposition on material surfaces.« less

Improved human observer performance in digital reconstructed radiograph verification in head and neck cancer radiotherapy.

PubMed

Sturgeon, Jared D; Cox, John A; Mayo, Lauren L; Gunn, G Brandon; Zhang, Lifei; Balter, Peter A; Dong, Lei; Awan, Musaddiq; Kocak-Uzel, Esengul; Mohamed, Abdallah Sherif Radwan; Rosenthal, David I; Fuller, Clifton David

2015-10-01

Digitally reconstructed radiographs (DRRs) are routinely used as an a priori reference for setup correction in radiotherapy. The spatial resolution of DRRs may be improved to reduce setup error in fractionated radiotherapy treatment protocols. The influence of finer CT slice thickness reconstruction (STR) and resultant increased resolution DRRs on physician setup accuracy was prospectively evaluated. Four head and neck patient CT-simulation images were acquired and used to create DRR cohorts by varying STRs at 0.5, 1, 2, 2.5, and 3 mm. DRRs were displaced relative to a fixed isocenter using 0-5 mm random shifts in the three cardinal axes. Physician observers reviewed DRRs of varying STRs and displacements and then aligned reference and test DRRs replicating daily KV imaging workflow. A total of 1,064 images were reviewed by four blinded physicians. Observer errors were analyzed using nonparametric statistics (Friedman's test) to determine whether STR cohorts had detectably different displacement profiles. Post hoc bootstrap resampling was applied to evaluate potential generalizability. The observer-based trial revealed a statistically significant difference between cohort means for observer displacement vector error ([Formula: see text]) and for [Formula: see text]-axis [Formula: see text]. Bootstrap analysis suggests a 15% gain in isocenter translational setup error with reduction of STR from 3 mm to [Formula: see text]2 mm, though interobserver variance was a larger feature than STR-associated measurement variance. Higher resolution DRRs generated using finer CT scan STR resulted in improved observer performance at shift detection and could decrease operator-dependent geometric error. Ideally, CT STRs [Formula: see text]2 mm should be utilized for DRR generation in the head and neck.

Population pharmacokinetic modeling and simulation of huperzine A in elderly Chinese subjects

PubMed Central

Sheng, Lei; Qu, Yi; Yan, Jing; Liu, Gang-yi; Wang, Wei-liang; Wang, Yi-jun; Wang, Hong-yi; Zhang, Meng-qi; Lu, Chuan; Liu, Yun; Jia, Jing-yin; Hu, Chao-ying; Li, Xue-ning; Yu, Chen; Xu, Hong-rong

2016-01-01

Aim: Our preliminary results show that huperzine A, an acetylcholinesterase inhibitor used to treat Alzheimer's disease (AD) patients in China, exhibits different pharmacokinetic features in elderly and young healthy subjects. However, its pharmacokinetic data in elderly subjects remains unavailable to date. Thus, we developed a population pharmacokinetic (PPK) model of huperzine A in elderly Chinese people, and identified the covariate affecting its pharmacokinetics for optimal individual administration. Methods: A total of 341 serum huperzine A concentration records was obtained from 2 completed clinical trials (14 elderly healthy subjects in a phase I pharmacokinetic study; 35 elderly AD patients in a phase II study). Population pharmacokinetic analysis was performed using the non-linear mixed-effect modeling software Phoenix NLME1.1.1. The effects of age, gender, body weight, height, creatinine, endogenous creatinine clearance rate as well as drugs administered concomitantly were analyzed. Bootstrap and visual predictive checks were used simultaneously to validate the final population pharmacokinetics models. Results: The plasma concentration-time profile of huperzine A was best described by a one-compartment model with first-order absorption and elimination. Age was identified as the covariate having significant influence on huperzine A clearance. The final PPK model of huperzine A was: CL (L/h)=2.4649*(age/86)(−3.3856), Ka=0.6750 h−1, V (L)=104.216. The final PPK model was demonstrated to be suitable and effective by the bootstrap and visual predictive checks. Conclusion: A PPK model of huperzine A in elderly Chinese subjects is established, which can be used to predict PPK parameters of huperzine A in the treatment of elderly AD patients. PMID:27180987

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shaffer, Richard, E-mail: rickyshaffer@yahoo.co.u; Department of Clinical Oncology, Imperial College London National Health Service Trust, London; Pickles, Tom

Purpose: Prior studies have derived low values of alpha-beta ratio (a/ss) for prostate cancer of approximately 1-2 Gy. These studies used poorly matched groups, differing definitions of biochemical failure, and insufficient follow-up. Methods and Materials: National Comprehensive Cancer Network low- or low-intermediate risk prostate cancer patients, treated with external beam radiotherapy or permanent prostate brachytherapy, were matched for prostate-specific antigen, Gleason score, T-stage, percentage of positive cores, androgen deprivation therapy, and era, yielding 118 patient pairs. The Phoenix definition of biochemical failure was used. The best-fitting value for a/ss was found for up to 90-month follow-up using maximum likelihood analysis,more » and the 95% confidence interval using the profile likelihood method. Linear quadratic formalism was applied with the radiobiological parameters of relative biological effectiveness = 1.0, potential doubling time = 45 days, and repair half-time = 1 hour. Bootstrap analysis was performed to estimate uncertainties in outcomes, and hence in a/ss. Sensitivity analysis was performed by varying the values of the radiobiological parameters to extreme values. Results: The value of a/ss best fitting the outcomes data was >30 Gy, with lower 95% confidence limit of 5.2 Gy. This was confirmed on bootstrap analysis. Varying parameters to extreme values still yielded best-fit a/ss of >30 Gy, although the lower 95% confidence interval limit was reduced to 0.6 Gy. Conclusions: Using carefully matched groups, long follow-up, the Phoenix definition of biochemical failure, and well-established statistical methods, the best estimate of a/ss for low and low-tier intermediate-risk prostate cancer is likely to be higher than that of normal tissues, although a low value cannot be excluded.« less

Significance tests for functional data with complex dependence structure.

PubMed

Staicu, Ana-Maria; Lahiri, Soumen N; Carroll, Raymond J

2015-01-01

We propose an L 2 -norm based global testing procedure for the null hypothesis that multiple group mean functions are equal, for functional data with complex dependence structure. Specifically, we consider the setting of functional data with a multilevel structure of the form groups-clusters or subjects-units, where the unit-level profiles are spatially correlated within the cluster, and the cluster-level data are independent. Orthogonal series expansions are used to approximate the group mean functions and the test statistic is estimated using the basis coefficients. The asymptotic null distribution of the test statistic is developed, under mild regularity conditions. To our knowledge this is the first work that studies hypothesis testing, when data have such complex multilevel functional and spatial structure. Two small-sample alternatives, including a novel block bootstrap for functional data, are proposed, and their performance is examined in simulation studies. The paper concludes with an illustration of a motivating experiment.

A combined approach of generalized additive model and bootstrap with small sample sets for fault diagnosis in fermentation process of glutamate.

PubMed

Liu, Chunbo; Pan, Feng; Li, Yun

2016-07-29

Glutamate is of great importance in food and pharmaceutical industries. There is still lack of effective statistical approaches for fault diagnosis in the fermentation process of glutamate. To date, the statistical approach based on generalized additive model (GAM) and bootstrap has not been used for fault diagnosis in fermentation processes, much less the fermentation process of glutamate with small samples sets. A combined approach of GAM and bootstrap was developed for the online fault diagnosis in the fermentation process of glutamate with small sample sets. GAM was first used to model the relationship between glutamate production and different fermentation parameters using online data from four normal fermentation experiments of glutamate. The fitted GAM with fermentation time, dissolved oxygen, oxygen uptake rate and carbon dioxide evolution rate captured 99.6 % variance of glutamate production during fermentation process. Bootstrap was then used to quantify the uncertainty of the estimated production of glutamate from the fitted GAM using 95 % confidence interval. The proposed approach was then used for the online fault diagnosis in the abnormal fermentation processes of glutamate, and a fault was defined as the estimated production of glutamate fell outside the 95 % confidence interval. The online fault diagnosis based on the proposed approach identified not only the start of the fault in the fermentation process, but also the end of the fault when the fermentation conditions were back to normal. The proposed approach only used a small sample sets from normal fermentations excitements to establish the approach, and then only required online recorded data on fermentation parameters for fault diagnosis in the fermentation process of glutamate. The proposed approach based on GAM and bootstrap provides a new and effective way for the fault diagnosis in the fermentation process of glutamate with small sample sets.

Examination of the reliability of the crash modification factors using empirical Bayes method with resampling technique.

PubMed

Wang, Jung-Han; Abdel-Aty, Mohamed; Wang, Ling

2017-07-01

There have been plenty of studies intended to use different methods, for example, empirical Bayes before-after methods, to get accurate estimation of CMFs. All of them have different assumptions toward crash count if there was no treatment. Additionally, another major assumption is that multiple sites share the same true CMF. Under this assumption, the CMF at an individual intersection is randomly drawn from a normally distributed population of CMFs at all intersections. Since CMFs are non-zero values, the population of all CMFs might not follow normal distributions, and even if it does, the true mean of CMFs at some intersections may be different from that at others. Therefore, a bootstrap method based on before-after empirical Bayes theory was proposed to estimate CMFs, but it did not make distributional assumptions. This bootstrap procedure has the added benefit of producing a measure of CMF stability. Furthermore, based on the bootstrapped CMF, a new CMF precision rating method was proposed to evaluate the reliability of CMFs. This study chose 29 urban four-legged intersections as treated sites, and their controls were changed from stop-controlled to signal-controlled. Meanwhile, 124 urban four-legged stop-controlled intersections were selected as reference sites. At first, different safety performance functions (SPFs) were applied to five crash categories, and it was found that each crash category had different optimal SPF form. Then, the CMFs of these five crash categories were estimated using the bootstrap empirical Bayes method. The results of the bootstrapped method showed that signalization significantly decreased Angle+Left-Turn crashes, and its CMF had the highest precision. While, the CMF for Rear-End crashes was unreliable. For KABCO, KABC, and KAB crashes, their CMFs were proved to be reliable for the majority of intersections, but the estimated effect of signalization may be not accurate at some sites. Copyright © 2017 Elsevier Ltd. All rights reserved.

Steady-state sustainment of high-β plasmas through stability control in Japan Atomic Energy Research Institute Tokamak-60 Upgradea)

NASA Astrophysics Data System (ADS)

Isayama, A.

2005-05-01

Recent results from steady-state sustainment of high-β plasma experiments in the Japan Atomic Energy Research Institute Tokamak-60 Upgrade (JT-60U) tokamak [A. Kitsunezaki et al., Fusion Sci. Technol. 42, 179 (2002)] are described. Extension of discharge duration to 65s (formerly 15s) has enabled physics research with long time scale. In long-duration high-β research, the normalized beta βN=2.5, which is comparable to that in the steady-state operation in International Thermonuclear Experimental Reactor (ITER) [R. Aymar, P. Barabaschi, and Y. Shimomura, Plasma Phys. Controlled Fusion 44, 519 (2002)], has been sustained for about 15s with confinement enhancement factor H89PL above 2, where the duration is about 80 times energy confinement time and ˜10 times current diffusion time (τR). In the scenario aiming at longer duration with βN˜1.9, which is comparable to that in the ITER standard operation scenario, duration has been extended to 24s (˜15τR). Also, from the viewpoint of collisionality and Larmor radius of the plasmas, these results are obtained in the ITER-relevant regime with a few times larger than the ITER values. No serious effect of current diffusion on instabilities is observed in the region of βN≲2.5, and in fact neoclassical tearing modes (NTMs), which limit the achievable β in the stationary high-βp H-mode discharges, are suppressed throughout the discharge. In high-β research with the duration of several times τR, a high-β plasma with βN˜2.9-3 has been sustained for 5-6s with two scenarios for NTM suppression: (a) NTM avoidance by modification of pressure and current profiles, and (b) NTM stabilization with electron cyclotron current drive (ECCD)/electron cyclotron heating (ECH). NTM stabilization with the second harmonic X-mode ECCD/ECH has been performed, and it is found that EC current density comparable to bootstrap current density at the mode location is required for complete stabilization. Structure of a magnetic island associated with an m /n=3/2 NTM has been measured in detail (m and n are poloidal and toroidal mode numbers, respectively). By applying newly developed analysis method using motional Stark effect (MSE) diagnostic, where change in current density is directly evaluated from change in MSE pitch angle without equilibrium reconstruction, localized decrease/increase in current density at the mode rational surface is observed for NTM growth/suppression. In addition, it is found that characteristic structure of electron temperature perturbation profile is deformed during NTM stabilization. Hypothesis that temperature increase inside the magnetic island well explains the experimental observations. It is also found that the characteristic structure is not formed for the case of ECCD/ECH before the mode, while the structure is seen for the case with ECCD/ECH just after the mode onset, suggesting the stronger stabilization effect of the early EC wave injection.

Deducing noninductive current profile from surface voltage evolution

DOE Office of Scientific and Technical Information (OSTI.GOV)

Litwin, C.; Wukitch, S.; Hershkowitz, N.

Solving the resistive diffusion equation in the presence of a noninductive current source determines the time-evolution of the surface voltage. By inverting the problem the current drive profile can be determined from the surface voltage evolution. We show that under wide range of conditions the deduced profile is unique. If the conductivity profile is known, this method can be employed to infer the noninductive current profile, and, ipso facto, the profile of the total current. We discuss the application of this method to analyze the Alfven wave current drive experiments in Phaedrus-T.

Elastic S-matrices in (1 + 1) dimensions and Toda field theories

DOE Office of Scientific and Technical Information (OSTI.GOV)

Christe, P.; Mussardo, G.

Particular deformations of 2-D conformal field theory lead to integrable massive quantum field theories. These can be characterized by the relative scattering data. This paper proposes a general scheme for classifying the elastic nondegenerate S-matrix in (1 + 1) dimensions starting from the possible boot-strap processes and the spins of the conserved currents. Their identification with the S-matrix coming from the Toda field theory is analyzed. The authors discuss both cases of Toda field theory constructed with the simply-laced Dynkin diagrams and the nonsimply-laced ones. The authors present the results of the perturbative analysis and their geometrical interpretations.

Quantitative body DW-MRI biomarkers uncertainty estimation using unscented wild-bootstrap.

PubMed

Freiman, M; Voss, S D; Mulkern, R V; Perez-Rossello, J M; Warfield, S K

2011-01-01

We present a new method for the uncertainty estimation of diffusion parameters for quantitative body DW-MRI assessment. Diffusion parameters uncertainty estimation from DW-MRI is necessary for clinical applications that use these parameters to assess pathology. However, uncertainty estimation using traditional techniques requires repeated acquisitions, which is undesirable in routine clinical use. Model-based bootstrap techniques, for example, assume an underlying linear model for residuals rescaling and cannot be utilized directly for body diffusion parameters uncertainty estimation due to the non-linearity of the body diffusion model. To offset this limitation, our method uses the Unscented transform to compute the residuals rescaling parameters from the non-linear body diffusion model, and then applies the wild-bootstrap method to infer the body diffusion parameters uncertainty. Validation through phantom and human subject experiments shows that our method identify the regions with higher uncertainty in body DWI-MRI model parameters correctly with realtive error of -36% in the uncertainty values.

Bootstrapping the (A1, A2) Argyres-Douglas theory

NASA Astrophysics Data System (ADS)

Cornagliotto, Martina; Lemos, Madalena; Liendo, Pedro

2018-03-01

We apply bootstrap techniques in order to constrain the CFT data of the ( A 1 , A 2) Argyres-Douglas theory, which is arguably the simplest of the Argyres-Douglas models. We study the four-point function of its single Coulomb branch chiral ring generator and put numerical bounds on the low-lying spectrum of the theory. Of particular interest is an infinite family of semi-short multiplets labeled by the spin ℓ. Although the conformal dimensions of these multiplets are protected, their three-point functions are not. Using the numerical bootstrap we impose rigorous upper and lower bounds on their values for spins up to ℓ = 20. Through a recently obtained inversion formula, we also estimate them for sufficiently large ℓ, and the comparison of both approaches shows consistent results. We also give a rigorous numerical range for the OPE coefficient of the next operator in the chiral ring, and estimates for the dimension of the first R-symmetry neutral non-protected multiplet for small spin.

Acculturation, Income and Vegetable Consumption Behaviors Among Latino Adults in the U.S.: A Mediation Analysis with the Bootstrapping Technique.

PubMed

López, Erick B; Yamashita, Takashi

2017-02-01

This study examined whether household income mediates the relationship between acculturation and vegetable consumption among Latino adults in the U.S. Data from the 2009 to 2010 National Health and Nutrition Examination Survey were analyzed. Vegetable consumption index was created based on the frequencies of five kinds of vegetables intake. Acculturation was measured with the degree of English language use at home. Path model with bootstrapping technique was employed for mediation analysis. A significant partial mediation relationship was identified. Greater acculturation [95 % bias corrected bootstrap confident interval (BCBCI) = (0.02, 0.33)] was associated with the higher income and in turn, greater vegetable consumption. At the same time, greater acculturation was associated with lower vegetable consumption [95 % BCBCI = (-0.88, -0.07)]. Findings regarding the income as a mediator of the acculturation-dietary behavior relationship inform unique intervention programs and policy changes to address health disparities by race/ethnicity.

Exploration of the factor structure of the Kirton Adaption-Innovation Inventory using bootstrapping estimation.

PubMed

Im, Subin; Min, Soonhong

2013-04-01

Exploratory factor analyses of the Kirton Adaption-Innovation Inventory (KAI), which serves to measure individual cognitive styles, generally indicate three factors: sufficiency of originality, efficiency, and rule/group conformity. In contrast, a 2005 study by Im and Hu using confirmatory factor analysis supported a four-factor structure, dividing the sufficiency of originality dimension into two subdimensions, idea generation and preference for change. This study extends Im and Hu's (2005) study of a derived version of the KAI by providing additional evidence of the four-factor structure. Specifically, the authors test the robustness of the parameter estimates to the violation of normality assumptions in the sample using bootstrap methods. A bias-corrected confidence interval bootstrapping procedure conducted among a sample of 356 participants--members of the Arkansas Household Research Panel, with middle SES and average age of 55.6 yr. (SD = 13.9)--showed that the four-factor model with two subdimensions of sufficiency of originality fits the data significantly better than the three-factor model in non-normality conditions.

How to bootstrap a human communication system.

PubMed

Fay, Nicolas; Arbib, Michael; Garrod, Simon

2013-01-01

How might a human communication system be bootstrapped in the absence of conventional language? We argue that motivated signs play an important role (i.e., signs that are linked to meaning by structural resemblance or by natural association). An experimental study is then reported in which participants try to communicate a range of pre-specified items to a partner using repeated non-linguistic vocalization, repeated gesture, or repeated non-linguistic vocalization plus gesture (but without using their existing language system). Gesture proved more effective (measured by communication success) and more efficient (measured by the time taken to communicate) than non-linguistic vocalization across a range of item categories (emotion, object, and action). Combining gesture and vocalization did not improve performance beyond gesture alone. We experimentally demonstrate that gesture is a more effective means of bootstrapping a human communication system. We argue that gesture outperforms non-linguistic vocalization because it lends itself more naturally to the production of motivated signs. © 2013 Cognitive Science Society, Inc.

Measuring and Benchmarking Technical Efficiency of Public Hospitals in Tianjin, China

PubMed Central

Li, Hao; Dong, Siping

2015-01-01

China has long been stuck in applying traditional data envelopment analysis (DEA) models to measure technical efficiency of public hospitals without bias correction of efficiency scores. In this article, we have introduced the Bootstrap-DEA approach from the international literature to analyze the technical efficiency of public hospitals in Tianjin (China) and tried to improve the application of this method for benchmarking and inter-organizational learning. It is found that the bias corrected efficiency scores of Bootstrap-DEA differ significantly from those of the traditional Banker, Charnes, and Cooper (BCC) model, which means that Chinese researchers need to update their DEA models for more scientific calculation of hospital efficiency scores. Our research has helped shorten the gap between China and the international world in relative efficiency measurement and improvement of hospitals. It is suggested that Bootstrap-DEA be widely applied into afterward research to measure relative efficiency and productivity of Chinese hospitals so as to better serve for efficiency improvement and related decision making. PMID:26396090

On combination of strict Bayesian principles with model reduction technique or how stochastic model calibration can become feasible for large-scale applications

NASA Astrophysics Data System (ADS)

Oladyshkin, S.; Schroeder, P.; Class, H.; Nowak, W.

2013-12-01

Predicting underground carbon dioxide (CO2) storage represents a challenging problem in a complex dynamic system. Due to lacking information about reservoir parameters, quantification of uncertainties may become the dominant question in risk assessment. Calibration on past observed data from pilot-scale test injection can improve the predictive power of the involved geological, flow, and transport models. The current work performs history matching to pressure time series from a pilot storage site operated in Europe, maintained during an injection period. Simulation of compressible two-phase flow and transport (CO2/brine) in the considered site is computationally very demanding, requiring about 12 days of CPU time for an individual model run. For that reason, brute-force approaches for calibration are not feasible. In the current work, we explore an advanced framework for history matching based on the arbitrary polynomial chaos expansion (aPC) and strict Bayesian principles. The aPC [1] offers a drastic but accurate stochastic model reduction. Unlike many previous chaos expansions, it can handle arbitrary probability distribution shapes of uncertain parameters, and can therefore handle directly the statistical information appearing during the matching procedure. We capture the dependence of model output on these multipliers with the expansion-based reduced model. In our study we keep the spatial heterogeneity suggested by geophysical methods, but consider uncertainty in the magnitude of permeability trough zone-wise permeability multipliers. Next combined the aPC with Bootstrap filtering (a brute-force but fully accurate Bayesian updating mechanism) in order to perform the matching. In comparison to (Ensemble) Kalman Filters, our method accounts for higher-order statistical moments and for the non-linearity of both the forward model and the inversion, and thus allows a rigorous quantification of calibrated model uncertainty. The usually high computational costs of accurate filtering become very feasible for our suggested aPC-based calibration framework. However, the power of aPC-based Bayesian updating strongly depends on the accuracy of prior information. In the current study, the prior assumptions on the model parameters were not satisfactory and strongly underestimate the reservoir pressure. Thus, the aPC-based response surface used in Bootstrap filtering is fitted to a distant and poorly chosen region within the parameter space. Thanks to the iterative procedure suggested in [2] we overcome this drawback with small computational costs. The iteration successively improves the accuracy of the expansion around the current estimation of the posterior distribution. The final result is a calibrated model of the site that can be used for further studies, with an excellent match to the data. References [1] Oladyshkin S. and Nowak W. Data-driven uncertainty quantification using the arbitrary polynomial chaos expansion. Reliability Engineering and System Safety, 106:179-190, 2012. [2] Oladyshkin S., Class H., Nowak W. Bayesian updating via Bootstrap filtering combined with data-driven polynomial chaos expansions: methodology and application to history matching for carbon dioxide storage in geological formations. Computational Geosciences, 17 (4), 671-687, 2013.

Bootstrapping quarks and gluons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chew, G.F.

1979-04-01

Dual topological unitarization (DTU) - the approach to S-matrix causality and unitarity through combinatorial topology - is reviewed. Amplitudes associated with triangulated spheres are shown to constitute the core of particle physics. Each sphere is covered by triangulated disc faces corresponding to hadrons. The leading current candidate for the hadron-face triangulation pattern employs 3-triangle basic subdiscs whose orientations correspond to baryon number and topological color. Additional peripheral triangles lie along the hadron-face perimeter. Certain combinations of peripheral triangles with a basic-disc triangle can be identified as quarks, the flavor of a quark corresponding to the orientation of its edges thatmore » lie on the hadron-face perimeter. Both baryon number and flavor are additively conserved. Quark helicity, which can be associated with triangle-interior orientation, is not uniformly conserved and interacts with particle momentum, whereas flavor does not. Three different colors attach to the 3 quarks associated with a single basic subdisc, but there is no additive physical conservation law associated with color. There is interplay between color and quark helicity. In hadron faces with more than one basic subdisc, there may occur pairs of adjacent flavorless but colored triangles with net helicity +-1 that are identifiable as gluons. Broken symmetry is an automatic feature of the bootstrap. T, C and P symmetries, as well as up-down flavor symmetry, persist on all orientable surfaces.« less

Predicting the risk for colorectal cancer with personal characteristics and fecal immunochemical test.

PubMed

Li, Wen; Zhao, Li-Zhong; Ma, Dong-Wang; Wang, De-Zheng; Shi, Lei; Wang, Hong-Lei; Dong, Mo; Zhang, Shu-Yi; Cao, Lei; Zhang, Wei-Hua; Zhang, Xi-Peng; Zhang, Qing-Huai; Yu, Lin; Qin, Hai; Wang, Xi-Mo; Chen, Sam Li-Sheng

2018-05-01

We aimed to predict colorectal cancer (CRC) based on the demographic features and clinical correlates of personal symptoms and signs from Tianjin community-based CRC screening data.A total of 891,199 residents who were aged 60 to 74 and were screened in 2012 were enrolled. The Lasso logistic regression model was used to identify the predictors for CRC. Predictive validity was assessed by the receiver operating characteristic (ROC) curve. Bootstrapping method was also performed to validate this prediction model.CRC was best predicted by a model that included age, sex, education level, occupations, diarrhea, constipation, colon mucosa and bleeding, gallbladder disease, a stressful life event, family history of CRC, and a positive fecal immunochemical test (FIT). The area under curve (AUC) for the questionnaire with a FIT was 84% (95% CI: 82%-86%), followed by 76% (95% CI: 74%-79%) for a FIT alone, and 73% (95% CI: 71%-76%) for the questionnaire alone. With 500 bootstrap replications, the estimated optimism (<0.005) shows good discrimination in validation of prediction model.A risk prediction model for CRC based on a series of symptoms and signs related to enteric diseases in combination with a FIT was developed from first round of screening. The results of the current study are useful for increasing the awareness of high-risk subjects and for individual-risk-guided invitations or strategies to achieve mass screening for CRC.

BusyBee Web: metagenomic data analysis by bootstrapped supervised binning and annotation

PubMed Central

Kiefer, Christina; Fehlmann, Tobias; Backes, Christina

2017-01-01

Abstract Metagenomics-based studies of mixed microbial communities are impacting biotechnology, life sciences and medicine. Computational binning of metagenomic data is a powerful approach for the culture-independent recovery of population-resolved genomic sequences, i.e. from individual or closely related, constituent microorganisms. Existing binning solutions often require a priori characterized reference genomes and/or dedicated compute resources. Extending currently available reference-independent binning tools, we developed the BusyBee Web server for the automated deconvolution of metagenomic data into population-level genomic bins using assembled contigs (Illumina) or long reads (Pacific Biosciences, Oxford Nanopore Technologies). A reversible compression step as well as bootstrapped supervised binning enable quick turnaround times. The binning results are represented in interactive 2D scatterplots. Moreover, bin quality estimates, taxonomic annotations and annotations of antibiotic resistance genes are computed and visualized. Ground truth-based benchmarks of BusyBee Web demonstrate comparably high performance to state-of-the-art binning solutions for assembled contigs and markedly improved performance for long reads (median F1 scores: 70.02–95.21%). Furthermore, the applicability to real-world metagenomic datasets is shown. In conclusion, our reference-independent approach automatically bins assembled contigs or long reads, exhibits high sensitivity and precision, enables intuitive inspection of the results, and only requires FASTA-formatted input. The web-based application is freely accessible at: https://ccb-microbe.cs.uni-saarland.de/busybee. PMID:28472498

Heterogeneity of (18)F-FDG PET combined with expression of EGFR may improve the prognostic stratification of advanced oropharyngeal carcinoma.

PubMed

Wang, Hung-Ming; Cheng, Nai-Ming; Lee, Li-Yu; Fang, Yu-Hua Dean; Chang, Joseph Tung-Chieh; Tsan, Din-Li; Ng, Shu-Hang; Liao, Chun-Ta; Yang, Lan-Yan; Yen, Tzu-Chen

2016-02-01

The Ang's risk profile (based on p16, smoking and cancer stage) is a well-known prognostic factor in oropharyngeal squamous cell carcinoma (OPSCC). Whether heterogeneity in (18)F-fluorodeoxyglucose (FDG) positron emission tomographic (PET) images and epidermal growth factor receptor (EGFR) expression could provide additional information on clinical outcomes in advanced-stage OPSCC was investigated. Patients with stage III-IV OPSCC who completed primary therapy were eligible. Zone-size nonuniformity (ZSNU) extracted from pretreatment FDG PET scans was used as an index of image heterogeneity. EGFR and p16 expression were examined by immunohistochemistry. Disease-specific survival (DSS) and overall survival (OS) served as outcome measures. Kaplan-Meier estimates and Cox proportional hazards regression models were used for survival analysis. A bootstrap resampling technique was applied to investigate the stability of outcomes. Finally, a recursive partitioning analysis (RPA)-based model was constructed. A total of 113 patients were included, of which 28 were p16-positive. Multivariate analysis identified the Ang's profile, EGFR and ZSNU as independent predictors of both DSS and OS. Using RPA, the three risk factors were used to devise a prognostic scoring system that successfully predicted DSS in both p16-positive and -negative cases. The c-statistic of the prognostic index for DSS was 0.81, a value which was significantly superior to both AJCC stage (0.60) and the Ang's risk profile (0.68). In patients showing an Ang's high-risk profile (N = 77), the use of our scoring system clearly identified three distinct prognostic subgroups. It was concluded that a novel index may improve the prognostic stratification of patients with advanced-stage OPSCC. © 2015 UICC.

Classifier performance prediction for computer-aided diagnosis using a limited dataset.

PubMed

Sahiner, Berkman; Chan, Heang-Ping; Hadjiiski, Lubomir

2008-04-01

In a practical classifier design problem, the true population is generally unknown and the available sample is finite-sized. A common approach is to use a resampling technique to estimate the performance of the classifier that will be trained with the available sample. We conducted a Monte Carlo simulation study to compare the ability of the different resampling techniques in training the classifier and predicting its performance under the constraint of a finite-sized sample. The true population for the two classes was assumed to be multivariate normal distributions with known covariance matrices. Finite sets of sample vectors were drawn from the population. The true performance of the classifier is defined as the area under the receiver operating characteristic curve (AUC) when the classifier designed with the specific sample is applied to the true population. We investigated methods based on the Fukunaga-Hayes and the leave-one-out techniques, as well as three different types of bootstrap methods, namely, the ordinary, 0.632, and 0.632+ bootstrap. The Fisher's linear discriminant analysis was used as the classifier. The dimensionality of the feature space was varied from 3 to 15. The sample size n2 from the positive class was varied between 25 and 60, while the number of cases from the negative class was either equal to n2 or 3n2. Each experiment was performed with an independent dataset randomly drawn from the true population. Using a total of 1000 experiments for each simulation condition, we compared the bias, the variance, and the root-mean-squared error (RMSE) of the AUC estimated using the different resampling techniques relative to the true AUC (obtained from training on a finite dataset and testing on the population). Our results indicated that, under the study conditions, there can be a large difference in the RMSE obtained using different resampling methods, especially when the feature space dimensionality is relatively large and the sample size is small. Under this type of conditions, the 0.632 and 0.632+ bootstrap methods have the lowest RMSE, indicating that the difference between the estimated and the true performances obtained using the 0.632 and 0.632+ bootstrap will be statistically smaller than those obtained using the other three resampling methods. Of the three bootstrap methods, the 0.632+ bootstrap provides the lowest bias. Although this investigation is performed under some specific conditions, it reveals important trends for the problem of classifier performance prediction under the constraint of a limited dataset.

Kinetic effects on the currents determining the stability of a magnetic island in tokamaks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Poli, E., E-mail: emanuele.poli@ipp.mpg.de; Bergmann, A.; Casson, F. J.

The role of the bootstrap and polarization currents for the stability of neoclassical tearing modes is investigated employing both a drift kinetic and a gyrokinetic approach. The adiabatic response of the ions around the island separatrix implies, for island widths below or around the ion thermal banana width, density flattening for islands rotating at the ion diamagnetic frequency, while for islands rotating at the electron diamagnetic frequency the density is unperturbed and the only contribution to the neoclassical drive arises from electron temperature flattening. As for the polarization current, the full inclusion of finite orbit width effects in the calculationmore » of the potential developing in a rotating island leads to a smoothing of the discontinuous derivatives exhibited by the analytic potential on which the polarization term used in the modeling is based. This leads to a reduction of the polarization-current contribution with respect to the analytic estimate, in line with other studies. Other contributions to the perpendicular ion current, related to the response of the particles around the island separatrix, are found to compete or even dominate the polarization-current term for realistic island rotation frequencies.« less

Maternal Depression and Trait Anger as Risk Factors for Escalated Physical Discipline

PubMed Central

Shay, Nicole L.; Knutson, John F.

2008-01-01

To test the hypothesized anger-mediated relation between maternal depression and escalation of physical discipline, 122 economically disadvantaged mothers were assessed for current and lifetime diagnoses of depression using the Current Depressive Episode, Past Depression, and Dysthymia sections of the Structured Clinical Interview for DSM-IV (SCID) and a measure of current depressive symptoms, the Beck Depression Inventory–Second Edition (BDI-II). Escalation of physical discipline was assessed using a video analog parenting task; maternal anger not specific to discipline was assessed using the Spielberger Trait Anger Expression Inventory. Reports of anger were associated with the diagnosis of depression and depressive symptoms. Bootstrap analyses of indirect effects indicated that the link between depression and escalated discipline was mediated by anger. Parallel analyses based on BDI-II scores identified a marginally significant indirect effect of depression on discipline. Findings suggest that anger and irritability are central to the putative link between depression and harsh discipline. PMID:18174347

Effect of resistivity profile on current decay time of initial phase of current quench in neon-gas-puff inducing disruptions of JT-60U

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kawakami, S.; Ohno, N.; Shibata, Y.

2013-11-15

According to an early work [Y. Shibata et al., Nucl. Fusion 50, 025015 (2010)] on the behavior of the plasma current decay in the JT-60U disruptive discharges caused by the radiative collapse with a massive neon-gas-puff, the increase of the internal inductance mainly determined the current decay time of plasma current during the initial phase of current quench. To investigate what determines the increase of the internal inductance, we focus attention on the relationship between the electron temperature (or the resistivity) profile and the time evolution of the current density profile and carry out numerical calculations. As a result, wemore » find the reason of the increase of the internal inductance: The current density profile at the start of the current quench is broader than an expected current density profile in the steady state, which is determined by the temperature (or resistivity) profile. The current density profile evolves into peaked one and the internal inductance is increasing.« less

Concept Innateness, Concept Continuity, and Bootstrapping

PubMed Central

Carey, Susan

2011-01-01

The commentators raised issues relevant to all three important theses of The Origin of Concepts (TOOC). Some questioned the very existence of innate representational primitives, and others questioned my claims about their richness and whether they should be thought of as concepts. Some questioned the existence of conceptual discontinuity in the course of knowledge acquisition and others argued that discontinuity is much more common than portrayed in TOOC. Some raised issues with my characterization of Quinian bootstrapping, and others questioned the dual factor theory of concepts motivated by my picture of conceptual development. PMID:23264705

Crossing symmetry in alpha space

NASA Astrophysics Data System (ADS)

Hogervorst, Matthijs; van Rees, Balt C.

2017-11-01

We initiate the study of the conformal bootstrap using Sturm-Liouville theory, specializing to four-point functions in one-dimensional CFTs. We do so by decomposing conformal correlators using a basis of eigenfunctions of the Casimir which are labeled by a complex number α. This leads to a systematic method for computing conformal block decompositions. Analyzing bootstrap equations in alpha space turns crossing symmetry into an eigenvalue problem for an integral operator K. The operator K is closely related to the Wilson transform, and some of its eigenfunctions can be found in closed form.

Direct measurement of fast transients by using boot-strapped waveform averaging

NASA Astrophysics Data System (ADS)

Olsson, Mattias; Edman, Fredrik; Karki, Khadga Jung

2018-03-01

An approximation to coherent sampling, also known as boot-strapped waveform averaging, is presented. The method uses digital cavities to determine the condition for coherent sampling. It can be used to increase the effective sampling rate of a repetitive signal and the signal to noise ratio simultaneously. The method is demonstrated by using it to directly measure the fluorescence lifetime from Rhodamine 6G by digitizing the signal from a fast avalanche photodiode. The obtained lifetime of 4.0 ns is in agreement with the known values.

Mapping and assessing variability in the Antarctic marginal ice zone, pack ice and coastal polynyas in two sea ice algorithms with implications on breeding success of snow petrels

NASA Astrophysics Data System (ADS)

Stroeve, Julienne C.; Jenouvrier, Stephanie; Campbell, G. Garrett; Barbraud, Christophe; Delord, Karine

2016-08-01

Sea ice variability within the marginal ice zone (MIZ) and polynyas plays an important role for phytoplankton productivity and krill abundance. Therefore, mapping their spatial extent as well as seasonal and interannual variability is essential for understanding how current and future changes in these biologically active regions may impact the Antarctic marine ecosystem. Knowledge of the distribution of MIZ, consolidated pack ice and coastal polynyas in the total Antarctic sea ice cover may also help to shed light on the factors contributing towards recent expansion of the Antarctic ice cover in some regions and contraction in others. The long-term passive microwave satellite data record provides the longest and most consistent record for assessing the proportion of the sea ice cover that is covered by each of these ice categories. However, estimates of the amount of MIZ, consolidated pack ice and polynyas depend strongly on which sea ice algorithm is used. This study uses two popular passive microwave sea ice algorithms, the NASA Team and Bootstrap, and applies the same thresholds to the sea ice concentrations to evaluate the distribution and variability in the MIZ, the consolidated pack ice and coastal polynyas. Results reveal that the seasonal cycle in the MIZ and pack ice is generally similar between both algorithms, yet the NASA Team algorithm has on average twice the MIZ and half the consolidated pack ice area as the Bootstrap algorithm. Trends also differ, with the Bootstrap algorithm suggesting statistically significant trends towards increased pack ice area and no statistically significant trends in the MIZ. The NASA Team algorithm on the other hand indicates statistically significant positive trends in the MIZ during spring. Potential coastal polynya area and amount of broken ice within the consolidated ice pack are also larger in the NASA Team algorithm. The timing of maximum polynya area may differ by as much as 5 months between algorithms. These differences lead to different relationships between sea ice characteristics and biological processes, as illustrated here with the breeding success of an Antarctic seabird.

Method-independent, Computationally Frugal Convergence Testing for Sensitivity Analysis Techniques

NASA Astrophysics Data System (ADS)

Mai, J.; Tolson, B.

2017-12-01

The increasing complexity and runtime of environmental models lead to the current situation that the calibration of all model parameters or the estimation of all of their uncertainty is often computationally infeasible. Hence, techniques to determine the sensitivity of model parameters are used to identify most important parameters. All subsequent model calibrations or uncertainty estimation procedures focus then only on these subsets of parameters and are hence less computational demanding. While the examination of the convergence of calibration and uncertainty methods is state-of-the-art, the convergence of the sensitivity methods is usually not checked. If any, bootstrapping of the sensitivity results is used to determine the reliability of the estimated indexes. Bootstrapping, however, might as well become computationally expensive in case of large model outputs and a high number of bootstraps. We, therefore, present a Model Variable Augmentation (MVA) approach to check the convergence of sensitivity indexes without performing any additional model run. This technique is method- and model-independent. It can be applied either during the sensitivity analysis (SA) or afterwards. The latter case enables the checking of already processed sensitivity indexes. To demonstrate the method's independency of the convergence testing method, we applied it to two widely used, global SA methods: the screening method known as Morris method or Elementary Effects (Morris 1991) and the variance-based Sobol' method (Solbol' 1993). The new convergence testing method is first scrutinized using 12 analytical benchmark functions (Cuntz & Mai et al. 2015) where the true indexes of aforementioned three methods are known. This proof of principle shows that the method reliably determines the uncertainty of the SA results when different budgets are used for the SA. The results show that the new frugal method is able to test the convergence and therefore the reliability of SA results in an efficient way. The appealing feature of this new technique is the necessity of no further model evaluation and therefore enables checking of already processed sensitivity results. This is one step towards reliable and transferable, published sensitivity results.

A risk-adjusted financial model to estimate the cost of a video-assisted thoracoscopic surgery lobectomy programme.

PubMed

Brunelli, Alessandro; Tentzeris, Vasileios; Sandri, Alberto; McKenna, Alexandra; Liew, Shan Liung; Milton, Richard; Chaudhuri, Nilanjan; Kefaloyannis, Emmanuel; Papagiannopoulos, Kostas

2016-05-01

To develop a clinically risk-adjusted financial model to estimate the cost associated with a video-assisted thoracoscopic surgery (VATS) lobectomy programme. Prospectively collected data of 236 VATS lobectomy patients (August 2012-December 2013) were analysed retrospectively. Fixed and variable intraoperative and postoperative costs were retrieved from the Hospital Accounting Department. Baseline and surgical variables were tested for a possible association with total cost using a multivariable linear regression and bootstrap analyses. Costs were calculated in GBP and expressed in Euros (EUR:GBP exchange rate 1.4). The average total cost of a VATS lobectomy was €11 368 (range €6992-€62 535). Average intraoperative (including surgical and anaesthetic time, overhead, disposable materials) and postoperative costs [including ward stay, high dependency unit (HDU) or intensive care unit (ICU) and variable costs associated with management of complications] were €8226 (range €5656-€13 296) and €3029 (range €529-€51 970), respectively. The following variables remained reliably associated with total costs after linear regression analysis and bootstrap: carbon monoxide lung diffusion capacity (DLCO) <60% predicted value (P = 0.02, bootstrap 63%) and chronic obstructive pulmonary disease (COPD; P = 0.035, bootstrap 57%). The following model was developed to estimate the total costs: 10 523 + 1894 × COPD + 2376 × DLCO < 60%. The comparison between predicted and observed costs was repeated in 1000 bootstrapped samples to verify the stability of the model. The two values were not different (P > 0.05) in 86% of the samples. A hypothetical patient with COPD and DLCO less than 60% would cost €4270 more than a patient without COPD and with higher DLCO values (€14 793 vs €10 523). Risk-adjusting financial data can help estimate the total cost associated with VATS lobectomy based on clinical factors. This model can be used to audit the internal financial performance of a VATS lobectomy programme for budgeting, planning and for appropriate bundled payment reimbursements. © The Author 2015. Published by Oxford University Press on behalf of the European Association for Cardio-Thoracic Surgery. All rights reserved.

Childhood trauma and problem behavior: Examining the mediating roles of experiential avoidance and mindfulness processes.

PubMed

Roche, Anne I; Kroska, Emily B; Miller, Michelle L; Kroska, Sydney K; O'Hara, Michael W

2018-03-22

Childhood trauma is associated with a variety of risky, unhealthy, or problem behaviors. The current study aimed to explore experiential avoidance and mindfulness processes as mechanisms through which childhood trauma and problem behavior are linked in a college sample. The sample consisted of college-aged young adults recruited November-December, 2016 (N = 414). Participants completed self-report measures of childhood trauma, current problem behavior, experiential avoidance, and mindfulness processes. Bootstrapped mediation analyses examined the mechanistic associations of interest. Mediation analyses indicated that experiential avoidance was a significant mediator of the association between childhood trauma and problem behavior. Additionally, multiple mediation analyses indicated that specific mindfulness facets-act with awareness and nonjudgment of inner experience-significantly mediated the same association. Interventions for college students who have experienced childhood trauma might profitably target mechanisms such as avoidance and mindfulness in order to minimize engagement in problem behavior.

Anomalous dimensions of spinning operators from conformal symmetry

NASA Astrophysics Data System (ADS)

Gliozzi, Ferdinando

2018-01-01

We compute, to the first non-trivial order in the ɛ-expansion of a perturbed scalar field theory, the anomalous dimensions of an infinite class of primary operators with arbitrary spin ℓ = 0, 1, . . . , including as a particular case the weakly broken higher-spin currents, using only constraints from conformal symmetry. Following the bootstrap philosophy, no reference is made to any Lagrangian, equations of motion or coupling constants. Even the space dimensions d are left free. The interaction is implicitly turned on through the local operators by letting them acquire anomalous dimensions. When matching certain four-point and five-point functions with the corresponding quantities of the free field theory in the ɛ → 0 limit, no free parameter remains. It turns out that only the expected discrete d values are permitted and the ensuing anomalous dimensions reproduce known results for the weakly broken higher-spin currents and provide new results for the other spinning operators.

Bootstrapping language acquisition.

PubMed

Abend, Omri; Kwiatkowski, Tom; Smith, Nathaniel J; Goldwater, Sharon; Steedman, Mark

2017-07-01

The semantic bootstrapping hypothesis proposes that children acquire their native language through exposure to sentences of the language paired with structured representations of their meaning, whose component substructures can be associated with words and syntactic structures used to express these concepts. The child's task is then to learn a language-specific grammar and lexicon based on (probably contextually ambiguous, possibly somewhat noisy) pairs of sentences and their meaning representations (logical forms). Starting from these assumptions, we develop a Bayesian probabilistic account of semantically bootstrapped first-language acquisition in the child, based on techniques from computational parsing and interpretation of unrestricted text. Our learner jointly models (a) word learning: the mapping between components of the given sentential meaning and lexical words (or phrases) of the language, and (b) syntax learning: the projection of lexical elements onto sentences by universal construction-free syntactic rules. Using an incremental learning algorithm, we apply the model to a dataset of real syntactically complex child-directed utterances and (pseudo) logical forms, the latter including contextually plausible but irrelevant distractors. Taking the Eve section of the CHILDES corpus as input, the model simulates several well-documented phenomena from the developmental literature. In particular, the model exhibits syntactic bootstrapping effects (in which previously learned constructions facilitate the learning of novel words), sudden jumps in learning without explicit parameter setting, acceleration of word-learning (the "vocabulary spurt"), an initial bias favoring the learning of nouns over verbs, and one-shot learning of words and their meanings. The learner thus demonstrates how statistical learning over structured representations can provide a unified account for these seemingly disparate phenomena. Copyright © 2017 Elsevier B.V. All rights reserved.

Effect of non-normality on test statistics for one-way independent groups designs.

PubMed

Cribbie, Robert A; Fiksenbaum, Lisa; Keselman, H J; Wilcox, Rand R

2012-02-01

The data obtained from one-way independent groups designs is typically non-normal in form and rarely equally variable across treatment populations (i.e., population variances are heterogeneous). Consequently, the classical test statistic that is used to assess statistical significance (i.e., the analysis of variance F test) typically provides invalid results (e.g., too many Type I errors, reduced power). For this reason, there has been considerable interest in finding a test statistic that is appropriate under conditions of non-normality and variance heterogeneity. Previously recommended procedures for analysing such data include the James test, the Welch test applied either to the usual least squares estimators of central tendency and variability, or the Welch test with robust estimators (i.e., trimmed means and Winsorized variances). A new statistic proposed by Krishnamoorthy, Lu, and Mathew, intended to deal with heterogeneous variances, though not non-normality, uses a parametric bootstrap procedure. In their investigation of the parametric bootstrap test, the authors examined its operating characteristics under limited conditions and did not compare it to the Welch test based on robust estimators. Thus, we investigated how the parametric bootstrap procedure and a modified parametric bootstrap procedure based on trimmed means perform relative to previously recommended procedures when data are non-normal and heterogeneous. The results indicated that the tests based on trimmed means offer the best Type I error control and power when variances are unequal and at least some of the distribution shapes are non-normal. © 2011 The British Psychological Society.

Determining the near-surface current profile from measurements of the wave dispersion relation

NASA Astrophysics Data System (ADS)

Smeltzer, Benjamin; Maxwell, Peter; Aesøy, Eirik; Ellingsen, Simen

2017-11-01

The current-induced Doppler shifts of waves can yield information about the background mean flow, providing an attractive method of inferring the current profile in the upper layer of the ocean. We present measurements of waves propagating on shear currents in a laboratory water channel, as well as theoretical investigations of inversion techniques for determining the vertical current structure. Spatial and temporal measurements of the free surface profile obtained using a synthetic Schlieren method are analyzed to determine the wave dispersion relation and Doppler shifts as a function of wavelength. The vertical current profile can then be inferred from the Doppler shifts using an inversion algorithm. Most existing algorithms rely on a priori assumptions of the shape of the current profile, and developing a method that uses less stringent assumptions is a focus of this study, allowing for measurement of more general current profiles. The accuracy of current inversion algorithms are evaluated by comparison to measurements of the mean flow profile from particle image velocimetry (PIV), and a discussion of the sensitivity to errors in the Doppler shifts is presented.

Quantification of variability and uncertainty for air toxic emission inventories with censored emission factor data.

PubMed

Frey, H Christopher; Zhao, Yuchao

2004-11-15

Probabilistic emission inventories were developed for urban air toxic emissions of benzene, formaldehyde, chromium, and arsenic for the example of Houston. Variability and uncertainty in emission factors were quantified for 71-97% of total emissions, depending upon the pollutant and data availability. Parametric distributions for interunit variability were fit using maximum likelihood estimation (MLE), and uncertainty in mean emission factors was estimated using parametric bootstrap simulation. For data sets containing one or more nondetected values, empirical bootstrap simulation was used to randomly sample detection limits for nondetected values and observations for sample values, and parametric distributions for variability were fit using MLE estimators for censored data. The goodness-of-fit for censored data was evaluated by comparison of cumulative distributions of bootstrap confidence intervals and empirical data. The emission inventory 95% uncertainty ranges are as small as -25% to +42% for chromium to as large as -75% to +224% for arsenic with correlated surrogates. Uncertainty was dominated by only a few source categories. Recommendations are made for future improvements to the analysis.

Bootstrapping non-commutative gauge theories from L∞ algebras

NASA Astrophysics Data System (ADS)

Blumenhagen, Ralph; Brunner, Ilka; Kupriyanov, Vladislav; Lüst, Dieter

2018-05-01

Non-commutative gauge theories with a non-constant NC-parameter are investigated. As a novel approach, we propose that such theories should admit an underlying L∞ algebra, that governs not only the action of the symmetries but also the dynamics of the theory. Our approach is well motivated from string theory. We recall that such field theories arise in the context of branes in WZW models and briefly comment on its appearance for integrable deformations of AdS5 sigma models. For the SU(2) WZW model, we show that the earlier proposed matrix valued gauge theory on the fuzzy 2-sphere can be bootstrapped via an L∞ algebra. We then apply this approach to the construction of non-commutative Chern-Simons and Yang-Mills theories on flat and curved backgrounds with non-constant NC-structure. More concretely, up to the second order, we demonstrate how derivative and curvature corrections to the equations of motion can be bootstrapped in an algebraic way from the L∞ algebra. The appearance of a non-trivial A∞ algebra is discussed, as well.

A symbol of uniqueness: the cluster bootstrap for the 3-loop MHV heptagon

DOE PAGES

Drummond, J. M.; Papathanasiou, G.; Spradlin, M.

2015-03-16

Seven-particle scattering amplitudes in planar super-Yang-Mills theory are believed to belong to a special class of generalised polylogarithm functions called heptagon functions. These are functions with physical branch cuts whose symbols may be written in terms of the 42 cluster A-coordinates on Gr(4, 7). Motivated by the success of the hexagon bootstrap programme for constructing six-particle amplitudes we initiate the systematic study of the symbols of heptagon functions. We find that there is exactly one such symbol of weight six which satisfies the MHV last-entry condition and is finite in the 7 ll 6 collinear limit. This unique symbol ismore » both dihedral and parity-symmetric, and remarkably its collinear limit is exactly the symbol of the three-loop six-particle MHV amplitude, although none of these properties were assumed a priori. It must therefore be the symbol of the threeloop seven-particle MHV amplitude. The simplicity of its construction suggests that the n-gon bootstrap may be surprisingly powerful for n > 6.« less

Review of Orbital Propellant Transfer Techniques and the Feasibility of a Thermal Bootstrap Propellant Transfer Concepts

NASA Technical Reports Server (NTRS)

Yoshikawa, H. H.; Madison, I. B.

1971-01-01

This study was performed in support of the NASA Task B-2 Study Plan for Space Basing. The nature of space-based operations implies that orbital transfer of propellant is a prime consideration. The intent of this report is (1) to report on the findings and recommendations of existing literature on space-based propellant transfer techniques, and (2) to determine possible alternatives to the recommended methods. The reviewed literature recommends, in general, the use of conventional liquid transfer techniques (i.e., pumping) in conjunction with an artificially induced gravitational field. An alternate concept that was studied, the Thermal Bootstrap Transfer Process, is based on the compression of a two-phase fluid with subsequent condensation to a liquid (vapor compression/condensation). This concept utilizes the intrinsic energy capacities of the tanks and propellant by exploiting temperature differentials and available energy differences. The results indicate the thermodynamic feasibility of the Thermal Bootstrap Transfer Process for a specific range of tank sizes, temperatures, fill-factors and receiver tank heat transfer coefficients.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lewis, John R.; Brooks, Dusty Marie

In pressurized water reactors, the prevention, detection, and repair of cracks within dissimilar metal welds is essential to ensure proper plant functionality and safety. Weld residual stresses, which are difficult to model and cannot be directly measured, contribute to the formation and growth of cracks due to primary water stress corrosion cracking. Additionally, the uncertainty in weld residual stress measurements and modeling predictions is not well understood, further complicating the prediction of crack evolution. The purpose of this document is to develop methodology to quantify the uncertainty associated with weld residual stress that can be applied to modeling predictions andmore » experimental measurements. Ultimately, the results can be used to assess the current state of uncertainty and to build confidence in both modeling and experimental procedures. The methodology consists of statistically modeling the variation in the weld residual stress profiles using functional data analysis techniques. Uncertainty is quantified using statistical bounds (e.g. confidence and tolerance bounds) constructed with a semi-parametric bootstrap procedure. Such bounds describe the range in which quantities of interest, such as means, are expected to lie as evidenced by the data. The methodology is extended to provide direct comparisons between experimental measurements and modeling predictions by constructing statistical confidence bounds for the average difference between the two quantities. The statistical bounds on the average difference can be used to assess the level of agreement between measurements and predictions. The methodology is applied to experimental measurements of residual stress obtained using two strain relief measurement methods and predictions from seven finite element models developed by different organizations during a round robin study.« less

Stability of DIII-D high-performance, negative central shear discharges

DOE PAGES

Hanson, Jeremy M.; Berkery, John W.; Bialek, James M.; ...

2017-03-20

Tokamak plasma experiments on the DIII-D device demonstrate high-performance, negative central shear (NCS) equilibria with enhanced stability when the minimum safety factor q min exceeds 2, qualitatively confirming theoretical predictions of favorable stability in the NCS regime. The discharges exhibit good confinement with an L-mode enhancement factor H 89 = 2.5, and are ultimately limited by the ideal-wall external kink stability boundary as predicted by ideal MHD theory, as long as tearing mode (TM) locking events, resistive wall modes (RWMs), and internal kink modes are properly avoided or controlled. Although the discharges exhibit rotating TMs, locking events are avoided asmore » long as a threshold minimum safety factor value q min > 2 is maintained. Fast timescale magnetic feedback control ameliorates RWM activity, expanding the stable operating space and allowing access to β N values approaching the ideal-wall limit. Quickly growing and rotating instabilities consistent with internal kink mode dynamics are encountered when the ideal-wall limit is reached. The RWM events largely occur between the no- and ideal-wall pressure limits predicted by ideal MHD. However, evaluating kinetic contributions to the RWM dispersion relation results in a prediction of passive stability in this regime due to high plasma rotation. In addition, the ideal MHD stability analysis predicts that the ideal-wall limit can be further increased to β N > 4 by broadening the current profile. Furthermore, this path toward improved stability has the potential advantage of being compatible with the bootstrap-dominated equilibria envisioned for advanced tokamak (AT) fusion reactors.« less

Stability of DIII-D high-performance, negative central shear discharges

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hanson, Jeremy M.; Berkery, John W.; Bialek, James M.

Tokamak plasma experiments on the DIII-D device demonstrate high-performance, negative central shear (NCS) equilibria with enhanced stability when the minimum safety factor q min exceeds 2, qualitatively confirming theoretical predictions of favorable stability in the NCS regime. The discharges exhibit good confinement with an L-mode enhancement factor H 89 = 2.5, and are ultimately limited by the ideal-wall external kink stability boundary as predicted by ideal MHD theory, as long as tearing mode (TM) locking events, resistive wall modes (RWMs), and internal kink modes are properly avoided or controlled. Although the discharges exhibit rotating TMs, locking events are avoided asmore » long as a threshold minimum safety factor value q min > 2 is maintained. Fast timescale magnetic feedback control ameliorates RWM activity, expanding the stable operating space and allowing access to β N values approaching the ideal-wall limit. Quickly growing and rotating instabilities consistent with internal kink mode dynamics are encountered when the ideal-wall limit is reached. The RWM events largely occur between the no- and ideal-wall pressure limits predicted by ideal MHD. However, evaluating kinetic contributions to the RWM dispersion relation results in a prediction of passive stability in this regime due to high plasma rotation. In addition, the ideal MHD stability analysis predicts that the ideal-wall limit can be further increased to β N > 4 by broadening the current profile. Furthermore, this path toward improved stability has the potential advantage of being compatible with the bootstrap-dominated equilibria envisioned for advanced tokamak (AT) fusion reactors.« less

Partnership for Edge Physics Simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kritz, Arnold H.; Rafiq, Tariq

A major goal of our participation in the Edge Physics Simulation project has been to contribute to the understanding of the self-organization of tokamak turbulence fluctuations resulting in the formation of a staircase structure in the ion temperature. A second important goal is to demonstrate how small scale turbulence in plasmas self-organizes with dynamically driven quasi-stationary flow shear. These goals have been accomplished through the analyses of the statistical properties of XGC1 flux driven Gyrokinetic electrostatic ion temperature gradient (ITG) turbulence simulation data in which neutrals are included. The ITG turbulence data, and in particular fluctuation data, were obtained frommore » a massively parallel flux-driven gyrokinetic full-f particle-in-cell simulation of a DIII-D like equilibrium. Below some the findings are summarized. It was observed that the emergence of staircase structure is related to the variations in the normalized temperature gradient length (R/LT) and the poloidal flow shear. Average turbulence intensity is found to be large in the vicinity of minima in R/LTi, where ITG growth is expected to be lower. The distributions of the occurrences of potential fluctuation are found to be Gaussian away from the staircase-step locations, but they are found to be non-Gaussian in the vicinity of staircase-step locations. The results of analytically derived expressions for the distribution of the occurrences of turbulence intensity and intensity flux were compared with the corresponding quantities computed using XGC1 simulation data and good agreement is found. The derived expressions predicts inward and outward propagation of turbulence intensity flux in an intermittent fashion. The outward propagation of turbulence intensity flux occurs at staircase-step locations and is related to the change in poloidal flow velocity shear and to the change in the ion temperature gradient. The standard deviation, skewness and kurtosis for turbulence quantities were computed and found to be large in the vicinity of the staircase-step structures. Large values of skewness and kurtosis can be explained by a temporary opening and closing of the structure which allows turbulence intensity events to propagate. The staircase patterns may reduce the ion heat transport and a manipulation of these patterns may be used to optimize heat transport in tokamaks. An additional objective of the research in support of the Edge Physics Simulation initiative has been to improve the understanding of scrape-off layer thermal transport. In planning experiments and designing future tokamaks, it is important to understand the physical effects that contribute to divertor heat-load fluxes. The research accomplished will contribute to developing new models for the scrape-off layer region. The XGC0 code was used to compute the heat fluxes and the heat-load width in the outer divertor plates of C-Mod and DIII-D tokamaks. It was observed that the width of the XGC0 neoclassical heat-load was approximately inversely proportional to the total plasma current. Anomalous transport in the H-mode pedestal region of five Alcator C-Mod discharges, representing a collisionality scan, was analyzed. The understanding of anomalous transport in the pedestal region is important for the development of a comprehensive model for the H-mode pedestal slope. It was found that the electron thermal anomalous diffusivities at the pedestal top increase with the electron collisionality. This dependence can point to the DRIBM as the modes that drive the anomalous transport in the plasma edge of highly collisional discharges. The effects of plasma shaping on the H-mode pedestal structure was also investigated. The differences in the predicted H-mode pedestal width and height for the DIII-D discharges with different elongation and triangularities were discussed. For the discharges with higher elongation, it was found that the gradients of the plasma profiles in the H-mode pedestal reach semi-steady states. In these simulations, the pedestal slowly continued to evolve to higher pedestal pressures and bootstrap currents until the peeling ballooning stability conditions were satisfied. The discharges with lower elongation do not reach the semi-steady state, and ELM crashes were triggered at earlier times. The plasma elongation was found to have a stronger stabilizing effect than the plasma triangularity. For the discharges with lower elongation and lower triangularity, the ELM frequency was large, and the H-mode pedestal evolves rapidly. It was found that the temperature of neutrals in the scrape-off-layer region can affect the dynamics of the H-mode pedestal buildup. However, the final pedestal profiles were nearly independent of the neutral temperature. The elongation and triangularity affected the pedestal widths of plasma density and electron temperature profiles differently. This study illustrated a new mechanism for controlling the pedestal bootstrap current and the pedestal stability.« less

Gyrokinetic Particle Simulations of Neoclassical Transport

NASA Astrophysics Data System (ADS)

Lin, Zhihong

A time varying weighting (delta f) scheme based on the small gyro-radius ordering is developed and applied to a steady state, multi-species gyrokinetic particle simulation of neoclassical transport. Accurate collision operators conserving momentum and energy are developed and implemented. Benchmark simulation results using these operators are found to agree very well with neoclassical theory. For example, it is dynamically demonstrated that like-particle collisions produce no particle flux and that the neoclassical fluxes are ambipolar for an ion -electron plasma. An important physics feature of the present scheme is the introduction of toroidal flow to the simulations. In agreement with the existing analytical neoclassical theory, ion energy flux is enhanced by the toroidal mass flow and the neoclassical viscosity is a Pfirsch-Schluter factor times the classical viscosity in the banana regime. In addition, the poloidal electric field associated with toroidal mass flow is found to enhance density gradient driven electron particle flux and the bootstrap current while reducing temperature gradient driven flux and current. Modifications of the neoclassical transport by the orbit squeezing effects due to the radial electric field associated with sheared toroidal flow are studied. Simulation results indicate a reduction of both ion thermal flux and neoclassical toroidal rotation. Neoclassical theory in the steep gradient profile regime, where conventional neoclassical theory fails, is examined by taking into account finite banana width effects. The relevance of these studies to interesting experimental conditions in tokamaks is discussed. Finally, the present numerical scheme is extended to general geometry equilibrium. This new formulation will be valuable for the development of new capabilities to address complex equilibria such as advanced stellarator configurations and possibly other alternate concepts for the magnetic confinement of plasmas. In general, the present work demonstrates a valuable new capability for studying important aspects of neoclassical transport inaccessible by conventional analytical calculation processes.

Parameterization of light absorption by components of seawater in optically complex coastal waters of the Crimea Peninsula (Black Sea).

PubMed

Dmitriev, Egor V; Khomenko, Georges; Chami, Malik; Sokolov, Anton A; Churilova, Tatyana Y; Korotaev, Gennady K

2009-03-01

The absorption of sunlight by oceanic constituents significantly contributes to the spectral distribution of the water-leaving radiance. Here it is shown that current parameterizations of absorption coefficients do not apply to the optically complex waters of the Crimea Peninsula. Based on in situ measurements, parameterizations of phytoplankton, nonalgal, and total particulate absorption coefficients are proposed. Their performance is evaluated using a log-log regression combined with a low-pass filter and the nonlinear least-square method. Statistical significance of the estimated parameters is verified using the bootstrap method. The parameterizations are relevant for chlorophyll a concentrations ranging from 0.45 up to 2 mg/m(3).

Use of high order, periodic orbits in the PIES code

NASA Astrophysics Data System (ADS)

Monticello, Donald; Reiman, Allan

2010-11-01

We have implemented a version of the PIES code (Princeton Iterative Equilibrium SolverootnotetextA. Reiman et al 2007 Nucl. Fusion 47 572) that uses high order periodic orbits to select the surfaces on which straight magnetic field line coordinates will be calculated. The use of high order periodic orbits has increase the robustness and speed of the PIES code. We now have more uniform treatment of in-phase and out-of-phase islands. This new version has better convergence properties and works well with a full Newton scheme. We now have the ability to shrink islands using a bootstrap like current and this includes the m=1 island in tokamaks.

First-Principles-Driven Model-Based Optimal Control of the Current Profile in NSTX-U

NASA Astrophysics Data System (ADS)

Ilhan, Zeki; Barton, Justin; Wehner, William; Schuster, Eugenio; Gates, David; Gerhardt, Stefan; Kolemen, Egemen; Menard, Jonathan

2014-10-01

Regulation in time of the toroidal current profile is one of the main challenges toward the realization of the next-step operational goals for NSTX-U. A nonlinear, control-oriented, physics-based model describing the temporal evolution of the current profile is obtained by combining the magnetic diffusion equation with empirical correlations obtained at NSTX-U for the electron density, electron temperature, and non-inductive current drives. In this work, the proposed model is embedded into the control design process to synthesize a time-variant, linear-quadratic-integral, optimal controller capable of regulating the safety factor profile around a desired target profile while rejecting disturbances. Neutral beam injectors and the total plasma current are used as actuators to shape the current profile. The effectiveness of the proposed controller in regulating the safety factor profile in NSTX-U is demonstrated via closed-loop predictive simulations carried out in PTRANSP. Supported by PPPL.

Three ways to solve critical ϕ4 theory on 4 ‑ 𝜖 dimensional real projective space: Perturbation, bootstrap, and Schwinger-Dyson equation

NASA Astrophysics Data System (ADS)

Hasegawa, Chika; Nakayama, Yu

2018-03-01

In this paper, we solve the two-point function of the lowest dimensional scalar operator in the critical ϕ4 theory on 4 ‑ 𝜖 dimensional real projective space in three different methods. The first is to use the conventional perturbation theory, and the second is to impose the cross-cap bootstrap equation, and the third is to solve the Schwinger-Dyson equation under the assumption of conformal invariance. We find that the three methods lead to mutually consistent results but each has its own advantage.

On critical exponents without Feynman diagrams

NASA Astrophysics Data System (ADS)

Sen, Kallol; Sinha, Aninda

2016-11-01

In order to achieve a better analytic handle on the modern conformal bootstrap program, we re-examine and extend the pioneering 1974 work of Polyakov’s, which was based on consistency between the operator product expansion and unitarity. As in the bootstrap approach, this method does not depend on evaluating Feynman diagrams. We show how this approach can be used to compute the anomalous dimensions of certain operators in the O(n) model at the Wilson-Fisher fixed point in 4-ɛ dimensions up to O({ɛ }2). AS dedicates this work to the loving memory of his mother.

Bootstrapping 3D fermions

DOE PAGES

Iliesiu, Luca; Kos, Filip; Poland, David; ...

2016-03-17

We study the conformal bootstrap for a 4-point function of fermions in 3D. We first introduce an embedding formalism for 3D spinors and compute the conformal blocks appearing in fermion 4-point functions. Using these results, we find general bounds on the dimensions of operators appearing in the ψ × ψ OPE, and also on the central charge C T. We observe features in our bounds that coincide with scaling dimensions in the GrossNeveu models at large N. Finally, we also speculate that other features could coincide with a fermionic CFT containing no relevant scalar operators.

Gene Discovery in Bladder Cancer Progression using cDNA Microarrays

PubMed Central

Sanchez-Carbayo, Marta; Socci, Nicholas D.; Lozano, Juan Jose; Li, Wentian; Charytonowicz, Elizabeth; Belbin, Thomas J.; Prystowsky, Michael B.; Ortiz, Angel R.; Childs, Geoffrey; Cordon-Cardo, Carlos

2003-01-01

To identify gene expression changes along progression of bladder cancer, we compared the expression profiles of early-stage and advanced bladder tumors using cDNA microarrays containing 17,842 known genes and expressed sequence tags. The application of bootstrapping techniques to hierarchical clustering segregated early-stage and invasive transitional carcinomas into two main clusters. Multidimensional analysis confirmed these clusters and more importantly, it separated carcinoma in situ from papillary superficial lesions and subgroups within early-stage and invasive tumors displaying different overall survival. Additionally, it recognized early-stage tumors showing gene profiles similar to invasive disease. Different techniques including standard t-test, single-gene logistic regression, and support vector machine algorithms were applied to identify relevant genes involved in bladder cancer progression. Cytokeratin 20, neuropilin-2, p21, and p33ING1 were selected among the top ranked molecular targets differentially expressed and validated by immunohistochemistry using tissue microarrays (n = 173). Their expression patterns were significantly associated with pathological stage, tumor grade, and altered retinoblastoma (RB) expression. Moreover, p33ING1 expression levels were significantly associated with overall survival. Analysis of the annotation of the most significant genes revealed the relevance of critical genes and pathways during bladder cancer progression, including the overexpression of oncogenic genes such as DEK in superficial tumors or immune response genes such as Cd86 antigen in invasive disease. Gene profiling successfully classified bladder tumors based on their progression and clinical outcome. The present study has identified molecular biomarkers of potential clinical significance and critical molecular targets associated with bladder cancer progression. PMID:12875971

New Methods for Estimating Seasonal Potential Climate Predictability

NASA Astrophysics Data System (ADS)

Feng, Xia

This study develops two new statistical approaches to assess the seasonal potential predictability of the observed climate variables. One is the univariate analysis of covariance (ANOCOVA) model, a combination of autoregressive (AR) model and analysis of variance (ANOVA). It has the advantage of taking into account the uncertainty of the estimated parameter due to sampling errors in statistical test, which is often neglected in AR based methods, and accounting for daily autocorrelation that is not considered in traditional ANOVA. In the ANOCOVA model, the seasonal signals arising from external forcing are determined to be identical or not to assess any interannual variability that may exist is potentially predictable. The bootstrap is an attractive alternative method that requires no hypothesis model and is available no matter how mathematically complicated the parameter estimator. This method builds up the empirical distribution of the interannual variance from the resamplings drawn with replacement from the given sample, in which the only predictability in seasonal means arises from the weather noise. These two methods are applied to temperature and water cycle components including precipitation and evaporation, to measure the extent to which the interannual variance of seasonal means exceeds the unpredictable weather noise compared with the previous methods, including Leith-Shukla-Gutzler (LSG), Madden, and Katz. The potential predictability of temperature from ANOCOVA model, bootstrap, LSG and Madden exhibits a pronounced tropical-extratropical contrast with much larger predictability in the tropics dominated by El Nino/Southern Oscillation (ENSO) than in higher latitudes where strong internal variability lowers predictability. Bootstrap tends to display highest predictability of the four methods, ANOCOVA lies in the middle, while LSG and Madden appear to generate lower predictability. Seasonal precipitation from ANOCOVA, bootstrap, and Katz, resembling that for temperature, is more predictable over the tropical regions, and less predictable in extropics. Bootstrap and ANOCOVA are in good agreement with each other, both methods generating larger predictability than Katz. The seasonal predictability of evaporation over land bears considerably similarity with that of temperature using ANOCOVA, bootstrap, LSG and Madden. The remote SST forcing and soil moisture reveal substantial seasonality in their relations with the potentially predictable seasonal signals. For selected regions, either SST or soil moisture or both shows significant relationships with predictable signals, hence providing indirect insight on slowly varying boundary processes involved to enable useful seasonal climate predication. A multivariate analysis of covariance (MANOCOVA) model is established to identify distinctive predictable patterns, which are uncorrelated with each other. Generally speaking, the seasonal predictability from multivariate model is consistent with that from ANOCOVA. Besides unveiling the spatial variability of predictability, MANOCOVA model also reveals the temporal variability of each predictable pattern, which could be linked to the periodic oscillations.

Identification of cephalopod species from the North and Baltic Seas using morphology, COI and 18S rDNA sequences

NASA Astrophysics Data System (ADS)

Gebhardt, Katharina; Knebelsberger, Thomas

2015-09-01

We morphologically analyzed 79 cephalopod specimens from the North and Baltic Seas belonging to 13 separate species. Another 29 specimens showed morphological features of either Alloteuthis mediaor Alloteuthis subulata or were found to be in between. Reliable identification features to distinguish between A. media and A. subulata are currently not available. The analysis of the DNA barcoding region of the COI gene revealed intraspecific distances (uncorrected p) ranging from 0 to 2.13 % (average 0.1 %) and interspecific distances between 3.31 and 22 % (average 15.52 %). All species formed monophyletic clusters in a neighbor-joining analysis and were supported by bootstrap values of ≥99 %. All COI haplotypes belonging to the 29 Alloteuthis specimens were grouped in one cluster. Neither COI nor 18S rDNA sequences helped to distinguish between the different Alloteuthis morphotypes. For species identification purposes, we recommend the use of COI, as it showed higher bootstrap support of species clusters and less amplification and sequencing failure compared to 18S. Our data strongly support the assumption that the genus Alloteuthis is only represented by a single species, at least in the North Sea. It remained unclear whether this species is A. subulata or A. media. All COI sequences including important metadata were uploaded to the Barcode of Life Data Systems and can be used as reference library for the molecular identification of more than 50 % of the cephalopod fauna known from the North and Baltic Seas.

Scoring system to guide decision making for the use of gentamicin-impregnated collagen sponge to prevent deep sternal wound infection.

PubMed

Benedetto, Umberto; Raja, Shahzad G

2014-11-01

The effectiveness of the routine retrosternal placement of a gentamicin-impregnated collagen sponge (GICS) implant before sternotomy closure is currently a matter of some controversy. We aimed to develop a scoring system to guide decision making for the use of GICS to prevent deep sternal wound infection. Fast backward elimination on predictors, including GICS, was performed using the Lawless and Singhal method. The scoring system was reported as a partial nomogram that can be used to manually obtain predicted individual risk of deep sternal wound infection from the regression model. Bootstrapping validation of the regression models was performed. The final populations consisted of 8750 adult patients undergoing cardiac surgery through full sternotomy during the study period. A total of 329 patients (3.8%) received GICS implant. The overall incidence of deep sternal wound infection was lower among patients who received GICS implant (0.6%) than patients who did not (2.01%) (P=.02). A nomogram to predict the individual risk for deep sternal wound infection was developed that included the use of GICS. Bootstrapping validation confirmed a good discriminative power of the models. The scoring system provides an impartial assessment of the decision-making process for clinicians to establish if GICS implant is effective in reducing the risk for deep sternal wound infection in individual patients undergoing cardiac surgery through full sternotomy. Copyright © 2014 The American Association for Thoracic Surgery. Published by Elsevier Inc. All rights reserved.

Advances in the high bootstrap fraction regime on DIII-D towards the Q  =  5 mission of ITER steady state

NASA Astrophysics Data System (ADS)

Qian, J. P.; Garofalo, A. M.; Gong, X. Z.; Ren, Q. L.; Ding, S. Y.; Solomon, W. M.; Xu, G. S.; Grierson, B. A.; Guo, W. F.; Holcomb, C. T.; McClenaghan, J.; McKee, G. R.; Pan, C. K.; Huang, J.; Staebler, G. M.; Wan, B. N.

2017-05-01

Recent EAST/DIII-D joint experiments on the high poloidal beta {β\\text{P}} regime in DIII-D have extended operation with internal transport barriers (ITBs) and excellent energy confinement (H 98y2 ~ 1.6) to higher plasma current, for lower q 95  ⩽  7.0, and more balanced neutral beam injection (NBI) (torque injection  <  2 Nm), for lower plasma rotation than previous results (Garofalo et al, IAEA 2014, Gong et al 2014 IAEA Int. Conf. on Fusion Energy). Transport analysis and experimental measurements at low toroidal rotation suggest that the E  ×  B shear effect is not key to the ITB formation in these high {β\\text{P}} discharges. Experiments and TGLF modeling show that the Shafranov shift has a key stabilizing effect on turbulence. Extrapolation of the DIII-D results using a 0D model shows that with the improved confinement, the high bootstrap fraction regime could achieve fusion gain Q  =  5 in ITER at {β\\text{N}} ~ 2.9 and q 95 ~ 7. With the optimization of q(0), the required improved confinement is achievable when using 1.5D TGLF-SAT1 for transport simulations. Results reported in this paper suggest that the DIII-D high {β\\text{P}} scenario could be a candidate for ITER steady state operation.

Mapping and Assessing Variability in the Antarctic Marginal Ice Zone, the Pack Ice and Coastal Polynyas

NASA Astrophysics Data System (ADS)

Stroeve, Julienne; Jenouvrier, Stephanie

2016-04-01

Sea ice variability within the marginal ice zone (MIZ) and polynyas plays an important role for phytoplankton productivity and krill abundance. Therefore mapping their spatial extent, seasonal and interannual variability is essential for understanding how current and future changes in these biological active regions may impact the Antarctic marine ecosystem. Knowledge of the distribution of different ice types to the total Antarctic sea ice cover may also help to shed light on the factors contributing towards recent expansion of the Antarctic ice cover in some regions and contraction in others. The long-term passive microwave satellite data record provides the longest and most consistent data record for assessing different ice types. However, estimates of the amount of MIZ, consolidated pack ice and polynyas depends strongly on what sea ice algorithm is used. This study uses two popular passive microwave sea ice algorithms, the NASA Team and Bootstrap to evaluate the distribution and variability in the MIZ, the consolidated pack ice and coastal polynyas. Results reveal the NASA Team algorithm has on average twice the MIZ and half the consolidated pack ice area as the Bootstrap algorithm. Polynya area is also larger in the NASA Team algorithm, and the timing of maximum polynya area may differ by as much as 5 months between algorithms. These differences lead to different relationships between sea ice characteristics and biological processes, as illustrated here with the breeding success of an Antarctic seabird.

Innovative Methods for Integrating Knowledge for Long-Term Monitoring of Contaminated Groundwater Sites: Understanding Microorganism Communities and their Associated Hydrochemical Environment

NASA Astrophysics Data System (ADS)

Mouser, P. J.; Rizzo, D. M.; Druschel, G.; O'Grady, P.; Stevens, L.

2005-12-01

This interdisciplinary study integrates hydrochemical and genome-based data to estimate the redox processes occurring at long-term monitoring sites. Groundwater samples have been collected from a well-characterized landfill-leachate contaminated aquifer in northeastern New York. Primers from the 16S rDNA gene were used to amplify Bacteria and Archaea in groundwater taken from monitoring wells located in clean, fringe, and contaminated locations within the aquifer. PCR-amplified rDNA were digested with restriction enzymes to evaluate terminal restriction fragment length polymorphism (T-RFLP) community profiles. The rDNA was cloned, sequenced, and partial sequences were matched against known organisms using the NCBI Blast database. Phylogenetic trees and bootstrapping were used to identify classifications of organisms and compare the communities from clean, fringe, and contaminated locations. We used Artificial Neural Network (ANN) models to incorporate microbial data with hydrochemical information for improving our understanding of subsurface processes.

Patient satisfaction after pulmonary resection for lung cancer: a multicenter comparative analysis.

PubMed

Pompili, Cecilia; Brunelli, Alessandro; Rocco, Gaetano; Salvi, Rosario; Xiumé, Francesco; La Rocca, Antonello; Sabbatini, Armando; Martucci, Nicola

2013-01-01

Patient satisfaction reflects the perception of the customer about the level of quality of care received during the episode of hospitalization. To compare the levels of satisfaction of patients submitted to lung resection in two different thoracic surgical units. Prospective analysis of 280 consecutive patients submitted to pulmonary resection for neoplastic disease in two centers (center A: 139 patients; center B: 141 patients; 2009-2010). Patients' satisfaction was assessed at discharge through the EORTC-InPatSat32 module, a 32-item, multi-scale self-administered anonymous questionnaire. Each scale (ranging from 0 to 100 in score) was compared between the two units. Multivariable regression and bootstrap were used to verify factors associated with the patients' general satisfaction (dependent variable). Patients from unit B reported a higher general satisfaction (91.5 vs. 88.3, p = 0.04), mainly due to a significantly higher satisfaction in the doctor-related scales (doctors' technical skill: p = 0.001; doctors' interpersonal skill: p = 0.008; doctors' availability: p = 0.005, and doctors information provision: p = 0.0006). Multivariable regression analysis and bootstrap confirmed that level of care in unit B (p = 0.006, bootstrap frequency 60%) along with lower level of education of the patient population (p = 0.02, bootstrap frequency 62%) were independent factors associated with a higher general patient satisfaction. We were able to show a different level of patient satisfaction in patients operated on in two different thoracic surgery units. A reduced level of patient satisfaction may trigger changes in the management policy of individual units in order to meet patients' expectations and improve organizational efficiency. Copyright © 2012 S. Karger AG, Basel.

Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support.

PubMed

Wilcox, Thomas P; Zwickl, Derrick J; Heath, Tracy A; Hillis, David M

2002-11-01

Four New World genera of dwarf boas (Exiliboa, Trachyboa, Tropidophis, and Ungaliophis) have been placed by many systematists in a single group (traditionally called Tropidophiidae). However, the monophyly of this group has been questioned in several studies. Moreover, the overall relationships among basal snake lineages, including the placement of the dwarf boas, are poorly understood. We obtained mtDNA sequence data for 12S, 16S, and intervening tRNA-val genes from 23 species of snakes representing most major snake lineages, including all four genera of New World dwarf boas. We then examined the phylogenetic position of these species by estimating the phylogeny of the basal snakes. Our phylogenetic analysis suggests that New World dwarf boas are not monophyletic. Instead, we find Exiliboa and Ungaliophis to be most closely related to sand boas (Erycinae), boas (Boinae), and advanced snakes (Caenophidea), whereas Tropidophis and Trachyboa form an independent clade that separated relatively early in snake radiation. Our estimate of snake phylogeny differs significantly in other ways from some previous estimates of snake phylogeny. For instance, pythons do not cluster with boas and sand boas, but instead show a strong relationship with Loxocemus and Xenopeltis. Additionally, uropeltids cluster strongly with Cylindrophis, and together are embedded in what has previously been considered the macrostomatan radiation. These relationships are supported by both bootstrapping (parametric and nonparametric approaches) and Bayesian analysis, although Bayesian support values are consistently higher than those obtained from nonparametric bootstrapping. Simulations show that Bayesian support values represent much better estimates of phylogenetic accuracy than do nonparametric bootstrap support values, at least under the conditions of our study. Copyright 2002 Elsevier Science (USA)

Explanation of Two Anomalous Results in Statistical Mediation Analysis.

PubMed

Fritz, Matthew S; Taylor, Aaron B; Mackinnon, David P

2012-01-01

Previous studies of different methods of testing mediation models have consistently found two anomalous results. The first result is elevated Type I error rates for the bias-corrected and accelerated bias-corrected bootstrap tests not found in nonresampling tests or in resampling tests that did not include a bias correction. This is of special concern as the bias-corrected bootstrap is often recommended and used due to its higher statistical power compared with other tests. The second result is statistical power reaching an asymptote far below 1.0 and in some conditions even declining slightly as the size of the relationship between X and M , a , increased. Two computer simulations were conducted to examine these findings in greater detail. Results from the first simulation found that the increased Type I error rates for the bias-corrected and accelerated bias-corrected bootstrap are a function of an interaction between the size of the individual paths making up the mediated effect and the sample size, such that elevated Type I error rates occur when the sample size is small and the effect size of the nonzero path is medium or larger. Results from the second simulation found that stagnation and decreases in statistical power as a function of the effect size of the a path occurred primarily when the path between M and Y , b , was small. Two empirical mediation examples are provided using data from a steroid prevention and health promotion program aimed at high school football players (Athletes Training and Learning to Avoid Steroids; Goldberg et al., 1996), one to illustrate a possible Type I error for the bias-corrected bootstrap test and a second to illustrate a loss in power related to the size of a . Implications of these findings are discussed.

Sample size determination for mediation analysis of longitudinal data.

PubMed

Pan, Haitao; Liu, Suyu; Miao, Danmin; Yuan, Ying

2018-03-27

Sample size planning for longitudinal data is crucial when designing mediation studies because sufficient statistical power is not only required in grant applications and peer-reviewed publications, but is essential to reliable research results. However, sample size determination is not straightforward for mediation analysis of longitudinal design. To facilitate planning the sample size for longitudinal mediation studies with a multilevel mediation model, this article provides the sample size required to achieve 80% power by simulations under various sizes of the mediation effect, within-subject correlations and numbers of repeated measures. The sample size calculation is based on three commonly used mediation tests: Sobel's method, distribution of product method and the bootstrap method. Among the three methods of testing the mediation effects, Sobel's method required the largest sample size to achieve 80% power. Bootstrapping and the distribution of the product method performed similarly and were more powerful than Sobel's method, as reflected by the relatively smaller sample sizes. For all three methods, the sample size required to achieve 80% power depended on the value of the ICC (i.e., within-subject correlation). A larger value of ICC typically required a larger sample size to achieve 80% power. Simulation results also illustrated the advantage of the longitudinal study design. The sample size tables for most encountered scenarios in practice have also been published for convenient use. Extensive simulations study showed that the distribution of the product method and bootstrapping method have superior performance to the Sobel's method, but the product method was recommended to use in practice in terms of less computation time load compared to the bootstrapping method. A R package has been developed for the product method of sample size determination in mediation longitudinal study design.

A Validated Prediction Model for Overall Survival From Stage III Non-Small Cell Lung Cancer: Toward Survival Prediction for Individual Patients.

PubMed

Oberije, Cary; De Ruysscher, Dirk; Houben, Ruud; van de Heuvel, Michel; Uyterlinde, Wilma; Deasy, Joseph O; Belderbos, Jose; Dingemans, Anne-Marie C; Rimner, Andreas; Din, Shaun; Lambin, Philippe

2015-07-15

Although patients with stage III non-small cell lung cancer (NSCLC) are homogeneous according to the TNM staging system, they form a heterogeneous group, which is reflected in the survival outcome. The increasing amount of information for an individual patient and the growing number of treatment options facilitate personalized treatment, but they also complicate treatment decision making. Decision support systems (DSS), which provide individualized prognostic information, can overcome this but are currently lacking. A DSS for stage III NSCLC requires the development and integration of multiple models. The current study takes the first step in this process by developing and validating a model that can provide physicians with a survival probability for an individual NSCLC patient. Data from 548 patients with stage III NSCLC were available to enable the development of a prediction model, using stratified Cox regression. Variables were selected by using a bootstrap procedure. Performance of the model was expressed as the c statistic, assessed internally and on 2 external data sets (n=174 and n=130). The final multivariate model, stratified for treatment, consisted of age, gender, World Health Organization performance status, overall treatment time, equivalent radiation dose, number of positive lymph node stations, and gross tumor volume. The bootstrapped c statistic was 0.62. The model could identify risk groups in external data sets. Nomograms were constructed to predict an individual patient's survival probability (www.predictcancer.org). The data set can be downloaded at https://www.cancerdata.org/10.1016/j.ijrobp.2015.02.048. The prediction model for overall survival of patients with stage III NSCLC highlights the importance of combining patient, clinical, and treatment variables. Nomograms were developed and validated. This tool could be used as a first building block for a decision support system. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Profiles of childhood adversities in pathological gamblers - A latent class analysis.

PubMed

Lotzin, Annett; Ulas, Mehmet; Buth, Sven; Milin, Sascha; Kalke, Jens; Schäfer, Ingo

2018-06-01

Despite of high rates of adverse childhood experiences (ACEs) in pathological gamblers, researchers have rarely studied which types of ACEs often co-occur and how these profiles of ACEs are related to current psychopathology. We aimed to identify profiles of ACEs in pathological gamblers and examined how these profiles were related to gambling-related characteristics and current general psychopathology. In 329 current or lifetime pathological gamblers, diagnosed with the Composite Diagnostic Interview for DSM-IV, 10 types of ACEs were measured using the Adverse Childhood Experiences Questionnaire. Global psychopathology was assessed using the Symptom Checklist SCL-27. ACE profiles were identified using latent class analysis. Differences between ACE profiles in gambling-related characteristics and global psychopathology were analyzed using MANOVA. We found that four out of five gamblers (n=257, 78.1%) reported at least one ACE. Four distinct ACE profiles were identified: 'Low ACE', 'High ACE', 'Physical and emotional abuse', and 'Neglect'. The number of the fulfilled pathological gambling criteria and the severity of current global psychopathology differed between the ACE profiles: Gamblers with a 'High ACE' profile fulfilled more pathological gambling criteria and showed a more severe current psychopathology than gamblers of the 'Low ACE' profile. Gamblers with a 'Physical and emotional abuse' or an 'Emotion neglect' profile showed an intermediate severity of psychopathology. Our findings indicate that four different ACE profiles can be distinguished in pathological gamblers that differed in their gambling-related characteristics and current psychopathology. Systematic assessment of profiles of ACEs in pathological gamblers may inform about the severity of current global psychopathology that might be important to be addressed in addition to gambling-specific treatment. Copyright © 2018 Elsevier Ltd. All rights reserved.

Profiling of the injected charge drift current transients by cross-sectional scanning technique

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gaubas, E., E-mail: eugenijus.gaubas@ff.vu.lt; Ceponis, T.; Pavlov, J.

2014-02-07

The electric field distribution and charge drift currents in Si particle detectors are analyzed. Profiling of the injected charge drift current transients has been implemented by varying charge injection position within a cross-sectional boundary of the particle detector. The obtained profiles of the induction current density and duration of the injected charge drift pulses fit well the simulated current variations. Induction current transients have been interpreted by different stages of the bipolar and monopolar drift of the injected carriers. Profiles of the injected charge current transients registered in the non-irradiated and neutron irradiated Si diodes are compared. It has beenmore » shown that the mixed regime of the competing processes of drift, recombination, and diffusion appears in the measured current profiles on the irradiated samples. The impact of the avalanche effects can be ignored based on the investigations presented. It has been shown that even a simplified dynamic model enabled us to reproduce the main features of the profiled transients of induced charge drift current.« less

Isozyme, ISSR and RAPD profiling of genotypes in marvel grass (Dichanthium annulatum).

PubMed

Saxena, Raghvendra; Chandra, Amaresh

2010-11-01

Genetic analysis of 30 accessions of marvel grass (Dichanthium annulatum Forsk.), a tropical range grass collected from grasslands and open fields of drier regions, was carried out with the objectives of identifying unique materials that could be used in developing the core germplasm for such regions as well as to explore gene (s) for drought tolerance. Five inter-simple sequence repeat (ISSR) primers [(CA)4, (AGAC), (GACA) 4; 27 random amplified polymorphic DNA (RAPD) and four enzyme systems were employed in the present study. In total, ISSR yielded 61 (52 polymorphic), RAPD 269 (253 polymorphic) and enzyme 55 isozymes (44 polymorphic) bands. The average polymorphic information content (PIC) and marker index (MI) across all polymorphic bands of 3 markers systems ranged from 0.419 to 0.480 and 4.34 to 5.25 respectively Dendrogram analysis revealed three main clusters with all three markers. Four enzymes namely esterase (EST), polyphenoloxidase (PPO), peroxidase (PRX) and superoxide dismutase (SOD) revealed 55 alleles from a total of 16 enzyme-coding loci. Of these, 14 loci and 44 alleles were polymorphic. The mean number of alleles per locus was 3.43. Mean heterozygosity observed among the polymorphic loci ranged from 0.406 (SOD) to 0.836 (EST) and accession wise from 0.679 (1G3108) to 0.743 (IGKMD-10). Though there was intermixing of few accessions of one agro-climatic region to another largely groupings of accessions were with their regions of collections. Bootstrap analysis at 1000 iterations also showed large numbers of nodes (11 to 17) having strong clustering (> 50 bootstrap values) in all three marker systems. The accessions of the arid and drier regions forming one cluster are assigned as distinct core collection of Dichanthium and can be targeted for isolation of gene (s) for drought tolerance. Variations in isozyme allele numbers and high PIC (0.48) and MI (4.98) as observed with ISSR markers indicated their usefulness for germplasm characterization.

Development of population pharmacokinetics model of icotinib with non-linear absorption characters in healthy Chinese volunteers to assess the CYP2C19 polymorphism and food-intake effect.

PubMed

Hu, Pei; Chen, Jia; Liu, Dongyang; Zheng, Xin; Zhao, Qian; Jiang, Ji

2015-07-01

Icotinib is a potent and selective inhibitor of epidermal growth factor receptors (EGFR) approved to treat non-small cell lung cancer (NSCLC). However, its high variability may impede its application. The objectives of this analysis were to assess plasma pharmacokinetics and identify covariates that may explain variability in icotinib absorption and/or disposition following single dose of icotinib in healthy volunteers. Data from two clinical studies (n = 22) were analyzed. One study was designed as three-period and Latin-squared (six sequence) trial to evaluate dose proportionality, and the other one was designed as two-way crossover trial to evaluate food effect on pharmacokinetics (PK) characters. Icotinib concentrations in plasma were analyzed using non-linear mixed-effects model (NONMEM) method. The model was used to assess influence of food, demographic characteristics, measurements of blood biochemistry, and CYP2C19 genotype on PK characters of icotinib in humans. The final model was diagnosed by goodness-of-fit plots and evaluated by visual predictive check (VPC) and bootstrap methods. A two-compartment model with saturated absorption character was developed to capture icotinib pharmacokinetics. Typical value of clearance, distribution clearance, central volume of distribution, maximum absorption rate were 29.5 L/h, 24.9 L/h, 18.5 L, 122.2 L and 204,245 μg/h, respectively. When icotinib was administrated with food, bioavailability was estimated to be increased by 48%. Inter-occasion variability was identified to affect on maximum absorption rate constant in food-effect study. CL was identified to be significantly influenced by age, albumin concentration (ALB), and CYP2C19 genotype. No obvious bias was found by VPC and bootstrap methods. The developed model can capture icotinib pharmacokinetics well in healthy volunteers. Food intake can increase icotinib exposure. Three covariates, age, albumin concentration, and CYP2C19 genotype, were identified to significantly affect icotinib PK profiles in healthy subjects.

Why do workaholics experience depression? A study with Chinese University teachers.

PubMed

Nie, Yingzhi; Sun, Haitao

2016-10-01

This study focuses on the relationships of workaholism to job burnout and depression of university teachers. The direct and indirect (via job burnout) effects of workaholism on depression were investigated in 412 Chinese university teachers. Structural equation modeling and bootstrap method were used. Results revealed that workaholism, job burnout, and depression significantly correlated with each other. Structural equation modeling and bootstrap test indicated the partial mediation role of job burnout on the relationship between workaholism and depression. The findings shed some light on how workaholism influenced depression and provided valuable evidence for prevention of depression in work. © The Author(s) 2015.

Governance and performance: the performance of Dutch hospitals explained by governance characteristics.

PubMed

Blank, Jos L T; van Hulst, Bart Laurents

2011-10-01

This paper describes the efficiency of Dutch hospitals using the Data Envelopment Analysis (DEA) method with bootstrapping. In particular, the analysis focuses on accounting for cost inefficiency measures on the part of hospital corporate governance. We use bootstrap techniques, as introduced by Simar and Wilson (J. Econom. 136(1):31-64, 2007), in order to obtain more efficient estimates of the effects of governance on the efficiency. The results show that part of the cost efficiency can be explained with governance. In particular we find that a higher remuneration of the board as well as a higher remuneration of the supervisory board does not implicate better performance.

Construction of prediction intervals for Palmer Drought Severity Index using bootstrap

NASA Astrophysics Data System (ADS)

Beyaztas, Ufuk; Bickici Arikan, Bugrayhan; Beyaztas, Beste Hamiye; Kahya, Ercan

2018-04-01

In this study, we propose an approach based on the residual-based bootstrap method to obtain valid prediction intervals using monthly, short-term (three-months) and mid-term (six-months) drought observations. The effects of North Atlantic and Arctic Oscillation indexes on the constructed prediction intervals are also examined. Performance of the proposed approach is evaluated for the Palmer Drought Severity Index (PDSI) obtained from Konya closed basin located in Central Anatolia, Turkey. The finite sample properties of the proposed method are further illustrated by an extensive simulation study. Our results revealed that the proposed approach is capable of producing valid prediction intervals for future PDSI values.

Differentiation of Trypanosoma cruzi I subgroups through characterization of cytochrome b gene sequences.

PubMed

Spotorno O, Angel E; Córdova, Luis; Solari I, Aldo

2008-12-01

To identify and characterize chilean samples of Trypanosoma cruzi and their association with hosts, the first 516 bp of the mitochondrial cytochrome b gene were sequenced from eight biological samples, and phylogenetically compared with other known 20 American sequences. The molecular characterization of these 28 sequences in a maximum likelihood phylogram (-lnL = 1255.12, tree length = 180, consistency index = 0.79) allowed the robust identification (bootstrap % > 99) of three previously known discrete typing units (DTU): DTU IIb, IIa, and I. An apparently undescribed new sequence found in four new chilean samples was detected and designated as DTU Ib; they were separated by 24.7 differences, but robustly related (bootstrap % = 97 in 500 replicates) to those of DTU I by sharing 12 substitutions, among which four were nonsynonymous ones. Such new DTU Ib was also robust (bootstrap % = 100), and characterized by 10 unambiguous substitutions, with a single nonsynonymous G to T change at site 409. The fact that two of such new sequences were found in parasites from a chilean endemic caviomorph rodent, Octodon degus, and that they were closely related to the ancient DTU I suggested old origins and a long association to caviomorph hosts.

A safe an easy method for building consensus HIV sequences from 454 massively parallel sequencing data.

PubMed

Fernández-Caballero Rico, Jose Ángel; Chueca Porcuna, Natalia; Álvarez Estévez, Marta; Mosquera Gutiérrez, María Del Mar; Marcos Maeso, María Ángeles; García, Federico

2018-02-01

To show how to generate a consensus sequence from the information of massive parallel sequences data obtained from routine HIV anti-retroviral resistance studies, and that may be suitable for molecular epidemiology studies. Paired Sanger (Trugene-Siemens) and next-generation sequencing (NGS) (454 GSJunior-Roche) HIV RT and protease sequences from 62 patients were studied. NGS consensus sequences were generated using Mesquite, using 10%, 15%, and 20% thresholds. Molecular evolutionary genetics analysis (MEGA) was used for phylogenetic studies. At a 10% threshold, NGS-Sanger sequences from 17/62 patients were phylogenetically related, with a median bootstrap-value of 88% (IQR83.5-95.5). Association increased to 36/62 sequences, median bootstrap 94% (IQR85.5-98)], using a 15% threshold. Maximum association was at the 20% threshold, with 61/62 sequences associated, and a median bootstrap value of 99% (IQR98-100). A safe method is presented to generate consensus sequences from HIV-NGS data at 20% threshold, which will prove useful for molecular epidemiological studies. Copyright © 2016 Elsevier España, S.L.U. and Sociedad Española de Enfermedades Infecciosas y Microbiología Clínica. All rights reserved.

The relationship between the number of loci and the statistical support for the topology of UPGMA trees obtained from genetic distance data.

PubMed

Highton, R

1993-12-01

An analysis of the relationship between the number of loci utilized in an electrophoretic study of genetic relationships and the statistical support for the topology of UPGMA trees is reported for two published data sets. These are Highton and Larson (Syst. Zool.28:579-599, 1979), an analysis of the relationships of 28 species of plethodonine salamanders, and Hedges (Syst. Zool., 35:1-21, 1986), a similar study of 30 taxa of Holarctic hylid frogs. As the number of loci increases, the statistical support for the topology at each node in UPGMA trees was determined by both the bootstrap and jackknife methods. The results show that the bootstrap and jackknife probabilities supporting the topology at some nodes of UPGMA trees increase as the number of loci utilized in a study is increased, as expected for nodes that have groupings that reflect phylogenetic relationships. The pattern of increase varies and is especially rapid in the case of groups with no close relatives. At nodes that likely do not represent correct phylogenetic relationships, the bootstrap probabilities do not increase and often decline with the addition of more loci.

Comparison of mode estimation methods and application in molecular clock analysis

NASA Technical Reports Server (NTRS)

Hedges, S. Blair; Shah, Prachi

2003-01-01

BACKGROUND: Distributions of time estimates in molecular clock studies are sometimes skewed or contain outliers. In those cases, the mode is a better estimator of the overall time of divergence than the mean or median. However, different methods are available for estimating the mode. We compared these methods in simulations to determine their strengths and weaknesses and further assessed their performance when applied to real data sets from a molecular clock study. RESULTS: We found that the half-range mode and robust parametric mode methods have a lower bias than other mode methods under a diversity of conditions. However, the half-range mode suffers from a relatively high variance and the robust parametric mode is more susceptible to bias by outliers. We determined that bootstrapping reduces the variance of both mode estimators. Application of the different methods to real data sets yielded results that were concordant with the simulations. CONCLUSION: Because the half-range mode is a simple and fast method, and produced less bias overall in our simulations, we recommend the bootstrapped version of it as a general-purpose mode estimator and suggest a bootstrap method for obtaining the standard error and 95% confidence interval of the mode.

Bootstrap percolation on spatial networks

NASA Astrophysics Data System (ADS)

Gao, Jian; Zhou, Tao; Hu, Yanqing

2015-10-01

Bootstrap percolation is a general representation of some networked activation process, which has found applications in explaining many important social phenomena, such as the propagation of information. Inspired by some recent findings on spatial structure of online social networks, here we study bootstrap percolation on undirected spatial networks, with the probability density function of long-range links’ lengths being a power law with tunable exponent. Setting the size of the giant active component as the order parameter, we find a parameter-dependent critical value for the power-law exponent, above which there is a double phase transition, mixed of a second-order phase transition and a hybrid phase transition with two varying critical points, otherwise there is only a second-order phase transition. We further find a parameter-independent critical value around -1, about which the two critical points for the double phase transition are almost constant. To our surprise, this critical value -1 is just equal or very close to the values of many real online social networks, including LiveJournal, HP Labs email network, Belgian mobile phone network, etc. This work helps us in better understanding the self-organization of spatial structure of online social networks, in terms of the effective function for information spreading.

A resampling strategy based on bootstrap to reduce the effect of large blunders in GPS absolute positioning

NASA Astrophysics Data System (ADS)

Angrisano, Antonio; Maratea, Antonio; Gaglione, Salvatore

2018-01-01

In the absence of obstacles, a GPS device is generally able to provide continuous and accurate estimates of position, while in urban scenarios buildings can generate multipath and echo-only phenomena that severely affect the continuity and the accuracy of the provided estimates. Receiver autonomous integrity monitoring (RAIM) techniques are able to reduce the negative consequences of large blunders in urban scenarios, but require both a good redundancy and a low contamination to be effective. In this paper a resampling strategy based on bootstrap is proposed as an alternative to RAIM, in order to estimate accurately position in case of low redundancy and multiple blunders: starting with the pseudorange measurement model, at each epoch the available measurements are bootstrapped—that is random sampled with replacement—and the generated a posteriori empirical distribution is exploited to derive the final position. Compared to standard bootstrap, in this paper the sampling probabilities are not uniform, but vary according to an indicator of the measurement quality. The proposed method has been compared with two different RAIM techniques on a data set collected in critical conditions, resulting in a clear improvement on all considered figures of merit.

Reanalysis of cancer mortality in Japanese A-bomb survivors exposed to low doses of radiation: bootstrap and simulation methods

PubMed Central

2009-01-01

Background The International Commission on Radiological Protection (ICRP) recommended annual occupational dose limit is 20 mSv. Cancer mortality in Japanese A-bomb survivors exposed to less than 20 mSv external radiation in 1945 was analysed previously, using a latency model with non-linear dose response. Questions were raised regarding statistical inference with this model. Methods Cancers with over 100 deaths in the 0 - 20 mSv subcohort of the 1950-1990 Life Span Study are analysed with Poisson regression models incorporating latency, allowing linear and non-linear dose response. Bootstrap percentile and Bias-corrected accelerated (BCa) methods and simulation of the Likelihood Ratio Test lead to Confidence Intervals for Excess Relative Risk (ERR) and tests against the linear model. Results The linear model shows significant large, positive values of ERR for liver and urinary cancers at latencies from 37 - 43 years. Dose response below 20 mSv is strongly non-linear at the optimal latencies for the stomach (11.89 years), liver (36.9), lung (13.6), leukaemia (23.66), and pancreas (11.86) and across broad latency ranges. Confidence Intervals for ERR are comparable using Bootstrap and Likelihood Ratio Test methods and BCa 95% Confidence Intervals are strictly positive across latency ranges for all 5 cancers. Similar risk estimates for 10 mSv (lagged dose) are obtained from the 0 - 20 mSv and 5 - 500 mSv data for the stomach, liver, lung and leukaemia. Dose response for the latter 3 cancers is significantly non-linear in the 5 - 500 mSv range. Conclusion Liver and urinary cancer mortality risk is significantly raised using a latency model with linear dose response. A non-linear model is strongly superior for the stomach, liver, lung, pancreas and leukaemia. Bootstrap and Likelihood-based confidence intervals are broadly comparable and ERR is strictly positive by bootstrap methods for all 5 cancers. Except for the pancreas, similar estimates of latency and risk from 10 mSv are obtained from the 0 - 20 mSv and 5 - 500 mSv subcohorts. Large and significant cancer risks for Japanese survivors exposed to less than 20 mSv external radiation from the atomic bombs in 1945 cast doubt on the ICRP recommended annual occupational dose limit. PMID:20003238

The pharmacokinetics of propofol in ICU patients undergoing long-term sedation.

PubMed

Smuszkiewicz, Piotr; Wiczling, Paweł; Przybyłowski, Krzysztof; Borsuk, Agnieszka; Trojanowska, Iwona; Paterska, Marta; Matysiak, Jan; Kokot, Zenon; Grześkowiak, Edmund; Bienert, Agnieszka

2016-11-01

The aim of this study was to characterize the pharmacokinetics (PK) of propofol in ICU patients undergoing long-term sedation and to assess the influence of routinely collected covariates on the PK parameters. Propofol concentration-time profiles were collected from 29 patients. Non-linear mixed-effects modelling in NONMEM 7.2 was used to analyse the observed data. The propofol pharmacokinetics was best described with a three-compartment disposition model. Non-parametric bootstrap and a visual predictive check were used to evaluate the adequacy of the developed model to describe the observations. The typical value of the propofol clearance (1.46 l/min) approximated the hepatic blood flow. The volume of distribution at steady state was high and was equal to 955.1 l, which is consistent with other studies involving propofol in ICU patients. There was no statistically significant covariate relationship between PK parameters and opioid type, SOFA score on the day of admission, APACHE II, predicted death rate, reason for ICU admission (sepsis, trauma or surgery), gender, body weight, age, infusion duration and C-reactive protein concentration. The population PK model was developed successfully to describe the time-course of propofol concentration in ICU patients undergoing prolonged sedation. Despite a very heterogeneous group of patients, consistent PK profiles were observed. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

RF current profile control studies in the alcator C-mod tokamak

NASA Astrophysics Data System (ADS)

Bonoli, P. T.; Porkolab, M.; Wukitch, S. J.; Bernabei, S.; Kaita, R.; Mikkelsen, D.; Phillips, C. K.; Schilling, G.

1999-09-01

Time dependent calculations of lower hybrid (LH) current profile control in Alcator C-Mod have been done using the TRANSP [1], FPPRF [2], and LSC [3] codes. Up to 3 MW of LH current drive power was applied in plasmas with high power ICRF minority heating (PICH=1.8-3 MW) and fast current ramp up. Using the experimentally measured temperature profiles, off-axis current generation resulted in nonmonotonic q-profiles with qmin~=1.6. Self-consistent effects of off-axis electron heating by the LH power were also included in the analysis and significant broadening of the electron temperature profile was found with qmin>~2 and a larger shear reversal radius.

Emotion dysregulation as a mediator between childhood emotional abuse and current depression in a low-income African-American sample.

PubMed

Crow, Thomas; Cross, Dorthie; Powers, Abigail; Bradley, Bekh

2014-10-01

Abuse and neglect in childhood are well-established risk factors for later psychopathology. Past research has suggested that childhood emotional abuse may be particularly harmful to psychological development. The current cross-sectional study employed multiple regression techniques to assess the effects of childhood trauma on adulthood depression and emotion dysregulation in a large sample of mostly low-income African Americans recruited in an urban hospital. Bootstrap analyses were used to test emotion dysregulation as a potential mediator between emotional abuse in childhood and current depression. Childhood emotional abuse significantly predicted depressive symptoms even when accounting for all other childhood trauma types, and we found support for a complementary mediation of this relationship by emotion dysregulation. Our findings highlight the importance of emotion dysregulation and childhood emotional abuse in relation to adult depression. Moving forward, clinicians should consider the particular importance of emotional abuse in the development of depression, and future research should seek to identify mechanisms through which emotional abuse increases risk for depression and emotion dysregulation. Copyright © 2014 Elsevier Ltd. All rights reserved.

Emotion dysregulation as a mediator between childhood emotional abuse and current depression in a low-income African-American sample☆

PubMed Central

Crow, Thomas; Cross, Dorthie; Powers, Abigail; Bradley, Bekh

2014-01-01

Abuse and neglect in childhood are well-established risk factors for later psychopathology. Past research has suggested that childhood emotional abuse may be particularly harmful to psychological development. The current cross-sectional study employed multiple regression techniques to assess the effects of childhood trauma on adulthood depression and emotion dysregulation in a large sample of mostly low-income African Americans recruited in an urban hospital. Bootstrap analyses were used to test emotion dysregulation as a potential mediator between emotional abuse in childhood and current depression. Childhood emotional abuse significantly predicted depressive symptoms even when accounting for all other childhood trauma types, and we found support for a complementary mediation of this relationship by emotion dysregulation. Our findings highlight the importance of emotion dysregulation and childhood emotional abuse in relation to adult depression. Moving forward, clinicians should consider the particular importance of emotional abuse in the development of depression, and future research should seek to identify mechanisms through which emotional abuse increases risk for depression and emotion dysregulation. PMID:25035171

Plasma stability analysis using Consistent Automatic Kinetic Equilibrium reconstruction (CAKE)

NASA Astrophysics Data System (ADS)

Roelofs, Matthijs; Kolemen, Egemen; Eldon, David; Glasser, Alex; Meneghini, Orso; Smith, Sterling P.

2017-10-01

Presented here is the Consistent Automatic Kinetic Equilibrium (CAKE) code. CAKE is being developed to perform real-time kinetic equilibrium reconstruction, aiming to do a reconstruction in less than 100ms. This is achieved by taking, next to real-time Motional Stark Effect (MSE) and magnetics data, real-time Thomson Scattering (TS) and real-time Charge Exchange Recombination (CER, still in development) data in to account. Electron densities and temperature are determined by TS, while ion density and pressures are determined using CER. These form, together with the temperature and density of neutrals, the additional pressure constraints. Extra current constraints are imposed in the core by the MSE diagnostics. The pedestal current density is estimated using Sauters equation for the bootstrap current density. By comparing the behaviour of the ideal MHD perturbed potential energy (δW) and the linear stability index (Δ') of CAKE to magnetics-only reconstruction, it can be seen that the use of diagnostics to reconstruct the pedestal have a large effect on stability. Supported by U.S. DOE DE-SC0015878 and DE-FC02-04ER54698.

Nonlinear Fluid Model Of 3-D Field Effects In Tokamak Plasmas

NASA Astrophysics Data System (ADS)

Callen, J. D.; Hegna, C. C.; Beidler, M. T.

2017-10-01

Extended MHD codes (e.g., NIMROD, M3D-C1) are beginning to explore nonlinear effects of small 3-D magnetic fields on tokamak plasmas. To facilitate development of analogous physically understandable reduced models, a fluid-based dynamic nonlinear model of these added 3-D field effects in the base axisymmetric tokamak magnetic field geometry is being developed. The model incorporates kinetic-based closures within an extended MHD framework. Key 3-D field effects models that have been developed include: 1) a comprehensive modified Rutherford equation for the growth of a magnetic island that includes the classical tearing and NTM perturbed bootstrap current drives, externally applied magnetic field and current drives, and classical and neoclassical polarization current effects, and 2) dynamic nonlinear evolution of the plasma toroidal flow (radial electric field) in response to the 3-D fields. An application of this model to RMP ELM suppression precipitated by an ELM crash will be discussed. Supported by Office of Fusion Energy Sciences, Office of Science, Dept. of Energy Grants DE-FG02-86ER53218 and DE-FG02-92ER54139.

Improved Design of Stellarator Coils for Current Carrying Plasmas

NASA Astrophysics Data System (ADS)

Drevlak, M.; Strumberger, E.; Hirshman, S.; Boozer, A.; Brooks, A.; Valanju, P.

1998-11-01

The method of automatic optimization (P. Merkel, Nucl. Fus. 27), (1987) 867; P. Merkel, M. Drevlak, Proc 25th EPS Conf. on Cont. Fus. and Plas. Phys., Prague, in print. for the design of stellarator coils consists essentially of determining filaments such that the average relative field error int dS [ (B_coil + B_j) \\cdot n]^2/B^2_coil is minimized on the prescribed plasma boundary. Bj is the magnetic field produced by the plasma currents of the given finite β fixed boundary equilibrium. For equilibria of the W7-X type, Bj can be neglected, because of the reduced parallel plasma currents. This is not true for quasi-axisymmetric stellarator (QAS) configurations (A. Reiman, et al., to be published.) with large equilibrium and net plasma (bootstrap) currents. Although the coils for QAS exhibit low values of the field error, free boundary calculations indicate that the shape of the plasma is usually not accurately reproduced , particularly when saddle coils are used. We investigate if the surface reconstruction can be improved by introducing a modified measure of the field error based on a measure of the resonant components of the normal field.

Attachment and alcohol use amongst athletes: the mediating role of conscientiousness and alexithymia.

PubMed

Andres, Fanny; Castanier, Carole; Le Scanff, Christine

2014-02-01

The present study aims to explore the mediating effects of conscientiousness and alexithymia in the relationship between parental attachment style and alcohol use in a large sample of athletic young people. Participants included 434 French sport sciences students. Alcohol use, parental attachment style, conscientiousness and alexithymia were assessed. The hypotheses were tested by using regression and bootstrapping mediation analyses. Maternal insecure attachment style is positively associated with alcohol use. The current study highlights a multiple pathway in this relationship. The results reveal the mediating effect of low conscientiousness and alexithymia between maternal insecure attachment and alcohol use. Athletes' alcohol use seems to be the result of a complex association of underlying psychological factors. © 2013.

Modifications to the edge current profile with auxiliary edge current drive and improved confinement in a reversed-field pinch

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chapman, B.E.; Biewer, T.M.; Chattopadhyay, P.K.

2000-09-01

Auxiliary edge current drive is routinely applied in the Madison Symmetric Torus [R.N. Dexter, D. W. Kerst, T.W. Lovell et.al., Fusion Technol. 19, 131 (1991)] with the goal of modifying the parallel current profile to reduce current- driven magnetic fluctuations and the associated particle and energy transport. Provided by an inductive electric field, the current drive successfully reduces energy transport. First-time measurements of the modified edge current profile reveal that, relative to discharges without auxiliary current drive, the edge current density decreases. This decrease is explicable in terms of newly measured reductions in the dynamo (fluctuation-based) electric field and themore » electrical conductivity. Induced by the current drive, these two changes to the edge plasma play as much of a role in determining the resultant edge current profile as does the current drive itself.« less

Method-independent, Computationally Frugal Convergence Testing for Sensitivity Analysis Techniques

NASA Astrophysics Data System (ADS)

Mai, Juliane; Tolson, Bryan

2017-04-01

The increasing complexity and runtime of environmental models lead to the current situation that the calibration of all model parameters or the estimation of all of their uncertainty is often computationally infeasible. Hence, techniques to determine the sensitivity of model parameters are used to identify most important parameters or model processes. All subsequent model calibrations or uncertainty estimation procedures focus then only on these subsets of parameters and are hence less computational demanding. While the examination of the convergence of calibration and uncertainty methods is state-of-the-art, the convergence of the sensitivity methods is usually not checked. If any, bootstrapping of the sensitivity results is used to determine the reliability of the estimated indexes. Bootstrapping, however, might as well become computationally expensive in case of large model outputs and a high number of bootstraps. We, therefore, present a Model Variable Augmentation (MVA) approach to check the convergence of sensitivity indexes without performing any additional model run. This technique is method- and model-independent. It can be applied either during the sensitivity analysis (SA) or afterwards. The latter case enables the checking of already processed sensitivity indexes. To demonstrate the method independency of the convergence testing method, we applied it to three widely used, global SA methods: the screening method known as Morris method or Elementary Effects (Morris 1991, Campolongo et al., 2000), the variance-based Sobol' method (Solbol' 1993, Saltelli et al. 2010) and a derivative-based method known as Parameter Importance index (Goehler et al. 2013). The new convergence testing method is first scrutinized using 12 analytical benchmark functions (Cuntz & Mai et al. 2015) where the true indexes of aforementioned three methods are known. This proof of principle shows that the method reliably determines the uncertainty of the SA results when different budgets are used for the SA. Subsequently, we focus on the model-independency by testing the frugal method using the hydrologic model mHM (www.ufz.de/mhm) with about 50 model parameters. The results show that the new frugal method is able to test the convergence and therefore the reliability of SA results in an efficient way. The appealing feature of this new technique is the necessity of no further model evaluation and therefore enables checking of already processed (and published) sensitivity results. This is one step towards reliable and transferable, published sensitivity results.

Performance Assessment of Model-Based Optimal Feedforward and Feedback Current Profile Control in NSTX-U using the TRANSP Code

NASA Astrophysics Data System (ADS)

Ilhan, Z.; Wehner, W. P.; Schuster, E.; Boyer, M. D.; Gates, D. A.; Gerhardt, S.; Menard, J.

2015-11-01

Active control of the toroidal current density profile is crucial to achieve and maintain high-performance, MHD-stable plasma operation in NSTX-U. A first-principles-driven, control-oriented model describing the temporal evolution of the current profile has been proposed earlier by combining the magnetic diffusion equation with empirical correlations obtained at NSTX-U for the electron density, electron temperature, and non-inductive current drives. A feedforward + feedback control scheme for the requlation of the current profile is constructed by embedding the proposed nonlinear, physics-based model into the control design process. Firstly, nonlinear optimization techniques are used to design feedforward actuator trajectories that steer the plasma to a desired operating state with the objective of supporting the traditional trial-and-error experimental process of advanced scenario planning. Secondly, a feedback control algorithm to track a desired current profile evolution is developed with the goal of adding robustness to the overall control scheme. The effectiveness of the combined feedforward + feedback control algorithm for current profile regulation is tested in predictive simulations carried out in TRANSP. Supported by PPPL.

Correlation of ion and beam current densities in Kaufman thrusters.

NASA Technical Reports Server (NTRS)

Wilbur, P. J.

1973-01-01

In the absence of direct impingement erosion, electrostatic thruster accelerator grid lifetime is defined by the charge exchange erosion that occurs at peak values of the ion beam current density. In order to maximize the thrust from an engine with a specified grid lifetime, the ion beam current density profile should therefore be as flat as possible. Knauer (1970) has suggested this can be achieved by establishing a radial plasma uniformity within the thruster discharge chamber; his tests with the radial field thruster provide an example of uniform plasma properties within the chamber and a flat ion beam profile occurring together. It is shown that, in particular, the ion density profile within the chamber determines the beam current density profile, and that a uniform ion density profile at the screen grid end of the discharge chamber should lead to a flat beam current density profile.

Integrated Scenario Modeling of NSTX Advanced Plasma Configurations

NASA Astrophysics Data System (ADS)

Kessel, Charles; Synakowski, Edward

2003-10-01

The Spherical Torus will provide an attractive fusion energy source if it can demonstrate the following major features: high elongation and triangularity, 100% non-inductive current with a credible path to high bootstrap fractions, non-solenoidal startup and current rampup, high beta with stabilization of RWM instabilities, and sufficiently high energy confinement. NSTX has specific experimental milestones to examine these features, and integrated scenario modeling is helping to understand how these configurations might be produced and what tools are needed to access this operating space. Simulations with the Tokamak Simulation Code (TSC), CURRAY, and JSOLVER/BALMSC/PEST2 have identified fully non-inductively sustained, high beta plasmas that rely on strong plasma shaping accomplished with a PF coil modification, off-axis current drive from Electron Bernstein Waves (EBW), flexible on-axis heating and CD from High Harmonic Fast Wave (HHFW) and Neutral Beam Injection (NBI), and density control. Ideal MHD stability shows that with wall stabilization through plasma rotation and/or RWM feedback coils, a beta of 40% is achievable, with 100% non-inductive current sustained for 4 current diffusion times. Experimental data and theory are combined to produce a best extrapolation to these regimes, which is continuously improved as the discharges approach these parameters, and theoretical/computational methods expand. Further investigations and development for integrated scenario modeling on NSTX is discussed.

Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees.

PubMed

Kück, Patrick; Meusemann, Karen; Dambach, Johannes; Thormann, Birthe; von Reumont, Björn M; Wägele, Johann W; Misof, Bernhard

2010-03-31

Methods of alignment masking, which refers to the technique of excluding alignment blocks prior to tree reconstructions, have been successful in improving the signal-to-noise ratio in sequence alignments. However, the lack of formally well defined methods to identify randomness in sequence alignments has prevented a routine application of alignment masking. In this study, we compared the effects on tree reconstructions of the most commonly used profiling method (GBLOCKS) which uses a predefined set of rules in combination with alignment masking, with a new profiling approach (ALISCORE) based on Monte Carlo resampling within a sliding window, using different data sets and alignment methods. While the GBLOCKS approach excludes variable sections above a certain threshold which choice is left arbitrary, the ALISCORE algorithm is free of a priori rating of parameter space and therefore more objective. ALISCORE was successfully extended to amino acids using a proportional model and empirical substitution matrices to score randomness in multiple sequence alignments. A complex bootstrap resampling leads to an even distribution of scores of randomly similar sequences to assess randomness of the observed sequence similarity. Testing performance on real data, both masking methods, GBLOCKS and ALISCORE, helped to improve tree resolution. The sliding window approach was less sensitive to different alignments of identical data sets and performed equally well on all data sets. Concurrently, ALISCORE is capable of dealing with different substitution patterns and heterogeneous base composition. ALISCORE and the most relaxed GBLOCKS gap parameter setting performed best on all data sets. Correspondingly, Neighbor-Net analyses showed the most decrease in conflict. Alignment masking improves signal-to-noise ratio in multiple sequence alignments prior to phylogenetic reconstruction. Given the robust performance of alignment profiling, alignment masking should routinely be used to improve tree reconstructions. Parametric methods of alignment profiling can be easily extended to more complex likelihood based models of sequence evolution which opens the possibility of further improvements.

Neural network evaluation of tokamak current profiles for real time control

NASA Astrophysics Data System (ADS)

Wróblewski, Dariusz

1997-02-01

Active feedback control of the current profile, requiring real-time determination of the current profile parameters, is envisioned for tokamaks operating in enhanced confinement regimes. The distribution of toroidal current in a tokamak is now routinely evaluated based on external (magnetic probes, flux loops) and internal (motional Stark effect) measurements of the poloidal magnetic field. However, the analysis involves reconstruction of magnetohydrodynamic equilibrium and is too intensive computationally to be performed in real time. In the present study, a neural network is used to provide a mapping from the magnetic measurements (internal and external) to selected parameters of the safety factor profile. The single-pass, feedforward calculation of output of a trained neural network is very fast, making this approach particularly suitable for real-time applications. The network was trained on a large set of simulated equilibrium data for the DIII-D tokamak. The database encompasses a large variety of current profiles including the hollow current profiles important for reversed central shear operation. The parameters of safety factor profile (a quantity related to the current profile through the magnetic field tilt angle) estimated by the neural network include central safety factor, q0, minimum value of q, qmin, and the location of qmin. Very good performance of the trained neural network both for simulated test data and for experimental datais demonstrated.

Neural network evaluation of tokamak current profiles for real time control (abstract)

NASA Astrophysics Data System (ADS)

Wróblewski, Dariusz

1997-01-01

Active feedback control of the current profile, requiring real-time determination of the current profile parameters, is envisioned for tokamaks operating in enhanced confinement regimes. The distribution of toroidal current in a tokamak is now routinely evaluated based on external (magnetic probes, flux loops) and internal (motional Stark effect) measurements of the poloidal magnetic field. However, the analysis involves reconstruction of magnetohydrodynamic equilibrium and is too intensive computationally to be performed in real time. In the present study, a neural network is used to provide a mapping from the magnetic measurements (internal and external) to selected parameters of the safety factor profile. The single-pass, feedforward calculation of output of a trained neural network is very fast, making this approach particularly suitable for real-time applications. The network was trained on a large set of simulated equilibrium data for the DIII-D tokamak. The database encompasses a large variety of current profiles including the hollow current profiles important for reversed central shear operation. The parameters of safety factor profile (a quantity related to the current profile through the magnetic field tilt angle) estimated by the neural network include central safety factor, q0, minimum value of q, qmin, and the location of qmin. Very good performance of the trained neural network both for simulated test data and for experimental data is demonstrated.

The use of generalised additive models (GAM) in dentistry.

PubMed

Helfenstein, U; Steiner, M; Menghini, G

1997-12-01

Ordinary multiple regression and logistic multiple regression are widely applied statistical methods which allow a researcher to 'explain' or 'predict' a response variable from a set of explanatory variables or predictors. In these models it is usually assumed that quantitative predictors such as age enter linearly into the model. During recent years these methods have been further developed to allow more flexibility in the way explanatory variables 'act' on a response variable. The methods are called 'generalised additive models' (GAM). The rigid linear terms characterising the association between response and predictors are replaced in an optimal way by flexible curved functions of the predictors (the 'profiles'). Plotting the 'profiles' allows the researcher to visualise easily the shape by which predictors 'act' over the whole range of values. The method facilitates detection of particular shapes such as 'bumps', 'U-shapes', 'J-shapes, 'threshold values' etc. Information about the shape of the association is not revealed by traditional methods. The shapes of the profiles may be checked by performing a Monte Carlo simulation ('bootstrapping'). After the presentation of the GAM a relevant case study is presented in order to demonstrate application and use of the method. The dependence of caries in primary teeth on a set of explanatory variables is investigated. Since GAMs may not be easily accessible to dentists, this article presents them in an introductory condensed form. It was thought that a nonmathematical summary and a worked example might encourage readers to consider the methods described. GAMs may be of great value to dentists in allowing visualisation of the shape by which predictors 'act' and obtaining a better understanding of the complex relationships between predictors and response.

A population pharmacokinetic model of valproic acid in pediatric patients with epilepsy: a non-linear pharmacokinetic model based on protein-binding saturation.

PubMed

Ding, Junjie; Wang, Yi; Lin, Weiwei; Wang, Changlian; Zhao, Limei; Li, Xingang; Zhao, Zhigang; Miao, Liyan; Jiao, Zheng

2015-03-01

Valproic acid (VPA) follows a non-linear pharmacokinetic profile in terms of protein-binding saturation. The total daily dose regarding VPA clearance is a simple power function, which may partially explain the non-linearity of the pharmacokinetic profile; however, it may be confounded by the therapeutic drug monitoring effect. The aim of this study was to develop a population pharmacokinetic model for VPA based on protein-binding saturation in pediatric patients with epilepsy. A total of 1,107 VPA serum trough concentrations at steady state were collected from 902 epileptic pediatric patients aged from 3 weeks to 14 years at three hospitals. The population pharmacokinetic model was developed using NONMEM(®) software. The ability of three candidate models (the simple power exponent model, the dose-dependent maximum effect [DDE] model, and the protein-binding model) to describe the non-linear pharmacokinetic profile of VPA was investigated, and potential covariates were screened using a stepwise approach. Bootstrap, normalized prediction distribution errors and external evaluations from two independent studies were performed to determine the stability and predictive performance of the candidate models. The age-dependent exponent model described the effects of body weight and age on the clearance well. Co-medication with carbamazepine was identified as a significant covariate. The DDE model best fitted the aim of this study, although there were no obvious differences in the predictive performances. The condition number was less than 500, and the precision of the parameter estimates was less than 30 %, indicating stability and validity of the final model. The DDE model successfully described the non-linear pharmacokinetics of VPA. Furthermore, the proposed population pharmacokinetic model of VPA can be used to design rational dosage regimens to achieve desirable serum concentrations.

Observation of instability-induced current redistribution in a spherical-torus plasma.

PubMed

Menard, J E; Bell, R E; Gates, D A; Kaye, S M; LeBlanc, B P; Levinton, F M; Medley, S S; Sabbagh, S A; Stutman, D; Tritz, K; Yuh, H

2006-09-01

A motional Stark effect diagnostic has been utilized to reconstruct the parallel current density profile in a spherical-torus plasma for the first time. The measured current profile compares favorably with neoclassical theory when no large-scale magnetohydrodynamic instabilities are present in the plasma. However, a current profile anomaly is observed during saturated interchange-type instability activity. This apparent anomaly can be explained by redistribution of neutral beam injection current drive and represents the first observation of interchange-type instabilities causing such redistribution. The associated current profile modifications contribute to sustaining the central safety factor above unity for over five resistive diffusion times, and similar processes may contribute to improved operational scenarios proposed for ITER.

Nonlinear mixed effects modelling for the analysis of longitudinal body core temperature data in healthy volunteers.

PubMed

Seng, Kok-Yong; Chen, Ying; Wang, Ting; Ming Chai, Adam Kian; Yuen Fun, David Chiok; Teo, Ya Shi; Sze Tan, Pearl Min; Ang, Wee Hon; Wei Lee, Jason Kai

2016-04-01

Many longitudinal studies have collected serial body core temperature (T c) data to understand thermal work strain of workers under various environmental and operational heat stress environments. This provides the opportunity for the development of mathematical models to analyse and forecast temporal T c changes across populations of subjects. Such models can reduce the need for invasive methods that continuously measure T c. This current work sought to develop a nonlinear mixed effects modelling framework to delineate the dynamic changes of T c and its association with a set of covariates of interest (e.g. heart rate, chest skin temperature), and the structure of the variability of T c in various longitudinal studies. Data to train and evaluate the model were derived from two laboratory investigations involving male soldiers who participated in either a 12 (N  =  18) or 15 km (N  =  16) foot march with varied clothing, load and heat acclimatisation status. Model qualification was conducted using nonparametric bootstrap and cross validation procedures. For cross validation, the trajectory of a new subject's T c was simulated via Bayesian maximum a posteriori estimation when using only the baseline T c or using the baseline T c as well as measured T c at the end of every work (march) phase. The final model described T c versus time profiles using a parametric function with its main parameters modelled as a sigmoid hyperbolic function of the load and/or chest skin temperature. Overall, T c predictions corresponded well with the measured data (root mean square deviation: 0.16 °C), and compared favourably with those provided by two recently published Kalman filter models.

Effect of the relative shift between the electron density and temperature pedestal position on the pedestal stability in JET-ILW and comparison with JET-C

NASA Astrophysics Data System (ADS)

Stefanikova, E.; Frassinetti, L.; Saarelma, S.; Loarte, A.; Nunes, I.; Garzotti, L.; Lomas, P.; Rimini, F.; Drewelow, P.; Kruezi, U.; Lomanowski, B.; de la Luna, E.; Meneses, L.; Peterka, M.; Viola, B.; Giroud, C.; Maggi, C.; contributors, JET

2018-05-01

The electron temperature and density pedestals tend to vary in their relative radial positions, as observed in DIII-D (Beurskens et al 2011 Phys. Plasmas 18 056120) and ASDEX Upgrade (Dunne et al 2017 Plasma Phys. Control. Fusion 59 14017). This so-called relative shift has an impact on the pedestal magnetohydrodynamic (MHD) stability and hence on the pedestal height (Osborne et al 2015 Nucl. Fusion 55 063018). The present work studies the effect of the relative shift on pedestal stability of JET ITER-like wall (JET-ILW) baseline low triangularity (δ) unseeded plasmas, and similar JET-C discharges. As shown in this paper, the increase of the pedestal relative shift is correlated with the reduction of the normalized pressure gradient, therefore playing a strong role in pedestal stability. Furthermore, JET-ILW tends to have a larger relative shift compared to JET carbon wall (JET-C), suggesting a possible role of the plasma facing materials in affecting the density profile location. Experimental results are then compared with stability analysis performed in terms of the peeling-ballooning model and with pedestal predictive model EUROPED (Saarelma et al 2017 Plasma Phys. Control. Fusion). Stability analysis is consistent with the experimental findings, showing an improvement of the pedestal stability, when the relative shift is reduced. This has been ascribed mainly to the increase of the edge bootstrap current, and to minor effects related to the increase of the pedestal pressure gradient and narrowing of the pedestal pressure width. Pedestal predictive model EUROPED shows a qualitative agreement with experiment, especially for low values of the relative shift.

Predicting phenotypes of asthma and eczema with machine learning

PubMed Central

2014-01-01

Background There is increasing recognition that asthma and eczema are heterogeneous diseases. We investigated the predictive ability of a spectrum of machine learning methods to disambiguate clinical sub-groups of asthma, wheeze and eczema, using a large heterogeneous set of attributes in an unselected population. The aim was to identify to what extent such heterogeneous information can be combined to reveal specific clinical manifestations. Methods The study population comprised a cross-sectional sample of adults, and included representatives of the general population enriched by subjects with asthma. Linear and non-linear machine learning methods, from logistic regression to random forests, were fit on a large attribute set including demographic, clinical and laboratory features, genetic profiles and environmental exposures. Outcome of interest were asthma, wheeze and eczema encoded by different operational definitions. Model validation was performed via bootstrapping. Results The study population included 554 adults, 42% male, 38% previous or current smokers. Proportion of asthma, wheeze, and eczema diagnoses was 16.7%, 12.3%, and 21.7%, respectively. Models were fit on 223 non-genetic variables plus 215 single nucleotide polymorphisms. In general, non-linear models achieved higher sensitivity and specificity than other methods, especially for asthma and wheeze, less for eczema, with areas under receiver operating characteristic curve of 84%, 76% and 64%, respectively. Our findings confirm that allergen sensitisation and lung function characterise asthma better in combination than separately. The predictive ability of genetic markers alone is limited. For eczema, new predictors such as bio-impedance were discovered. Conclusions More usefully-complex modelling is the key to a better understanding of disease mechanisms and personalised healthcare: further advances are likely with the incorporation of more factors/attributes and longitudinal measures. PMID:25077568

Stability of DIII-D high-performance, negative central shear discharges

NASA Astrophysics Data System (ADS)

Hanson, J. M.; Berkery, J. W.; Bialek, J.; Clement, M.; Ferron, J. R.; Garofalo, A. M.; Holcomb, C. T.; La Haye, R. J.; Lanctot, M. J.; Luce, T. C.; Navratil, G. A.; Olofsson, K. E. J.; Strait, E. J.; Turco, F.; Turnbull, A. D.

2017-05-01

Tokamak plasma experiments on the DIII-D device (Luxon et al 2005 Fusion Sci. Tech. 48 807) demonstrate high-performance, negative central shear (NCS) equilibria with enhanced stability when the minimum safety factor {{q}\\text{min}} exceeds 2, qualitatively confirming theoretical predictions of favorable stability in the NCS regime. The discharges exhibit good confinement with an L-mode enhancement factor H 89  =  2.5, and are ultimately limited by the ideal-wall external kink stability boundary as predicted by ideal MHD theory, as long as tearing mode (TM) locking events, resistive wall modes (RWMs), and internal kink modes are properly avoided or controlled. Although the discharges exhibit rotating TMs, locking events are avoided as long as a threshold minimum safety factor value {{q}\\text{min}}>2 is maintained. Fast timescale magnetic feedback control ameliorates RWM activity, expanding the stable operating space and allowing access to {β\\text{N}} values approaching the ideal-wall limit. Quickly growing and rotating instabilities consistent with internal kink mode dynamics are encountered when the ideal-wall limit is reached. The RWM events largely occur between the no- and ideal-wall pressure limits predicted by ideal MHD. However, evaluating kinetic contributions to the RWM dispersion relation results in a prediction of passive stability in this regime due to high plasma rotation. In addition, the ideal MHD stability analysis predicts that the ideal-wall limit can be further increased to {β\\text{N}}>4 by broadening the current profile. This path toward improved stability has the potential advantage of being compatible with the bootstrap-dominated equilibria envisioned for advanced tokamak (AT) fusion reactors.

The role of sleep problems in the relationship between peer victimization and antisocial behavior: A five-year longitudinal study.

PubMed

Chang, Ling-Yin; Wu, Wen-Chi; Wu, Chi-Chen; Lin, Linen Nymphas; Yen, Lee-Lan; Chang, Hsing-Yi

2017-01-01

Peer victimization in children and adolescents is a serious public health concern. Growing evidence exists for negative consequences of peer victimization, but research has mostly been short term and little is known about the mechanisms that moderate and mediate the impacts of peer victimization on subsequent antisocial behavior. The current study intended to examine the longitudinal relationship between peer victimization in adolescence and antisocial behavior in young adulthood and to determine whether sleep problems influence this relationship. In total, 2006 adolescents participated in a prospective study from 2009 to 2013. The moderating role of sleep problems was examined by testing the significance of the interaction between peer victimization and sleep problems. The mediating role of sleep problems was tested by using bootstrapping mediational analyses. All analyses were conducted using SAS 9.3 software. We found that peer victimization during adolescence was positively and significantly associated with antisocial behavior in young adulthood (β = 0.10, p < 0.0001). This association was mediated, but not moderated by sleep problems. Specifically, peer victimization first increased levels of sleep problems, which in turn elevated the risk of antisocial behavior (indirect effect: 0.01, 95% bootstrap confidence interval: 0.004, 0.021). These findings imply that sleep problems may operate as a potential mechanism through which peer victimization during adolescence leads to increases in antisocial behavior in young adulthood. Prevention and intervention programs that target sleep problems may yield benefits for decreasing antisocial behavior in adolescents who have been victimized by peers. Copyright © 2016 Elsevier Ltd. All rights reserved.

mBEEF-vdW: Robust fitting of error estimation density functionals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lundgaard, Keld T.; Wellendorff, Jess; Voss, Johannes

Here, we propose a general-purpose semilocal/nonlocal exchange-correlation functional approximation, named mBEEF-vdW. The exchange is a meta generalized gradient approximation, and the correlation is a semilocal and nonlocal mixture, with the Rutgers-Chalmers approximation for van der Waals (vdW) forces. The functional is fitted within the Bayesian error estimation functional (BEEF) framework. We improve the previously used fitting procedures by introducing a robust MM-estimator based loss function, reducing the sensitivity to outliers in the datasets. To more reliably determine the optimal model complexity, we furthermore introduce a generalization of the bootstrap 0.632 estimator with hierarchical bootstrap sampling and geometric mean estimator overmore » the training datasets. Using this estimator, we show that the robust loss function leads to a 10% improvement in the estimated prediction error over the previously used least-squares loss function. The mBEEF-vdW functional is benchmarked against popular density functional approximations over a wide range of datasets relevant for heterogeneous catalysis, including datasets that were not used for its training. Overall, we find that mBEEF-vdW has a higher general accuracy than competing popular functionals, and it is one of the best performing functionals on chemisorption systems, surface energies, lattice constants, and dispersion. We also show the potential-energy curve of graphene on the nickel(111) surface, where mBEEF-vdW matches the experimental binding length. mBEEF-vdW is currently available in gpaw and other density functional theory codes through Libxc, version 3.0.0.« less

mBEEF-vdW: Robust fitting of error estimation density functionals

DOE PAGES

Lundgaard, Keld T.; Wellendorff, Jess; Voss, Johannes; ...

2016-06-15

Here, we propose a general-purpose semilocal/nonlocal exchange-correlation functional approximation, named mBEEF-vdW. The exchange is a meta generalized gradient approximation, and the correlation is a semilocal and nonlocal mixture, with the Rutgers-Chalmers approximation for van der Waals (vdW) forces. The functional is fitted within the Bayesian error estimation functional (BEEF) framework. We improve the previously used fitting procedures by introducing a robust MM-estimator based loss function, reducing the sensitivity to outliers in the datasets. To more reliably determine the optimal model complexity, we furthermore introduce a generalization of the bootstrap 0.632 estimator with hierarchical bootstrap sampling and geometric mean estimator overmore » the training datasets. Using this estimator, we show that the robust loss function leads to a 10% improvement in the estimated prediction error over the previously used least-squares loss function. The mBEEF-vdW functional is benchmarked against popular density functional approximations over a wide range of datasets relevant for heterogeneous catalysis, including datasets that were not used for its training. Overall, we find that mBEEF-vdW has a higher general accuracy than competing popular functionals, and it is one of the best performing functionals on chemisorption systems, surface energies, lattice constants, and dispersion. We also show the potential-energy curve of graphene on the nickel(111) surface, where mBEEF-vdW matches the experimental binding length. mBEEF-vdW is currently available in gpaw and other density functional theory codes through Libxc, version 3.0.0.« less

Efficient statistical tests to compare Youden index: accounting for contingency correlation.

PubMed

Chen, Fangyao; Xue, Yuqiang; Tan, Ming T; Chen, Pingyan

2015-04-30

Youden index is widely utilized in studies evaluating accuracy of diagnostic tests and performance of predictive, prognostic, or risk models. However, both one and two independent sample tests on Youden index have been derived ignoring the dependence (association) between sensitivity and specificity, resulting in potentially misleading findings. Besides, paired sample test on Youden index is currently unavailable. This article develops efficient statistical inference procedures for one sample, independent, and paired sample tests on Youden index by accounting for contingency correlation, namely associations between sensitivity and specificity and paired samples typically represented in contingency tables. For one and two independent sample tests, the variances are estimated by Delta method, and the statistical inference is based on the central limit theory, which are then verified by bootstrap estimates. For paired samples test, we show that the estimated covariance of the two sensitivities and specificities can be represented as a function of kappa statistic so the test can be readily carried out. We then show the remarkable accuracy of the estimated variance using a constrained optimization approach. Simulation is performed to evaluate the statistical properties of the derived tests. The proposed approaches yield more stable type I errors at the nominal level and substantially higher power (efficiency) than does the original Youden's approach. Therefore, the simple explicit large sample solution performs very well. Because we can readily implement the asymptotic and exact bootstrap computation with common software like R, the method is broadly applicable to the evaluation of diagnostic tests and model performance. Copyright © 2015 John Wiley & Sons, Ltd.

Understanding London's Water Supply Tradeoffs When Scheduling Interventions Under Deep Uncertainty

NASA Astrophysics Data System (ADS)

Huskova, I.; Matrosov, E. S.; Harou, J. J.; Kasprzyk, J. R.; Reed, P. M.

2015-12-01

Water supply planning in many major world cities faces several challenges associated with but not limited to climate change, population growth and insufficient land availability for infrastructure development. Long-term plans to maintain supply-demand balance and ecosystem services require careful consideration of uncertainties associated with future conditions. The current approach for London's water supply planning utilizes least cost optimization of future intervention schedules with limited uncertainty consideration. Recently, the focus of the long-term plans has shifted from solely least cost performance to robustness and resilience of the system. Identifying robust scheduling of interventions requires optimizing over a statistically representative sample of stochastic inputs which may be computationally difficult to achieve. In this study we optimize schedules using an ensemble of plausible scenarios and assess how manipulating that ensemble influences the different Pareto-approximate intervention schedules. We investigate how a major stress event's location in time as well as the optimization problem formulation influence the Pareto-approximate schedules. A bootstrapping method that respects the non-stationary trend of climate change scenarios and ensures the even distribution of the major stress event in the scenario ensemble is proposed. Different bootstrapped hydrological scenario ensembles are assessed using many-objective scenario optimization of London's future water supply and demand intervention scheduling. However, such a "fixed" scheduling of interventions approach does not aim to embed flexibility or adapt effectively as the future unfolds. Alternatively, making decisions based on the observations of occurred conditions could help planners who prefer adaptive planning. We will show how rules to guide the implementation of interventions based on observations may result in more flexible strategies.

BATEMANATER: a computer program to estimate and bootstrap mating system variables based on Bateman's principles.

PubMed

Jones, Adam G

2015-11-01

Bateman's principles continue to play a major role in the characterization of genetic mating systems in natural populations. The modern manifestations of Bateman's ideas include the opportunity for sexual selection (i.e. I(s) - the variance in relative mating success), the opportunity for selection (i.e. I - the variance in relative reproductive success) and the Bateman gradient (i.e. β(ss) - the slope of the least-squares regression of reproductive success on mating success). These variables serve as the foundation for one convenient approach for the quantification of mating systems. However, their estimation presents at least two challenges, which I address here with a new Windows-based computer software package called BATEMANATER. The first challenge is that confidence intervals for these variables are not easy to calculate. BATEMANATER solves this problem using a bootstrapping approach. The second, more serious, problem is that direct estimates of mating system variables from open populations will typically be biased if some potential progeny or adults are missing from the analysed sample. BATEMANATER addresses this problem using a maximum-likelihood approach to estimate mating system variables from incompletely sampled breeding populations. The current version of BATEMANATER addresses the problem for systems in which progeny can be collected in groups of half- or full-siblings, as would occur when eggs are laid in discrete masses or offspring occur in pregnant females. BATEMANATER has a user-friendly graphical interface and thus represents a new, convenient tool for the characterization and comparison of genetic mating systems. © 2015 John Wiley & Sons Ltd.

Exploration of spherical torus physics in the NSTX device

NASA Astrophysics Data System (ADS)

Ono, M.; Kaye, S. M.; Peng, Y.-K. M.; Barnes, G.; Blanchard, W.; Carter, M. D.; Chrzanowski, J.; Dudek, L.; Ewig, R.; Gates, D.; Hatcher, R. E.; Jarboe, T.; Jardin, S. C.; Johnson, D.; Kaita, R.; Kalish, M.; Kessel, C. E.; Kugel, H. W.; Maingi, R.; Majeski, R.; Manickam, J.; McCormack, B.; Menard, J.; Mueller, D.; Nelson, B. A.; Nelson, B. E.; Neumeyer, C.; Oliaro, G.; Paoletti, F.; Parsells, R.; Perry, E.; Pomphrey, N.; Ramakrishnan, S.; Raman, R.; Rewoldt, G.; Robinson, J.; Roquemore, A. L.; Ryan, P.; Sabbagh, S.; Swain, D.; Synakowski, E. J.; Viola, M.; Williams, M.; Wilson, J. R.; NSTX Team

2000-03-01

The National Spherical Torus Experiment (NSTX) is being built at Princeton Plasma Physics Laboratory to test the fusion physics principles for the spherical torus concept at the MA level. The NSTX nominal plasma parameters are R0 = 85 cm, a = 67 cm, R/a >= 1.26, Bt = 3 kG, Ip = 1 MA, q95 = 14, elongation κ <= 2.2, triangularity δ <= 0.5 and a plasma pulse length of up to 5 s. The plasma heating/current drive tools are high harmonic fast wave (6 MW, 5 s), neutral beam injection (5 MW, 80 keV, 5 s) and coaxial helicity injection. Theoretical calculations predict that NSTX should provide exciting possibilities for exploring a number of important new physics regimes, including very high plasma β, naturally high plasma elongation, high bootstrap current fraction, absolute magnetic well and high pressure driven sheared flow. In addition, the NSTX programme plans to explore fully non-inductive plasma startup as well as a dispersive scrape-off layer for heat and particle flux handling.

A high-efficiency low-voltage CMOS rectifier for harvesting energy in implantable devices.

PubMed

Hashemi, S Saeid; Sawan, Mohamad; Savaria, Yvon

2012-08-01

We present, in this paper, a new full-wave CMOS rectifier dedicated for wirelessly-powered low-voltage biomedical implants. It uses bootstrapped capacitors to reduce the effective threshold voltage of selected MOS switches. It achieves a significant increase in its overall power efficiency and low voltage-drop. Therefore, the rectifier is good for applications with low-voltage power supplies and large load current. The rectifier topology does not require complex circuit design. The highest voltages available in the circuit are used to drive the gates of selected transistors in order to reduce leakage current and to lower their channel on-resistance, while having high transconductance. The proposed rectifier was fabricated using the standard TSMC 0.18 μm CMOS process. When connected to a sinusoidal source of 3.3 V peak amplitude, it allows improving the overall power efficiency by 11% compared to the best recently published results given by a gate cross-coupled-based structure.

Monte Carlo based statistical power analysis for mediation models: methods and software.

PubMed

Zhang, Zhiyong

2014-12-01

The existing literature on statistical power analysis for mediation models often assumes data normality and is based on a less powerful Sobel test instead of the more powerful bootstrap test. This study proposes to estimate statistical power to detect mediation effects on the basis of the bootstrap method through Monte Carlo simulation. Nonnormal data with excessive skewness and kurtosis are allowed in the proposed method. A free R package called bmem is developed to conduct the power analysis discussed in this study. Four examples, including a simple mediation model, a multiple-mediator model with a latent mediator, a multiple-group mediation model, and a longitudinal mediation model, are provided to illustrate the proposed method.

SOCIAL COMPETENCE AND PSYCHOLOGICAL VULNERABILITY: THE MEDIATING ROLE OF FLOURISHING.

PubMed

Uysal, Recep

2015-10-01

This study examined whether flourishing mediated the social competence and psychological vulnerability. Participants were 259 university students (147 women, 112 men; M age = 21.3 yr., SD = 1.7) who completed the Turkish versions of the Perceived Social Competence Scale, the Flourishing Scale, and the Psychological Vulnerability Scale. Mediation models were tested using the bootstrapping method to examine indirect effects. Consistent with the hypotheses, the results indicated a positive relationship between social competence and flourishing, and a negative relationship between social competence and psychological vulnerability. Results of the bootstrapping method revealed that flourishing significantly mediated the relationship between social competence and psychological vulnerability. The significance and limitations of the results were discussed.

Transformational leadership in the consumer service workgroup: competing models of job satisfaction, change commitment, and cooperative conflict resolution.

PubMed

Yang, Yi-Feng

2014-02-01

This paper discusses the effects of transformational leadership on cooperative conflict resolution (management) by evaluating several alternative models related to the mediating role of job satisfaction and change commitment. Samples of data from customer service personnel in Taiwan were analyzed. Based on the bootstrap sample technique, an empirical study was carried out to yield the best fitting model. The procedure of hierarchical nested model analysis was used, incorporating the methods of bootstrapping mediation, PRODCLIN2, and structural equation modeling (SEM) comparison. The analysis suggests that leadership that promotes integration (change commitment) and provides inspiration and motivation (job satisfaction), in the proper order, creates the means for cooperative conflict resolution.

Examining Competing Models of Transformational Leadership, Leadership Trust, Change Commitment, and Job Satisfaction.

PubMed

Yang, Yi-Feng

2016-08-01

This study discusses the influence of transformational leadership on job satisfaction through assessing six alternative models related to the mediators of leadership trust and change commitment utilizing a data sample (N = 341; M age = 32.5 year, SD = 5.2) for service promotion personnel in Taiwan. The bootstrap sampling technique was used to select the better fitting model. The tool of hierarchical nested model analysis was applied, along with the approaches of bootstrapping mediation, PRODCLIN2, and structural equation modeling comparison. The results overall demonstrate that leadership is important and that leadership role identification (trust) and workgroup cohesiveness (commitment) form an ordered serial relationship. © The Author(s) 2016.

On the appropriate definition of soil profile configuration and initial conditions for land surface-hydrology models in cold regions

NASA Astrophysics Data System (ADS)

Sapriza-Azuri, Gonzalo; Gamazo, Pablo; Razavi, Saman; Wheater, Howard S.

2018-06-01

Arctic and subarctic regions are amongst the most susceptible regions on Earth to global warming and climate change. Understanding and predicting the impact of climate change in these regions require a proper process representation of the interactions between climate, carbon cycle, and hydrology in Earth system models. This study focuses on land surface models (LSMs) that represent the lower boundary condition of general circulation models (GCMs) and regional climate models (RCMs), which simulate climate change evolution at the global and regional scales, respectively. LSMs typically utilize a standard soil configuration with a depth of no more than 4 m, whereas for cold, permafrost regions, field experiments show that attention to deep soil profiles is needed to understand and close the water and energy balances, which are tightly coupled through the phase change. To address this gap, we design and run a series of model experiments with a one-dimensional LSM, called CLASS (Canadian Land Surface Scheme), as embedded in the MESH (Modélisation Environmentale Communautaire - Surface and Hydrology) modelling system, to (1) characterize the effect of soil profile depth under different climate conditions and in the presence of parameter uncertainty; (2) assess the effect of including or excluding the geothermal flux in the LSM at the bottom of the soil column; and (3) develop a methodology for temperature profile initialization in permafrost regions, where the system has an extended memory, by the use of paleo-records and bootstrapping. Our study area is in Norman Wells, Northwest Territories of Canada, where measurements of soil temperature profiles and historical reconstructed climate data are available. Our results demonstrate a dominant role for parameter uncertainty, that is often neglected in LSMs. Considering such high sensitivity to parameter values and dependency on the climate condition, we show that a minimum depth of 20 m is essential to adequately represent the temperature dynamics. We further show that our proposed initialization procedure is effective and robust to uncertainty in paleo-climate reconstructions and that more than 300 years of reconstructed climate time series are needed for proper model initialization.

Modifications to the edge current profile with auxiliary edge current drive and improved confinement in a reversed-field pinch

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chapman, B. E.; Biewer, T. M.; Chattopadhyay, P. K.

2000-09-01

Auxiliary edge current drive is routinely applied in the Madison Symmetric Torus [R. N. Dexter, D. W. Kerst, T. W. Lovell et al., Fusion Technol. 19, 131 (1991)] with the goal of modifying the parallel current profile to reduce current-driven magnetic fluctuations and the associated particle and energy transport. Provided by an inductive electric field, the current drive successfully reduces fluctuations and transport. First-time measurements of the modified edge current profile reveal that, relative to discharges without auxiliary current drive, the edge current density decreases. This decrease is explicable in terms of newly measured reductions in the dynamo (fluctuation-based) electricmore » field and the electrical conductivity. Induced by the current drive, these two changes to the edge plasma play as much of a role in determining the resultant edge current profile as does the current drive itself. (c) 2000 American Institute of Physics.« less

Surface currents associated with external kink modes in tokamak plasmas during a major disruption

NASA Astrophysics Data System (ADS)

Ng, C. S.; Bhattacharjee, A.

2017-10-01

The surface current on the plasma-vacuum interface during a disruption event involving kink instability can play an important role in driving current into the vacuum vessel. However, there have been disagreements over the nature or even the sign of the surface current in recent theoretical calculations based on idealized step-function background plasma profiles. We revisit such calculations by replacing step-function profiles with more realistic profiles characterized by a strong but finite gradient along the radial direction. It is shown that the resulting surface current is no longer a delta-function current density, but a finite and smooth current density profile with an internal structure, concentrated within the region with a strong plasma pressure gradient. Moreover, this current density profile has peaks of both signs, unlike the delta-function case with a sign opposite to, or the same as the plasma current. We show analytically and numerically that such current density can be separated into two parts, with one of them, called the convective current density, describing the transport of the background plasma density by the displacement, and the other part that remains, called the residual current density. It is argued that consideration of both types of current density is important and can resolve past controversies.

Modeling of the control of the driven current profile in ICRF MCCD on EAST plasma

NASA Astrophysics Data System (ADS)

Yin, L.; Yang, C.; Gong, X. Y.; Lu, X. Q.; Cao, J. J.; Wu, Z. Y.; Chen, Y.; Du, D.

2018-05-01

Control of the current profile is a crucial issue for improved confinement and the inhibition of instability in advanced tokamak operation. Using typical discharge data for the Experimental Advanced Superconducting Tokamak, numerical simulations of driven-current profile control in mode conversion current drive (MCCD) in the ion cyclotron range of frequencies were performed employing a full-wave method and Ehst-Karney efficiency formula. Results indicate that the driven current profile in MCCD can be effectively modified by shifting the mode conversion layer. The peak of the driven current can be located at an aimed position in the normalized minor radius range (-0.60 ≤r/a≤0) by changing the radiofrequency and the minority-ion concentration. The efficiency of the off-axis MCCD can reach 233 kA/MW through optimization, and the mode converted ion cyclotron wave plays an important role in such scenarios. The effects of electron temperature and plasma density on the driven current profile are also investigated.

[Molecular variability in the commom shrew Sorex araneus L. from European Russia and Siberia inferred from the length polymorphism of DNA regions flanked by short interspersed elements (Inter-SINE PCR) and the relationships between the Moscow and Seliger chromosome races].

PubMed

Bannikova, A A; Bulatova, N Sh; Kramerov, D A

2006-06-01

Genetic exchange among chromosomal races of the common shrew Sorex araneus and the problem of reproductive barriers have been extensively studied by means of such molecular markers as mtDNA, microsatellites, and allozymes. In the present study, the interpopulation and interracial polymorphism in the common shrew was derived, using fingerprints generated by amplified DNA regions flanked by short interspersed repeats (SINEs)-interSINE PCR (IS-PCR). We used primers, complementary to consensus sequences of two short retroposons: mammalian element MIR and the SOR element from the genome of Sorex araneus. Genetic differentiation among eleven populations of the common shrew from eight chromosome races was estimated. The NP and MJ analyses, as well as multidimensional scaling showed that all samples examined grouped into two main clusters, corresponding to European Russia and Siberia. The bootstrap support of the European Russia cluster in the NJ and MP analyses was respectively 76 and 61%. The bootstrap index for the Siberian cluster was 100% in both analyses; the Tomsk race, included into this cluster, was separated with the bootstrap support of NJ/MP 92/95%.

Wavelet-based time series bootstrap model for multidecadal streamflow simulation using climate indicators

NASA Astrophysics Data System (ADS)

Erkyihun, Solomon Tassew; Rajagopalan, Balaji; Zagona, Edith; Lall, Upmanu; Nowak, Kenneth

2016-05-01

A model to generate stochastic streamflow projections conditioned on quasi-oscillatory climate indices such as Pacific Decadal Oscillation (PDO) and Atlantic Multi-decadal Oscillation (AMO) is presented. Recognizing that each climate index has underlying band-limited components that contribute most of the energy of the signals, we first pursue a wavelet decomposition of the signals to identify and reconstruct these features from annually resolved historical data and proxy based paleoreconstructions of each climate index covering the period from 1650 to 2012. A K-Nearest Neighbor block bootstrap approach is then developed to simulate the total signal of each of these climate index series while preserving its time-frequency structure and marginal distributions. Finally, given the simulated climate signal time series, a K-Nearest Neighbor bootstrap is used to simulate annual streamflow series conditional on the joint state space defined by the simulated climate index for each year. We demonstrate this method by applying it to simulation of streamflow at Lees Ferry gauge on the Colorado River using indices of two large scale climate forcings: Pacific Decadal Oscillation (PDO) and Atlantic Multi-decadal Oscillation (AMO), which are known to modulate the Colorado River Basin (CRB) hydrology at multidecadal time scales. Skill in stochastic simulation of multidecadal projections of flow using this approach is demonstrated.

Uncertainty estimation of Intensity-Duration-Frequency relationships: A regional analysis

NASA Astrophysics Data System (ADS)

Mélèse, Victor; Blanchet, Juliette; Molinié, Gilles

2018-03-01

We propose in this article a regional study of uncertainties in IDF curves derived from point-rainfall maxima. We develop two generalized extreme value models based on the simple scaling assumption, first in the frequentist framework and second in the Bayesian framework. Within the frequentist framework, uncertainties are obtained i) from the Gaussian density stemming from the asymptotic normality theorem of the maximum likelihood and ii) with a bootstrap procedure. Within the Bayesian framework, uncertainties are obtained from the posterior densities. We confront these two frameworks on the same database covering a large region of 100, 000 km2 in southern France with contrasted rainfall regime, in order to be able to draw conclusion that are not specific to the data. The two frameworks are applied to 405 hourly stations with data back to the 1980's, accumulated in the range 3 h-120 h. We show that i) the Bayesian framework is more robust than the frequentist one to the starting point of the estimation procedure, ii) the posterior and the bootstrap densities are able to better adjust uncertainty estimation to the data than the Gaussian density, and iii) the bootstrap density give unreasonable confidence intervals, in particular for return levels associated to large return period. Therefore our recommendation goes towards the use of the Bayesian framework to compute uncertainty.

A bootstrapping method for development of Treebank

NASA Astrophysics Data System (ADS)

Zarei, F.; Basirat, A.; Faili, H.; Mirain, M.

2017-01-01

Using statistical approaches beside the traditional methods of natural language processing could significantly improve both the quality and performance of several natural language processing (NLP) tasks. The effective usage of these approaches is subject to the availability of the informative, accurate and detailed corpora on which the learners are trained. This article introduces a bootstrapping method for developing annotated corpora based on a complex and rich linguistically motivated elementary structure called supertag. To this end, a hybrid method for supertagging is proposed that combines both of the generative and discriminative methods of supertagging. The method was applied on a subset of Wall Street Journal (WSJ) in order to annotate its sentences with a set of linguistically motivated elementary structures of the English XTAG grammar that is using a lexicalised tree-adjoining grammar formalism. The empirical results confirm that the bootstrapping method provides a satisfactory way for annotating the English sentences with the mentioned structures. The experiments show that the method could automatically annotate about 20% of WSJ with the accuracy of F-measure about 80% of which is particularly 12% higher than the F-measure of the XTAG Treebank automatically generated from the approach proposed by Basirat and Faili [(2013). Bridge the gap between statistical and hand-crafted grammars. Computer Speech and Language, 27, 1085-1104].

Confidence intervals for correlations when data are not normal.

PubMed

Bishara, Anthony J; Hittner, James B

2017-02-01

With nonnormal data, the typical confidence interval of the correlation (Fisher z') may be inaccurate. The literature has been unclear as to which of several alternative methods should be used instead, and how extreme a violation of normality is needed to justify an alternative. Through Monte Carlo simulation, 11 confidence interval methods were compared, including Fisher z', two Spearman rank-order methods, the Box-Cox transformation, rank-based inverse normal (RIN) transformation, and various bootstrap methods. Nonnormality often distorted the Fisher z' confidence interval-for example, leading to a 95 % confidence interval that had actual coverage as low as 68 %. Increasing the sample size sometimes worsened this problem. Inaccurate Fisher z' intervals could be predicted by a sample kurtosis of at least 2, an absolute sample skewness of at least 1, or significant violations of normality hypothesis tests. Only the Spearman rank-order and RIN transformation methods were universally robust to nonnormality. Among the bootstrap methods, an observed imposed bootstrap came closest to accurate coverage, though it often resulted in an overly long interval. The results suggest that sample nonnormality can justify avoidance of the Fisher z' interval in favor of a more robust alternative. R code for the relevant methods is provided in supplementary materials.

Using Landsat Surface Reflectance Data as a Reference Target for Multiswath Hyperspectral Data Collected Over Mixed Agricultural Rangeland Areas

DOE Office of Scientific and Technical Information (OSTI.GOV)

McCann, Cooper; Repasky, Kevin S.; Morin, Mikindra

Low-cost flight-based hyperspectral imaging systems have the potential to provide important information for ecosystem and environmental studies as well as aide in land management. To realize this potential, methods must be developed to provide large-area surface reflectance data allowing for temporal data sets at the mesoscale. This paper describes a bootstrap method of producing a large-area, radiometrically referenced hyperspectral data set using the Landsat surface reflectance (LaSRC) data product as a reference target. The bootstrap method uses standard hyperspectral processing techniques that are extended to remove uneven illumination conditions between flight passes, allowing for radiometrically self-consistent data after mosaicking. Throughmore » selective spectral and spatial resampling, LaSRC data are used as a radiometric reference target. Advantages of the bootstrap method include the need for minimal site access, no ancillary instrumentation, and automated data processing. Data from two hyperspectral flights over the same managed agricultural and unmanaged range land covering approximately 5.8 km 2 acquired on June 21, 2014 and June 24, 2015 are presented. As a result, data from a flight over agricultural land collected on June 6, 2016 are compared with concurrently collected ground-based reflectance spectra as a means of validation.« less

Using Landsat Surface Reflectance Data as a Reference Target for Multiswath Hyperspectral Data Collected Over Mixed Agricultural Rangeland Areas

DOE PAGES

McCann, Cooper; Repasky, Kevin S.; Morin, Mikindra; ...

2017-07-25

Low-cost flight-based hyperspectral imaging systems have the potential to provide important information for ecosystem and environmental studies as well as aide in land management. To realize this potential, methods must be developed to provide large-area surface reflectance data allowing for temporal data sets at the mesoscale. This paper describes a bootstrap method of producing a large-area, radiometrically referenced hyperspectral data set using the Landsat surface reflectance (LaSRC) data product as a reference target. The bootstrap method uses standard hyperspectral processing techniques that are extended to remove uneven illumination conditions between flight passes, allowing for radiometrically self-consistent data after mosaicking. Throughmore » selective spectral and spatial resampling, LaSRC data are used as a radiometric reference target. Advantages of the bootstrap method include the need for minimal site access, no ancillary instrumentation, and automated data processing. Data from two hyperspectral flights over the same managed agricultural and unmanaged range land covering approximately 5.8 km 2 acquired on June 21, 2014 and June 24, 2015 are presented. As a result, data from a flight over agricultural land collected on June 6, 2016 are compared with concurrently collected ground-based reflectance spectra as a means of validation.« less

Confidence intervals for distinguishing ordinal and disordinal interactions in multiple regression.

PubMed

Lee, Sunbok; Lei, Man-Kit; Brody, Gene H

2015-06-01

Distinguishing between ordinal and disordinal interaction in multiple regression is useful in testing many interesting theoretical hypotheses. Because the distinction is made based on the location of a crossover point of 2 simple regression lines, confidence intervals of the crossover point can be used to distinguish ordinal and disordinal interactions. This study examined 2 factors that need to be considered in constructing confidence intervals of the crossover point: (a) the assumption about the sampling distribution of the crossover point, and (b) the possibility of abnormally wide confidence intervals for the crossover point. A Monte Carlo simulation study was conducted to compare 6 different methods for constructing confidence intervals of the crossover point in terms of the coverage rate, the proportion of true values that fall to the left or right of the confidence intervals, and the average width of the confidence intervals. The methods include the reparameterization, delta, Fieller, basic bootstrap, percentile bootstrap, and bias-corrected accelerated bootstrap methods. The results of our Monte Carlo simulation study suggest that statistical inference using confidence intervals to distinguish ordinal and disordinal interaction requires sample sizes more than 500 to be able to provide sufficiently narrow confidence intervals to identify the location of the crossover point. (c) 2015 APA, all rights reserved).

A Pilot Investigation of the Relationship between Climate Variability and Milk Compounds under the Bootstrap Technique

PubMed Central

Marami Milani, Mohammad Reza; Hense, Andreas; Rahmani, Elham; Ploeger, Angelika

2015-01-01

This study analyzes the linear relationship between climate variables and milk components in Iran by applying bootstrapping to include and assess the uncertainty. The climate parameters, Temperature Humidity Index (THI) and Equivalent Temperature Index (ETI) are computed from the NASA-Modern Era Retrospective-Analysis for Research and Applications (NASA-MERRA) reanalysis (2002–2010). Milk data for fat, protein (measured on fresh matter bases), and milk yield are taken from 936,227 milk records for the same period, using cows fed by natural pasture from April to September. Confidence intervals for the regression model are calculated using the bootstrap technique. This method is applied to the original times series, generating statistically equivalent surrogate samples. As a result, despite the short time data and the related uncertainties, an interesting behavior of the relationships between milk compound and the climate parameters is visible. During spring only, a weak dependency of milk yield and climate variations is obvious, while fat and protein concentrations show reasonable correlations. In summer, milk yield shows a similar level of relationship with ETI, but not with temperature and THI. We suggest this methodology for studies in the field of the impacts of climate change and agriculture, also environment and food with short-term data. PMID:28231215

Detecting temporal trends in species assemblages with bootstrapping procedures and hierarchical models

USGS Publications Warehouse

Gotelli, Nicholas J.; Dorazio, Robert M.; Ellison, Aaron M.; Grossman, Gary D.

2010-01-01

Quantifying patterns of temporal trends in species assemblages is an important analytical challenge in community ecology. We describe methods of analysis that can be applied to a matrix of counts of individuals that is organized by species (rows) and time-ordered sampling periods (columns). We first developed a bootstrapping procedure to test the null hypothesis of random sampling from a stationary species abundance distribution with temporally varying sampling probabilities. This procedure can be modified to account for undetected species. We next developed a hierarchical model to estimate species-specific trends in abundance while accounting for species-specific probabilities of detection. We analysed two long-term datasets on stream fishes and grassland insects to demonstrate these methods. For both assemblages, the bootstrap test indicated that temporal trends in abundance were more heterogeneous than expected under the null model. We used the hierarchical model to estimate trends in abundance and identified sets of species in each assemblage that were steadily increasing, decreasing or remaining constant in abundance over more than a decade of standardized annual surveys. Our methods of analysis are broadly applicable to other ecological datasets, and they represent an advance over most existing procedures, which do not incorporate effects of incomplete sampling and imperfect detection.

Modality specificity and integration in working memory: Insights from visuospatial bootstrapping.

PubMed

Allen, Richard J; Havelka, Jelena; Falcon, Thomas; Evans, Sally; Darling, Stephen

2015-05-01

The question of how meaningful associations between verbal and spatial information might be utilized to facilitate working memory performance is potentially highly instructive for models of memory function. The present study explored how separable processing capacities within specialized domains might each contribute to this, by examining the disruptive impacts of simple verbal and spatial concurrent tasks on young adults' recall of visually presented digit sequences encountered either in a single location or within a meaningful spatial "keypad" configuration. The previously observed advantage for recall in the latter condition (the "visuospatial bootstrapping effect") consistently emerged across 3 experiments, indicating use of familiar spatial information in boosting verbal memory. The magnitude of this effect interacted with concurrent activity; articulatory suppression during encoding disrupted recall to a greater extent when digits were presented in single locations (Experiment 1), while spatial tapping during encoding had a larger impact on the keypad condition and abolished the visuospatial bootstrapping advantage (Experiment 2). When spatial tapping was performed during recall (Experiment 3), no task by display interaction was observed. Outcomes are discussed within the context of the multicomponent model of working memory, with a particular emphasis on cross-domain storage in the episodic buffer (Baddeley, 2000). (c) 2015 APA, all rights reserved).

Bootstrap-based procedures for inference in nonparametric receiver-operating characteristic curve regression analysis.

PubMed

Rodríguez-Álvarez, María Xosé; Roca-Pardiñas, Javier; Cadarso-Suárez, Carmen; Tahoces, Pablo G

2018-03-01

Prior to using a diagnostic test in a routine clinical setting, the rigorous evaluation of its diagnostic accuracy is essential. The receiver-operating characteristic curve is the measure of accuracy most widely used for continuous diagnostic tests. However, the possible impact of extra information about the patient (or even the environment) on diagnostic accuracy also needs to be assessed. In this paper, we focus on an estimator for the covariate-specific receiver-operating characteristic curve based on direct regression modelling and nonparametric smoothing techniques. This approach defines the class of generalised additive models for the receiver-operating characteristic curve. The main aim of the paper is to offer new inferential procedures for testing the effect of covariates on the conditional receiver-operating characteristic curve within the above-mentioned class. Specifically, two different bootstrap-based tests are suggested to check (a) the possible effect of continuous covariates on the receiver-operating characteristic curve and (b) the presence of factor-by-curve interaction terms. The validity of the proposed bootstrap-based procedures is supported by simulations. To facilitate the application of these new procedures in practice, an R-package, known as npROCRegression, is provided and briefly described. Finally, data derived from a computer-aided diagnostic system for the automatic detection of tumour masses in breast cancer is analysed.

Phylogenetic Analysis of Prevalent Tuberculosis and Non-Tuberculosis Mycobacteria in Isfahan, Iran, Based on a 360 bp Sequence of the rpoB Gene

PubMed Central

Nasr Esfahani, Bahram; Moghim, Sharareh; Ghasemian Safaei, Hajieh; Moghoofei, Mohsen; Sedighi, Mansour; Hadifar, Shima

2016-01-01

Background Taxonomic and phylogenetic studies of Mycobacterium species have been based around the 16sRNA gene for many years. However, due to the high strain similarity between species in the Mycobacterium genus (94.3% - 100%), defining a valid phylogenetic tree is difficult; consequently, its use in estimating the boundaries between species is limited. The sequence of the rpoB gene makes it an appropriate gene for phylogenetic analysis, especially in bacteria with limited variation. Objectives In the present study, a 360bp sequence of rpoB was used for precise classification of Mycobacterium strains isolated in Isfahan, Iran. Materials and Methods From February to October 2013, 57 clinical and environmental isolates were collected, subcultured, and identified by phenotypic methods. After DNA extraction, a 360bp fragment was PCR-amplified and sequenced. The phylogenetic tree was constructed based on consensus sequence data, using MEGA5 software. Results Slow and fast-growing groups of the Mycobacterium strains were clearly differentiated based on the constructed tree of 56 common Mycobacterium isolates. Each species with a unique title in the tree was identified; in total, 13 nods with a bootstrap value of over 50% were supported. Among the slow-growing group was Mycobacterium kansasii, with M. tuberculosis in a cluster with a bootstrap value of 98% and M. gordonae in another cluster with a bootstrap value of 90%. In the fast-growing group, one cluster with a bootstrap value of 89% was defined, including all fast-growing members present in this study. Conclusions The results suggest that only the application of the rpoB gene sequence is sufficient for taxonomic categorization and definition of a new Mycobacterium species, due to its high resolution power and proper variation in its sequence (85% - 100%); the resulting tree has high validity. PMID:27284397

Emergence of Joint Attention through Bootstrap Learning based on the Mechanisms of Visual Attention and Learning with Self-evaluation

NASA Astrophysics Data System (ADS)

Nagai, Yukie; Hosoda, Koh; Morita, Akio; Asada, Minoru

This study argues how human infants acquire the ability of joint attention through interactions with their caregivers from a viewpoint of cognitive developmental robotics. In this paper, a mechanism by which a robot acquires sensorimotor coordination for joint attention through bootstrap learning is described. Bootstrap learning is a process by which a learner acquires higher capabilities through interactions with its environment based on embedded lower capabilities even if the learner does not receive any external evaluation nor the environment is controlled. The proposed mechanism for bootstrap learning of joint attention consists of the robot's embedded mechanisms: visual attention and learning with self-evaluation. The former is to find and attend to a salient object in the field of the robot's view, and the latter is to evaluate the success of visual attention, not joint attention, and then to learn the sensorimotor coordination. Since the object which the robot looks at based on visual attention does not always correspond to the object which the caregiver is looking at in an environment including multiple objects, the robot may have incorrect learning situations for joint attention as well as correct ones. However, the robot is expected to statistically lose the learning data of the incorrect ones as outliers because of its weaker correlation between the sensor input and the motor output than that of the correct ones, and consequently to acquire appropriate sensorimotor coordination for joint attention even if the caregiver does not provide any task evaluation to the robot. The experimental results show the validity of the proposed mechanism. It is suggested that the proposed mechanism could explain the developmental mechanism of infants' joint attention because the learning process of the robot's joint attention can be regarded as equivalent to the developmental process of infants' one.

Uncertainty quantification of CO₂ saturation estimated from electrical resistance tomography data at the Cranfield site

DOE PAGES

Yang, Xianjin; Chen, Xiao; Carrigan, Charles R.; ...

2014-06-03

A parametric bootstrap approach is presented for uncertainty quantification (UQ) of CO₂ saturation derived from electrical resistance tomography (ERT) data collected at the Cranfield, Mississippi (USA) carbon sequestration site. There are many sources of uncertainty in ERT-derived CO₂ saturation, but we focus on how the ERT observation errors propagate to the estimated CO₂ saturation in a nonlinear inversion process. Our UQ approach consists of three steps. We first estimated the observational errors from a large number of reciprocal ERT measurements. The second step was to invert the pre-injection baseline data and the resulting resistivity tomograph was used as the priormore » information for nonlinear inversion of time-lapse data. We assigned a 3% random noise to the baseline model. Finally, we used a parametric bootstrap method to obtain bootstrap CO₂ saturation samples by deterministically solving a nonlinear inverse problem many times with resampled data and resampled baseline models. Then the mean and standard deviation of CO₂ saturation were calculated from the bootstrap samples. We found that the maximum standard deviation of CO₂ saturation was around 6% with a corresponding maximum saturation of 30% for a data set collected 100 days after injection began. There was no apparent spatial correlation between the mean and standard deviation of CO₂ saturation but the standard deviation values increased with time as the saturation increased. The uncertainty in CO₂ saturation also depends on the ERT reciprocal error threshold used to identify and remove noisy data and inversion constraints such as temporal roughness. Five hundred realizations requiring 3.5 h on a single 12-core node were needed for the nonlinear Monte Carlo inversion to arrive at stationary variances while the Markov Chain Monte Carlo (MCMC) stochastic inverse approach may expend days for a global search. This indicates that UQ of 2D or 3D ERT inverse problems can be performed on a laptop or desktop PC.« less

Analyzing hospitalization data: potential limitations of Poisson regression.

PubMed

Weaver, Colin G; Ravani, Pietro; Oliver, Matthew J; Austin, Peter C; Quinn, Robert R

2015-08-01

Poisson regression is commonly used to analyze hospitalization data when outcomes are expressed as counts (e.g. number of days in hospital). However, data often violate the assumptions on which Poisson regression is based. More appropriate extensions of this model, while available, are rarely used. We compared hospitalization data between 206 patients treated with hemodialysis (HD) and 107 treated with peritoneal dialysis (PD) using Poisson regression and compared results from standard Poisson regression with those obtained using three other approaches for modeling count data: negative binomial (NB) regression, zero-inflated Poisson (ZIP) regression and zero-inflated negative binomial (ZINB) regression. We examined the appropriateness of each model and compared the results obtained with each approach. During a mean 1.9 years of follow-up, 183 of 313 patients (58%) were never hospitalized (indicating an excess of 'zeros'). The data also displayed overdispersion (variance greater than mean), violating another assumption of the Poisson model. Using four criteria, we determined that the NB and ZINB models performed best. According to these two models, patients treated with HD experienced similar hospitalization rates as those receiving PD {NB rate ratio (RR): 1.04 [bootstrapped 95% confidence interval (CI): 0.49-2.20]; ZINB summary RR: 1.21 (bootstrapped 95% CI 0.60-2.46)}. Poisson and ZIP models fit the data poorly and had much larger point estimates than the NB and ZINB models [Poisson RR: 1.93 (bootstrapped 95% CI 0.88-4.23); ZIP summary RR: 1.84 (bootstrapped 95% CI 0.88-3.84)]. We found substantially different results when modeling hospitalization data, depending on the approach used. Our results argue strongly for a sound model selection process and improved reporting around statistical methods used for modeling count data. © The Author 2015. Published by Oxford University Press on behalf of ERA-EDTA. All rights reserved.

A Bootstrap Approach to an Affordable Exploration Program

NASA Technical Reports Server (NTRS)

Oeftering, Richard C.

2011-01-01

This paper examines the potential to build an affordable sustainable exploration program by adopting an approach that requires investing in technologies that can be used to build a space infrastructure from very modest initial capabilities. Human exploration has had a history of flight programs that have high development and operational costs. Since Apollo, human exploration has had very constrained budgets and they are expected be constrained in the future. Due to their high operations costs it becomes necessary to consider retiring established space facilities in order to move on to the next exploration challenge. This practice may save cost in the near term but it does so by sacrificing part of the program s future architecture. Human exploration also has a history of sacrificing fully functional flight hardware to achieve mission objectives. An affordable exploration program cannot be built when it involves billions of dollars of discarded space flight hardware, instead, the program must emphasize preserving its high value space assets and building a suitable permanent infrastructure. Further this infrastructure must reduce operational and logistics cost. The paper examines the importance of achieving a high level of logistics independence by minimizing resource consumption, minimizing the dependency on external logistics, and maximizing the utility of resources available. The approach involves the development and deployment of a core suite of technologies that have minimum initial needs yet are able expand upon initial capability in an incremental bootstrap fashion. The bootstrap approach incrementally creates an infrastructure that grows and becomes self sustaining and eventually begins producing the energy, products and consumable propellants that support human exploration. The bootstrap technologies involve new methods of delivering and manipulating energy and materials. These technologies will exploit the space environment, minimize dependencies, and minimize the need for imported resources. They will provide the widest range of utility in a resource scarce environment and pave the way to an affordable exploration program.

The value of value of information: best informing research design and prioritization using current methods.

PubMed

Eckermann, Simon; Karnon, Jon; Willan, Andrew R

2010-01-01

Value of information (VOI) methods have been proposed as a systematic approach to inform optimal research design and prioritization. Four related questions arise that VOI methods could address. (i) Is further research for a health technology assessment (HTA) potentially worthwhile? (ii) Is the cost of a given research design less than its expected value? (iii) What is the optimal research design for an HTA? (iv) How can research funding be best prioritized across alternative HTAs? Following Occam's razor, we consider the usefulness of VOI methods in informing questions 1-4 relative to their simplicity of use. Expected value of perfect information (EVPI) with current information, while simple to calculate, is shown to provide neither a necessary nor a sufficient condition to address question 1, given that what EVPI needs to exceed varies with the cost of research design, which can vary from very large down to negligible. Hence, for any given HTA, EVPI does not discriminate, as it can be large and further research not worthwhile or small and further research worthwhile. In contrast, each of questions 1-4 are shown to be fully addressed (necessary and sufficient) where VOI methods are applied to maximize expected value of sample information (EVSI) minus expected costs across designs. In comparing complexity in use of VOI methods, applying the central limit theorem (CLT) simplifies analysis to enable easy estimation of EVSI and optimal overall research design, and has been shown to outperform bootstrapping, particularly with small samples. Consequently, VOI methods applying the CLT to inform optimal overall research design satisfy Occam's razor in both improving decision making and reducing complexity. Furthermore, they enable consideration of relevant decision contexts, including option value and opportunity cost of delay, time, imperfect implementation and optimal design across jurisdictions. More complex VOI methods such as bootstrapping of the expected value of partial EVPI may have potential value in refining overall research design. However, Occam's razor must be seriously considered in application of these VOI methods, given their increased complexity and current limitations in informing decision making, with restriction to EVPI rather than EVSI and not allowing for important decision-making contexts. Initial use of CLT methods to focus these more complex partial VOI methods towards where they may be useful in refining optimal overall trial design is suggested. Integrating CLT methods with such partial VOI methods to allow estimation of partial EVSI is suggested in future research to add value to the current VOI toolkit.

Neoclassical transport in toroidal plasmas with nonaxisymmetric flux surfaces

DOE PAGES

Belli, Emily A.; Candy, Jefferey M.

2015-04-15

The capability to treat nonaxisymmetric flux surface geometry has been added to the drift-kinetic code NEO. Geometric quantities (i.e. metric elements) are supplied by a recently-developed local 3D equilibrium solver, allowing neoclassical transport coefficients to be systematically computed while varying the 3D plasma shape in a simple and intuitive manner. Code verification is accomplished via detailed comparison with 3D Pfirsch–Schlüter theory. A discussion of the various collisionality regimes associated with 3D transport is given, with an emphasis on non-ambipolar particle flux, neoclassical toroidal viscosity, energy flux and bootstrap current. As a result, we compute the transport in the presence ofmore » ripple-type perturbations in a DIII-D-like H-mode edge plasma.« less

Kappa statistic for the clustered dichotomous responses from physicians and patients

PubMed Central

Kang, Chaeryon; Qaqish, Bahjat; Monaco, Jane; Sheridan, Stacey L.; Cai, Jianwen

2013-01-01

The bootstrap method for estimating the standard error of the kappa statistic in the presence of clustered data is evaluated. Such data arise, for example, in assessing agreement between physicians and their patients regarding their understanding of the physician-patient interaction and discussions. We propose a computationally efficient procedure for generating correlated dichotomous responses for physicians and assigned patients for simulation studies. The simulation result demonstrates that the proposed bootstrap method produces better estimate of the standard error and better coverage performance compared to the asymptotic standard error estimate that ignores dependence among patients within physicians with at least a moderately large number of clusters. An example of an application to a coronary heart disease prevention study is presented. PMID:23533082

Tests of Mediation: Paradoxical Decline in Statistical Power as a Function of Mediator Collinearity

PubMed Central

Beasley, T. Mark

2013-01-01

Increasing the correlation between the independent variable and the mediator (a coefficient) increases the effect size (ab) for mediation analysis; however, increasing a by definition increases collinearity in mediation models. As a result, the standard error of product tests increase. The variance inflation due to increases in a at some point outweighs the increase of the effect size (ab) and results in a loss of statistical power. This phenomenon also occurs with nonparametric bootstrapping approaches because the variance of the bootstrap distribution of ab approximates the variance expected from normal theory. Both variances increase dramatically when a exceeds the b coefficient, thus explaining the power decline with increases in a. Implications for statistical analysis and applied researchers are discussed. PMID:24954952

The Bootstrap, the Jackknife, and the Randomization Test: A Sampling Taxonomy.

PubMed

Rodgers, J L

1999-10-01

A simple sampling taxonomy is defined that shows the differences between and relationships among the bootstrap, the jackknife, and the randomization test. Each method has as its goal the creation of an empirical sampling distribution that can be used to test statistical hypotheses, estimate standard errors, and/or create confidence intervals. Distinctions between the methods can be made based on the sampling approach (with replacement versus without replacement) and the sample size (replacing the whole original sample versus replacing a subset of the original sample). The taxonomy is useful for teaching the goals and purposes of resampling schemes. An extension of the taxonomy implies other possible resampling approaches that have not previously been considered. Univariate and multivariate examples are presented.

Abstractness and Continuity in the Syntactic Development of Young Children with Autism

PubMed Central

Naigles, Letitia R.; Kelty, Emma; Jaffery, Rose; Fein, Deborah

2011-01-01

Grammar is frequently considered to be a strength in the cognitive profile of individuals with autism spectrum disorders (ASDs); however, few studies have investigated how abstract (i.e., distinct from specific lexical items) is the grammatical knowledge of individuals with ASD. In this study, we examine the extent to which children with ASD have abstracted the transitive (SVO) frame in English. Participants in a longitudinal study of language acquisition in children with autism (17 children with ASD averaging 41 months of age, 18 TD children averaging 28 months of age) were taught two novel verbs in transitive sentences and asked (via intermodal preferential looking) whether these verbs mapped onto novel causative vs. noncausative actions. Both groups consistently mapped the verbs onto the causative actions (i.e., they engaged in syntactic bootstrapping). Moreover, the children with ASD’s performance on this task was significantly and independently predicted by both vocabulary and sentence-processing measures obtained eight months earlier. We conclude that many children with ASD are able to generalize grammatical patterns, and this ability may derive from earlier lexical and grammatical knowledge. PMID:22012625

Corrected confidence bands for functional data using principal components.

PubMed

Goldsmith, J; Greven, S; Crainiceanu, C

2013-03-01

Functional principal components (FPC) analysis is widely used to decompose and express functional observations. Curve estimates implicitly condition on basis functions and other quantities derived from FPC decompositions; however these objects are unknown in practice. In this article, we propose a method for obtaining correct curve estimates by accounting for uncertainty in FPC decompositions. Additionally, pointwise and simultaneous confidence intervals that account for both model- and decomposition-based variability are constructed. Standard mixed model representations of functional expansions are used to construct curve estimates and variances conditional on a specific decomposition. Iterated expectation and variance formulas combine model-based conditional estimates across the distribution of decompositions. A bootstrap procedure is implemented to understand the uncertainty in principal component decomposition quantities. Our method compares favorably to competing approaches in simulation studies that include both densely and sparsely observed functions. We apply our method to sparse observations of CD4 cell counts and to dense white-matter tract profiles. Code for the analyses and simulations is publicly available, and our method is implemented in the R package refund on CRAN. Copyright © 2013, The International Biometric Society.

Corrected Confidence Bands for Functional Data Using Principal Components

PubMed Central

Goldsmith, J.; Greven, S.; Crainiceanu, C.

2014-01-01

Functional principal components (FPC) analysis is widely used to decompose and express functional observations. Curve estimates implicitly condition on basis functions and other quantities derived from FPC decompositions; however these objects are unknown in practice. In this article, we propose a method for obtaining correct curve estimates by accounting for uncertainty in FPC decompositions. Additionally, pointwise and simultaneous confidence intervals that account for both model- and decomposition-based variability are constructed. Standard mixed model representations of functional expansions are used to construct curve estimates and variances conditional on a specific decomposition. Iterated expectation and variance formulas combine model-based conditional estimates across the distribution of decompositions. A bootstrap procedure is implemented to understand the uncertainty in principal component decomposition quantities. Our method compares favorably to competing approaches in simulation studies that include both densely and sparsely observed functions. We apply our method to sparse observations of CD4 cell counts and to dense white-matter tract profiles. Code for the analyses and simulations is publicly available, and our method is implemented in the R package refund on CRAN. PMID:23003003

Near-Inertial and Tidal Currents Detected with a Vessel Mounted Acoustic Doppler Current Profiler in the Western Mediterranean Sea

NASA Technical Reports Server (NTRS)

Garcia-Gorriz, E.; Candela, J.; Font, J.

1998-01-01

The Acoustic Doppler Current Profiler (ADCP) combined with accurate navigation provides absolute current velocities which include information from all the frequencies which have a dynamical presence in the ocean.

Evaluation of a Magnetically-Filtered Faraday Probe for Measuring the ion Current Density Profile of a Hall Thruster

DTIC Science & Technology

2004-07-01

The ability of a magnetically-filtered Faraday probe (MFFP) to obtain the ion current density profile of a Hall thruster is investigated. The MFFP is...MFFP, boxed Faraday probe (BFP), and nude Faraday probe are used to measure the ion current density profile of a 5 kW Hall thruster operated over the

Non-Solenoidal Startup Research Directions on the Pegasus Toroidal Experiment

NASA Astrophysics Data System (ADS)

Fonck, R. J.; Bongard, M. W.; Lewicki, B. T.; Reusch, J. A.; Winz, G. R.

2017-10-01

The Pegasus research program has been focused on developing a physical understanding and predictive models for non-solenoidal tokamak plasma startup using Local Helicity Injection (LHI). LHI employs strong localized electron currents injected along magnetic field lines in the plasma edge that relax through magnetic turbulence to form a tokamak-like plasma. Pending approval, the Pegasus program will address a broader, more comprehensive examination of non-solenoidal tokamak startup techniques. New capabilities may include: increasing the toroidal field to 0.6 T to support critical scaling tests to near-NSTX-U field levels; deploying internal plasma diagnostics; installing a coaxial helicity injection (CHI) capability in the upper divertor region; and deploying a modest (200-400 kW) electron cyclotron RF capability. These efforts will address scaling of relevant physics to higher BT, separate and comparative studies of helicity injection techniques, efficiency of handoff to consequent current sustainment techniques, and the use of ECH to synergistically improve the target plasma for consequent bootstrap and neutral beam current drive sustainment. This has an ultimate goal of validating techniques to produce a 1 MA target plasma in NSTX-U and beyond. Work supported by US DOE Grant DE-FG02-96ER54375.

Test of electical resistivity and current diffusion modelling on MAST and JET

NASA Astrophysics Data System (ADS)

Keeling, D. L.; Challis, C. D.; Jenkins, I.; Hawkes, N. C.; Lupelli, I.; Michael, C.; de Bock, M. F. M.; the MAST Team; contributors, JET

2018-01-01

Experiments have been carried out on the MAST and JET tokamaks intended to compare the electrical resistivity of the plasma with theoretical formulations. The tests consist of obtaining motional stark effect (MSE) measurements in MHD-free plasmas during plasma current ramp-up (JET and MAST), ramp-down (MAST) and in stationary state (JET and MAST). Simulations of these plasmas are then performed in which the current profile evolution is calculated according to the poloidal field diffusion equation (PFDE) with classical or neoclassical resistivity. Synthetic MSE data are produced in the simulations for direct comparison with the experimental data. It is found that the toroidal current profile evolution modelled using neoclassical resistivity did not match the experimental observations on either device during current ramp-up or ramp-down as concluded from comparison of experimental and synthetic MSE profiles. In these phases, use of neoclassical resistivity in the modelling systematically overestimates the rate of current profile evolution. During the stationary state however, the modelled toroidal current profile matched experimental observations to a high degree of accuracy on both devices using neoclassical resistivity. Whilst no solution to the mismatch in the dynamic phases of the plasma is proposed, it is suggested that some physical process other than MHD which is not captured by the simple diffusive model of current profile evolution is responsible.

Rubiaceae in Brazilian Atlantic Forest remnants: floristic similarity and implications for conservation.

PubMed

de Paiva, Alessandra Marques; Barberena, Felipe Fajardo Villela Antolin; Lopes, Rosana Conrado

2016-06-01

Brazil holds most of the Atlantic Forest Domain and is also one of the Rubiaceae diversity centers in the Neotropics. Despite the urban expansion in the state of Rio de Janeiro, large areas of continuous vegetation with high connectivity degree can still be found. Recently, new Rubiaceae species have been described in the Rio de Janeiro flora, which present small populations and very particular distribution. The current paper analyzed the similarity in the floristic composition of the Rubiaceae in eight Atlantic Forest remnants of Rio de Janeiro state protected by Conservation Units. We also surveyed and set guidelines for conservation of microendemic species. The similarity analysis were based on previously published studies in Área de Proteção Ambiental de Grumari, Área de Proteção Ambiental Palmares, Parque Estadual da Serra da Tiririca, Parque Nacional do Itatiaia, Parque Nacional de Jurubatiba, Reserva Biológica de Poço das Antas, Reserva Biológica do Tinguá and Reserva Ecológica de Macaé de Cima - using the PAST software (“Paleontological Statistics”) with Sørensen coefficient. The floristic similarity analysis revealed two groups with distinct physiographic characteristics and different vegetation types. Group A consisted in two Restinga areas, Área de Proteção Ambiental de Grumari and Parque Nacional de Jurubatiba, which showed strong bootstrap support (98 %). Group B included forest remnants with distinct phytophisiognomies or altitudes, but with moderate bootstrap support. Low similarity levels among the eight areas were found due to the habitats’ heterogeneity. The current study pointed out 19 microendemic species from the Atlantic Forest, they present a single-site distribution or a distribution restricted to Mountain and Metropolitan regions of Rio de Janeiro state. Concerning the conservation status of microendemic species, discrepancies between the Catalogue of Flora of Rio de Janeiro and the Red Book of Brazilian Flora (two of the main reference catalogs of Brazilian flora) have been identified. We have also highlighted the need for recollecting microendemic species from the Atlantic Forest, and for properly assessing the degree of threat faced by these taxons early.

Off-axis current drive and real-time control of current profile in JT-60U

NASA Astrophysics Data System (ADS)

Suzuki, T.; Ide, S.; Oikawa, T.; Fujita, T.; Ishikawa, M.; Seki, M.; Matsunaga, G.; Hatae, T.; Naito, O.; Hamamatsu, K.; Sueoka, M.; Hosoyama, H.; Nakazato, M.; JT-60 Team

2008-04-01

Aiming at optimization of current profile in high-β plasmas for higher confinement and stability, a real-time control system of the minimum of the safety factor (qmin) using the off-axis current drive has been developed. The off-axis current drive can raise the safety factor in the centre and help to avoid instability that limits the performance of the plasma. The system controls the injection power of lower-hybrid waves, and hence its off-axis driven current in order to control qmin. The real-time control of qmin is demonstrated in a high-β plasma, where qmin follows the temporally changing reference qmin,ref from 1.3 to 1.7. Applying the control to another high-β discharge (βN = 1.7, βp = 1.5) with m/n = 2/1 neo-classical tearing mode (NTM), qmin was raised above 2 and the NTM was suppressed. The stored energy increased by 16% with the NTM suppressed, since the resonant rational surface was eliminated. For the future use for current profile control, current density profile for off-axis neutral beam current drive (NBCD) is for the first time measured, using the motional Stark effect diagnostic. Spatially localized NBCD profile was clearly observed at the normalized minor radius ρ of about 0.6-0.8. The location was also confirmed by multi-chordal neutron emission profile measurement. The total amount of the measured beam driven current was consistent with the theoretical calculation using the ACCOME code. The CD location in the calculation was inward shifted than the measurement.

Tests for informative cluster size using a novel balanced bootstrap scheme.

PubMed

Nevalainen, Jaakko; Oja, Hannu; Datta, Somnath

2017-07-20

Clustered data are often encountered in biomedical studies, and to date, a number of approaches have been proposed to analyze such data. However, the phenomenon of informative cluster size (ICS) is a challenging problem, and its presence has an impact on the choice of a correct analysis methodology. For example, Dutta and Datta (2015, Biometrics) presented a number of marginal distributions that could be tested. Depending on the nature and degree of informativeness of the cluster size, these marginal distributions may differ, as do the choices of the appropriate test. In particular, they applied their new test to a periodontal data set where the plausibility of the informativeness was mentioned, but no formal test for the same was conducted. We propose bootstrap tests for testing the presence of ICS. A balanced bootstrap method is developed to successfully estimate the null distribution by merging the re-sampled observations with closely matching counterparts. Relying on the assumption of exchangeability within clusters, the proposed procedure performs well in simulations even with a small number of clusters, at different distributions and against different alternative hypotheses, thus making it an omnibus test. We also explain how to extend the ICS test to a regression setting and thereby enhancing its practical utility. The methodologies are illustrated using the periodontal data set mentioned earlier. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

Signal detection theory and vestibular perception: III. Estimating unbiased fit parameters for psychometric functions.

PubMed

Chaudhuri, Shomesh E; Merfeld, Daniel M

2013-03-01

Psychophysics generally relies on estimating a subject's ability to perform a specific task as a function of an observed stimulus. For threshold studies, the fitted functions are called psychometric functions. While fitting psychometric functions to data acquired using adaptive sampling procedures (e.g., "staircase" procedures), investigators have encountered a bias in the spread ("slope" or "threshold") parameter that has been attributed to the serial dependency of the adaptive data. Using simulations, we confirm this bias for cumulative Gaussian parametric maximum likelihood fits on data collected via adaptive sampling procedures, and then present a bias-reduced maximum likelihood fit that substantially reduces the bias without reducing the precision of the spread parameter estimate and without reducing the accuracy or precision of the other fit parameters. As a separate topic, we explain how to implement this bias reduction technique using generalized linear model fits as well as other numeric maximum likelihood techniques such as the Nelder-Mead simplex. We then provide a comparison of the iterative bootstrap and observed information matrix techniques for estimating parameter fit variance from adaptive sampling procedure data sets. The iterative bootstrap technique is shown to be slightly more accurate; however, the observed information technique executes in a small fraction (0.005 %) of the time required by the iterative bootstrap technique, which is an advantage when a real-time estimate of parameter fit variance is required.

Bootstrap Enhanced Penalized Regression for Variable Selection with Neuroimaging Data.

PubMed

Abram, Samantha V; Helwig, Nathaniel E; Moodie, Craig A; DeYoung, Colin G; MacDonald, Angus W; Waller, Niels G

2016-01-01

Recent advances in fMRI research highlight the use of multivariate methods for examining whole-brain connectivity. Complementary data-driven methods are needed for determining the subset of predictors related to individual differences. Although commonly used for this purpose, ordinary least squares (OLS) regression may not be ideal due to multi-collinearity and over-fitting issues. Penalized regression is a promising and underutilized alternative to OLS regression. In this paper, we propose a nonparametric bootstrap quantile (QNT) approach for variable selection with neuroimaging data. We use real and simulated data, as well as annotated R code, to demonstrate the benefits of our proposed method. Our results illustrate the practical potential of our proposed bootstrap QNT approach. Our real data example demonstrates how our method can be used to relate individual differences in neural network connectivity with an externalizing personality measure. Also, our simulation results reveal that the QNT method is effective under a variety of data conditions. Penalized regression yields more stable estimates and sparser models than OLS regression in situations with large numbers of highly correlated neural predictors. Our results demonstrate that penalized regression is a promising method for examining associations between neural predictors and clinically relevant traits or behaviors. These findings have important implications for the growing field of functional connectivity research, where multivariate methods produce numerous, highly correlated brain networks.

More N =4 superconformal bootstrap

NASA Astrophysics Data System (ADS)

Beem, Christopher; Rastelli, Leonardo; van Rees, Balt C.

2017-08-01

In this long overdue second installment, we continue to develop the conformal bootstrap program for N =4 superconformal field theories (SCFTs) in four dimensions via an analysis of the correlation function of four stress-tensor supermultiplets. We review analytic results for this correlator and make contact with the SCFT/chiral algebra correspondence of Beem et al. [Commun. Math. Phys. 336, 1359 (2015), 10.1007/s00220-014-2272-x]. We demonstrate that the constraints of unitarity and crossing symmetry require the central charge c to be greater than or equal to 3 /4 in any interacting N =4 SCFT. We apply numerical bootstrap methods to derive upper bounds on scaling dimensions and operator product expansion coefficients for several low-lying, unprotected operators as a function of the central charge. We interpret our bounds in the context of N =4 super Yang-Mills theories, formulating a series of conjectures regarding the embedding of the conformal manifold—parametrized by the complexified gauge coupling—into the space of scaling dimensions and operator product expansion coefficients. Our conjectures assign a distinguished role to points on the conformal manifold that are self-dual under a subgroup of the S -duality group. This paper contains a more detailed exposition of a number of results previously reported in Beem et al. [Phys. Rev. Lett. 111, 071601 (2013), 10.1103/PhysRevLett.111.071601] in addition to new results.