Adaptive Monte Carlo methods

NASA Astrophysics Data System (ADS)

Fasnacht, Marc

We develop adaptive Monte Carlo methods for the calculation of the free energy as a function of a parameter of interest. The methods presented are particularly well-suited for systems with complex energy landscapes, where standard sampling techniques have difficulties. The Adaptive Histogram Method uses a biasing potential derived from histograms recorded during the simulation to achieve uniform sampling in the parameter of interest. The Adaptive Integration method directly calculates an estimate of the free energy from the average derivative of the Hamiltonian with respect to the parameter of interest and uses it as a biasing potential. We compare both methods to a state of the art method, and demonstrate that they compare favorably for the calculation of potentials of mean force of dense Lennard-Jones fluids. We use the Adaptive Integration Method to calculate accurate potentials of mean force for different types of simple particles in a Lennard-Jones fluid. Our approach allows us to separate the contributions of the solvent to the potential of mean force from the effect of the direct interaction between the particles. With contributions of the solvent determined, we can find the potential of mean force directly for any other direct interaction without additional simulations. We also test the accuracy of the Adaptive Integration Method on a thermodynamic cycle, which allows us to perform a consistency check between potentials of mean force and chemical potentials calculated using the Adaptive Integration Method. The results demonstrate a high degree of consistency of the method.

Free energy landscapes of small peptides in an implicit solvent model determined by force-biased multicanonical molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Watanabe, Yukihisa S.; Kim, Jae Gil; Fukunishi, Yoshifumi; Nakamura, Haruki

2004-12-01

In order to investigate whether the implicit solvent (GB/SA) model could reproduce the free energy landscapes of peptides, the potential of mean forces (PMFs) of eight tripeptides was examined and compared with the PMFs of the explicit water model. The force-biased multicanonical molecular dynamics method was used for the enhanced conformational sampling. Consequently, the GB/SA model reproduced almost all the global and local minima in the PMFs observed with the explicit water model. However, the GB/SA model overestimated frequencies of the structures that are stabilized by intra-peptide hydrogen bonds.

Exploring the free-energy landscape of a short peptide using an average force

NASA Astrophysics Data System (ADS)

Chipot, Christophe; Hénin, Jérôme

2005-12-01

The reversible folding of deca-alanine is chosen as a test case for characterizing a method that uses an adaptive biasing force (ABF) to escape from the minima and overcome the barriers of the free-energy landscape. This approach relies on the continuous estimation of a biasing force that yields a Hamiltonian in which no average force is exerted along the ordering parameter ξ. Optimizing the parameters that control how the ABF is applied, the method is shown to be extremely effective when a nonequivocal ordering parameter can be defined to explore the folding pathway of the peptide. Starting from a β-turn motif and restraining ξ to a region of the conformational space that extends from the α-helical state to an ensemble of extended structures, the ABF scheme is successful in folding the peptide chain into a compact α helix. Sampling of this conformation is, however, marginal when the range of ξ values embraces arrangements of greater compactness, hence demonstrating the inherent limitations of free-energy methods when ambiguous ordering parameters are utilized.

Using collective variables to drive molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Fiorin, Giacomo; Klein, Michael L.; Hénin, Jérôme

2013-12-01

A software framework is introduced that facilitates the application of biasing algorithms to collective variables of the type commonly employed to drive massively parallel molecular dynamics (MD) simulations. The modular framework that is presented enables one to combine existing collective variables into new ones, and combine any chosen collective variable with available biasing methods. The latter include the classic time-dependent biases referred to as steered MD and targeted MD, the temperature-accelerated MD algorithm, as well as the adaptive free-energy biases called metadynamics and adaptive biasing force. The present modular software is extensible, and portable between commonly used MD simulation engines.

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

Makhnovskii, Yurii A.; Berezhkovskii, Alexander M.; Antipov, Anatoly E.

This paper is devoted to particle transport in a tube formed by alternating wide and narrow sections, in the presence of an external biasing force. The focus is on the effective transport coefficients—mobility and diffusivity, as functions of the biasing force and the geometric parameters of the tube. Dependences of the effective mobility and diffusivity on the tube geometric parameters are known in the limiting cases of no bias and strong bias. The approximations used to obtain these results are inapplicable at intermediate values of the biasing force. To bridge the two limits Brownian dynamics simulations were run to determinemore » the transport coefficients at intermediate values of the force. The simulations were performed for a representative set of tube geometries over a wide range of the biasing force. They revealed that there is a range of the narrow section length, where the force dependence of the mobility has a maximum. In contrast, the diffusivity is a monotonically increasing function of the force. A simple formula is proposed, which reduces to the known dependences of the diffusivity on the tube geometric parameters in both limits of zero and strong bias. At intermediate values of the biasing force, the formula catches the diffusivity dependence on the narrow section length, if the radius of these sections is not too small.« less

Free Energy Computations by Minimization of Kullback-Leibler Divergence: An Efficient Adaptive Biasing Potential Method for Sparse Representations

DTIC Science & Technology

2011-10-14

landscapes. It is motivated by statistical learning arguments and unifies the tasks of biasing the molecular dynamics to escape free energy wells and...statistical learning arguments and unifies the tasks of biasing the molecular dynamics to escape free energy wells and estimating the free energy...experimentally, to characterize global changes as well as investigate relative stabilities. In most applications, a brute- force computation based on

Assessing the utility of frequency dependent nudging for reducing biases in biogeochemical models

NASA Astrophysics Data System (ADS)

Lagman, Karl B.; Fennel, Katja; Thompson, Keith R.; Bianucci, Laura

2014-09-01

Bias errors, resulting from inaccurate boundary and forcing conditions, incorrect model parameterization, etc. are a common problem in environmental models including biogeochemical ocean models. While it is important to correct bias errors wherever possible, it is unlikely that any environmental model will ever be entirely free of such errors. Hence, methods for bias reduction are necessary. A widely used technique for online bias reduction is nudging, where simulated fields are continuously forced toward observations or a climatology. Nudging is robust and easy to implement, but suppresses high-frequency variability and introduces artificial phase shifts. As a solution to this problem Thompson et al. (2006) introduced frequency dependent nudging where nudging occurs only in prescribed frequency bands, typically centered on the mean and the annual cycle. They showed this method to be effective for eddy resolving ocean circulation models. Here we add a stability term to the previous form of frequency dependent nudging which makes the method more robust for non-linear biological models. Then we assess the utility of frequency dependent nudging for biological models by first applying the method to a simple predator-prey model and then to a 1D ocean biogeochemical model. In both cases we only nudge in two frequency bands centered on the mean and the annual cycle, and then assess how well the variability in higher frequency bands is recovered. We evaluate the effectiveness of frequency dependent nudging in comparison to conventional nudging and find significant improvements with the former.

Children's classification and lexicalization of attractiveness, gender, and race: differential displays of these concepts and relatedness to bias and flexibility.

PubMed

Rennels, Jennifer L; Langlois, Judith H

2014-10-01

Minimal research has examined children's functional use of attractiveness to classify and label others, an important step in the development of children's biases. This study compared 3- to 11-year-olds' classification, sorting, and labeling of others and themselves based on attractiveness, gender, and race and also investigated whether these abilities and other characteristics predicted children's bias and flexibility. Relative to gender and race, children rarely used attractiveness to spontaneously classify people and were less accurate at sorting and labeling others and themselves by attractiveness, suggesting that they have a less explicit concept of attractiveness. Predictors of bias differed depending on domain and assessment method (forced choice or non-forced choice), showing that children's bias is affected by both individual differences and task characteristics. Predictors of flexibility differed based on whether children were assigning positive or negative traits to target children, demonstrating that the valence of attributes is an important consideration when conceptualizing children's flexibility. Copyright © 2014 Elsevier Inc. All rights reserved.

Children’s Classification and Lexicalization of Attractiveness, Gender, and Race: Differential Displays of These Concepts and Relatedness to Bias and Flexibility

PubMed Central

Rennels, Jennifer L.; Langlois, Judith H.

2014-01-01

Minimal research has examined children’s functional use of attractiveness to classify and label others, an important step in the development of children’s biases. This study compared 3-to 11-year-olds’ classification, sorting, and labeling of others and themselves based on attractiveness, gender, and race, and investigated whether these abilities and other characteristics predicted children’s bias and flexibility. Relative to gender and race, children rarely used attractiveness to spontaneously classify people and were less accurate at sorting and labeling others and themselves by attractiveness, suggesting they have a less explicit concept of attractiveness. Predictors of bias differed depending upon domain and assessment method (forced choice or non-forced choice), showing that children’s bias is affected by both individual differences and task characteristics. Predictors of flexibility differed based on whether children were assigning positive or negative traits to target children, demonstrating that the valence of attributes is an important consideration when conceptualizing children’s flexibility. PMID:24842583

Predictive Methods for Dense Polymer Networks: Combating Bias with Bio-Based Structures

DTIC Science & Technology

2016-03-16

Informatics Tools Acknowledgements: Air Force Office of Scientific Research, Air Force Research Laboratory, Office of Naval Research, Strategic...Sources and Methods • Bio-based cyanate esters have been made from anethole, resveratrol, eugenol, cresol, lignin, vanillin, and even creosote oils ...not large by informatics standards, it nonetheless represents a significant amount of synthetic effort. Because the data is limited, minimizing

Implications of the methodological choices for hydrologic portrayals of climate change over the contiguous United States: Statistically downscaled forcing data and hydrologic models

USGS Publications Warehouse

Mizukami, Naoki; Clark, Martyn P.; Gutmann, Ethan D.; Mendoza, Pablo A.; Newman, Andrew J.; Nijssen, Bart; Livneh, Ben; Hay, Lauren E.; Arnold, Jeffrey R.; Brekke, Levi D.

2016-01-01

Continental-domain assessments of climate change impacts on water resources typically rely on statistically downscaled climate model outputs to force hydrologic models at a finer spatial resolution. This study examines the effects of four statistical downscaling methods [bias-corrected constructed analog (BCCA), bias-corrected spatial disaggregation applied at daily (BCSDd) and monthly scales (BCSDm), and asynchronous regression (AR)] on retrospective hydrologic simulations using three hydrologic models with their default parameters (the Community Land Model, version 4.0; the Variable Infiltration Capacity model, version 4.1.2; and the Precipitation–Runoff Modeling System, version 3.0.4) over the contiguous United States (CONUS). Biases of hydrologic simulations forced by statistically downscaled climate data relative to the simulation with observation-based gridded data are presented. Each statistical downscaling method produces different meteorological portrayals including precipitation amount, wet-day frequency, and the energy input (i.e., shortwave radiation), and their interplay affects estimations of precipitation partitioning between evapotranspiration and runoff, extreme runoff, and hydrologic states (i.e., snow and soil moisture). The analyses show that BCCA underestimates annual precipitation by as much as −250 mm, leading to unreasonable hydrologic portrayals over the CONUS for all models. Although the other three statistical downscaling methods produce a comparable precipitation bias ranging from −10 to 8 mm across the CONUS, BCSDd severely overestimates the wet-day fraction by up to 0.25, leading to different precipitation partitioning compared to the simulations with other downscaled data. Overall, the choice of downscaling method contributes to less spread in runoff estimates (by a factor of 1.5–3) than the choice of hydrologic model with use of the default parameters if BCCA is excluded.

Bias correction of surface downwelling longwave and shortwave radiation for the EWEMBI dataset

NASA Astrophysics Data System (ADS)

Lange, Stefan

2018-05-01

Many meteorological forcing datasets include bias-corrected surface downwelling longwave and shortwave radiation (rlds and rsds). Methods used for such bias corrections range from multi-year monthly mean value scaling to quantile mapping at the daily timescale. An additional downscaling is necessary if the data to be corrected have a higher spatial resolution than the observational data used to determine the biases. This was the case when EartH2Observe (E2OBS; Calton et al., 2016) rlds and rsds were bias-corrected using more coarsely resolved Surface Radiation Budget (SRB; Stackhouse Jr. et al., 2011) data for the production of the meteorological forcing dataset EWEMBI (Lange, 2016). This article systematically compares various parametric quantile mapping methods designed specifically for this purpose, including those used for the production of EWEMBI rlds and rsds. The methods vary in the timescale at which they operate, in their way of accounting for physical upper radiation limits, and in their approach to bridging the spatial resolution gap between E2OBS and SRB. It is shown how temporal and spatial variability deflation related to bilinear interpolation and other deterministic downscaling approaches can be overcome by downscaling the target statistics of quantile mapping from the SRB to the E2OBS grid such that the sub-SRB-grid-scale spatial variability present in the original E2OBS data is retained. Cross validations at the daily and monthly timescales reveal that it is worthwhile to take empirical estimates of physical upper limits into account when adjusting either radiation component and that, overall, bias correction at the daily timescale is more effective than bias correction at the monthly timescale if sampling errors are taken into account.

Adaptive Variable Bias Magnetic Bearing Control

NASA Technical Reports Server (NTRS)

Johnson, Dexter; Brown, Gerald V.; Inman, Daniel J.

1998-01-01

Most magnetic bearing control schemes use a bias current with a superimposed control current to linearize the relationship between the control current and the force it delivers. With the existence of the bias current, even in no load conditions, there is always some power consumption. In aerospace applications, power consumption becomes an important concern. In response to this concern, an alternative magnetic bearing control method, called Adaptive Variable Bias Control (AVBC), has been developed and its performance examined. The AVBC operates primarily as a proportional-derivative controller with a relatively slow, bias current dependent, time-varying gain. The AVBC is shown to reduce electrical power loss, be nominally stable, and provide control performance similar to conventional bias control. Analytical, computer simulation, and experimental results are presented in this paper.

Encoding specificity manipulations do affect retrieval from memory.

PubMed

Zeelenberg, René

2005-05-01

In a recent article, P.A. Higham (2002) [Strong cues are not necessarily weak: Thomson and Tulving (1970) and the encoding specificity principle revisited. Memory &Cognition, 30, 67-80] proposed a new way to analyze cued recall performance in terms of three separable aspects of memory (retrieval, monitoring, and report bias) by comparing performance under both free-report and forced-report instructions. He used this method to derive estimates of these aspects of memory in an encoding specificity experiment similar to that reported by D.M. Thomson and E. Tulving (1970) [Associative encoding and retrieval: weak and strong cues. Journal of Experimental Psychology, 86, 255-262]. Under forced-report instructions, the encoding specificity manipulation did not affect performance. Higham concluded that the manipulation affected monitoring and report bias, but not retrieval. I argue that this interpretation of the results is problematic because the Thomson and Tulving paradigm is confounded, and show in three experiments using a more appropriate design that encoding specificity manipulations do affect performance in forced-report cued recall. Because in Higham's framework forced-report performance provides a measure of retrieval that is uncontaminated by monitoring and report bias it is concluded that encoding specificity manipulations do affect retrieval from memory.

Quantification of in-contact probe-sample electrostatic forces with dynamic atomic force microscopy.

PubMed

Balke, Nina; Jesse, Stephen; Carmichael, Ben; Okatan, M Baris; Kravchenko, Ivan I; Kalinin, Sergei V; Tselev, Alexander

2017-01-04

Atomic force microscopy (AFM) methods utilizing resonant mechanical vibrations of cantilevers in contact with a sample surface have shown sensitivities as high as few picometers for detecting surface displacements. Such a high sensitivity is harnessed in several AFM imaging modes. Here, we demonstrate a cantilever-resonance-based method to quantify electrostatic forces on a probe in the probe-sample junction in the presence of a surface potential or when a bias voltage is applied to the AFM probe. We find that the electrostatic forces acting on the probe tip apex can produce signals equivalent to a few pm of surface displacement. In combination with modeling, the measurements of the force were used to access the strength of the electrical field at the probe tip apex in contact with a sample. We find an evidence that the electric field strength in the junction can reach ca. 1 V nm -1 at a bias voltage of a few volts and is limited by non-ideality of the tip-sample contact. This field is sufficiently strong to significantly influence material states and kinetic processes through charge injection, Maxwell stress, shifts of phase equilibria, and reduction of energy barriers for activated processes. Besides, the results provide a baseline for accounting for the effects of local electrostatic forces in electromechanical AFM measurements as well as offer additional means to probe ionic mobility and field-induced phenomena in solids.

Probing local bias-induced transitions using photothermal excitation contact resonance atomic force microscopy and voltage spectroscopy

DOE PAGES

Li, Qian; Jesse, Stephen; Tselev, Alexander; ...

2015-01-05

In this paper, nanomechanical properties are closely related to the states of matter, including chemical composition, crystal structure, mesoscopic domain configuration, etc. Investigation of these properties at the nanoscale requires not only static imaging methods, e.g., contact resonance atomic force microscopy (CR-AFM), but also spectroscopic methods capable of revealing their dependence on various external stimuli. Here we demonstrate the voltage spectroscopy of CR-AFM, which was realized by combining photothermal excitation (as opposed to the conventional piezoacoustic excitation method) with the band excitation technique. We applied this spectroscopy to explore local bias-induced phenomena ranging from purely physical to surface electromechanical andmore » electrochemical processes. Our measurements show that the changes in the surface properties associated with these bias-induced transitions can be accurately assessed in a fast and dynamic manner, using resonance frequency as a signature. Finally, with many of the advantages offered by photothermal excitation, contact resonance voltage spectroscopy not only is expected to find applications in a broader field of nanoscience but also will provide a basis for future development of other nanoscale elastic spectroscopies.« less

Specific and Non-Specific Protein Association in Solution: Computation of Solvent Effects and Prediction of First-Encounter Modes for Efficient Configurational Bias Monte Carlo Simulations

PubMed Central

Cardone, Antonio; Pant, Harish; Hassan, Sergio A.

2013-01-01

Weak and ultra-weak protein-protein association play a role in molecular recognition, and can drive spontaneous self-assembly and aggregation. Such interactions are difficult to detect experimentally, and are a challenge to the force field and sampling technique. A method is proposed to identify low-population protein-protein binding modes in aqueous solution. The method is designed to identify preferential first-encounter complexes from which the final complex(es) at equilibrium evolves. A continuum model is used to represent the effects of the solvent, which accounts for short- and long-range effects of water exclusion and for liquid-structure forces at protein/liquid interfaces. These effects control the behavior of proteins in close proximity and are optimized based on binding enthalpy data and simulations. An algorithm is described to construct a biasing function for self-adaptive configurational-bias Monte Carlo of a set of interacting proteins. The function allows mixing large and local changes in the spatial distribution of proteins, thereby enhancing sampling of relevant microstates. The method is applied to three binary systems. Generalization to multiprotein complexes is discussed. PMID:24044772

Nanohardness and Residual Stress in TiN Coatings.

PubMed

Hernández, Luis Carlos; Ponce, Luis; Fundora, Abel; López, Enrique; Pérez, Eduardo

2011-05-17

TiN films were prepared by the Cathodic arc evaporation deposition method under different negative substrate bias. AFM image analyses show that the growth mode of biased coatings changes from 3D island to lateral when the negative bias potential is increased. Nanohardness of the thin films was measured by nanoindentation, and residual stress was determined using Grazing incidence X ray diffraction. The maximum value of residual stress is reached at -100 V substrate bias coinciding with the biggest values of adhesion and nanohardness. Nanoindentation measurement proves that the force-depth curve shifts due to residual stress. The experimental results demonstrate that nanohardness is seriously affected by the residual stress.

Optimization and Experimentation of Dual-Mass MEMS Gyroscope Quadrature Error Correction Methods

PubMed Central

Cao, Huiliang; Li, Hongsheng; Kou, Zhiwei; Shi, Yunbo; Tang, Jun; Ma, Zongmin; Shen, Chong; Liu, Jun

2016-01-01

This paper focuses on an optimal quadrature error correction method for the dual-mass MEMS gyroscope, in order to reduce the long term bias drift. It is known that the coupling stiffness and demodulation error are important elements causing bias drift. The coupling stiffness in dual-mass structures is analyzed. The experiment proves that the left and right masses’ quadrature errors are different, and the quadrature correction system should be arranged independently. The process leading to quadrature error is proposed, and the Charge Injecting Correction (CIC), Quadrature Force Correction (QFC) and Coupling Stiffness Correction (CSC) methods are introduced. The correction objects of these three methods are the quadrature error signal, force and the coupling stiffness, respectively. The three methods are investigated through control theory analysis, model simulation and circuit experiments, and the results support the theoretical analysis. The bias stability results based on CIC, QFC and CSC are 48 °/h, 9.9 °/h and 3.7 °/h, respectively, and this value is 38 °/h before quadrature error correction. The CSC method is proved to be the better method for quadrature correction, and it improves the Angle Random Walking (ARW) value, increasing it from 0.66 °/√h to 0.21 °/√h. The CSC system general test results show that it works well across the full temperature range, and the bias stabilities of the six groups’ output data are 3.8 °/h, 3.6 °/h, 3.4 °/h, 3.1 °/h, 3.0 °/h and 4.2 °/h, respectively, which proves the system has excellent repeatability. PMID:26751455

Optimization and Experimentation of Dual-Mass MEMS Gyroscope Quadrature Error Correction Methods.

PubMed

Cao, Huiliang; Li, Hongsheng; Kou, Zhiwei; Shi, Yunbo; Tang, Jun; Ma, Zongmin; Shen, Chong; Liu, Jun

2016-01-07

This paper focuses on an optimal quadrature error correction method for the dual-mass MEMS gyroscope, in order to reduce the long term bias drift. It is known that the coupling stiffness and demodulation error are important elements causing bias drift. The coupling stiffness in dual-mass structures is analyzed. The experiment proves that the left and right masses' quadrature errors are different, and the quadrature correction system should be arranged independently. The process leading to quadrature error is proposed, and the Charge Injecting Correction (CIC), Quadrature Force Correction (QFC) and Coupling Stiffness Correction (CSC) methods are introduced. The correction objects of these three methods are the quadrature error signal, force and the coupling stiffness, respectively. The three methods are investigated through control theory analysis, model simulation and circuit experiments, and the results support the theoretical analysis. The bias stability results based on CIC, QFC and CSC are 48 °/h, 9.9 °/h and 3.7 °/h, respectively, and this value is 38 °/h before quadrature error correction. The CSC method is proved to be the better method for quadrature correction, and it improves the Angle Random Walking (ARW) value, increasing it from 0.66 °/√h to 0.21 °/√h. The CSC system general test results show that it works well across the full temperature range, and the bias stabilities of the six groups' output data are 3.8 °/h, 3.6 °/h, 3.4 °/h, 3.1 °/h, 3.0 °/h and 4.2 °/h, respectively, which proves the system has excellent repeatability.

Quantification of tension to explain bias dependence of driven polymer translocation dynamics

NASA Astrophysics Data System (ADS)

Suhonen, P. M.; Piili, J.; Linna, R. P.

2017-12-01

Motivated by identifying the origin of the bias dependence of tension propagation, we investigate methods for measuring tension propagation quantitatively in computer simulations of driven polymer translocation. Here, the motion of flexible polymer chains through a narrow pore is simulated using Langevin dynamics. We measure tension forces, bead velocities, bead distances, and bond angles along the polymer at all stages of translocation with unprecedented precision. Measurements are done at a standard temperature used in simulations and at zero temperature to pin down the effect of fluctuations. The measured quantities were found to give qualitatively similar characteristics, but the bias dependence could be determined only using tension force. We find that in the scaling relation τ ˜Nβfdα for translocation time τ , the polymer length N , and the bias force fd, the increase of the exponent β with bias is caused by center-of-mass diffusion of the polymer toward the pore on the cis side. We find that this diffusion also causes the exponent α to deviate from the ideal value -1 . The bias dependence of β was found to result from combination of diffusion and pore friction and so be relevant for polymers that are too short to be considered asymptotically long. The effect is relevant in experiments all of which are made using polymers whose lengths are far below the asymptotic limit. Thereby, our results also corroborate the theoretical prediction by Sakaue's theory [Polymers 8, 424 (2016), 10.3390/polym8120424] that there should not be bias dependence of β for asymptotically long polymers. By excluding fluctuations we also show that monomer crowding at the pore exit cannot have a measurable effect on translocation dynamics under realistic conditions.

Impact of Acoustic Radiation Force Excitation Geometry on Shear Wave Dispersion and Attenuation Estimates.

PubMed

Lipman, Samantha L; Rouze, Ned C; Palmeri, Mark L; Nightingale, Kathryn R

2018-04-01

Shear wave elasticity imaging (SWEI) characterizes the mechanical properties of human tissues to differentiate healthy from diseased tissue. Commercial scanners tend to reconstruct shear wave speeds for a region of interest using time-of-flight methods reporting a single shear wave speed (or elastic modulus) to the end user under the assumptions that tissue is elastic and shear wave speeds are not dependent on the frequency content of the shear waves. Human tissues, however, are known to be viscoelastic, resulting in dispersion and attenuation. Shear wave spectroscopy and spectral methods have been previously reported in the literature to quantify shear wave dispersion and attenuation, commonly making an assumption that the acoustic radiation force excitation acts as a cylindrical source with a known geometric shear wave amplitude decay. This work quantifies the bias in shear dispersion and attenuation estimates associated with making this cylindrical wave assumption when applied to shear wave sources with finite depth extents, as commonly occurs with realistic focal geometries, in elastic and viscoelastic media. Bias is quantified using analytically derived shear wave data and shear wave data generated using finite-element method models. Shear wave dispersion and attenuation bias (up to 15% for dispersion and 41% for attenuation) is greater for more tightly focused acoustic radiation force sources with smaller depths of field relative to their lateral extent (height-to-width ratios <16). Dispersion and attenuation errors associated with assuming a cylindrical geometric shear wave decay in SWEI can be appreciable and should be considered when analyzing the viscoelastic properties of tissues with acoustic radiation force source distributions with limited depths of field. Copyright © 2018 World Federation for Ultrasound in Medicine and Biology. Published by Elsevier Inc. All rights reserved.

Single-molecule force spectroscopy study of interactions between angiotensin II type 1 receptor and different biased ligands in living cells.

PubMed

Li, Wenhui; Xu, Jiachao; Kou, Xiaolong; Zhao, Rong; Zhou, Wei; Fang, Xiaohong

2018-05-01

Angiotensin II type 1 receptor (AT1R), a typical G protein-coupled receptor, plays a key role in regulating many cardiovascular functions. Different ligands can bind with AT1R to selectively activate either G protein (Gq) or β-arrestin (β-arr) pathway, or both pathways, but the molecular mechanism is not clear yet. In this work, we used, for the first time, atomic force microscopy-based single molecule force spectroscopy (SMFS) to study the interactions of AT1R with three types of ligands, balanced ligand, Gq-biased ligand, and β-arr-biased ligand, in living cells. The results revealed their difference in binding force and binding stability. The complex of the Gq-biased ligand-AT1R overcame two energy barriers with an intermediate state during dissociation, whereas that of β-arr-biased ligand-AT1R complex overcame one energy barrier. This indicated that AT1R had different ligand-binding conformational substates and underwent different structural changes to activate downstream signaling pathways with variable agonist efficacies. Quantitative analysis of AT1R-ligand binding in living cells at the single-molecule level offers a new tool to study the molecular mechanism of AT1R biased activation. Graphical Abstract Single-molecule force measurement on the living cell expressing AT1R-eGFP with a ligand modified AFM tip (left), the dynamic force spectra of β-arrestin biased ligands-AT1R (middle), and Gq-biased ligands-AT1R (right). The complexes of β-arr-biased ligand-AT1R overcame one energy barrier, with one linear region in the spectra, whereas the Gq-biased ligand-AT1R complexes overcame two energy barriers with two linear regions.

Bias-correction of CORDEX-MENA projections using the Distribution Based Scaling method

NASA Astrophysics Data System (ADS)

Bosshard, Thomas; Yang, Wei; Sjökvist, Elin; Arheimer, Berit; Graham, L. Phil

2014-05-01

Within the Regional Initiative for the Assessment of the Impact of Climate Change on Water Resources and Socio-Economic Vulnerability in the Arab Region (RICCAR) lead by UN ESCWA, CORDEX RCM projections for the Middle East Northern Africa (MENA) domain are used to drive hydrological impacts models. Bias-correction of newly available CORDEX-MENA projections is a central part of this project. In this study, the distribution based scaling (DBS) method has been applied to 6 regional climate model projections driven by 2 RCP emission scenarios. The DBS method uses a quantile mapping approach and features a conditional temperature correction dependent on the wet/dry state in the climate model data. The CORDEX-MENA domain is particularly challenging for bias-correction as it spans very diverse climates showing pronounced dry and wet seasons. Results show that the regional climate models simulate too low temperatures and often have a displaced rainfall band compared to WATCH ERA-Interim forcing data in the reference period 1979-2008. DBS is able to correct the temperature biases as well as some aspects of the precipitation biases. Special focus is given to the analysis of the influence of the dry-frequency bias (i.e. climate models simulating too few rain days) on the bias-corrected projections and on the modification of the climate change signal by the DBS method.

Nanoscale amorphization of GeTe nanowire with conductive atomic force microscope.

PubMed

Kim, JunHo

2014-10-01

We fabricated GeTe nanowires by using Au catalysis mediated vapor-liquid-solid method. The fabricated nanowires were confirmed by X-ray diffraction, scanning electron microscopy and transmission electron microscopy. For a nanowire with - 150 nm diameter, we performed amorphization experiment with conductive atomic force microscope. We examined the structural change of the nanowire with several bias voltages from 0 V to 10 V. Above bias voltage of 6-7 V, some points of the nanowire showed transition to amorphous phase. The consumed energy for the amorphization was estimated to be 4-5 nJ, which was close to the other result of nanowire tested with a four probe device.

Frequency-varying synchronous micro-vibration suppression for a MSFW with application of small-gain theorem

NASA Astrophysics Data System (ADS)

Peng, Cong; Fan, Yahong; Huang, Ziyuan; Han, Bangcheng; Fang, Jiancheng

2017-01-01

This paper presents a novel synchronous micro-vibration suppression method on the basis of the small gain theorem to reduce the frequency-varying synchronous micro-vibration forces for a magnetically suspended flywheel (MSFW). The proposed synchronous micro-vibration suppression method not only eliminates the synchronous current fluctuations to force the rotor spinning around the inertia axis, but also considers the compensation caused by the displacement stiffness in the permanent-magnet (PM)-biased magnetic bearings. Moreover, the stability of the proposed control system is exactly analyzed by using small gain theorem. The effectiveness of the proposed micro-vibration suppression method is demonstrated via the direct measurement of the disturbance forces for a MSFW. The main merit of the proposed method is that it provides a simple and practical method in suppressing the frequency varying micro-vibration forces and preserving the nominal performance of the baseline control system.

Quantification of in-contact probe-sample electrostatic forces with dynamic atomic force microscopy

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

Balke, Nina Wisinger; Jesse, Stephen; Carmichael, Ben D.

Here, atomic force microscopy (AFM) methods utilizing resonant mechanical vibrations of cantilevers in contact with a sample surface have shown sensitivities as high as few picometers for detecting surface displacements. Such a high sensitivity is harnessed in several AFM imaging modes. Here, we demonstrate a cantilever-resonance-based method to quantify electrostatic forces on a probe in the probe-sample junction in the presence of a surface potential or when a bias voltage is applied to the AFM probe. We find that the electrostatic forces acting on the probe tip apex can produce signals equivalent to a few pm of surface displacement. Inmore » combination with modeling, the measurements of the force were used to access the strength of the electrical field at the probe tip apex in contact with a sample. We find an evidence that the electric field strength in the junction can reach ca. 1 V nm –1 at a bias voltage of a few volts and is limited by non-ideality of the tip-sample contact. This field is sufficiently strong to significantly influence material states and kinetic processes through charge injection, Maxwell stress, shifts of phase equilibria, and reduction of energy barriers for activated processes. Besides, the results provide a baseline for accounting for the effects of local electrostatic forces in electromechanical AFM measurements as well as offer additional means to probe ionic mobility and field-induced phenomena in solids.« less

Quantification of In-Contact Probe-Sample Electrostatic Forces with Dynamic Atomic Force Microscopy.

PubMed

Balke, Nina; Jesse, Stephen; Carmichael, Ben; Okatan, M; Kravchenko, Ivan; Kalinin, Sergei; Tselev, Alexander

2016-12-13

Atomic Force Microscopy (AFM) methods utilizing resonant mechanical vibrations of cantilevers in contact with a sample surface have shown sensitivities as high as few picometers for detecting surface displacements. Such a high sensitivity is harnessed in several AFM imaging modes. Here, we demonstrate a cantilever-resonance-based method to quantify electrostatic forces on a probe in the probe-sample junction in the presence of a surface potential or when a bias voltage is applied to the AFM probe. We find that the electrostatic forces acting on the probe tip apex can produce signals equivalent to a few pm of surface displacement. In combination with modeling, the measurements of the force were used to access the strength of the electrical field at the probe tip apex in contact with a sample. We find an evidence that the electric field strength in the junction can reach ca. 1 V/nm at a bias voltage of a few volts and is limited by non-ideality of the tip-sample contact. This field is sufficiently strong to significantly influence material states and kinetic processes through charge injection, Maxwell stress, shifts of phase equilibria, and reduction of energy barriers for activated processes. Besides, the results provide a baseline for accounting for the effects of local electrostatic forces in electromechanical AFM measurements as well as offer additional means to probe ionic mobility and field-induced phenomena in solids. Copyright 2016 IOP Publishing Ltd.

Quantification of in-contact probe-sample electrostatic forces with dynamic atomic force microscopy

DOE PAGES

Balke, Nina Wisinger; Jesse, Stephen; Carmichael, Ben D.; ...

2017-01-04

Here, atomic force microscopy (AFM) methods utilizing resonant mechanical vibrations of cantilevers in contact with a sample surface have shown sensitivities as high as few picometers for detecting surface displacements. Such a high sensitivity is harnessed in several AFM imaging modes. Here, we demonstrate a cantilever-resonance-based method to quantify electrostatic forces on a probe in the probe-sample junction in the presence of a surface potential or when a bias voltage is applied to the AFM probe. We find that the electrostatic forces acting on the probe tip apex can produce signals equivalent to a few pm of surface displacement. Inmore » combination with modeling, the measurements of the force were used to access the strength of the electrical field at the probe tip apex in contact with a sample. We find an evidence that the electric field strength in the junction can reach ca. 1 V nm –1 at a bias voltage of a few volts and is limited by non-ideality of the tip-sample contact. This field is sufficiently strong to significantly influence material states and kinetic processes through charge injection, Maxwell stress, shifts of phase equilibria, and reduction of energy barriers for activated processes. Besides, the results provide a baseline for accounting for the effects of local electrostatic forces in electromechanical AFM measurements as well as offer additional means to probe ionic mobility and field-induced phenomena in solids.« less

Pressurized fluid torque driver control and method

NASA Technical Reports Server (NTRS)

Cook, Joseph S., Jr. (Inventor)

1994-01-01

Methods and apparatus are provided for a torque driver including a displaceable gear to limit torque transfer to a fastener at a precisely controlled torque limit. A biasing assembly biases a first gear into engagement with a second gear for torque transfer between the first and second gear. The biasing assembly includes a pressurized cylinder controlled at a constant pressure that corresponds to a torque limit. A calibrated gage and valve is used to set the desired torque limit. One or more coiled output linkages connect the first gear with the fastener adaptor which may be a socket for a nut. A gear tooth profile provides a separation force that overcomes the bias to limit torque at the desired torque limit. Multiple fasteners may be rotated simultaneously to a desired torque limit if additional output spur gears are provided. The torque limit is adjustable and may be different for fasteners within the same fastener configuration.

Enhanced sub-micron colloidal particle separation with interdigitated microelectrode arrays using mixed AC/DC dielectrophoretic scheme.

PubMed

Swaminathan, Vikhram V; Shannon, Mark A; Bashir, Rashid

2015-04-01

Dielectrophoretic separation of particles finds a variety of applications in the capture of species such as cells, viruses, proteins, DNA from biological systems, as well as other organic and inorganic contaminants from water. The ability to capture particles is constrained by poor volumetric scaling of separation force with respect to particle diameter, as well as the weak penetration of electric fields in the media. In order to improve the separation of sub-micron colloids, we present a scheme based on multiple interdigitated electrode arrays under mixed AC/DC bias. The use of high frequency longitudinal AC bias breaks the shielding effects through electroosmotic micromixing to enhance electric fields through the electrolyte, while a transverse DC bias between the electrode arrays enables penetration of the separation force to capture particles from the bulk of the microchannel. We determine the favorable biasing conditions for field enhancement with the help of analytical models, and experimentally demonstrate the improved capture from sub-micron colloidal suspensions with the mixed AC/DC electrostatic excitation scheme over conventional AC-DEP methods.

Development of reactive force fields using ab initio molecular dynamics simulation minimally biased to experimental data

NASA Astrophysics Data System (ADS)

Chen, Chen; Arntsen, Christopher; Voth, Gregory A.

2017-10-01

Incorporation of quantum mechanical electronic structure data is necessary to properly capture the physics of many chemical processes. Proton hopping in water, which involves rearrangement of chemical and hydrogen bonds, is one such example of an inherently quantum mechanical process. Standard ab initio molecular dynamics (AIMD) methods, however, do not yet accurately predict the structure of water and are therefore less than optimal for developing force fields. We have instead utilized a recently developed method which minimally biases AIMD simulations to match limited experimental data to develop novel multiscale reactive molecular dynamics (MS-RMD) force fields by using relative entropy minimization. In this paper, we present two new MS-RMD models using such a parameterization: one which employs water with harmonic internal vibrations and another which uses anharmonic water. We show that the newly developed MS-RMD models very closely reproduce the solvation structure of the hydrated excess proton in the target AIMD data. We also find that the use of anharmonic water increases proton hopping, thereby increasing the proton diffusion constant.

The Role of Response Bias in Perceptual Learning

PubMed Central

2015-01-01

Sensory judgments improve with practice. Such perceptual learning is often thought to reflect an increase in perceptual sensitivity. However, it may also represent a decrease in response bias, with unpracticed observers acting in part on a priori hunches rather than sensory evidence. To examine whether this is the case, 55 observers practiced making a basic auditory judgment (yes/no amplitude-modulation detection or forced-choice frequency/amplitude discrimination) over multiple days. With all tasks, bias was present initially, but decreased with practice. Notably, this was the case even on supposedly “bias-free,” 2-alternative forced-choice, tasks. In those tasks, observers did not favor the same response throughout (stationary bias), but did favor whichever response had been correct on previous trials (nonstationary bias). Means of correcting for bias are described. When applied, these showed that at least 13% of perceptual learning on a forced-choice task was due to reduction in bias. In other situations, changes in bias were shown to obscure the true extent of learning, with changes in estimated sensitivity increasing once bias was corrected for. The possible causes of bias and the implications for our understanding of perceptual learning are discussed. PMID:25867609

Electrostatic force spectroscopy revealing the degree of reduction of individual graphene oxide sheets.

PubMed

Shen, Yue; Wang, Ying; Zhou, Yuan; Hai, Chunxi; Hu, Jun; Zhang, Yi

2018-01-01

Electrostatic force spectroscopy (EFS) is a method for monitoring the electrostatic force microscopy (EFM) phase with high resolution as a function of the electrical direct current bias applied either to the probe or sample. Based on the dielectric constant difference of graphene oxide (GO) sheets (reduced using various methods), EFS can be used to characterize the degree of reduction of uniformly reduced one-atom-thick GO sheets at the nanoscale. In this paper, using thermally or chemically reduced individual GO sheets on mica substrates as examples, we characterize their degree of reduction at the nanoscale using EFS. For the reduced graphene oxide (rGO) sheets with a given degree of reduction (sample n), the EFS curve is very close to a parabola within a restricted area. We found that the change in parabola opening direction (or sign the parabola opening value) indicates the onset of reduction on GO sheets. Moreover, the parabola opening value, the peak bias value (tip bias leads to the peak or valley EFM phases) and the EFM phase contrast at a certain tip bias less than the peak value can all indicate the degree of reduction of rGO samples, which is positively correlated with the dielectric constant. In addition, we gave the ranking of degree for reduction on thermally or chemically reduced GO sheets and evaluated the effects of the reducing conditions. The identification of the degree of reduction of GO sheets using EFS is important for reduction strategy optimization and mass application of GO, which is highly desired owing to its mechanical, thermal, optical and electronic applications. Furthermore, as a general and quantitative technique for evaluating the small differences in the dielectric properties of nanomaterials, the EFS technique will extend and facilitate its nanoscale electronic devices applications in the future.

Experimental investigation of SDBD plasma actuator driven by AC high voltage with a superimposed positive pulse bias voltage

NASA Astrophysics Data System (ADS)

Qi, Xiao-Hua; Yan, Hui-Jie; Yang, Liang; Hua, Yue; Ren, Chun-Sheng

2017-08-01

In this work, a driven voltage consisting of AC high voltage with a superimposed positive pulse bias voltage ("AC+ Positive pulse bias" voltage) is adopted to study the performance of a surface dielectric barrier discharge plasma actuator under atmospheric conditions. To compare the performance of the actuator driven by single-AC voltage and "AC+ Positive pulse bias" voltage, the actuator-induced thrust force and power consumption are measured as a function of the applied AC voltage, and the measured results indicate that the thrust force can be promoted significantly after superimposing the positive pulse bias voltage. The physical mechanism behind the thrust force changes is analyzed by measuring the optical properties, electrical characteristics, and surface potential distribution. Experimental results indicate that the glow-like discharge in the AC voltage half-cycle, next to the cycle where a bias voltage pulse has been applied, is enhanced after applying the positive pulse bias voltage, and this perhaps is the main reason for the thrust force increase. Moreover, surface potential measurement results reveal that the spatial electric field formed by the surface charge accumulation after positive pulse discharge can significantly affect the applied external electric field, and this perhaps can be responsible for the experimental phenomenon that the decrease of thrust force is delayed by pulse bias voltage action after the filament discharge occurs in the glow-like discharge region. The schlieren images further verify that the actuator-induced airflow velocity increases with the positive pulse voltage.

AGCM Biases in Evaporation Regime: Impacts on Soil Moisture Memory and Land-Atmosphere Feedback

NASA Technical Reports Server (NTRS)

Mahanama, Sarith P. P.; Koster, Randal D.

2005-01-01

Because precipitation and net radiation in an atmospheric general circulation model (AGCM) are typically biased relative to observations, the simulated evaporative regime of a region may be biased, with consequent negative effects on the AGCM s ability to translate an initialized soil moisture anomaly into an improved seasonal prediction. These potential problems are investigated through extensive offline analyses with the Mosaic land surface model (LSM). We first forced the LSM globally with a 15-year observations-based dataset. We then repeated the simulation after imposing a representative set of GCM climate biases onto the forcings - the observational forcings were scaled so that their mean seasonal cycles matched those simulated by the NSIPP-1 (NASA Global Modeling and Assimilation Office) AGCM over the same period-The AGCM s climate biases do indeed lead to significant biases in evaporative regime in certain regions, with the expected impacts on soil moisture memory timescales. Furthermore, the offline simulations suggest that the biased forcing in the AGCM should contribute to overestimated feedback in certain parts of North America - parts already identified in previous studies as having excessive feedback. The present study thus supports the notion that the reduction of climate biases in the AGCM will lead to more appropriate translations of soil moisture initialization into seasonal prediction skill.

Adaptive enhanced sampling with a path-variable for the simulation of protein folding and aggregation

NASA Astrophysics Data System (ADS)

Peter, Emanuel K.

2017-12-01

In this article, we present a novel adaptive enhanced sampling molecular dynamics (MD) method for the accelerated simulation of protein folding and aggregation. We introduce a path-variable L based on the un-biased momenta p and displacements dq for the definition of the bias s applied to the system and derive 3 algorithms: general adaptive bias MD, adaptive path-sampling, and a hybrid method which combines the first 2 methodologies. Through the analysis of the correlations between the bias and the un-biased gradient in the system, we find that the hybrid methodology leads to an improved force correlation and acceleration in the sampling of the phase space. We apply our method on SPC/E water, where we find a conservation of the average water structure. We then use our method to sample dialanine and the folding of TrpCage, where we find a good agreement with simulation data reported in the literature. Finally, we apply our methodologies on the initial stages of aggregation of a hexamer of Alzheimer's amyloid β fragment 25-35 (Aβ 25-35) and find that transitions within the hexameric aggregate are dominated by entropic barriers, while we speculate that especially the conformation entropy plays a major role in the formation of the fibril as a rate limiting factor.

Adaptive enhanced sampling with a path-variable for the simulation of protein folding and aggregation.

PubMed

Peter, Emanuel K

2017-12-07

In this article, we present a novel adaptive enhanced sampling molecular dynamics (MD) method for the accelerated simulation of protein folding and aggregation. We introduce a path-variable L based on the un-biased momenta p and displacements dq for the definition of the bias s applied to the system and derive 3 algorithms: general adaptive bias MD, adaptive path-sampling, and a hybrid method which combines the first 2 methodologies. Through the analysis of the correlations between the bias and the un-biased gradient in the system, we find that the hybrid methodology leads to an improved force correlation and acceleration in the sampling of the phase space. We apply our method on SPC/E water, where we find a conservation of the average water structure. We then use our method to sample dialanine and the folding of TrpCage, where we find a good agreement with simulation data reported in the literature. Finally, we apply our methodologies on the initial stages of aggregation of a hexamer of Alzheimer's amyloid β fragment 25-35 (Aβ 25-35) and find that transitions within the hexameric aggregate are dominated by entropic barriers, while we speculate that especially the conformation entropy plays a major role in the formation of the fibril as a rate limiting factor.

Power spectrum analysis with least-squares fitting: amplitude bias and its elimination, with application to optical tweezers and atomic force microscope cantilevers.

PubMed

Nørrelykke, Simon F; Flyvbjerg, Henrik

2010-07-01

Optical tweezers and atomic force microscope (AFM) cantilevers are often calibrated by fitting their experimental power spectra of Brownian motion. We demonstrate here that if this is done with typical weighted least-squares methods, the result is a bias of relative size between -2/n and +1/n on the value of the fitted diffusion coefficient. Here, n is the number of power spectra averaged over, so typical calibrations contain 10%-20% bias. Both the sign and the size of the bias depend on the weighting scheme applied. Hence, so do length-scale calibrations based on the diffusion coefficient. The fitted value for the characteristic frequency is not affected by this bias. For the AFM then, force measurements are not affected provided an independent length-scale calibration is available. For optical tweezers there is no such luck, since the spring constant is found as the ratio of the characteristic frequency and the diffusion coefficient. We give analytical results for the weight-dependent bias for the wide class of systems whose dynamics is described by a linear (integro)differential equation with additive noise, white or colored. Examples are optical tweezers with hydrodynamic self-interaction and aliasing, calibration of Ornstein-Uhlenbeck models in finance, models for cell migration in biology, etc. Because the bias takes the form of a simple multiplicative factor on the fitted amplitude (e.g. the diffusion coefficient), it is straightforward to remove and the user will need minimal modifications to his or her favorite least-squares fitting programs. Results are demonstrated and illustrated using synthetic data, so we can compare fits with known true values. We also fit some commonly occurring power spectra once-and-for-all in the sense that we give their parameter values and associated error bars as explicit functions of experimental power-spectral values.

Evaluation of a single column model at the Southern Great Plains climate research facility

NASA Astrophysics Data System (ADS)

Kennedy, Aaron D.

Despite recent advancements in global climate modeling, models produce a large range of climate sensitivities for the Earth. This range of sensitivities results in part from uncertainties in modeling clouds. To understand and to improve cloud parameterizations in Global Climate Models (GCMs), simulations should be evaluated using observations of clouds. Detailed studies can be conducted at Atmospheric Radiation Measurements (ARM) sites which provide adequate observations and forcing for Single Column Model (SCM) studies. Unfortunately, forcing for SCMs is sparse and not available for many locations or times. This study had two main goals: (1) evaluate clouds from the GISS Model E AR5 SCM at the ARM Southern Great Plains site and (2) determine whether reanalysis-based forcing was feasible at this location. To accomplish these goals, multiple model runs were conducted from 1999--2008 using forcing provided by ARM and forcing developed from the North American Regional Reanalysis (NARR). To better understand cloud biases and differences in the forcings, atmospheric states were classified using Self Organizing Maps (SOMs). Although model simulations had many similarities with the observations, there were several noticeable biases. Deep clouds had a negative bias year-round and this was attributed to clouds being too thin during frontal systems and a lack of convection during the spring and summer. These results were consistent regardless of the forcing used. During August, SCM simulations had a positive bias for low clouds. This bias varied with the forcing suggesting that part of the problem was tied to errors in the forcing. NARR forcing had many favorable characteristics when compared to ARM observations and forcing. In particular, temperature and wind information were more accurate than ARM when compared to balloon soundings. During the cool season, NARR forcing produced results similar to ARM with reasonable precipitation and a similar cloud field. Although NARR vertical velocities were weaker than ARM during the convective season, these simulations were able to capture the majority of convective events. The limiting factor for NARR was humidity biases in the upper troposphere during the summer months. Prior to releasing this forcing to the modeling community, this issue must be investigated further.

Regulatory and evolutionary signatures of sex-biased genes on both the X chromosome and the autosomes.

PubMed

Shen, Jiangshan J; Wang, Ting-You; Yang, Wanling

2017-11-02

Sex is an important but understudied factor in the genetics of human diseases. Analyses using a combination of gene expression data, ENCODE data, and evolutionary data of sex-biased gene expression in human tissues can give insight into the regulatory and evolutionary forces acting on sex-biased genes. In this study, we analyzed the differentially expressed genes between males and females. On the X chromosome, we used a novel method and investigated the status of genes that escape X-chromosome inactivation (escape genes), taking into account the clonality of lymphoblastoid cell lines (LCLs). To investigate the regulation of sex-biased differentially expressed genes (sDEG), we conducted pathway and transcription factor enrichment analyses on the sDEGs, as well as analyses on the genomic distribution of sDEGs. Evolutionary analyses were also conducted on both sDEGs and escape genes. Genome-wide, we characterized differential gene expression between sexes in 462 RNA-seq samples and identified 587 sex-biased genes, or 3.2% of the genes surveyed. On the X chromosome, sDEGs were distributed in evolutionary strata in a similar pattern as escape genes. We found a trend of negative correlation between the gene expression breadth and nonsynonymous over synonymous mutation (dN/dS) ratios, showing a possible pleiotropic constraint on evolution of genes. Genome-wide, nine transcription factors were found enriched in binding to the regions surrounding the transcription start sites of female-biased genes. Many pathways and protein domains were enriched in sex-biased genes, some of which hint at sex-biased physiological processes. These findings lend insight into the regulatory and evolutionary forces shaping sex-biased gene expression and their involvement in the physiological and pathological processes in human health and diseases.

Unconstrained Enhanced Sampling for Free Energy Calculations of Biomolecules: A Review

PubMed Central

Miao, Yinglong; McCammon, J. Andrew

2016-01-01

Free energy calculations are central to understanding the structure, dynamics and function of biomolecules. Yet insufficient sampling of biomolecular configurations is often regarded as one of the main sources of error. Many enhanced sampling techniques have been developed to address this issue. Notably, enhanced sampling methods based on biasing collective variables (CVs), including the widely used umbrella sampling, adaptive biasing force and metadynamics, have been discussed in a recent excellent review (Abrams and Bussi, Entropy, 2014). Here, we aim to review enhanced sampling methods that do not require predefined system-dependent CVs for biomolecular simulations and as such do not suffer from the hidden energy barrier problem as encountered in the CV-biasing methods. These methods include, but are not limited to, replica exchange/parallel tempering, self-guided molecular/Langevin dynamics, essential energy space random walk and accelerated molecular dynamics. While it is overwhelming to describe all details of each method, we provide a summary of the methods along with the applications and offer our perspectives. We conclude with challenges and prospects of the unconstrained enhanced sampling methods for accurate biomolecular free energy calculations. PMID:27453631

Unconstrained Enhanced Sampling for Free Energy Calculations of Biomolecules: A Review.

PubMed

Miao, Yinglong; McCammon, J Andrew

Free energy calculations are central to understanding the structure, dynamics and function of biomolecules. Yet insufficient sampling of biomolecular configurations is often regarded as one of the main sources of error. Many enhanced sampling techniques have been developed to address this issue. Notably, enhanced sampling methods based on biasing collective variables (CVs), including the widely used umbrella sampling, adaptive biasing force and metadynamics, have been discussed in a recent excellent review (Abrams and Bussi, Entropy, 2014). Here, we aim to review enhanced sampling methods that do not require predefined system-dependent CVs for biomolecular simulations and as such do not suffer from the hidden energy barrier problem as encountered in the CV-biasing methods. These methods include, but are not limited to, replica exchange/parallel tempering, self-guided molecular/Langevin dynamics, essential energy space random walk and accelerated molecular dynamics. While it is overwhelming to describe all details of each method, we provide a summary of the methods along with the applications and offer our perspectives. We conclude with challenges and prospects of the unconstrained enhanced sampling methods for accurate biomolecular free energy calculations.

The Bias in the Presentation of Stimulation when the Up and Down Method is Used with Forced Choice Responding.

DTIC Science & Technology

1980-07-01

where this technique has been used to measure sensory thresholds. In the psychological literature the up and down method is sometimes called the staircase...1969. 6. Smith, J. E. K., Stimulus programming in psychophysics. Psychometrika, 26: 27-33, 1961. 7. Taylor, M. M., and Creelman , C. D., PEST

Effect of a direct current bias on the electrohydrodynamic performance of a surface dielectric barrier discharge actuator for airflow control

NASA Astrophysics Data System (ADS)

Yan, Huijie; Yang, Liang; Qi, Xiaohua; Ren, Chunsheng

2015-02-01

The effect of a DC bias on the electrohydrodynamics (EHD) force induced by a surface dielectric barrier AC discharge actuator for airflow control at the atmospheric pressure is investigated. The measurement of the surface potential due to charge deposition at different DC biases is carried out by using a special designed corona like discharge potential probe. From the surface potential data, the plasma electromotive force is shown not affected much by the DC biases except for some reduction of the DC bias near the exposed electrode edge for the sheath-like configuration. The total thrust is measured by an analytical balance, and an almost linear relationship to the potential voltage at the exposed electrode edge is found for the direct thrust force. The temporally averaged ionic wind characteristics are investigated by Pitot tube sensor and schlieren visualization system. It is found that the ionic wind velocity profiles with different DC biases are almost the same in the AC discharge plasma area but gradually diversified in the further downstream area as well as the upper space away from the discharge plasma area. Also, the DC bias can significantly modify the topology of the ionic wind produced by the AC discharge actuator. These results can provide an insight into how the DC biases to affect the force generation.

Omens of coupled model biases in the CMIP5 AMIP simulations

NASA Astrophysics Data System (ADS)

Găinuşă-Bogdan, Alina; Hourdin, Frédéric; Traore, Abdoul Khadre; Braconnot, Pascale

2018-02-01

Despite decades of efforts and improvements in the representation of processes as well as in model resolution, current global climate models still suffer from a set of important, systematic biases in sea surface temperature (SST), not much different from the previous generation of climate models. Many studies have looked at errors in the wind field, cloud representation or oceanic upwelling in coupled models to explain the SST errors. In this paper we highlight the relationship between latent heat flux (LH) biases in forced atmospheric simulations and the SST biases models develop in coupled mode, at the scale of the entire intertropical domain. By analyzing 22 pairs of forced atmospheric and coupled ocean-atmosphere simulations from the CMIP5 database, we show a systematic, negative correlation between the spatial patterns of these two biases. This link between forced and coupled bias patterns is also confirmed by two sets of dedicated sensitivity experiments with the IPSL-CM5A-LR model. The analysis of the sources of the atmospheric LH bias pattern reveals that the near-surface wind speed bias dominates the zonal structure of the LH bias and that the near-surface relative humidity dominates the east-west contrasts.

Measurement method for determining the magnetic hysteresis effects of reluctance actuators by evaluation of the force and flux variation.

PubMed

Vrijsen, N H; Jansen, J W; Compter, J C; Lomonova, E A

2013-07-01

A measurement method is presented which identifies the magnetic hysteresis effects present in the force of linear reluctance actuators. The measurement method is applied to determine the magnetic hysteresis in the force of an E-core reluctance actuator, with and without pre-biasing permanent magnet. The force measurements are conducted with a piezoelectric load cell (Kistler type 9272). This high-bandwidth force measurement instrument is identified in the frequency domain using a voice-coil actuator that has negligible magnetic hysteresis and eddy currents. Specifically, the phase delay between the current and force of the voice-coil actuator is used for the calibration of the measurement instrument. This phase delay is also obtained by evaluation of the measured force and flux variation in the E-core actuator, both with and without permanent magnet on the middle tooth. The measured magnetic flux variation is used to distinguish the phase delay due to magnetic hysteresis from the measured phase delay between the current and the force of the E-core actuator. Finally, an open loop steady-state ac model is presented that predicts the magnetic hysteresis effects in the force of the E-core actuator.

Post-processing ECMWF precipitation and temperature ensemble reforecasts for operational hydrologic forecasting at various spatial scales

NASA Astrophysics Data System (ADS)

Verkade, J. S.; Brown, J. D.; Reggiani, P.; Weerts, A. H.

2013-09-01

The ECMWF temperature and precipitation ensemble reforecasts are evaluated for biases in the mean, spread and forecast probabilities, and how these biases propagate to streamflow ensemble forecasts. The forcing ensembles are subsequently post-processed to reduce bias and increase skill, and to investigate whether this leads to improved streamflow ensemble forecasts. Multiple post-processing techniques are used: quantile-to-quantile transform, linear regression with an assumption of bivariate normality and logistic regression. Both the raw and post-processed ensembles are run through a hydrologic model of the river Rhine to create streamflow ensembles. The results are compared using multiple verification metrics and skill scores: relative mean error, Brier skill score and its decompositions, mean continuous ranked probability skill score and its decomposition, and the ROC score. Verification of the streamflow ensembles is performed at multiple spatial scales: relatively small headwater basins, large tributaries and the Rhine outlet at Lobith. The streamflow ensembles are verified against simulated streamflow, in order to isolate the effects of biases in the forcing ensembles and any improvements therein. The results indicate that the forcing ensembles contain significant biases, and that these cascade to the streamflow ensembles. Some of the bias in the forcing ensembles is unconditional in nature; this was resolved by a simple quantile-to-quantile transform. Improvements in conditional bias and skill of the forcing ensembles vary with forecast lead time, amount, and spatial scale, but are generally moderate. The translation to streamflow forecast skill is further muted, and several explanations are considered, including limitations in the modelling of the space-time covariability of the forcing ensembles and the presence of storages.

First principles calculation of current-induced forces in atomic gold contacts

NASA Astrophysics Data System (ADS)

Brandbyge, Mads; Stokbro, Kurt; Taylor, Jeremy; Mozos, Jose-Luis; Ordejon, Pablo

2002-03-01

We have recently developed an first principles method [1] for calculating the electronic structure, electronic transport, and forces acting on the atoms, for atomic scale systems connected to semi-infinite electrodes and with an applied voltage bias. Our method is based on the density functional theory (DFT) as implemented in the well tested SIESTA program [2]. We fully deal with the atomistic structure of the whole system, treating both the contact and the electrodes on the same footing. The effect of the finite bias (including selfconsistency and the solution of the electrostatic problem) is taken into account using nonequilibrium Green's functions. In this talk we show results for the forces acting on the contact atoms due to the nonequilibrium situation in the electronic subsystem, i.e. in the presence of an electronic current. We concentrate on one atom wide gold contacts/wires connected to bulk gold electrodes. References [1] Our implementation is called TranSIESTA and is described in M. Brandbyge, J. Taylor, K. Stokbro, J-L. Mozos, and P. Ordejon, cond-mat/0110650 [2] D. Sanchez-Portal, P. Ordejon, E. Artacho and J. Soler, Int. J. Quantum Chem. 65, 453 (1997).

Probing of multiple magnetic responses in magnetic inductors using atomic force microscopy.

PubMed

Park, Seongjae; Seo, Hosung; Seol, Daehee; Yoon, Young-Hwan; Kim, Mi Yang; Kim, Yunseok

2016-02-08

Even though nanoscale analysis of magnetic properties is of significant interest, probing methods are relatively less developed compared to the significance of the technique, which has multiple potential applications. Here, we demonstrate an approach for probing various magnetic properties associated with eddy current, coil current and magnetic domains in magnetic inductors using multidimensional magnetic force microscopy (MMFM). The MMFM images provide combined magnetic responses from the three different origins, however, each contribution to the MMFM response can be differentiated through analysis based on the bias dependence of the response. In particular, the bias dependent MMFM images show locally different eddy current behavior with values dependent on the type of materials that comprise the MI. This approach for probing magnetic responses can be further extended to the analysis of local physical features.

Strain Gauge Balance Uncertainty Analysis at NASA Langley: A Technical Review

NASA Technical Reports Server (NTRS)

Tripp, John S.

1999-01-01

This paper describes a method to determine the uncertainties of measured forces and moments from multi-component force balances used in wind tunnel tests. A multivariate regression technique is first employed to estimate the uncertainties of the six balance sensitivities and 156 interaction coefficients derived from established balance calibration procedures. These uncertainties are then employed to calculate the uncertainties of force-moment values computed from observed balance output readings obtained during tests. Confidence and prediction intervals are obtained for each computed force and moment as functions of the actual measurands. Techniques are discussed for separate estimation of balance bias and precision uncertainties.

On the climate model simulation of Indian monsoon low pressure systems and the effect of remote disturbances and systematic biases

NASA Astrophysics Data System (ADS)

Levine, Richard C.; Martin, Gill M.

2018-06-01

Monsoon low pressure systems (LPS) are synoptic-scale systems forming over the Indian monsoon trough region, contributing substantially to seasonal mean summer monsoon rainfall there. Many current global climate models (GCMs), including the Met Office Unified Model (MetUM), show deficient rainfall in this region, much of which has previously been attributed to remote systematic biases such as excessive equatorial Indian Ocean (EIO) convection, while also substantially under-representing LPS and associated rainfall as they travel westwards across India. Here the sources and sensitivities of LPS to local, remote and short-timescale forcing are examined, in order to understand the poor representation in GCMs. An LPS tracking method is presented using TRACK feature tracking software for comparison between re-analysis data-sets, MetUM GCM and regional climate model (RCM) simulations. RCM simulations, at similar horizontal resolution to the GCM and forced with re-analysis data at the lateral boundaries, are carried out with different domains to examine the effects of remote biases. The results suggest that remote biases contribute significantly to the poor simulation of LPS in the GCM. As these remote systematic biases are common amongst many current GCMs, it is likely that GCMs are intrinsically capable of representing LPS, even at relatively low resolution. The main problem areas are time-mean excessive EIO convection and poor representation of precursor disturbances transmitted from the Western Pacific. The important contribution of the latter is established using RCM simulations forced by climatological 6-hourly lateral boundary conditions, which also highlight the role of LPS in moving rainfall from steep orography towards Central India.

Simulation of phase equilibria

NASA Astrophysics Data System (ADS)

Martin, Marcus Gary

The focus of this thesis is on the use of configurational bias Monte Carlo in the Gibbs ensemble. Unlike Metropolis Monte Carlo, which is reviewed in chapter I, configurational bias Monte Carlo uses an underlying Markov chain transition matrix which is asymmetric in such a way that it is more likely to attempt to move to a molecular conformation which has a lower energy than to one with a higher energy. Chapter II explains how this enables efficient simulation of molecules with complex architectures (long chains and branched molecules) for coexisting fluid phases (liquid, vapor, or supercritical), and also presents several of our recent extensions to this method. In chapter III we discuss the development of the Transferable Potentials for Phase Equilibria United Atom (TraPPE-UA) force field which accurately describes the fluid phase coexistence for linear and branched alkanes. Finally, in the fourth chapter the methods and the force field are applied to systems ranging from supercritical extraction to gas chromatography to illustrate the power and versatility of our approach.

Communication: Estimating the initial biasing potential for λ-local-elevation umbrella-sampling (λ-LEUS) simulations via slow growth

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

Bieler, Noah S.; Hünenberger, Philippe H., E-mail: phil@igc.phys.chem.ethz.ch

2014-11-28

In a recent article [Bieler et al., J. Chem. Theory Comput. 10, 3006–3022 (2014)], we introduced a combination of the λ-dynamics (λD) approach for calculating alchemical free-energy differences and of the local-elevation umbrella-sampling (LEUS) memory-based biasing method to enhance the sampling along the alchemical coordinate. The combined scheme, referred to as λ-LEUS, was applied to the perturbation of hydroquinone to benzene in water as a test system, and found to represent an improvement over thermodynamic integration (TI) in terms of sampling efficiency at equivalent accuracy. However, the preoptimization of the biasing potential required in the λ-LEUS method requires “filling up”more » all the basins in the potential of mean force. This introduces a non-productive pre-sampling time that is system-dependent, and generally exceeds the corresponding equilibration time in a TI calculation. In this letter, a remedy is proposed to this problem, termed the slow growth memory guessing (SGMG) approach. Instead of initializing the biasing potential to zero at the start of the preoptimization, an approximate potential of mean force is estimated from a short slow growth calculation, and its negative used to construct the initial memory. Considering the same test system as in the preceding article, it is shown that of the application of SGMG in λ-LEUS permits to reduce the preoptimization time by about a factor of four.« less

Communication: Estimating the initial biasing potential for λ-local-elevation umbrella-sampling (λ-LEUS) simulations via slow growth

NASA Astrophysics Data System (ADS)

Bieler, Noah S.; Hünenberger, Philippe H.

2014-11-01

In a recent article [Bieler et al., J. Chem. Theory Comput. 10, 3006-3022 (2014)], we introduced a combination of the λ-dynamics (λD) approach for calculating alchemical free-energy differences and of the local-elevation umbrella-sampling (LEUS) memory-based biasing method to enhance the sampling along the alchemical coordinate. The combined scheme, referred to as λ-LEUS, was applied to the perturbation of hydroquinone to benzene in water as a test system, and found to represent an improvement over thermodynamic integration (TI) in terms of sampling efficiency at equivalent accuracy. However, the preoptimization of the biasing potential required in the λ-LEUS method requires "filling up" all the basins in the potential of mean force. This introduces a non-productive pre-sampling time that is system-dependent, and generally exceeds the corresponding equilibration time in a TI calculation. In this letter, a remedy is proposed to this problem, termed the slow growth memory guessing (SGMG) approach. Instead of initializing the biasing potential to zero at the start of the preoptimization, an approximate potential of mean force is estimated from a short slow growth calculation, and its negative used to construct the initial memory. Considering the same test system as in the preceding article, it is shown that of the application of SGMG in λ-LEUS permits to reduce the preoptimization time by about a factor of four.

Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering.

PubMed

Gil-Ley, Alejandro; Bussi, Giovanni

2015-03-10

The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated in a Hamiltonian replica-exchange scheme. The ladder of replicas is built with different strengths of the bias potential exploiting the tunability of well-tempered metadynamics. Using this method, free-energy barriers of individual collective variables are significantly reduced compared with simple force-field scaling. The introduced methodology is flexible and allows adaptive bias potentials to be self-consistently constructed for a large number of simple collective variables, such as distances and dihedral angles. The method is tested on alanine dipeptide and applied to the difficult problem of conformational sampling in a tetranucleotide.

Opposing Forces of A/T-Biased Mutations and G/C-Biased Gene Conversions Shape the Genome of the Nematode Pristionchus pacificus

PubMed Central

Weller, Andreas M.; Rödelsperger, Christian; Eberhardt, Gabi; Molnar, Ruxandra I.; Sommer, Ralf J.

2014-01-01

Base substitution mutations are a major source of genetic novelty and mutation accumulation line (MAL) studies revealed a nearly universal AT bias in de novo mutation spectra. While a comparison of de novo mutation spectra with the actual nucleotide composition in the genome suggests the existence of general counterbalancing mechanisms, little is known about the evolutionary and historical details of these opposing forces. Here, we correlate MAL-derived mutation spectra with patterns observed from population resequencing. Variation observed in natural populations has already been subject to evolutionary forces. Distinction between rare and common alleles, the latter of which are close to fixation and of presumably older age, can provide insight into mutational processes and their influence on genome evolution. We provide a genome-wide analysis of de novo mutations in 22 MALs of the nematode Pristionchus pacificus and compare the spectra with natural variants observed in resequencing of 104 natural isolates. MALs show an AT bias of 5.3, one of the highest values observed to date. In contrast, the AT bias in natural variants is much lower. Specifically, rare derived alleles show an AT bias of 2.4, whereas common derived alleles close to fixation show no AT bias at all. These results indicate the existence of a strong opposing force and they suggest that the GC content of the P. pacificus genome is in equilibrium. We discuss GC-biased gene conversion as a potential mechanism acting against AT-biased mutations. This study provides insight into genome evolution by combining MAL studies with natural variation. PMID:24414549

The Air Force Officer Qualifying Test: Validity, Fairness, and Bias. Technical Report

ERIC Educational Resources Information Center

Hardison, Chaitra M.; Sims, Carra S.; Wong, Eunice C.

2010-01-01

The Air Force has long recognized the importance of selecting the most qualified officers possible. For more than 60 years, it has relied on the Air Force Officer Qualifying Test (AFOQT) as one measure of those qualifications. A variety of concerns have been raised about whether the AFOQT is biased, too expensive, or even valid for predicting…

Permanent magnet flux-biased magnetic actuator with flux feedback

NASA Technical Reports Server (NTRS)

Groom, Nelson J. (Inventor)

1991-01-01

The invention is a permanent magnet flux-biased magnetic actuator with flux feedback for adjustably suspending an element on a single axis. The magnetic actuator includes a pair of opposing electromagnets and provides bi-directional forces along the single axis to the suspended element. Permanent magnets in flux feedback loops from the opposing electromagnets establish a reference permanent magnet flux-bias to linearize the force characteristics of the electromagnets to extend the linear range of the actuator without the need for continuous bias currents in the electromagnets.

Displaceable Spur Gear Torque Controlled Driver and Method

NASA Technical Reports Server (NTRS)

Cook, Joseph S., Jr. (Inventor)

1996-01-01

Methods and apparatus are provided for a torque driver including a laterally displaceable gear support member to carry an output spur gear. A biasing assembly biases the output spur gear into engagement with a pinion to which is applied an input torque greater than a desired output torque limit for a threaded fastener such as a nut or screw. A coiled output linkage connects the output spur gear with a fastener adaptor which may be a socket for a nut. A gear tooth profile provides a separation force that overcomes the bias to limit torque at the desired torque limit. Multiple fasteners may be rotated simultaneously to a desired torque limit if additional output spur gears are provided. A gauged selector mechanism is provided to laterally displace multiple driven members for fasteners arranged in differing configurations. The torque limit is selectably adjustable and may be different for fasteners within the same fastener configuration.

Displaceable spur gear torque controlled driver and method

NASA Technical Reports Server (NTRS)

Cook, Joseph S., Jr. (Inventor)

1994-01-01

Methods and apparatus are provided for a torque driver including a laterally displaceable gear support member to carry an output spur gear. A biasing assembly biases the output spur gear into engagement with a pinion to which is applied an input torque greater than a desired output torque limit for a threaded fastener such as a nut or screw. A coiled output linkage connects the output spur gear with a fastener adaptor which may be a socket for a nut. A gear tooth profile provides a separation force that overcomes the bias to limit torque at the desired torque limit. Multiple fasteners may be rotated simultaneously to a desired torque limit if additional output spur gears are provided. A gauged selector mechanism is provided to laterally displace multiple driver members for fasteners arranged in differing configurations. The torque limit is selectably adjustable and may be different for fasteners within the same fastener configuration.

The Air Force Officer Qualifying Test: Validity, Fairness, and Bias

DTIC Science & Technology

2010-01-01

scores. The Standards for Educational and Psychological Testing (AERA, APA, and NCME, 1999) provides a set of guidelines published and endorsed by the...determining the validity and bias of selection tests falls upon professionals in the discipline of industrial/organizational psychology 20 See Roper v. Dep’t...i). 30 The Air Force Officer Qualifying Test : Validity, Fairness, and Bias and closely related fields (e.g., educational psychology and

Simulation of uphill/downhill running on a level treadmill using additional horizontal force.

PubMed

Gimenez, Philippe; Arnal, Pierrick J; Samozino, Pierre; Millet, Guillaume Y; Morin, Jean-Benoit

2014-07-18

Tilting treadmills allow a convenient study of biomechanics during uphill/downhill running, but they are not commonly available and there is even fewer tilting force-measuring treadmill. The aim of the present study was to compare uphill/downhill running on a treadmill (inclination of ± 8%) with running on a level treadmill using additional backward or forward pulling forces to simulate the effect of gravity. This comparison specifically focused on the energy cost of running, stride frequency (SF), electromyographic activity (EMG), leg and foot angles at foot strike, and ground impact shock. The main results are that SF, impact shock, and leg and foot angle parameters determined were very similar and significantly correlated between the two methods, the intercept and slope of the linear regression not differing significantly from zero and unity, respectively. The correlation of oxygen uptake (V̇O2) data between both methods was not significant during uphill running (r=0.42; P>0.05). V̇O2 data were correlated during downhill running (r=0.74; P<0.01) but there was a significant difference between the methods (bias=-2.51 ± 1.94 ml min(-1) kg(-1)). Linear regressions for EMG of vastus lateralis, biceps femoris, gastrocnemius lateralis, soleus and tibialis anterior were not different from the identity line but the systematic bias was elevated for this parameter. In conclusion, this method seems appropriate for the study of SF, leg and foot angle, impact shock parameters but is less applicable for physiological variables (EMG and energy cost) during uphill/downhill running when using a tilting force-measuring treadmill is not possible. Copyright © 2014 Elsevier Ltd. All rights reserved.

Combined frequency modulated atomic force microscopy and scanning tunneling microscopy detection for multi-tip scanning probe microscopy applications

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

Morawski, Ireneusz; Institute of Experimental Physics, University of Wrocław, pl. M. Borna 9, 50-204 Wrocław; Spiegelberg, Richard

A method which allows scanning tunneling microscopy (STM) tip biasing independent of the sample bias during frequency modulated atomic force microscopy (AFM) operation is presented. The AFM sensor is supplied by an electronic circuit combining both a frequency shift signal and a tunneling current signal by means of an inductive coupling. This solution enables a control of the tip potential independent of the sample potential. Individual tip biasing is specifically important in order to implement multi-tip STM/AFM applications. An extensional quartz sensor (needle sensor) with a conductive tip is applied to record simultaneously topography and conductivity of the sample. Themore » high resonance frequency of the needle sensor (1 MHz) allows scanning of a large area of the surface being investigated in a reasonably short time. A recipe for the amplitude calibration which is based only on the frequency shift signal and does not require the tip being in contact is presented. Additionally, we show spectral measurements of the mechanical vibration noise of the scanning system used in the investigations.« less

A bias-corrected CMIP5 dataset for Africa using the CDF-t method - a contribution to agricultural impact studies

NASA Astrophysics Data System (ADS)

Moise Famien, Adjoua; Janicot, Serge; Delfin Ochou, Abe; Vrac, Mathieu; Defrance, Dimitri; Sultan, Benjamin; Noël, Thomas

2018-03-01

The objective of this paper is to present a new dataset of bias-corrected CMIP5 global climate model (GCM) daily data over Africa. This dataset was obtained using the cumulative distribution function transform (CDF-t) method, a method that has been applied to several regions and contexts but never to Africa. Here CDF-t has been applied over the period 1950-2099 combining Historical runs and climate change scenarios for six variables: precipitation, mean near-surface air temperature, near-surface maximum air temperature, near-surface minimum air temperature, surface downwelling shortwave radiation, and wind speed, which are critical variables for agricultural purposes. WFDEI has been used as the reference dataset to correct the GCMs. Evaluation of the results over West Africa has been carried out on a list of priority user-based metrics that were discussed and selected with stakeholders. It includes simulated yield using a crop model simulating maize growth. These bias-corrected GCM data have been compared with another available dataset of bias-corrected GCMs using WATCH Forcing Data as the reference dataset. The impact of WFD, WFDEI, and also EWEMBI reference datasets has been also examined in detail. It is shown that CDF-t is very effective at removing the biases and reducing the high inter-GCM scattering. Differences with other bias-corrected GCM data are mainly due to the differences among the reference datasets. This is particularly true for surface downwelling shortwave radiation, which has a significant impact in terms of simulated maize yields. Projections of future yields over West Africa are quite different, depending on the bias-correction method used. However all these projections show a similar relative decreasing trend over the 21st century.

An improved bias correction method of daily rainfall data using a sliding window technique for climate change impact assessment

NASA Astrophysics Data System (ADS)

Smitha, P. S.; Narasimhan, B.; Sudheer, K. P.; Annamalai, H.

2018-01-01

Regional climate models (RCMs) are used to downscale the coarse resolution General Circulation Model (GCM) outputs to a finer resolution for hydrological impact studies. However, RCM outputs often deviate from the observed climatological data, and therefore need bias correction before they are used for hydrological simulations. While there are a number of methods for bias correction, most of them use monthly statistics to derive correction factors, which may cause errors in the rainfall magnitude when applied on a daily scale. This study proposes a sliding window based daily correction factor derivations that help build reliable daily rainfall data from climate models. The procedure is applied to five existing bias correction methods, and is tested on six watersheds in different climatic zones of India for assessing the effectiveness of the corrected rainfall and the consequent hydrological simulations. The bias correction was performed on rainfall data downscaled using Conformal Cubic Atmospheric Model (CCAM) to 0.5° × 0.5° from two different CMIP5 models (CNRM-CM5.0, GFDL-CM3.0). The India Meteorological Department (IMD) gridded (0.25° × 0.25°) observed rainfall data was considered to test the effectiveness of the proposed bias correction method. The quantile-quantile (Q-Q) plots and Nash Sutcliffe efficiency (NSE) were employed for evaluation of different methods of bias correction. The analysis suggested that the proposed method effectively corrects the daily bias in rainfall as compared to using monthly factors. The methods such as local intensity scaling, modified power transformation and distribution mapping, which adjusted the wet day frequencies, performed superior compared to the other methods, which did not consider adjustment of wet day frequencies. The distribution mapping method with daily correction factors was able to replicate the daily rainfall pattern of observed data with NSE value above 0.81 over most parts of India. Hydrological simulations forced using the bias corrected rainfall (distribution mapping and modified power transformation methods that used the proposed daily correction factors) was similar to those simulated by the IMD rainfall. The results demonstrate that the methods and the time scales used for bias correction of RCM rainfall data have a larger impact on the accuracy of the daily rainfall and consequently the simulated streamflow. The analysis suggests that the distribution mapping with daily correction factors can be preferred for adjusting RCM rainfall data irrespective of seasons or climate zones for realistic simulation of streamflow.

Vertebrate codon bias indicates a highly GC-rich ancestral genome.

PubMed

Nabiyouni, Maryam; Prakash, Ashwin; Fedorov, Alexei

2013-04-25

Two factors are thought to have contributed to the origin of codon usage bias in eukaryotes: 1) genome-wide mutational forces that shape overall GC-content and create context-dependent nucleotide bias, and 2) positive selection for codons that maximize efficient and accurate translation. Particularly in vertebrates, these two explanations contradict each other and cloud the origin of codon bias in the taxon. On the one hand, mutational forces fail to explain GC-richness (~60%) of third codon positions, given the GC-poor overall genomic composition among vertebrates (~40%). On the other hand, positive selection cannot easily explain strict regularities in codon preferences. Large-scale bioinformatic assessment, of nucleotide composition of coding and non-coding sequences in vertebrates and other taxa, suggests a simple possible resolution for this contradiction. Specifically, we propose that the last common vertebrate ancestor had a GC-rich genome (~65% GC). The data suggest that whole-genome mutational bias is the major driving force for generating codon bias. As the bias becomes prominent, it begins to affect translation and can result in positive selection for optimal codons. The positive selection can, in turn, significantly modulate codon preferences. Copyright © 2013 Elsevier B.V. All rights reserved.

The Role of Scale and Model Bias in ADAPT's Photospheric Eatimation

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

Godinez Vazquez, Humberto C.; Hickmann, Kyle Scott; Arge, Charles Nicholas

2015-05-20

The Air Force Assimilative Photospheric flux Transport model (ADAPT), is a magnetic flux propagation based on Worden-Harvey (WH) model. ADAPT would be used to provide a global photospheric map of the Earth. A data assimilation method based on the Ensemble Kalman Filter (EnKF), a method of Monte Carlo approximation tied with Kalman filtering, is used in calculating the ADAPT models.

The role of electrostatic charge in the adhesion of spherical particles onto planar surfaces in atmospheric systems

DOE PAGES

Kweon, Hyojin; Yiacoumi, Sotira Z.; Tsouris, Costas

2015-06-19

In this study, the influence of electrostatic charge on the adhesive force between spherical particles and planar surfaces in atmospheric systems was studied using atomic force microscopy. Electrical bias was applied to modify the surface charge, and it was found that application of a stronger positive bias to a particle induces a stronger total adhesive force. The sensitivity of the system to changes in the bias depended on the surface charge density. For larger-size particles, the contribution of the electrostatic force decreased, and the capillary force became the major contributor to the total adhesive force. The influence of water adsorptionmore » on the total adhesive force and, specifically, on the contribution of the electrostatic force depended on the hydrophobicity of interacting surfaces. For a hydrophilic surface, water adsorption either attenuated the surface charge or screened the effect of surface potential. An excessive amount of adsorbed water provided a path to surface charge leakage, which might cancel out the electrostatic force, leading to a reduction in the adhesive force. Theoretically calculated forces were comparable with measured adhesive forces except for mica which has a highly localized surface potential. The results of this study provide information on the behavior of charged colloidal particles in atmospheric systems.« less

Diffusion of Brownian particles in a tilted periodic potential under the influence of an external Ornstein-Uhlenbeck noise

NASA Astrophysics Data System (ADS)

Bai, Zhan-Wu; Zhang, Wei

2018-01-01

The diffusion behaviors of Brownian particles in a tilted periodic potential under the influence of an internal white noise and an external Ornstein-Uhlenbeck noise are investigated through numerical simulation. In contrast to the case when the bias force is smaller or absent, the diffusion coefficient exhibits a nonmonotonic dependence on the correlation time of the external noise when bias force is large. A mechanism different from locked-to-running transition theory is presented for the diffusion enhancement by a bias force in intermediate to large damping. In the underdamped regime and the presence of external noise, the diffusion coefficient is a monotonically decreasing function of low temperature rather than a nonmonotonic function when external noise is absent. The diffusive process undergoes four regimes when bias force approaches but is less than its critical value and noises intensities are small. These behaviors can be attributed to the locked-to-running transition of particles.

Contributions of the atmosphere-land and ocean-sea ice model components to the tropical Atlantic SST bias in CESM1

NASA Astrophysics Data System (ADS)

Song, Z.; Lee, S. K.; Wang, C.; Kirtman, B. P.; Qiao, F.

2016-02-01

In order to identify and quantify intrinsic errors in the atmosphere-land and ocean-sea ice model components of the Community Earth System Model version 1 (CESM1) and their contributions to the tropical Atlantic sea surface temperature (SST) bias in CESM1, we propose a new method of diagnosis and apply it to a set of CESM1 simulations. Our analyses of the model simulations indicate that both the atmosphere-land and ocean-sea ice model components of CESM1 contain large errors in the tropical Atlantic. When the two model components are fully coupled, the intrinsic errors in the two components emerge quickly within a year with strong seasonality in their growth rates. In particular, the ocean-sea ice model contributes significantly in forcing the eastern equatorial Atlantic warm SST bias in early boreal summer. Further analysis shows that the upper thermocline water underneath the eastern equatorial Atlantic surface mixed layer is too warm in a stand-alone ocean-sea ice simulation of CESM1 forced with observed surface flux fields, suggesting that the mixed layer cooling associated with the entrainment of upper thermocline water is too weak in early boreal summer. Therefore, although we acknowledge the potential importance of the westerly wind bias in the western equatorial Atlantic and the low-level stratus cloud bias in the southeastern tropical Atlantic, both of which originate from the atmosphere-land model, we emphasize here that solving those problems in the atmosphere-land model alone does not resolve the equatorial Atlantic warm bias in CESM1.

Enhanced Conformational Sampling Using Replica Exchange with Collective-Variable Tempering

PubMed Central

2015-01-01

The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated in a Hamiltonian replica-exchange scheme. The ladder of replicas is built with different strengths of the bias potential exploiting the tunability of well-tempered metadynamics. Using this method, free-energy barriers of individual collective variables are significantly reduced compared with simple force-field scaling. The introduced methodology is flexible and allows adaptive bias potentials to be self-consistently constructed for a large number of simple collective variables, such as distances and dihedral angles. The method is tested on alanine dipeptide and applied to the difficult problem of conformational sampling in a tetranucleotide. PMID:25838811

Structural tuning of nanogaps using electromigration induced by field emission current with bipolar biasing

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

Yagi, Mamiko; Ito, Mitsuki; Shirakashi, Jun-ichi, E-mail: shrakash@cc.tuat.ac.jp

We report a new method for fabrication of Ni nanogaps based on electromigration induced by a field emission current. This method is called “activation” and is demonstrated here using a current source with alternately reversing polarities. The activation procedure with alternating current bias, in which the current source polarity alternates between positive and negative bias conditions, is performed with planar Ni nanogaps defined on SiO{sub 2}/Si substrates at room temperature. During negative biasing, a Fowler-Nordheim field emission current flows from the source (cathode) to the drain (anode) electrode. The Ni atoms at the tip of the drain electrode are thusmore » activated and then migrate across the gap from the drain to the source electrode. In contrast, in the positive bias case, the field emission current moves the activated atoms from the source to the drain electrode. These two procedures are repeated until the tunnel resistance of the nanogaps is successively reduced from 100 TΩ to 48 kΩ. Scanning electron microscopy and atomic force microscopy studies showed that the gap separation narrowed from approximately 95 nm to less than 10 nm because of the Ni atoms that accumulated at the tips of both the source and drain electrodes. These results show that the alternately biased activation process, which is a newly proposed atom transfer technique, can successfully control the tunnel resistance of the Ni nanogaps and is a suitable method for formation of ultrasmall nanogap structures.« less

Vertical electrostatic force in MEMS cantilever IR sensor

NASA Astrophysics Data System (ADS)

Rezadad, Imen; Boroumand Azad, Javaneh; Smith, Evan M.; Alhasan, Ammar; Peale, Robert E.

2014-06-01

A MEMS cantilever IR detector that repetitively lifts from the surface under the influence of a saw-tooth electrostatic force, where the contact duty cycle is a measure of the absorbed IR radiation, is analyzed. The design is comprised of three parallel conducting plates. Fixed buried and surface plates are held at opposite potential. A moveable cantilever is biased the same as the surface plate. Calculations based on energy methods with position-dependent capacity and electrostatic induction coefficients demonstrate the upward sign of the force on the cantilever and determine the force magnitude. 2D finite element method calculations of the local fields confirm the sign of the force and determine its distribution across the cantilever. The upward force is maximized when the surface plate is slightly larger than the other two. The electrostatic repulsion is compared with Casimir sticking force to determine the maximum useful contact area. MEMS devices were fabricated and the vertical displacement of the cantilever was observed in a number of experiments. The approach may be applied also to MEMS actuators and micromirrors.

Toward structure prediction of cyclic peptides.

PubMed

Yu, Hongtao; Lin, Yu-Shan

2015-02-14

Cyclic peptides are a promising class of molecules that can be used to target specific protein-protein interactions. A computational method to accurately predict their structures would substantially advance the development of cyclic peptides as modulators of protein-protein interactions. Here, we develop a computational method that integrates bias-exchange metadynamics simulations, a Boltzmann reweighting scheme, dihedral principal component analysis and a modified density peak-based cluster analysis to provide a converged structural description for cyclic peptides. Using this method, we evaluate the performance of a number of popular protein force fields on a model cyclic peptide. All the tested force fields seem to over-stabilize the α-helix and PPII/β regions in the Ramachandran plot, commonly populated by linear peptides and proteins. Our findings suggest that re-parameterization of a force field that well describes the full Ramachandran plot is necessary to accurately model cyclic peptides.

Children’s Beliefs in Reciprocation of Biases and Flexibility

PubMed Central

Rennels, Jennifer L.

2015-01-01

Children display positive and negative biases based on peers’ attractiveness, gender, and race, but it is unclear whether children who associate positive attributes with certain peers also believe those peers think positively of them. In each domain (attractiveness, gender, race), we measured 3- to 11-year-olds’ (N=102) biases and flexibility and their beliefs in reciprocity of bias and flexibility by asking who would think positively of them. Children could choose one of two unfamiliar peers (forced choice assessment) or had the additional options of choosing both or neither peer (non-forced choice assessment). We found children often displayed beliefs in reciprocation, with beliefs in positive bias reciprocation from attractive girls showing the largest effect sizes. These beliefs significantly correlated with and were predictive of children’s positive and negative biases and flexibility. The duality of children’s beliefs may contribute to strengthening their biases and segregating social groups. PMID:25918015

Displaceable Gear Torque Controlled Driver

NASA Technical Reports Server (NTRS)

Cook, Joseph S., Jr. (Inventor)

1997-01-01

Methods and apparatus are provided for a torque driver including a displaceable gear to limit torque transfer to a fastener at a precisely controlled torque limit. A biasing assembly biases a first gear into engagement with a second gear for torque transfer between the first and second gear. The biasing assembly includes a pressurized cylinder controlled at a constant pressure that corresponds to a torque limit. A calibrated gage and valve is used to set the desired torque limit. One or more coiled output linkages connect the first gear with the fastener adaptor which may be a socket for a nut. A gear tooth profile provides a separation force that overcomes the bias to limit torque at the desired torque limit. Multiple fasteners may be rotated simultaneously to a desired torque limit if additional output spur gears are provided. The torque limit is adjustable and may be different for fasteners within the same fastener configuration.

Guidelines for Nonsexist Use of Language

ERIC Educational Resources Information Center

School Counselor, 1976

1976-01-01

An APA task force, after critically analyzing graduate level psychology textbooks, found sex bias in the style of these books as well as in reporting more studies by males than by females. To avoid future bias, the task force has issued certain guidelines and principles which are listed in this article. (SE)

Bias current dependence of resistivity in Co0.4Fe0.4B0.2 ultrathin film prepared by RF magnetron sputtering

NASA Astrophysics Data System (ADS)

Mandal, Snehal; Mazumdar, Dipak; Das, I.

2018-04-01

Ultrathin film of Co0.4Fe0.4B0.2 was prepared on p-type Si (100) substrate by RF magnetron sputtering. X-Ray Reflectivity and Atomic Force Microscopy measurements were performed to estimate the thickness and surface roughness of the film. Electrical transport measurements were performed by four-probe method in a current-in-plane (CIP) geometry. Presence of non-linearity in the current-voltage (I-V) characteristics was observed at higher current range. The electrical resistivity was found to change by several orders of magnitude (105) by changing the bias current from nano-ampere (nA) to milli-ampere (mA) range. This bias current dependence of the resistivity has been explained by different transport mechanisms.

Processing of Swarm Accelerometer Data into Thermospheric Neutral Densities

NASA Astrophysics Data System (ADS)

Doornbos, E.; Siemes, C.; Encarnacao, J.; Peřestý, R.; Grunwaldt, L.; Kraus, J.; Holmdahl Olsen, P. E.; van den IJssel, J.; Flury, J.; Apelbaum, G.

2015-12-01

The Swarm satellites were launched on 22 November 2013 and carry accelerometers and GPS receivers as part of their scientific payload. The GPS receivers are not only used for locating the position and time of the magnetic measurements, but also for determining non-gravitational forces like drag and radiation pressure acting on the spacecraft. The accelerometers measure these forces directly, at much finer resolution than the GPS receivers, from which thermospheric neutral densities and potentially winds can be derived. Unfortunately, the acceleration measurements suffer from a variety of disturbances, the most prominent being slow temperature-induced bias variations and sudden bias changes. These disturbances have caused a significant delay of the accelerometer data release. In this presentation, we describe the new three-stage processing that is required for transforming the disturbed acceleration measurements into scientifically valuable thermospheric neutral densities. In the first stage, the sudden bias changes in the acceleration measurements are removed using a dedicated software tool. The second stage is the calibration of the accelerometer measurements against the non-gravitational accelerations derived from the GPS receiver, which includes the correction for the slow temperature-induced bias variations. The third stage consists of transforming the corrected and calibrated accelerations into thermospheric neutral densities. We describe the methods used in each stage, highlight the difficulties encountered, and comment on the quality of the thermospheric neutral density data set, which covers the geomagnetic storm on 17 March 2015.

Importance of Preserving Cross-correlation in developing Statistically Downscaled Climate Forcings and in estimating Land-surface Fluxes and States

NASA Astrophysics Data System (ADS)

Das Bhowmik, R.; Arumugam, S.

2015-12-01

Multivariate downscaling techniques exhibited superiority over univariate regression schemes in terms of preserving cross-correlations between multiple variables- precipitation and temperature - from GCMs. This study focuses on two aspects: (a) develop an analytical solutions on estimating biases in cross-correlations from univariate downscaling approaches and (b) quantify the uncertainty in land-surface states and fluxes due to biases in cross-correlations in downscaled climate forcings. Both these aspects are evaluated using climate forcings available from both historical climate simulations and CMIP5 hindcasts over the entire US. The analytical solution basically relates the univariate regression parameters, co-efficient of determination of regression and the co-variance ratio between GCM and downscaled values. The analytical solutions are compared with the downscaled univariate forcings by choosing the desired p-value (Type-1 error) in preserving the observed cross-correlation. . For quantifying the impacts of biases on cross-correlation on estimating streamflow and groundwater, we corrupt the downscaled climate forcings with different cross-correlation structure.

Free Energy Reconstruction from Metadynamics or Adiabatic Free Energy Dynamics Simulations.

PubMed

Cuendet, Michel A; Tuckerman, Mark E

2014-08-12

In molecular dynamics simulations, most enhanced sampling methods are traditionally associated with one particular estimator to calculate the free energy surface (FES), such as the histogram, the mean force, or the bias potential. Here, we start from the realization that four enhanced sampling methods, metadynamics and well-tempered metadynamics (in their extended Lagrangian form), as well as driven adiabatic free energy dynamics (dAFED) and unified free energy dynamics (UFED), can be used in combination with any of the three above-mentioned FES estimators. We compare the convergence properties of these estimators on the alanine dipeptide and a sodium ion solvation shell. We find that the mean force estimator is superior in all cases. We also show that it can be marginally beneficial to combine information from the histogram and the force, provided that both are of comparable accuracy.

Efficient Determination of Free Energy Landscapes in Multiple Dimensions from Biased Umbrella Sampling Simulations Using Linear Regression.

PubMed

Meng, Yilin; Roux, Benoît

2015-08-11

The weighted histogram analysis method (WHAM) is a standard protocol for postprocessing the information from biased umbrella sampling simulations to construct the potential of mean force with respect to a set of order parameters. By virtue of the WHAM equations, the unbiased density of state is determined by satisfying a self-consistent condition through an iterative procedure. While the method works very effectively when the number of order parameters is small, its computational cost grows rapidly in higher dimension. Here, we present a simple and efficient alternative strategy, which avoids solving the self-consistent WHAM equations iteratively. An efficient multivariate linear regression framework is utilized to link the biased probability densities of individual umbrella windows and yield an unbiased global free energy landscape in the space of order parameters. It is demonstrated with practical examples that free energy landscapes that are comparable in accuracy to WHAM can be generated at a small fraction of the cost.

Efficient Determination of Free Energy Landscapes in Multiple Dimensions from Biased Umbrella Sampling Simulations Using Linear Regression

PubMed Central

2015-01-01

The weighted histogram analysis method (WHAM) is a standard protocol for postprocessing the information from biased umbrella sampling simulations to construct the potential of mean force with respect to a set of order parameters. By virtue of the WHAM equations, the unbiased density of state is determined by satisfying a self-consistent condition through an iterative procedure. While the method works very effectively when the number of order parameters is small, its computational cost grows rapidly in higher dimension. Here, we present a simple and efficient alternative strategy, which avoids solving the self-consistent WHAM equations iteratively. An efficient multivariate linear regression framework is utilized to link the biased probability densities of individual umbrella windows and yield an unbiased global free energy landscape in the space of order parameters. It is demonstrated with practical examples that free energy landscapes that are comparable in accuracy to WHAM can be generated at a small fraction of the cost. PMID:26574437

Subsurface imaging of carbon nanotube networks in polymers with DC-biased multifrequency dynamic atomic force microscopy.

PubMed

Thompson, Hank T; Barroso-Bujans, Fabienne; Herrero, Julio Gomez; Reifenberger, Ron; Raman, Arvind

2013-04-05

The characterization of dispersion and connectivity of carbon nanotube (CNT) networks inside polymers is of great interest in polymer nanocomposites in new material systems, organic photovoltaics, and in electrodes for batteries and supercapacitors. We focus on a technique using amplitude modulation atomic force microscopy (AM-AFM) in the attractive regime of operation, using both single and dual mode excitation, which upon the application of a DC tip bias voltage allows, via the phase channel, the in situ, nanoscale, subsurface imaging of CNT networks dispersed in a polymer matrix at depths of 10-100 nm. We present an in-depth study of the origins of phase contrast in this technique and demonstrate that an electrical energy dissipation mechanism in the Coulomb attractive regime is key to the formation of the phase contrast which maps the spatial variations in the local capacitance and resistance due to the CNT network. We also note that dual frequency excitation can, under some conditions, improve the contrast for such samples. These methods open up the possibility for DC-biased amplitude modulation AFM to be used for mapping the variations in local capacitance and resistance in nanocomposites with conducting networks.

OMIP contribution to CMIP6: experimental and diagnostic protocol for the physical component of the Ocean Model Intercomparison Project

NASA Astrophysics Data System (ADS)

Griffies, Stephen M.; Danabasoglu, Gokhan; Durack, Paul J.; Adcroft, Alistair J.; Balaji, V.; Böning, Claus W.; Chassignet, Eric P.; Curchitser, Enrique; Deshayes, Julie; Drange, Helge; Fox-Kemper, Baylor; Gleckler, Peter J.; Gregory, Jonathan M.; Haak, Helmuth; Hallberg, Robert W.; Heimbach, Patrick; Hewitt, Helene T.; Holland, David M.; Ilyina, Tatiana; Jungclaus, Johann H.; Komuro, Yoshiki; Krasting, John P.; Large, William G.; Marsland, Simon J.; Masina, Simona; McDougall, Trevor J.; Nurser, A. J. George; Orr, James C.; Pirani, Anna; Qiao, Fangli; Stouffer, Ronald J.; Taylor, Karl E.; Treguier, Anne Marie; Tsujino, Hiroyuki; Uotila, Petteri; Valdivieso, Maria; Wang, Qiang; Winton, Michael; Yeager, Stephen G.

2016-09-01

The Ocean Model Intercomparison Project (OMIP) is an endorsed project in the Coupled Model Intercomparison Project Phase 6 (CMIP6). OMIP addresses CMIP6 science questions, investigating the origins and consequences of systematic model biases. It does so by providing a framework for evaluating (including assessment of systematic biases), understanding, and improving ocean, sea-ice, tracer, and biogeochemical components of climate and earth system models contributing to CMIP6. Among the WCRP Grand Challenges in climate science (GCs), OMIP primarily contributes to the regional sea level change and near-term (climate/decadal) prediction GCs.OMIP provides (a) an experimental protocol for global ocean/sea-ice models run with a prescribed atmospheric forcing; and (b) a protocol for ocean diagnostics to be saved as part of CMIP6. We focus here on the physical component of OMIP, with a companion paper (Orr et al., 2016) detailing methods for the inert chemistry and interactive biogeochemistry. The physical portion of the OMIP experimental protocol follows the interannual Coordinated Ocean-ice Reference Experiments (CORE-II). Since 2009, CORE-I (Normal Year Forcing) and CORE-II (Interannual Forcing) have become the standard methods to evaluate global ocean/sea-ice simulations and to examine mechanisms for forced ocean climate variability. The OMIP diagnostic protocol is relevant for any ocean model component of CMIP6, including the DECK (Diagnostic, Evaluation and Characterization of Klima experiments), historical simulations, FAFMIP (Flux Anomaly Forced MIP), C4MIP (Coupled Carbon Cycle Climate MIP), DAMIP (Detection and Attribution MIP), DCPP (Decadal Climate Prediction Project), ScenarioMIP, HighResMIP (High Resolution MIP), as well as the ocean/sea-ice OMIP simulations.

Bias in masked word identification: unconscious influences of repetition priming.

PubMed

Masson, Michael E J

2002-12-01

The beneficial influence of a prior study episode on subsequent identification of a word includes a large bias component, revealed in the forced-choice variant of the masked word identification test. In that type of test, subjects show a preference for a studied probe over a nonstudied probe, regardless of which one matches the masked target word. The forced-choice test was used in the present experiments to test the possibility that this bias effect is due to conscious recollection. Results show that bias was strongly attenuated (1) by changes in modality between study and test, and (2) under certain conditions, by using a conceptually driven study task. The bias effect was found only when probes were orthographically similar to one another, as predicted by the counter model (Ratcliff & McKoon, 1997). These results provide strong evidence that the bias effect is not mediated by conscious recollection.

A Comparison of Vertical Stiffness Values Calculated from Different Measures of Center of Mass Displacement in Single-Leg Hopping.

PubMed

Mudie, Kurt L; Gupta, Amitabh; Green, Simon; Hobara, Hiroaki; Clothier, Peter J

2017-02-01

This study assessed the agreement between K vert calculated from 4 different methods of estimating vertical displacement of the center of mass (COM) during single-leg hopping. Healthy participants (N = 38) completed a 10-s single-leg hopping effort on a force plate, with 3D motion of the lower limb, pelvis, and trunk captured. Derived variables were calculated for a total of 753 hop cycles using 4 methods, including: double integration of the vertical ground reaction force, law of falling bodies, a marker cluster on the sacrum, and a segmental analysis method. Bland-Altman plots demonstrated that K vert calculated using segmental analysis and double integration methods have a relatively small bias (0.93 kN⋅m -1 ) and 95% limits of agreement (-1.89 to 3.75 kN⋅m -1 ). In contrast, a greater bias was revealed between sacral marker cluster and segmental analysis (-2.32 kN⋅m -1 ), sacral marker cluster and double integration (-3.25 kN⋅m -1 ), and the law of falling bodies compared with all methods (17.26-20.52 kN⋅m -1 ). These findings suggest the segmental analysis and double integration methods can be used interchangeably for the calculation of K vert during single-leg hopping. The authors propose the segmental analysis method to be considered the gold standard for the calculation of K vert during single-leg, on-the-spot hopping.

Children's beliefs in reciprocation of biases and flexibility.

PubMed

Rennels, Jennifer L; Langlois, Judith H

2015-09-01

Children display positive and negative biases based on peers' attractiveness, gender, and race, but it is unclear whether children who associate positive attributes with certain peers also believe those peers think positively of them. In each domain (attractiveness, gender, and race), we measured 3- to 11-year-olds' (N = 102) biases and flexibility and their beliefs in reciprocity of bias and flexibility by asking who would think positively of them. Children could choose one of two unfamiliar peers (forced choice assessment) or had the additional options of choosing both peers or neither peer (non-forced choice assessment). We found that children often displayed beliefs in reciprocation, with beliefs in positive bias reciprocation from attractive girls showing the largest effect sizes. These beliefs were significantly correlated with and were predictive of children's positive and negative biases and flexibility. The duality of children's beliefs may contribute to strengthening their biases and segregating social groups. Copyright © 2015 Elsevier Inc. All rights reserved.

Portuguese Armed Forces in the International Security and Assistance Force in Afghanistan: Psychological Support for the Command of Kabul International Airport

DTIC Science & Technology

2006-04-01

all other results are higher than the reference population averages. One should not neglect the bias of the results due to the “ social desirability...scales applied in this paper, the hypothesis of a bias ( social desirability) is also to be taken into account, in spite of the fact that the force...the main adjustment factors are: • Social competences (interpersonal relationship capability and team integration); • Family support; • Emotional

Effect of Position- and Velocity-Dependent Forces on Reaching Movements at Different Speeds

PubMed Central

Summa, Susanna; Casadio, Maura; Sanguineti, Vittorio

2016-01-01

The speed of voluntary movements is determined by the conflicting needs of maximizing accuracy and minimizing mechanical effort. Dynamic perturbations, e.g., force fields, may be used to manipulate movements in order to investigate these mechanisms. Here, we focus on how the presence of position- and velocity-dependent force fields affects the relation between speed and accuracy during hand reaching movements. Participants were instructed to perform reaching movements under visual control in two directions, corresponding to either low or high arm inertia. The subjects were required to maintain four different movement durations (very slow, slow, fast, very fast). The experimental protocol included three phases: (i) familiarization—the robot generated no force; (ii) force field—the robot generated a force; and (iii) after-effect—again, no force. Participants were randomly assigned to four groups, depending on the type of force that was applied during the “force field” phase. The robot was programmed to generate position-dependent forces—with positive (K+) or negative stiffness (K−)—or velocity-dependent forces, with either positive (B+) or negative viscosity (B−). We focused on path curvature, smoothness, and endpoint error; in the latter we distinguished between bias and variability components. Movements in the high-inertia direction are smoother and less curved; smoothness also increases with movement speed. Endpoint bias and variability are greater in, respectively, the high and low inertia directions. A robust dependence on movement speed was only observed in the longitudinal components of both bias and variability. The strongest and more consistent effects of perturbation were observed with negative viscosity (B−), which resulted in increased variability during force field adaptation and in a reduction of the endpoint bias, which was retained in the subsequent after-effect phase. These findings confirm that training with negative viscosity produces lasting effects in movement accuracy at all speeds. PMID:27965559

The Role of Convective Gustiness in Reducing Seasonal Precipitation Biases in the Tropical West Pacific

NASA Astrophysics Data System (ADS)

Harrop, Bryce E.; Ma, Po-Lun; Rasch, Philip J.; Neale, Richard B.; Hannay, Cecile

2018-04-01

Precipitation is an important climate quantity that is critically relevant to society. In spite of intense efforts, significant precipitation biases remain in most climate models. One pervasive and persistent bias found in many general circulation models occurs in the Tropical West Pacific where northern hemisphere summer-time precipitation is often underestimated compared to observations. Using the DOE-E3SM model, the inclusion of a missing process, convective gustiness, is shown to reduce those biases through a net increase in surface evaporation. Gustiness in surface wind fields is assumed to arise empirically in proportion to the intensity of convective precipitation. The increased evaporation can be treated as an increase in the moist static energy forcing into the atmosphere. A Normalized Gross Moist Stability (NGMS) framework (which characterizes the relationship between convective forcing and convective response) is used to explore the processes responsible for the precipitation bias, and the impact of the gustiness parameterization in reducing that bias. Because the NGMS of the Tropical West Pacific is less than unity in the E3SMv1 model, the increase in energy forcing amplifies the increase in precipitation to exceed that of the evaporative flux. Convective gustiness favors increased precipitation in regions where the resolved surface winds are weak and convection is present.

The Role of Convective Gustiness in Reducing Seasonal Precipitation Biases in the Tropical West Pacific

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

Harrop, Bryce E.; Ma, Po -Lun; Rasch, Philip J.

Precipitation is an important climate quantity that is critically relevant to society. In spite of intense efforts, significant precipitation biases remain in most climate models. One pervasive and persistent bias found in many general circulation models occurs in the Tropical West Pacific where northern hemisphere summer-time precipitation is often underestimated compared to observations. Using the DOE-E3SM model, the inclusion of a missing process, convective gustiness, is shown to reduce those biases through a net increase in surface evaporation. Gustiness in surface wind fields is assumed to arise empirically in proportion to the intensity of convective precipitation. The increased evaporation canmore » be treated as an increase in the moist static energy forcing into the atmosphere. A Normalized Gross Moist Stability (NGMS) framework (which characterizes the relationship between convective forcing and convective response) is used to explore the processes responsible for the precipitation bias, and the impact of the gustiness parameterization in reducing that bias. Because the NGMS of the Tropical West Pacific is less than unity in the E3SMv1 model, the increase in energy forcing amplifies the increase in precipitation to exceed that of the evaporative flux. Convective gustiness favors increased precipitation in regions where the resolved surface winds are weak and convection is present.« less

The Role of Convective Gustiness in Reducing Seasonal Precipitation Biases in the Tropical West Pacific

DOE PAGES

Harrop, Bryce E.; Ma, Po -Lun; Rasch, Philip J.; ...

2018-03-12

Precipitation is an important climate quantity that is critically relevant to society. In spite of intense efforts, significant precipitation biases remain in most climate models. One pervasive and persistent bias found in many general circulation models occurs in the Tropical West Pacific where northern hemisphere summer-time precipitation is often underestimated compared to observations. Using the DOE-E3SM model, the inclusion of a missing process, convective gustiness, is shown to reduce those biases through a net increase in surface evaporation. Gustiness in surface wind fields is assumed to arise empirically in proportion to the intensity of convective precipitation. The increased evaporation canmore » be treated as an increase in the moist static energy forcing into the atmosphere. A Normalized Gross Moist Stability (NGMS) framework (which characterizes the relationship between convective forcing and convective response) is used to explore the processes responsible for the precipitation bias, and the impact of the gustiness parameterization in reducing that bias. Because the NGMS of the Tropical West Pacific is less than unity in the E3SMv1 model, the increase in energy forcing amplifies the increase in precipitation to exceed that of the evaporative flux. Convective gustiness favors increased precipitation in regions where the resolved surface winds are weak and convection is present.« less

A Comparison of MERRA and NARR Reanalysis Datasets with the DOE ARM SGP Continuous Forcing data

NASA Technical Reports Server (NTRS)

Kennedy, Aaron D.; Dong, Xiquan; Xi, Baike; Xie, Shaocheng; Zhang, Yunyan; Chen, Junye

2010-01-01

In this study, the atmospheric state, precipitation, cloud fraction, and radiative fluxes from Modern Era Retrospective-analysis for Research and Applications (MERRA) and North American Regional Reanalysis (NARR) are collected and compared with the Atmospheric Radiation Measurement (ARM) Southern Great Plains (SGP) continuous forcing during the period 1999-2001. For the atmospheric state, the three datasets have excellent agreement for the horizontal wind components and air temperature. NARR and ARM have generally good agreement for humidity, except for several biases in the PBL and in the upper troposphere. MERRA, on the other hand, suffers from a year-round negative bias in humidity except for the month of June. For the vertical pressure velocity, significant differences exist with the largest biases occurring during the spring upwelling and summer downwelling periods. Although NARR and MERRA share many resemblances to each other, ARM outperforms these reanalyses in terms of correlation with cloud fraction. Because the ARM forcing is constrained by observed precipitation that gives the adequate mass, heat, and moisture budgets, much of the precipitation (specifically during the late spring/early summer) is caused by smaller-scale forcing that is not captured by the reanalyses. Both NARR and MERRA capture the seasonal variation of CF observed by ARM radar-lidar and GOES with high correlations (0.92-0.78), but having negative biases of 14% and 3%, respectively. Compared to the ARM observations, MERRA shows a better agreement for both SW and LW fluxes except for LW-down (due to a negative bias in water vapor), NARR has significant positive bias for SW-down and negative bias for LW-down under clear- and all-sky conditions . The NARR biases result from a combination of too few clouds and a lack of sufficient extinction by aerosols and water vapor in the atmospheric column. The results presented here represent only one location for a limited time period, and more comparisons at different locations and longer time period are needed.

Validity of a Simple Method for Measuring Force-Velocity-Power Profile in Countermovement Jump.

PubMed

Jiménez-Reyes, Pedro; Samozino, Pierre; Pareja-Blanco, Fernando; Conceição, Filipe; Cuadrado-Peñafiel, Víctor; González-Badillo, Juan José; Morin, Jean-Benoît

2017-01-01

To analyze the reliability and validity of a simple computation method to evaluate force (F), velocity (v), and power (P) output during a countermovement jump (CMJ) suitable for use in field conditions and to verify the validity of this computation method to compute the CMJ force-velocity (F-v) profile (including unloaded and loaded jumps) in trained athletes. Sixteen high-level male sprinters and jumpers performed maximal CMJs under 6 different load conditions (0-87 kg). A force plate sampling at 1000 Hz was used to record vertical ground-reaction force and derive vertical-displacement data during CMJ trials. For each condition, mean F, v, and P of the push-off phase were determined from both force-plate data (reference method) and simple computation measures based on body mass, jump height (from flight time), and push-off distance and used to establish the linear F-v relationship for each individual. Mean absolute bias values were 0.9% (± 1.6%), 4.7% (± 6.2%), 3.7% (± 4.8%), and 5% (± 6.8%) for F, v, P, and slope of the F-v relationship (S Fv ), respectively. Both methods showed high correlations for F-v-profile-related variables (r = .985-.991). Finally, all variables computed from the simple method showed high reliability, with ICC >.980 and CV <1.0%. These results suggest that the simple method presented here is valid and reliable for computing CMJ force, velocity, power, and F-v profiles in athletes and could be used in practice under field conditions when body mass, push-off distance, and jump height are known.

Direct calculation of 1-octanol-water partition coefficients from adaptive biasing force molecular dynamics simulations.

PubMed

Bhatnagar, Navendu; Kamath, Ganesh; Chelst, Issac; Potoff, Jeffrey J

2012-07-07

The 1-octanol-water partition coefficient log K(ow) of a solute is a key parameter used in the prediction of a wide variety of complex phenomena such as drug availability and bioaccumulation potential of trace contaminants. In this work, adaptive biasing force molecular dynamics simulations are used to determine absolute free energies of hydration, solvation, and 1-octanol-water partition coefficients for n-alkanes from methane to octane. Two approaches are evaluated; the direct transfer of the solute from 1-octanol to water phase, and separate transfers of the solute from the water or 1-octanol phase to vacuum, with both methods yielding statistically indistinguishable results. Calculations performed with the TIP4P and SPC∕E water models and the TraPPE united-atom force field for n-alkanes show that the choice of water model has a negligible effect on predicted free energies of transfer and partition coefficients for n-alkanes. A comparison of calculations using wet and dry octanol phases shows that the predictions for log K(ow) using wet octanol are 0.2-0.4 log units lower than for dry octanol, although this is within the statistical uncertainty of the calculation.

Male Mutation Bias Is the Main Force Shaping Chromosomal Substitution Rates in Monotreme Mammals

PubMed Central

Link, Vivian; Aguilar-Gómez, Diana; Ramírez-Suástegui, Ciro; Hurst, Laurence D.

2017-01-01

Abstract In many species, spermatogenesis involves more cell divisions than oogenesis, and the male germline, therefore, accumulates more DNA replication errors, a phenomenon known as male mutation bias. The extent of male mutation bias (α) is estimated by comparing substitution rates of the X, Y, and autosomal chromosomes, as these chromosomes spend different proportions of their time in the germlines of the two sexes. Male mutation bias has been characterized in placental and marsupial mammals as well as birds, but analyses in monotremes failed to detect any such bias. Monotremes are an ancient lineage of egg-laying mammals with distinct biological properties, which include unique germline features. Here, we sought to assess the presence and potential characteristics of male mutation bias in platypus and the short-beaked echidna based on substitution rate analyses of X, Y, and autosomes. We established the presence of moderate male mutation bias in monotremes, corresponding to an α value of 2.12–3.69. Given that it has been unclear what proportion of the variation in substitution rates on the different chromosomal classes is really due to differential number of replications, we analyzed the influence of other confounding forces (selection, replication-timing, etc.) and found that male mutation bias is the main force explaining the between-chromosome classes differences in substitution rates. Finally, we estimated the proportion of variation at the gene level in substitution rates that is owing to replication effects and found that this phenomenon can explain >68% of these variations in monotremes, and in control species, rodents, and primates. PMID:28922870

Bite force measurement system using pressure-sensitive sheet and silicone impression material.

PubMed

Ando, Katsuya; Fuwa, Yuji; Kurosawa, Masahiro; Kondo, Takamasa; Goto, Shigemi

2009-03-01

This study was conducted to reduce the bias in measured values caused by the thickness of materials used in occlusal examinations. To this end, a silicone impression material for bite force measurement and an experimental model of a simplified stomatognathic system were employed in this study. By means of this experimental model, results showed that the effect of bias toward the posterior arch could be reduced in the anterior-posterior distribution of bite forces and in the occlusal contact areas due to the thickness of the materials used in occlusal examinations.

The South American Land Data Assimilation System (SALDAS) 5-Year Retrospective Atmospheric Forcing Datasets

NASA Technical Reports Server (NTRS)

deGoncalves, Luis Gustavo G.; Shuttleworth, William J.; Vila, Daniel; Larroza, Elaine; Bottino, Marcus J.; Herdies, Dirceu L.; Aravequia, Jose A.; De Mattos, Joao G. Z.; Toll, David L.; Rodell, Matthew;

The role of personal biases in the explanation of confabulation.

PubMed

Metcalf, Kasey; Langdon, Robyn; Coltheart, Max

2010-01-01

Previous research has demonstrated that motivational forces play an important role in determining the content of confabulation. In particular the content of confabulation has been shown to contain a positive emotional bias. This study investigated the role of personal biases in the confabulations of six patients with diverse aetiologies. Confabulations were elicited with a series of structured interviews. We then compared the patients' confabulations to their actual situations. Further analyses compared confabulations about current (i.e., the postmorbid period) and past (i.e., premorbid events and general life circumstances) events. Group analysis confirmed a general bias to recall events that were more positive than the reality. However, examination of individual cases revealed that positive biases were not universal. Confabulations about current circumstances showed the positive bias, whereas an emotional bias was not evident in past confabulations. We conclude that motivational forces play a role in determining the content of confabulations but conceive of this role primarily in terms of a need to maintain a consistent self-concept (whether positive or negative) overlaid upon the ease with which an individual can retrieve familiar premorbid daily activities and routines.

Opto electronic tweezers based smart sweeper for cells/micro-particles sorting

NASA Astrophysics Data System (ADS)

Verma, R. S.; Kumar, N.

2018-04-01

We report on use of opto-electronic tweezers based sorting approach, termed as smart sweepers, for sorting the microscopic particles by using the Dielectrophoretic (DEP) force response of cells on applied a.c. bias frequency. The applied a.c. bias was kept in negative DEP region, close to the crossover frequency of one of the particles. A line shaped intensity pattern, generated by a cylindrical lens, was scanned across the mixture sample. The particles whose cross over frequency was close to the applied bias frequency, experienced negligible negative DEP(n-DEP) force. On the other hand, the other type of particle experienced large repelling force and were forced to move along the scanning direction of the line shaped intensity profile. We, as a proof of concept, demonstrated the working principle of opto electronic smart sweepers by sweeping out the polystyrene particles from a mixture consisting of polystyrene microspheres (PSM) and red blood cells (RBCs) and leaving RBCs in the region of interest.

Free energy surface of an intrinsically disordered protein: comparison between temperature replica exchange molecular dynamics and bias-exchange metadynamics.

PubMed

Zerze, Gül H; Miller, Cayla M; Granata, Daniele; Mittal, Jeetain

2015-06-09

Intrinsically disordered proteins (IDPs), which are expected to be largely unstructured under physiological conditions, make up a large fraction of eukaryotic proteins. Molecular dynamics simulations have been utilized to probe structural characteristics of these proteins, which are not always easily accessible to experiments. However, exploration of the conformational space by brute force molecular dynamics simulations is often limited by short time scales. Present literature provides a number of enhanced sampling methods to explore protein conformational space in molecular simulations more efficiently. In this work, we present a comparison of two enhanced sampling methods: temperature replica exchange molecular dynamics and bias exchange metadynamics. By investigating both the free energy landscape as a function of pertinent order parameters and the per-residue secondary structures of an IDP, namely, human islet amyloid polypeptide, we found that the two methods yield similar results as expected. We also highlight the practical difference between the two methods by describing the path that we followed to obtain both sets of data.

Efficient multidimensional free energy calculations for ab initio molecular dynamics using classical bias potentials

NASA Astrophysics Data System (ADS)

VandeVondele, Joost; Rothlisberger, Ursula

2000-09-01

We present a method for calculating multidimensional free energy surfaces within the limited time scale of a first-principles molecular dynamics scheme. The sampling efficiency is enhanced using selected terms of a classical force field as a bias potential. This simple procedure yields a very substantial increase in sampling accuracy while retaining the high quality of the underlying ab initio potential surface and can thus be used for a parameter free calculation of free energy surfaces. The success of the method is demonstrated by the applications to two gas phase molecules, ethane and peroxynitrous acid, as test case systems. A statistical analysis of the results shows that the entire free energy landscape is well converged within a 40 ps simulation at 500 K, even for a system with barriers as high as 15 kcal/mol.

Good research practices for comparative effectiveness research: approaches to mitigate bias and confounding in the design of nonrandomized studies of treatment effects using secondary data sources: the International Society for Pharmacoeconomics and Outcomes Research Good Research Practices for Retrospective Database Analysis Task Force Report--Part II.

PubMed

Cox, Emily; Martin, Bradley C; Van Staa, Tjeerd; Garbe, Edeltraut; Siebert, Uwe; Johnson, Michael L

2009-01-01

The goal of comparative effectiveness analysis is to examine the relationship between two variables, treatment, or exposure and effectiveness or outcome. Unlike data obtained through randomized controlled trials, researchers face greater challenges with causal inference with observational studies. Recognizing these challenges, a task force was formed to develop a guidance document on methodological approaches to addresses these biases. The task force was commissioned and a Chair was selected by the International Society for Pharmacoeconomics and Outcomes Research Board of Directors in October 2007. This report, the second of three reported in this issue of the Journal, discusses the inherent biases when using secondary data sources for comparative effectiveness analysis and provides methodological recommendations to help mitigate these biases. The task force report provides recommendations and tools for researchers to mitigate threats to validity from bias and confounding in measurement of exposure and outcome. Recommendations on design of study included: the need for data analysis plan with causal diagrams; detailed attention to classification bias in definition of exposure and clinical outcome; careful and appropriate use of restriction; extreme care to identify and control for confounding factors, including time-dependent confounding. Design of nonrandomized studies of comparative effectiveness face several daunting issues, including measurement of exposure and outcome challenged by misclassification and confounding. Use of causal diagrams and restriction are two techniques that can improve the theoretical basis for analyzing treatment effects in study populations of more homogeneity, with reduced loss of generalizability.

Anti-Bias Education: Reflections

ERIC Educational Resources Information Center

Derman-Sparks, Louise

2011-01-01

It is 30 years since NAEYC published "Anti-Bias Curriculum Tools for Empowering Young Children" (Derman-Sparks & ABC Task Force, 1989). Since then, anti-bias education concepts have become part of the early childhood education (ECE) narrative in the United States and many other countries. It has brought a fresh way of thinking about…

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

Pereyra, Pedro, E-mail: pereyrapedro@gmail.com; Mendoza-Figueroa, M. G.

Transport properties of electrons through biased double barrier semiconductor structures with finite transverse width w{sub y}, in the presence of a channel-mixing transverse electric field E{sub T} (along the y-axis), were studied. We solve the multichannel Schrödinger equation using the transfer matrix method and transport properties, like the conductance G and the transmission coefficients T{sub ij} have been evaluated as functions of the electrons' energy E and the transverse and longitudinal (bias) electric forces, f{sub T} and f{sub b}. We show that peak-suppression effects appear, due to the applied bias. Similarly, coherent interference of wave-guide states induced by the transversemore » field is obtained. We show also that the coherent interference of resonant wave-guide states gives rise to resonant conductance, which can be tuned to produce broad resonant peaks, implying operation frequencies of the order of 10 THz or larger.« less

Bias Reduction in Short Records of Satellite Soil Moisture

NASA Technical Reports Server (NTRS)

Reichle, Rolf H.; Koster, Randal D.

2004-01-01

Although surface soil moisture data from different sources (satellite retrievals, ground measurements, and land model integrations of observed meteorological forcing data) have been shown to contain consistent and useful information in their seasonal cycle and anomaly signals, they typically exhibit very different mean values and variability. These biases pose a severe obstacle to exploiting the useful information contained in satellite retrievals through data assimilation. A simple method of bias removal is to match the cumulative distribution functions (cdf) of the satellite and model data. However, accurate cdf estimation typically requires a long record of satellite data. We demonstrate here that by wing spatial sampling with a 2 degree moving window we can obtain local statistics based on a one-year satellite record that are a good approximation to those that would be derived from a much longer time series. This result should increase the usefulness of relatively short satellite data records.

Exploring the impact of forcing error characteristics on physically based snow simulations within a global sensitivity analysis framework

NASA Astrophysics Data System (ADS)

Raleigh, M. S.; Lundquist, J. D.; Clark, M. P.

2015-07-01

Physically based models provide insights into key hydrologic processes but are associated with uncertainties due to deficiencies in forcing data, model parameters, and model structure. Forcing uncertainty is enhanced in snow-affected catchments, where weather stations are scarce and prone to measurement errors, and meteorological variables exhibit high variability. Hence, there is limited understanding of how forcing error characteristics affect simulations of cold region hydrology and which error characteristics are most important. Here we employ global sensitivity analysis to explore how (1) different error types (i.e., bias, random errors), (2) different error probability distributions, and (3) different error magnitudes influence physically based simulations of four snow variables (snow water equivalent, ablation rates, snow disappearance, and sublimation). We use the Sobol' global sensitivity analysis, which is typically used for model parameters but adapted here for testing model sensitivity to coexisting errors in all forcings. We quantify the Utah Energy Balance model's sensitivity to forcing errors with 1 840 000 Monte Carlo simulations across four sites and five different scenarios. Model outputs were (1) consistently more sensitive to forcing biases than random errors, (2) generally less sensitive to forcing error distributions, and (3) critically sensitive to different forcings depending on the relative magnitude of errors. For typical error magnitudes found in areas with drifting snow, precipitation bias was the most important factor for snow water equivalent, ablation rates, and snow disappearance timing, but other forcings had a more dominant impact when precipitation uncertainty was due solely to gauge undercatch. Additionally, the relative importance of forcing errors depended on the model output of interest. Sensitivity analysis can reveal which forcing error characteristics matter most for hydrologic modeling.

Accounting for elite indoor 200 m sprint results.

PubMed

Usherwood, James R; Wilson, Alan M

2006-03-22

Times for indoor 200 m sprint races are notably worse than those for outdoor races. In addition, there is a considerable bias against competitors drawn in inside lanes (with smaller bend radii). Centripetal acceleration requirements increase average forces during sprinting around bends. These increased forces can be modulated by changes in duty factor (the proportion of stride the limb is in contact with the ground). If duty factor is increased to keep limb forces constant, and protraction time and distance travelled during stance are unchanging, bend-running speeds are reduced. Here, we use results from the 2004 Olympics and World Indoor Championships to show quantitatively that the decreased performances in indoor competition, and the bias by lane number, are consistent with this 'constant limb force' hypothesis. Even elite athletes appear constrained by limb forces.

Male Mutation Bias Is the Main Force Shaping Chromosomal Substitution Rates in Monotreme Mammals.

PubMed

Link, Vivian; Aguilar-Gómez, Diana; Ramírez-Suástegui, Ciro; Hurst, Laurence D; Cortez, Diego

2017-09-01

In many species, spermatogenesis involves more cell divisions than oogenesis, and the male germline, therefore, accumulates more DNA replication errors, a phenomenon known as male mutation bias. The extent of male mutation bias (α) is estimated by comparing substitution rates of the X, Y, and autosomal chromosomes, as these chromosomes spend different proportions of their time in the germlines of the two sexes. Male mutation bias has been characterized in placental and marsupial mammals as well as birds, but analyses in monotremes failed to detect any such bias. Monotremes are an ancient lineage of egg-laying mammals with distinct biological properties, which include unique germline features. Here, we sought to assess the presence and potential characteristics of male mutation bias in platypus and the short-beaked echidna based on substitution rate analyses of X, Y, and autosomes. We established the presence of moderate male mutation bias in monotremes, corresponding to an α value of 2.12-3.69. Given that it has been unclear what proportion of the variation in substitution rates on the different chromosomal classes is really due to differential number of replications, we analyzed the influence of other confounding forces (selection, replication-timing, etc.) and found that male mutation bias is the main force explaining the between-chromosome classes differences in substitution rates. Finally, we estimated the proportion of variation at the gene level in substitution rates that is owing to replication effects and found that this phenomenon can explain >68% of these variations in monotremes, and in control species, rodents, and primates. © The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.

Evaluation of ACCMIP Outgoing Longwave Radiation from Tropospheric Ozone Using TES Satellite Observations.

NASA Technical Reports Server (NTRS)

Bowman, Kevin W.; Shindell, Drew Todd; Worden, H. M.; Lamarque, J. F.; Young, P. J.; Stevenson, D. S.; Qu, Z.; delaTorre, M.; Bergmann, D.; Cameron-Smith, P. J.;

A New Paradigm for Diagnosing Contributions to Model Aerosol Forcing Error: Diagnosing Model Aerosol Forcing Error

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

Jones, A. L.; Feldman, D. R.; Freidenreich, S.

A new paradigm in benchmark absorption-scattering radiative transfer is presented that enables both the globally averaged and spatially resolved testing of climate model radiation parameterizations in order to uncover persistent sources of biases in the aerosol instantaneous radiative effect (IRE). A proof of concept is demonstrated with the Geophysical Fluid Dynamics Laboratory AM4 and Community Earth System Model 1.2.2 climate models. Instead of prescribing atmospheric conditions and aerosols, as in prior intercomparisons, native snapshots of the atmospheric state and aerosol optical properties from the participating models are used as inputs to an accurate radiation solver to uncover model-relevant biases. Thesemore » diagnostic results show that the models' aerosol IRE bias is of the same magnitude as the persistent range cited (~1 W/m 2) and also varies spatially and with intrinsic aerosol optical properties. The findings presented here underscore the significance of native model error analysis and its dispositive ability to diagnose global biases, confirming its fundamental value for the Radiative Forcing Model Intercomparison Project.« less

A New Paradigm for Diagnosing Contributions to Model Aerosol Forcing Error: Diagnosing Model Aerosol Forcing Error

DOE PAGES

Jones, A. L.; Feldman, D. R.; Freidenreich, S.; ...

2017-12-07

A new paradigm in benchmark absorption-scattering radiative transfer is presented that enables both the globally averaged and spatially resolved testing of climate model radiation parameterizations in order to uncover persistent sources of biases in the aerosol instantaneous radiative effect (IRE). A proof of concept is demonstrated with the Geophysical Fluid Dynamics Laboratory AM4 and Community Earth System Model 1.2.2 climate models. Instead of prescribing atmospheric conditions and aerosols, as in prior intercomparisons, native snapshots of the atmospheric state and aerosol optical properties from the participating models are used as inputs to an accurate radiation solver to uncover model-relevant biases. Thesemore » diagnostic results show that the models' aerosol IRE bias is of the same magnitude as the persistent range cited (~1 W/m 2) and also varies spatially and with intrinsic aerosol optical properties. The findings presented here underscore the significance of native model error analysis and its dispositive ability to diagnose global biases, confirming its fundamental value for the Radiative Forcing Model Intercomparison Project.« less

An ensemble constrained variational analysis of atmospheric forcing data and its application to evaluate clouds in CAM5: Ensemble 3DCVA and Its Application

DOE PAGES

Tang, Shuaiqi; Zhang, Minghua; Xie, Shaocheng

2016-01-05

Large-scale atmospheric forcing data can greatly impact the simulations of atmospheric process models including Large Eddy Simulations (LES), Cloud Resolving Models (CRMs) and Single-Column Models (SCMs), and impact the development of physical parameterizations in global climate models. This study describes the development of an ensemble variationally constrained objective analysis of atmospheric large-scale forcing data and its application to evaluate the cloud biases in the Community Atmospheric Model (CAM5). Sensitivities of the variational objective analysis to background data, error covariance matrix and constraint variables are described and used to quantify the uncertainties in the large-scale forcing data. Application of the ensemblemore » forcing in the CAM5 SCM during March 2000 intensive operational period (IOP) at the Southern Great Plains (SGP) of the Atmospheric Radiation Measurement (ARM) program shows systematic biases in the model simulations that cannot be explained by the uncertainty of large-scale forcing data, which points to the deficiencies of physical parameterizations. The SCM is shown to overestimate high clouds and underestimate low clouds. These biases are found to also exist in the global simulation of CAM5 when it is compared with satellite data.« less

An ensemble constrained variational analysis of atmospheric forcing data and its application to evaluate clouds in CAM5: Ensemble 3DCVA and Its Application

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

Tang, Shuaiqi; Zhang, Minghua; Xie, Shaocheng

Large-scale atmospheric forcing data can greatly impact the simulations of atmospheric process models including Large Eddy Simulations (LES), Cloud Resolving Models (CRMs) and Single-Column Models (SCMs), and impact the development of physical parameterizations in global climate models. This study describes the development of an ensemble variationally constrained objective analysis of atmospheric large-scale forcing data and its application to evaluate the cloud biases in the Community Atmospheric Model (CAM5). Sensitivities of the variational objective analysis to background data, error covariance matrix and constraint variables are described and used to quantify the uncertainties in the large-scale forcing data. Application of the ensemblemore » forcing in the CAM5 SCM during March 2000 intensive operational period (IOP) at the Southern Great Plains (SGP) of the Atmospheric Radiation Measurement (ARM) program shows systematic biases in the model simulations that cannot be explained by the uncertainty of large-scale forcing data, which points to the deficiencies of physical parameterizations. The SCM is shown to overestimate high clouds and underestimate low clouds. These biases are found to also exist in the global simulation of CAM5 when it is compared with satellite data.« less

How suspect race affects police use of force in an interaction over time.

PubMed

Kahn, Kimberly Barsamian; Steele, Joel S; McMahon, Jean M; Stewart, Greg

2017-04-01

Although studies often find racial disparities in policing outcomes, less is known about how suspect race biases police interactions as they unfold. This study examines what is differentially occurring during police-suspect interactions for White, Black, and Latino suspects across time. It is hypothesized that racial bias may be more evident earlier in interactions, when less information about the situation is available. One hundred thirty-nine (62 White, 42 Black, and 35 Latino) use-of-force case files and associated written narratives from a medium to large size urban police department in the United States were analyzed. Trained coders broke down the interaction narratives into discrete "sequences," or dyadic action-reaction steps involving a suspect action (level of resistance) and an officer response (level of force). A linear mixed-effects model was run on amount of police use of force by suspect race and time, with suspect resistance and suspect actions toward third-party/self as controls. Results demonstrated that Black and Latino suspects receive more force in the beginning stages of the interaction, whereas Whites escalated in level of force faster after initial levels. By breaking down police-suspect interactions into discrete sequences, the current study reveals a better understanding of when bias originates in police use of force and informs how to focus policing interventions. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Bias-dependent local structure of water molecules at an electrochemical interface

NASA Astrophysics Data System (ADS)

Pedroza, Luana; Brandimarte, Pedro; Rocha, Alexandre R.; Fernandez-Serra, Marivi

2015-03-01

Following the need for new - and renewable - sources of energy worldwide, fuel cells using electrocatalysts can be thought of as a viable option. Understanding the local structure of water molecules at the interfaces of the metallic electrodes is a key problem. Notably the system is under an external potential bias, which makes the task of simulating this setup difficult. A first principle description of all components of the system is the most appropriate methodology in order to advance understanding of electrochemical processes. There, the metal is usually charged. To correctly compute the effect of an external bias potential applied to electrodes, we combine density functional theory (DFT) and non-equilibrium Green's functions methods (NEGF), with and without van der Waals interactions. In this work, we apply this methodology to study the electronic properties and forces of one water molecule and water monolayer at the interface of gold electrodes. We find that the water molecule has a different torque direction depending on the sign of the bias applied. We also show that it changes the position of the most stable configuration indicating that the external bias plays an important role in the structural properties of the interface. We acknowledge financial support from FAPESP.

Reproducing multi-model ensemble average with Ensemble-averaged Reconstructed Forcings (ERF) in regional climate modeling

NASA Astrophysics Data System (ADS)

Erfanian, A.; Fomenko, L.; Wang, G.

2016-12-01

Multi-model ensemble (MME) average is considered the most reliable for simulating both present-day and future climates. It has been a primary reference for making conclusions in major coordinated studies i.e. IPCC Assessment Reports and CORDEX. The biases of individual models cancel out each other in MME average, enabling the ensemble mean to outperform individual members in simulating the mean climate. This enhancement however comes with tremendous computational cost, which is especially inhibiting for regional climate modeling as model uncertainties can originate from both RCMs and the driving GCMs. Here we propose the Ensemble-based Reconstructed Forcings (ERF) approach to regional climate modeling that achieves a similar level of bias reduction at a fraction of cost compared with the conventional MME approach. The new method constructs a single set of initial and boundary conditions (IBCs) by averaging the IBCs of multiple GCMs, and drives the RCM with this ensemble average of IBCs to conduct a single run. Using a regional climate model (RegCM4.3.4-CLM4.5), we tested the method over West Africa for multiple combination of (up to six) GCMs. Our results indicate that the performance of the ERF method is comparable to that of the MME average in simulating the mean climate. The bias reduction seen in ERF simulations is achieved by using more realistic IBCs in solving the system of equations underlying the RCM physics and dynamics. This endows the new method with a theoretical advantage in addition to reducing computational cost. The ERF output is an unaltered solution of the RCM as opposed to a climate state that might not be physically plausible due to the averaging of multiple solutions with the conventional MME approach. The ERF approach should be considered for use in major international efforts such as CORDEX. Key words: Multi-model ensemble, ensemble analysis, ERF, regional climate modeling

The impact of work-limiting disability on labor force participation.

PubMed

Webber, Douglas A; Bjelland, Melissa J

2015-03-01

According to the justification hypothesis, non-employed individuals may over-report their level of work limitation, leading to biased census/survey estimates of the prevalence of severe disabilities and the associated labor force participation rate. For researchers studying policies which impact the disabled or elderly (e.g., Supplemental Security Income, Disability Insurance, and Early Retirement), this could lead to significant bias in key parameters of interest. Using the American Community Survey, we examine the potential for both inflated and deflated reported disability status and generate a general index of disability, which can be used to reduce the bias of these self-reports in other studies. We find that at least 4.8 million individuals have left the labor force because of a work-limiting disability, at least four times greater than the impact implied by our replication of previous models. Copyright © 2013 John Wiley & Sons, Ltd.

Flexible binding simulation by a novel and improved version of virtual-system coupled adaptive umbrella sampling

NASA Astrophysics Data System (ADS)

Dasgupta, Bhaskar; Nakamura, Haruki; Higo, Junichi

2016-10-01

Virtual-system coupled adaptive umbrella sampling (VAUS) enhances sampling along a reaction coordinate by using a virtual degree of freedom. However, VAUS and regular adaptive umbrella sampling (AUS) methods are yet computationally expensive. To decrease the computational burden further, improvements of VAUS for all-atom explicit solvent simulation are presented here. The improvements include probability distribution calculation by a Markov approximation; parameterization of biasing forces by iterative polynomial fitting; and force scaling. These when applied to study Ala-pentapeptide dimerization in explicit solvent showed advantage over regular AUS. By using improved VAUS larger biological systems are amenable.

Coupling of Lever Arm Swing and Biased Brownian Motion in Actomyosin

PubMed Central

Nie, Qing-Miao; Togashi, Akio; Sasaki, Takeshi N.; Takano, Mitsunori; Sasai, Masaki; Terada, Tomoki P.

2014-01-01

An important unresolved problem associated with actomyosin motors is the role of Brownian motion in the process of force generation. On the basis of structural observations of myosins and actins, the widely held lever-arm hypothesis has been proposed, in which proteins are assumed to show sequential structural changes among observed and hypothesized structures to exert mechanical force. An alternative hypothesis, the Brownian motion hypothesis, has been supported by single-molecule experiments and emphasizes more on the roles of fluctuating protein movement. In this study, we address the long-standing controversy between the lever-arm hypothesis and the Brownian motion hypothesis through in silico observations of an actomyosin system. We study a system composed of myosin II and actin filament by calculating free-energy landscapes of actin-myosin interactions using the molecular dynamics method and by simulating transitions among dynamically changing free-energy landscapes using the Monte Carlo method. The results obtained by this combined multi-scale calculation show that myosin with inorganic phosphate (Pi) and ADP weakly binds to actin and that after releasing Pi and ADP, myosin moves along the actin filament toward the strong-binding site by exhibiting the biased Brownian motion, a behavior consistent with the observed single-molecular behavior of myosin. Conformational flexibility of loops at the actin-interface of myosin and the N-terminus of actin subunit is necessary for the distinct bias in the Brownian motion. Both the 5.5–11 nm displacement due to the biased Brownian motion and the 3–5 nm displacement due to lever-arm swing contribute to the net displacement of myosin. The calculated results further suggest that the recovery stroke of the lever arm plays an important role in enhancing the displacement of myosin through multiple cycles of ATP hydrolysis, suggesting a unified movement mechanism for various members of the myosin family. PMID:24762409

Coupling of lever arm swing and biased Brownian motion in actomyosin.

PubMed

Nie, Qing-Miao; Togashi, Akio; Sasaki, Takeshi N; Takano, Mitsunori; Sasai, Masaki; Terada, Tomoki P

2014-04-01

An important unresolved problem associated with actomyosin motors is the role of Brownian motion in the process of force generation. On the basis of structural observations of myosins and actins, the widely held lever-arm hypothesis has been proposed, in which proteins are assumed to show sequential structural changes among observed and hypothesized structures to exert mechanical force. An alternative hypothesis, the Brownian motion hypothesis, has been supported by single-molecule experiments and emphasizes more on the roles of fluctuating protein movement. In this study, we address the long-standing controversy between the lever-arm hypothesis and the Brownian motion hypothesis through in silico observations of an actomyosin system. We study a system composed of myosin II and actin filament by calculating free-energy landscapes of actin-myosin interactions using the molecular dynamics method and by simulating transitions among dynamically changing free-energy landscapes using the Monte Carlo method. The results obtained by this combined multi-scale calculation show that myosin with inorganic phosphate (Pi) and ADP weakly binds to actin and that after releasing Pi and ADP, myosin moves along the actin filament toward the strong-binding site by exhibiting the biased Brownian motion, a behavior consistent with the observed single-molecular behavior of myosin. Conformational flexibility of loops at the actin-interface of myosin and the N-terminus of actin subunit is necessary for the distinct bias in the Brownian motion. Both the 5.5-11 nm displacement due to the biased Brownian motion and the 3-5 nm displacement due to lever-arm swing contribute to the net displacement of myosin. The calculated results further suggest that the recovery stroke of the lever arm plays an important role in enhancing the displacement of myosin through multiple cycles of ATP hydrolysis, suggesting a unified movement mechanism for various members of the myosin family.

Development of a Prototype Miniature Silicon Microgyroscope

PubMed Central

Xia, Dunzhu; Chen, Shuling; Wang, Shourong

2009-01-01

A miniature vacuum-packaged silicon microgyroscope (SMG) with symmetrical and decoupled structure was designed to prevent unintended coupling between drive and sense modes. To ensure high resonant stability and strong disturbance resisting capacity, a self-oscillating closed-loop circuit including an automatic gain control (AGC) loop based on electrostatic force feedback is adopted in drive mode, while, dual-channel decomposition and reconstruction closed loops are applied in sense mode. Moreover, the temperature effect on its zero bias was characterized experimentally and a practical compensation method is given. The testing results demonstrate that the useful signal and quadrature signal will not interact with each other because their phases are decoupled. Under a scale factor condition of 9.6 mV/°/s, in full measurement range of ± 300 deg/s, the zero bias stability reaches 15°/h with worse-case nonlinearity of 400 ppm, and the temperature variation trend of the SMG bias is thus largely eliminated, so that the maximum bias value is reduced to one tenth of the original after compensation from -40 °C to 80 °C. PMID:22408543

A Saturation Balancing Control Method for Enhancing Dynamic Vehicle Stability (PREPRINT)

DTIC Science & Technology

2011-03-01

force estimation; axle saturation level; independent drive; torque biasing; 1. Introduction Vehicle stability control ( VSC ) systems have widely been...shown to reduce accidents by minimizing driver’s loss of control during aggressive emergency maneuvers. VSC systems manipulate one or more of the... VSC (also referred to as vehicle dynamics control (VDC)) systems available on the market today are brake-based systems which extend the functionality

Free Energies of Quantum Particles: The Coupled-Perturbed Quantum Umbrella Sampling Method.

PubMed

Glover, William J; Casey, Jennifer R; Schwartz, Benjamin J

2014-10-14

We introduce a new simulation method called Coupled-Perturbed Quantum Umbrella Sampling that extends the classical umbrella sampling approach to reaction coordinates involving quantum mechanical degrees of freedom. The central idea in our method is to solve coupled-perturbed equations to find the response of the quantum system's wave function along a reaction coordinate of interest. This allows for propagation of the system's dynamics under the influence of a quantum biasing umbrella potential and provides a method to rigorously undo the effects of the bias to compute equilibrium ensemble averages. In this way, one can drag electrons into regions of high free energy where they would otherwise not go, thus enabling chemistry by fiat. We demonstrate the applicability of our method for two condensed-phase systems of interest. First, we consider the interaction of a hydrated electron with an aqueous sodium cation, and we calculate a potential of mean force that shows that an e(-):Na(+) contact pair is the thermodynamically favored product starting from either a neutral sodium atom or the separate cation and electron species. Second, we present the first determination of a hydrated electron's free-energy profile relative to an air/water interface. For the particular model parameters used, we find that the hydrated electron is more thermodynamically stable in the bulk rather than at the interface. Our analysis suggests that the primary driving force keeping the electron away from the interface is the long-range electron-solvent polarization interaction rather than the short-range details of the chosen pseudopotential.

Linear Response Path Following: A Molecular Dynamics Method To Simulate Global Conformational Changes of Protein upon Ligand Binding.

PubMed

Tamura, Koichi; Hayashi, Shigehiko

2015-07-14

Molecular functions of proteins are often fulfilled by global conformational changes that couple with local events such as the binding of ligand molecules. High molecular complexity of proteins has, however, been an obstacle to obtain an atomistic view of the global conformational transitions, imposing a limitation on the mechanistic understanding of the functional processes. In this study, we developed a new method of molecular dynamics (MD) simulation called the linear response path following (LRPF) to simulate a protein's global conformational changes upon ligand binding. The method introduces a biasing force based on a linear response theory, which determines a local reaction coordinate in the configuration space that represents linear coupling between local events of ligand binding and global conformational changes and thus provides one with fully atomistic models undergoing large conformational changes without knowledge of a target structure. The overall transition process involving nonlinear conformational changes is simulated through iterative cycles consisting of a biased MD simulation with an updated linear response force and a following unbiased MD simulation for relaxation. We applied the method to the simulation of global conformational changes of the yeast calmodulin N-terminal domain and successfully searched out the end conformation. The atomistically detailed trajectories revealed a sequence of molecular events that properly lead to the global conformational changes and identified key steps of local-global coupling that induce the conformational transitions. The LRPF method provides one with a powerful means to model conformational changes of proteins such as motors and transporters where local-global coupling plays a pivotal role in their functional processes.

Cultural transmission results in convergence towards colour term universals

PubMed Central

Xu, Jing; Dowman, Mike; Griffiths, Thomas L.

2013-01-01

As in biological evolution, multiple forces are involved in cultural evolution. One force is analogous to selection, and acts on differences in the fitness of aspects of culture by influencing who people choose to learn from. Another force is analogous to mutation, and influences how culture changes over time owing to errors in learning and the effects of cognitive biases. Which of these forces need to be appealed to in explaining any particular aspect of human cultures is an open question. We present a study that explores this question empirically, examining the role that the cognitive biases that influence cultural transmission might play in universals of colour naming. In a large-scale laboratory experiment, participants were shown labelled examples from novel artificial systems of colour terms and were asked to classify other colours on the basis of those examples. The responses of each participant were used to generate the examples seen by subsequent participants. By simulating cultural transmission in the laboratory, we were able to isolate a single evolutionary force—the effects of cognitive biases, analogous to mutation—and examine its consequences. Our results show that this process produces convergence towards systems of colour terms similar to those seen across human languages, providing support for the conclusion that the effects of cognitive biases, brought out through cultural transmission, can account for universals in colour naming. PMID:23486436

Magnetic force microscopy with frequency-modulated capacitive tip-sample distance control

NASA Astrophysics Data System (ADS)

Zhao, X.; Schwenk, J.; Mandru, A. O.; Penedo, M.; Baćani, M.; Marioni, M. A.; Hug, H. J.

2018-01-01

In a step towards routinely achieving 10 nm spatial resolution with magnetic force microscopy, we have developed a robust method for active tip-sample distance control based on frequency modulation of the cantilever oscillation. It allows us to keep a well-defined tip-sample distance of the order of 10 nm within better than +/- 0.4 nm precision throughout the measurement even in the presence of energy dissipative processes, and is adequate for single-passage non-contact operation in vacuum. The cantilever is excited mechanically in a phase-locked loop to oscillate at constant amplitude on its first flexural resonance mode. This frequency is modulated by an electrostatic force gradient generated by tip-sample bias oscillating from a few hundred Hz up to a few kHz. The sum of the side bands’ amplitudes is a proxy for the tip-sample distance and can be used for tip-sample distance control. This method can also be extended to other scanning probe microscopy techniques.

Rightward Biases in Free-Viewing Visual Bisection Tasks: Implications for Leftward Responses Biases on Similar Tasks

ERIC Educational Resources Information Center

Elias, Lorin J.; Robinson, Brent; Saucier, Deborah M.

2005-01-01

Neurologically normal individuals exhibit strong leftward response biases during free-viewing perceptual judgments of brightness, quantity, and size. When participants view two mirror-reversed objects and they are forced to choose which object appears darker, more numerous, or larger, the stimulus with the relevant feature on the left side is…

Training Toddlers Seated on Mobile Robots to Steer Using Force-Feedback Joystick.

PubMed

Agrawal, S K; Xi Chen; Ragonesi, C; Galloway, J C

2012-01-01

The broader goal of our research is to train infants with special needs to safely and purposefully drive a mobile robot to explore the environment. The hypothesis is that these impaired infants will benefit from mobility in their early years and attain childhood milestones, similar to their healthy peers. In this paper, we present an algorithm and training method using a force-feedback joystick with an "assist-as-needed" paradigm for driving training. In this "assist-as-needed" approach, if the child steers the joystick outside a force tunnel centered on the desired direction, the driver experiences a bias force on the hand. We show results with a group study on typically developing toddlers that such a haptic guidance algorithm is superior to training with a conventional joystick. We also provide a case study on two special needs children, under three years old, who learn to make sharp turns during driving, when trained over a five-day period with the force-feedback joystick using the algorithm.

Multi-muscle FES force control of the human arm for arbitrary goals.

PubMed

Schearer, Eric M; Liao, Yu-Wei; Perreault, Eric J; Tresch, Matthew C; Memberg, William D; Kirsch, Robert F; Lynch, Kevin M

2014-05-01

We present a method for controlling a neuroprosthesis for a paralyzed human arm using functional electrical stimulation (FES) and characterize the errors of the controller. The subject has surgically implanted electrodes for stimulating muscles in her shoulder and arm. Using input/output data, a model mapping muscle stimulations to isometric endpoint forces measured at the subject's hand was identified. We inverted the model of this redundant and coupled multiple-input multiple-output system by minimizing muscle activations and used this inverse for feedforward control. The magnitude of the total root mean square error over a grid in the volume of achievable isometric endpoint force targets was 11% of the total range of achievable forces. Major sources of error were random error due to trial-to-trial variability and model bias due to nonstationary system properties. Because the muscles working collectively are the actuators of the skeletal system, the quantification of errors in force control guides designs of motion controllers for multi-joint, multi-muscle FES systems that can achieve arbitrary goals.

High-Force Dielectric Electroactive Polymer (DEAP) membrane actuator

NASA Astrophysics Data System (ADS)

Hau, Steffen; York, Alexander; Seelecke, Stefan

2016-04-01

Energy efficiency, lightweight and scalability are key features for actuators in applications such as valves, pumps or any portable system. Dielectric electroactive Polymer (DEAP) technology is able to fulfill these requirements1 better than commonly used technology e.g. solenoids, but has limitations concerning force and stroke. However, the circular DEAP membrane actuator shows a potential increase in stroke in the mm range, when combined with an appropriate biasing mechanism2. Although, thus far, their force range is limited to the single-digit Newton range, or less3,4. This work describes how this force limit of DEAP membrane actuators can be pushed to the high double-digit Newton range and beyond. The concept for such an actuator consists of a stack of double-layered DEAPs membrane actuator combined with a biasing mechanism. These two components are combined in a novel way, which allows a compact design by integrating the biasing mechanism into the DEAP membrane actuator stack. Subsequently, the single components are manufactured, tested, and their force-displacement characteristic is documented. Utilizing this data allows assembling them into actuator systems for different applications. Two different actuators are assembled and tested (dimensions: 85x85x30mm3 (LxWxH)). The first one is able to lift 7.5kg. The second one can generate a force of 66N while acting against a spring load.

Setup for potential bias experiments on the Saha Institute of Nuclear Physics tokamak

NASA Astrophysics Data System (ADS)

Ghosh, J.; Pal, R.; Chattopadhyay, P. K.

1999-12-01

An experimental setup for studying the influence of the radial electric field on very low qa plasma on the Saha Institute of Nuclear Physics tokamak is presented. A high current, high voltage pulsed power supply, using a semiconductor controlled rectifier (SCR) as a dc switch is developed and used to bias a tungsten electrode inserted inside the plasma. The electrode's exposed length and its position inside the plasma are controlled by a double bellows assembly to optimize the electrode-exposed length. We show that using the force commutation method to turn the SCR off to get the power pulse desired has good potential for carrying out similar kinds of studies, especially in a low budget small tokamak.

Accuracy and Bias in Perception of Distress Level and Distress Change Among Same-Sex College Student Roommate Dyads.

PubMed

Xu, Qi; Shrout, Patrick E

2018-06-01

University students often experience high levels of stress and, in some cases, the stress leads to tragic outcomes. An important question is whether roommates can perceive the level and change in distress in their peers. We examined self- and other-reports of 187 same-sex undergraduate dyads at two times in a spring semester. Using the truth and bias model, we found that roommates tended to underestimate their partner's distress at both time points, and that ratings were equally influenced by truth and self-focus bias forces. For change, however, there was no evidence of directional (average) bias, and perceived change was only significantly related to the truth force. There were no consistent moderation effects by closeness or gender. These findings are interpreted in the context of person perception theory and the practical need for early warning about extreme distress in college students.

Overcenter collet space station truss fastener

NASA Technical Reports Server (NTRS)

Sheridan, Philip L. (Inventor)

1991-01-01

A quick-connect fastener is arranged with a tubular body that is arranged to be engaged against the exterior surface of a hollow attachment fitting and coincidentally aligned with an opening in the fitting. A collet having normally-contracted fingers with outwardly-enlarged ends is operatively arranged in the body to be moved forwardly by an expander member mounted in the tubular body for advancing the collet fingers through the opening in the attachment fitting. Biasing means are arranged between the expander member and a toggle linkage in the tubular body which is selectively operated to urge the expander member forwardly into engagement with the collet fingers with an initial biasing force to advance their forward portions through the body opening and then expand them outwardly. The biasing means also provide a subsequent biasing force for retaining the collet members in their expanded positions once their enlarged forward end portions are on the opposite side of the body.

May common model biases reduce CMIP5's ability to simulate the recent Pacific La Niña-like cooling?

NASA Astrophysics Data System (ADS)

Luo, Jing-Jia; Wang, Gang; Dommenget, Dietmar

2018-02-01

Over the recent three decades sea surface temperate (SST) in the eastern equatorial Pacific has decreased, which helps reduce the rate of global warming. However, most CMIP5 model simulations with historical radiative forcing do not reproduce this Pacific La Niña-like cooling. Based on the assumption of "perfect" models, previous studies have suggested that errors in simulated internal climate variations and/or external radiative forcing may cause the discrepancy between the multi-model simulations and the observation. But the exact causes remain unclear. Recent studies have suggested that observed SST warming in the other two ocean basins in past decades and the thermostat mechanism in the Pacific in response to increased radiative forcing may also play an important role in driving this La Niña-like cooling. Here, we investigate an alternative hypothesis that common biases of current state-of-the-art climate models may deteriorate the models' ability and can also contribute to this multi-model simulations-observation discrepancy. Our results suggest that underestimated inter-basin warming contrast across the three tropical oceans, overestimated surface net heat flux and underestimated local SST-cloud negative feedback in the equatorial Pacific may favor an El Niño-like warming bias in the models. Effects of the three common model biases do not cancel one another and jointly explain 50% of the total variance of the discrepancies between the observation and individual models' ensemble mean simulations of the Pacific SST trend. Further efforts on reducing common model biases could help improve simulations of the externally forced climate trends and the multi-decadal climate fluctuations.

Antecedents and Consequences of Supplier Performance Evaluation Efficacy

DTIC Science & Technology

2016-06-30

forming groups of high and low values. These tests are contingent on the reliable and valid measure of high and low rating inflation and high and...year)? Future research could deploy a SPM system as a test case on a limited set of transactions. Using a quasi-experimental design , comparisons...single source, common method bias must be of concern. Harmon’s one -factor test showed that when latent-indicator items were forced onto a single

Racial Targeting of Sexual Violence in Darfur

PubMed Central

Rymond-Richmond, Wenona; Palloni, Alberto

2009-01-01

Objectives. We used the Atrocities Documentation Survey to determine whether Sudanese government forces were involved in racially targeting sexual victimization toward ethnically African women in the Darfur region of western Sudan. Methods. The US State Department conducted the survey by interviewing a randomized multistage probability sample of 1136 Darfur refugees at 20 sites in Chad in 2004. For a subset of 932 respondents who had fled from village clusters that accounted for 15 or more respondents per cluster, we used hierarchical linear models to analyze village-level patterns of reported sexual violence. We statistically controlled for individual sexual victimization to remove bias. Results. Respondents reported being subjected to racial epithets associated with sexual victimization significantly more often during combined attacks by Sudanese government forces and Janjaweed militia forces than during separate attacks by either force. Conclusions. Combined attacks by Sudanese government forces and Janjaweed militia forces led to racial epithets being used more often during sexual victimization in Darfur. Our results suggest that the Sudanese government is participating in the use of sexual assault as a racially targeted weapon against ethnically African civilians. PMID:19542043

A Configurational-Bias-Monte-Carlo Back-Mapping Algorithm for Efficient and Rapid Conversion of Coarse-Grained Water Structures Into Atomistic Models.

PubMed

Loeffler, Troy David; Chan, Henry; Narayanan, Badri; Cherukara, Mathew J; Gray, Stephen K; Sankaranarayanan, Subramanian K R S

2018-06-20

Coarse-grained molecular dynamics (MD) simulations represent a powerful approach to simulate longer time scale and larger length scale phenomena than those accessible to all-atom models. The gain in efficiency, however, comes at the cost of atomistic details. The reverse transformation, also known as back-mapping, of coarse grained beads into their atomistic constituents represents a major challenge. Most existing approaches are limited to specific molecules or specific force-fields and often rely on running a long time atomistic MD of the back-mapped configuration to arrive at an optimal solution. Such approaches are problematic when dealing with systems with high diffusion barriers. Here, we introduce a new extension of the configurational-bias-Monte-Carlo (CBMC) algorithm, which we term the crystalline-configurational-bias-Monte-Carlo (C-CBMC) algortihm, that allows rapid and efficient conversion of a coarse-grained model back into its atomistic representation. Although the method is generic, we use a coarse-grained water model as a representative example and demonstrate the back-mapping or reverse transformation for model systems ranging from the ice-liquid water interface to amorphous and crystalline ice configurations. A series of simulations using the TIP4P/Ice model are performed to compare the new CBMC method to several other standard Monte Carlo and Molecular Dynamics based back-mapping techniques. In all the cases, the C-CBMC algorithm is able to find optimal hydrogen bonded configuration many thousand evaluations/steps sooner than the other methods compared within this paper. For crystalline ice structures such as a hexagonal, cubic, and cubic-hexagonal stacking disorder structures, the C-CBMC was able to find structures that were between 0.05 and 0.1 eV/water molecule lower in energy than the ground state energies predicted by the other methods. Detailed analysis of the atomistic structures show a significantly better global hydrogen positioning when contrasted with the existing simpler back-mapping methods. Our results demonstrate the efficiency and efficacy of our new back-mapping approach, especially for crystalline systems where simple force-field based relaxations have a tendency to get trapped in local minima.

The utility of satellite precipitation products for hydrologic prediction in topographically complex regions: The Chehalis River Basin, WA as a case study

NASA Astrophysics Data System (ADS)

Cao, Q.; Mehran, A.; Lettenmaier, D. P.; Mass, C.; Johnson, N.

2015-12-01

Accurate measurements of precipitation are of great importance in hydrologic predictions especially for floods, which are a pervasive natural hazard. One of the primary objectives of Global Precipitation Measurement (GPM) mission is to provide a basis for hydrologic predictions using satellite sensors. A major advance in GPM relative to the Tropical Rainfall Measuring Mission (TRMM) is that it observes atmospheric river (AR) events, most of which have landfall too far north to be tracked by TRMM. These events are responsible for most major floods along the U.S. West Coast. We address the question of whether, for hydrologic modeling purposes, it is better to use precipitation products derived directly from GPM and/or other precipitation fields from weather models that have assimilated satellite data. Our overall strategy is to compare different methods for prediction of flood and/or high flow events by different forcings on the hydrologic model. We examine four different configurations of the Distroibute Hydrology Soil Vegetation Model (DHSVM) over the Chehalis River Basin that use a) precipitation forcings based on gridded station data; b) precipitation forcings based on NWS WSR-88D data, c) forcings based from short-term precipitation forecasts using the Weather Research and Forecasting (WRF) mesoscale atmospheric model, and d) satellite-based precipitation estimates (TMPA and IMERG). We find that in general, biases in the radar and satellite products result in much larger errors than with either gridded station data or WRF forcings, but if these biases are removed, comparable performance in flood predictions can be achieved by Satellite-based precipitation estimates (TMPA and IMERG).

Spontaneous lateral atomic recoil force close to a photonic topological material

NASA Astrophysics Data System (ADS)

Hassani Gangaraj, S. Ali; Hanson, George W.; Antezza, Mauro; Silveirinha, Mário G.

2018-05-01

We investigate the quantum recoil force acting on an excited atom close to the surface of a nonreciprocal photonic topological insulator (PTI). The main atomic emission channel is the unidirectional surface plasmon propagating at the PTI-vacuum interface, and we show that it enables a spontaneous lateral recoil force that scales at short distances as 1 /d4 , where d is the atom-PTI separation. Remarkably, the sign of the recoil force is polarization and orientation independent, and it occurs in a translation-invariant homogeneous system in thermal equilibrium. Surprisingly, the recoil force persists for very small values of the gyration pseudovector, which, for a biased plasma, corresponds to very low cyclotron frequencies. The ultrastrong recoil force is rooted in the quasihyperbolic dispersion of the surface plasmons. We consider both an initially excited atom and a continuous pump scenario, the latter giving rise to a steady lateral force whose direction can be changed at will by simply varying the orientation of the biasing magnetic field. Our predictions may be tested in experiments with cold Rydberg atoms and superconducting qubits.

Impact of tropical Atlantic sea-surface temperature biases on the simulated atmospheric circulation and precipitation over the Atlantic region: An ECHAM6 model study

NASA Astrophysics Data System (ADS)

Eichhorn, Astrid; Bader, Jürgen

2017-09-01

As many coupled atmosphere-ocean general circulation models, the coupled Earth System Model developed at the Max Planck Institute for Meteorology suffers from severe sea-surface temperature (SST) biases in the tropical Atlantic. We performed a set of SST sensitivity experiments with its atmospheric model component ECHAM6 to understand the impact of tropical Atlantic SST biases on atmospheric circulation and precipitation. The model was forced by a climatology of observed global SSTs to focus on simulated seasonal and annual mean state climate. Through the superposition of varying tropical Atlantic bias patterns extracted from the MPI-ESM on top of the control field, this study investigates the relevance of the seasonal variation and spatial structure of tropical Atlantic biases for the simulated response. Results show that the position and structure of the Intertropical Convergence Zone (ITCZ) across the Atlantic is significantly affected, exhibiting a dynamically forced shift of annual mean precipitation maximum to the east of the Atlantic basin as well as a southward shift of the oceanic rain belt. The SST-induced changes in the ITCZ in turn affect seasonal rainfall over adjacent continents. However not only the ITCZ position but also other effects arising from biases in tropical Atlantic SSTs, e.g. variations in the wind field, change the simulation of precipitation over land. The seasonal variation and spatial pattern of tropical Atlantic SST biases turns out to be crucial for the simulated atmospheric response and is essential for analyzing the contribution of SST biases to coupled model mean state biases. Our experiments show that MPI-ESM mean-state biases in the Atlantic sector are mainly driven by SST biases in the tropical Atlantic while teleconnections from other basins seem to play a minor role.

The long-term trend in the diurnal temperature range over Asia and its natural and anthropogenic causes

NASA Astrophysics Data System (ADS)

Liu, Lin; Li, Zhanqing; Yang, Xin; Gong, Hainan; Li, Chao; Xiong, Anyuan

2016-04-01

Understanding the causes of long-term temperature trends is at the core of climate change studies. Any observed trend can result from natural variability or anthropogenic influences or both. In the present study, we evaluated the performance of 18 climate models from the Coupled Model Intercomparison Project Phase 5 on simulating the Asian diurnal temperature range (DTR) and explored the potential causes of the long-term trend in the DTR by examining the response of the DTR to natural forcing (volcanic aerosols and solar variability) and anthropogenic forcing (anthropogenic greenhouse gases (GHG) and aerosols) in the historical period of 1961-2005. For the climatology, the multimodel ensemble mean reproduced the geographical distribution and amplitude of the DTR over eastern China and India but underestimated the magnitudes of the DTR over the Tibetan Plateau and the high-latitude regions of the Asian continent. These negative biases in the DTR over frigid zones existed in most models. Seasonal biases in the DTR pattern from models were similar to the bias in the annual mean DTR pattern. Based on three selected state-of-the-art models, the observed decreasing trend in the DTR over Asia was reasonably reproduced in the all-forcing run. A comparison of separate forcing experiments revealed that anthropogenic forcing plays the dominant role in the declining trend in the DTR. Observations and model simulations showed that GHG forcing is mainly responsible for the negative trends in the DTR over Asia but that anthropogenic aerosol forcing was also behind the decreasing trend in the DTR over China and especially over eastern China.

Accounting for elite indoor 200 m sprint results

PubMed Central

Usherwood, James R; Wilson, Alan M

2005-01-01

Times for indoor 200 m sprint races are notably worse than those for outdoor races. In addition, there is a considerable bias against competitors drawn in inside lanes (with smaller bend radii). Centripetal acceleration requirements increase average forces during sprinting around bends. These increased forces can be modulated by changes in duty factor (the proportion of stride the limb is in contact with the ground). If duty factor is increased to keep limb forces constant, and protraction time and distance travelled during stance are unchanging, bend-running speeds are reduced. Here, we use results from the 2004 Olympics and World Indoor Championships to show quantitatively that the decreased performances in indoor competition, and the bias by lane number, are consistent with this ‘constant limb force’ hypothesis. Even elite athletes appear constrained by limb forces. PMID:17148323

Automated optimal coordination of multiple-DOF neuromuscular actions in feedforward neuroprostheses.

PubMed

Lujan, J Luis; Crago, Patrick E

2009-01-01

This paper describes a new method for designing feedforward controllers for multiple-muscle, multiple-DOF, motor system neural prostheses. The design process is based on experimental measurement of the forward input/output properties of the neuromechanical system and numerical optimization of stimulation patterns to meet muscle coactivation criteria, thus resolving the muscle redundancy (i.e., overcontrol) and the coupled DOF problems inherent in neuromechanical systems. We designed feedforward controllers to control the isometric forces at the tip of the thumb in two directions during stimulation of three thumb muscles as a model system. We tested the method experimentally in ten able-bodied individuals and one patient with spinal cord injury. Good control of isometric force in both DOFs was observed, with rms errors less than 10% of the force range in seven experiments and statistically significant correlations between the actual and target forces in all ten experiments. Systematic bias and slope errors were observed in a few experiments, likely due to the neuromuscular fatigue. Overall, the tests demonstrated the ability of a general design approach to satisfy both control and coactivation criteria in multiple-muscle, multiple-axis neuromechanical systems, which is applicable to a wide range of neuromechanical systems and stimulation electrodes.

Towards identification of relevant variables in the observed aerosol optical depth bias between MODIS and AERONET observations

NASA Astrophysics Data System (ADS)

Malakar, N. K.; Lary, D. J.; Gencaga, D.; Albayrak, A.; Wei, J.

2013-08-01

Measurements made by satellite remote sensing, Moderate Resolution Imaging Spectroradiometer (MODIS), and globally distributed Aerosol Robotic Network (AERONET) are compared. Comparison of the two datasets measurements for aerosol optical depth values show that there are biases between the two data products. In this paper, we present a general framework towards identifying relevant set of variables responsible for the observed bias. We present a general framework to identify the possible factors influencing the bias, which might be associated with the measurement conditions such as the solar and sensor zenith angles, the solar and sensor azimuth, scattering angles, and surface reflectivity at the various measured wavelengths, etc. Specifically, we performed analysis for remote sensing Aqua-Land data set, and used machine learning technique, neural network in this case, to perform multivariate regression between the ground-truth and the training data sets. Finally, we used mutual information between the observed and the predicted values as the measure of similarity to identify the most relevant set of variables. The search is brute force method as we have to consider all possible combinations. The computations involves a huge number crunching exercise, and we implemented it by writing a job-parallel program.

Effect of substrate bias voltage on tensile properties of single crystal silicon microstructure fully coated with plasma CVD diamond-like carbon film

NASA Astrophysics Data System (ADS)

Zhang, Wenlei; Hirai, Yoshikazu; Tsuchiya, Toshiyuki; Tabata, Osamu

2018-06-01

Tensile strength and strength distribution in a microstructure of single crystal silicon (SCS) were improved significantly by coating the surface with a diamond-like carbon (DLC) film. To explore the influence of coating parameters and the mechanism of film fracture, SCS microstructure surfaces (120 × 4 × 5 μm3) were fully coated by plasma enhanced chemical vapor deposition (PECVD) of a DLC at five different bias voltages. After the depositions, Raman spectroscopy, X-ray photoelectron spectroscopy (XPS), thermal desorption spectrometry (TDS), surface profilometry, atomic force microscope (AFM) measurement, and nanoindentation methods were used to study the chemical and mechanical properties of the deposited DLC films. Tensile test indicated that the average strength of coated samples was 13.2-29.6% higher than that of the SCS sample, and samples fabricated with a -400 V bias voltage were strongest. The fracture toughness of the DLC film was the dominant factor in the observed tensile strength. Deviations in strength were reduced with increasingly negative bias voltage. The effect of residual stress on the tensile properties is discussed in detail.

Reduction of uncertainty in global black carbon direct radiative forcing constrained by observations

NASA Astrophysics Data System (ADS)

Wang, R.; Balkanski, Y.; Boucher, O.; Ciais, P.; Schuster, G. L.; Chevallier, F.; Samset, B. H.; Valari, M.; Liu, J.; Tao, S.

2017-12-01

Black carbon (BC) absorbs sunlight and contributes to global warming. However, the size of this effect, namely the direct radiative forcing (DRF), ranges from +0.1 to +1.0 W m-2, largely due to discrepancies between modeled and observed BC radiation absorption. Studies that adjusted emissions to correct biases of models resulted in a revised upward estimate of the BC DRF. However, the observation-based BC RF was not optimized against observations in a rigorous mathematical manner, because uncertainties in emissions and the representativeness errors due to use of coarse-resolution models were not fully assessed. Here we simulated the absorption of solar radiation by BC from all sources at the 10-km resolution by combining a nested aerosol model with a downscaling method. The normalized mean bias in BC radiation absorption was reduced from -51% to -24% in Asia and from -57% to -50% elsewhere. We applied a Bayesian method that account for model, representativeness and observational uncertainties to estimate the BC RF and its uncertainty. Using the high-resolution model reduces uncertainty in BC DRF from -101%/+152% to -70%/+71% over Asia and from -83%/+108% to -64%/+68% over other continental regions. We derived an observation-based BC DRF of 0.61 Wm-2 (0.16 to 1.40 as 90% confidence) as our best estimate.

Silicone based dielectric elastomer strip actuators coupled with nonlinear biasing elements for large actuation strains

NASA Astrophysics Data System (ADS)

Hau, S.; Bruch, D.; Rizzello, G.; Motzki, P.; Seelecke, S.

2018-07-01

There are two major categories of dielectric elastomer actuators (DEAs), which differ from the way in which the actuation is exploited: stack DEAs, using the thickness compression, and membrane DEAs, which exploit the expansion in area. In this work we focus on a specific type of membrane DEAs, i.e., silicone-based strip-in-plane (SIP) DEAs with screen printed electrodes. The performance of such actuators strongly depends on their geometry and on the adopted mechanical biasing system. Typically, the biasing is based on elastomer pre-stretch or on dead loads, which results in relatively low actuation strain. Biasing systems characterized by a negative rate spring have proven to significantly increase the performance of circular out-of-plane DEAs. However, this kind of biasing has never been systematically applied to silicone SIP DEAs. In this work, the biasing design based on negative rate springs is extended to strip DEAs as well, allowing to improve speed, strain, and force of the resulting actuator. At first, the DEAs are characterized under electrical and mechanical loading. Afterwards, two actuator systems are studied and compared in terms of actuation strain, force output, and actuation speed. In a first design stage, the DEA is coupled with a linear spring. Subsequently, the membrane is loaded with a combination of linear and nonlinear spring (working in a negative stiffness region). The resulting stroke output of the second systems is more than 9 times higher in comparison to the first one. An actuation strain of up to 45% (11.2 millimeter) and a force output of 0.38 Newton are measured. A maximum speed of 0.29 m s‑1 is achieved, which is about 60 times faster than the one typically measured for similar systems based on VHB.

On CD-AFM bias related to probe bending

NASA Astrophysics Data System (ADS)

Ukraintsev, V. A.; Orji, N. G.; Vorburger, T. V.; Dixson, R. G.; Fu, J.; Silver, R. M.

2012-03-01

Critical Dimension AFM (CD-AFM) is a widely used reference metrology. To characterize modern semiconductor devices, very small and flexible probes, often 15 nm to 20 nm in diameter, are now frequently used. Several recent publications have reported on uncontrolled and significant probe-to-probe bias variation during linewidth and sidewall angle measurements [1,2]. Results obtained in this work suggest that probe bending can be on the order of several nanometers and thus potentially can explain much of the observed CD-AFM probe-to-probe bias variation. We have developed and experimentally tested one-dimensional (1D) and two-dimensional (2D) models to describe the bending of cylindrical probes. An earlier 1D bending model reported by Watanabe et al. [3] was refined. Contributions from several new phenomena were considered, including: probe misalignment, diameter variation near the carbon nanotube tip (CNT) apex, probe bending before snapping, distributed van der Waals-London force, etc. The methodology for extraction of the Hamaker probe-surface interaction energy from experimental probe bending data was developed. To overcome limitations of the 1D model, a new 2D distributed force (DF) model was developed. Comparison of the new model with the 1D single point force (SPF) model revealed about 27 % difference in probe bending bias between the two. A simple linear relation between biases predicted by the 1D SPF and 2D DF models was found. This finding simplifies use of the advanced 2D DF model of probe bending in various CD-AFM applications. New 2D and three-dimensional (3D) CDAFM data analysis software is needed to take full advantage of the new bias correction modeling capabilities.

Overcoming free energy barriers using unconstrained molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Hénin, Jérôme; Chipot, Christophe

2004-08-01

Association of unconstrained molecular dynamics (MD) and the formalisms of thermodynamic integration and average force [Darve and Pohorille, J. Chem. Phys. 115, 9169 (2001)] have been employed to determine potentials of mean force. When implemented in a general MD code, the additional computational effort, compared to other standard, unconstrained simulations, is marginal. The force acting along a chosen reaction coordinate ξ is estimated from the individual forces exerted on the chemical system and accumulated as the simulation progresses. The estimated free energy derivative computed for small intervals of ξ is canceled by an adaptive bias to overcome the barriers of the free energy landscape. Evolution of the system along the reaction coordinate is, thus, limited by its sole self-diffusion properties. The illustrative examples of the reversible unfolding of deca-L-alanine, the association of acetate and guanidinium ions in water, the dimerization of methane in water, and its transfer across the water liquid-vapor interface are examined to probe the efficiency of the method.

Overcoming free energy barriers using unconstrained molecular dynamics simulations.

PubMed

Hénin, Jérôme; Chipot, Christophe

2004-08-15

Association of unconstrained molecular dynamics (MD) and the formalisms of thermodynamic integration and average force [Darve and Pohorille, J. Chem. Phys. 115, 9169 (2001)] have been employed to determine potentials of mean force. When implemented in a general MD code, the additional computational effort, compared to other standard, unconstrained simulations, is marginal. The force acting along a chosen reaction coordinate xi is estimated from the individual forces exerted on the chemical system and accumulated as the simulation progresses. The estimated free energy derivative computed for small intervals of xi is canceled by an adaptive bias to overcome the barriers of the free energy landscape. Evolution of the system along the reaction coordinate is, thus, limited by its sole self-diffusion properties. The illustrative examples of the reversible unfolding of deca-L-alanine, the association of acetate and guanidinium ions in water, the dimerization of methane in water, and its transfer across the water liquid-vapor interface are examined to probe the efficiency of the method. (c) 2004 American Institute of Physics.

A New Paradigm for Diagnosing Contributions to Model Aerosol Forcing Error

NASA Astrophysics Data System (ADS)

Jones, A. L.; Feldman, D. R.; Freidenreich, S.; Paynter, D.; Ramaswamy, V.; Collins, W. D.; Pincus, R.

2017-12-01

A new paradigm in benchmark absorption-scattering radiative transfer is presented that enables both the globally averaged and spatially resolved testing of climate model radiation parameterizations in order to uncover persistent sources of biases in the aerosol instantaneous radiative effect (IRE). A proof of concept is demonstrated with the Geophysical Fluid Dynamics Laboratory AM4 and Community Earth System Model 1.2.2 climate models. Instead of prescribing atmospheric conditions and aerosols, as in prior intercomparisons, native snapshots of the atmospheric state and aerosol optical properties from the participating models are used as inputs to an accurate radiation solver to uncover model-relevant biases. These diagnostic results show that the models' aerosol IRE bias is of the same magnitude as the persistent range cited ( 1 W/m2) and also varies spatially and with intrinsic aerosol optical properties. The findings underscore the significance of native model error analysis and its dispositive ability to diagnose global biases, confirming its fundamental value for the Radiative Forcing Model Intercomparison Project.

No Own-Age Bias in 3-Year-Old Children: More Evidence for the Role of Early Experience in Building Face-Processing Biases

ERIC Educational Resources Information Center

Cassia, Viola Macchi; Pisacane, Antonella; Gava, Lucia

2012-01-01

This study aimed to investigate the presence of an own-age bias in young children who accumulated different amounts of early experience with child faces. Discrimination abilities for upright and inverted adult and child faces were tested using a delayed two-alternative, forced-choice matching-to-sample task in two groups of 3-year-old children,…

Application of the inverse analysis for determining the material properties of the woven fabrics for macroscopic approach

NASA Astrophysics Data System (ADS)

Oleksik, Mihaela; Oleksik, Valentin

2013-05-01

The current paper intends to realise a fast method for determining the material characteristics in the case of composite materials used in the airbags manufacturing. For determining the material data needed for other complex numerical simulations at macroscopic level there was used the inverse analysis method. In fact, there were carried out tensile tests for the composite material extracted along two directions - the direction of the weft and the direction of the warp and afterwards there were realised numerical simulations (using the Ls-Dyna software). A second stage consisted in the numerical simulation through the finite element method and the experimental testing for the Bias test. The material characteristics of the composite fabric material were then obtained by applying a multicriterial analysis using the Ls-Opt software, for which there was imposed a decrease of the mismatch between the force-displacement curves obtained numerically and experimentally, respectively, for both directions (weft and warp) as well as the decrease of the mismatch between the strain - extension curves for two points at the Bias test.

A Meso-Climatology Study of the High-Resolution Tower Network Over the Florida Spaceport

NASA Technical Reports Server (NTRS)

Case, Jonathan L.; Bauman, William H., III

2004-01-01

Forecasters at the US Air Force 45th Weather Squadron (45 WS) use wind and temperature data from the tower network over the Kennedy Space Center (KSC) and Cape Canaveral Air Force Station (CCAFS) to evaluate Launch Commit Criteria and to issue and verify temperature and wind advisories, watches, and warnings for ground operations. The Spaceflight Meteorology Group at the Johnson Space Center in Houston, TX also uses these data when issuing forecasts for shuttle landings at the KSC Shuttle Landing Facility. Systematic biases in these parameters at any of the towers could adversely affect an analysis, forecast, or verification for all of these operations. In addition, substantial geographical variations in temperature and wind speed can occur under specific wind directions. Therefore, the Applied Meteorology Unit (AMU), operated by ENSCO Inc., was tasked to develop a monthly and hourly climatology of temperatures and winds from the tower network, and identify the geographical variation, tower biases, and the magnitude of those biases. This paper presents a sub-set of results from a nine-year climatology of the KSC/CCAFS tower network, highlighting the geographical variations based on location, month, times of day, and specific wind direction regime. Section 2 provides a description of the tower mesonetwork and instrumentation characteristics. Section 3 presents the methodology used to construct the tower climatology including QC methods and data processing. The results of the tower climatology are presented in Section 4 and Section 5 summarizes the paper.

Force and light tuning vertical tunneling current in the atomic layered MoS2.

PubMed

Li, Feng; Lu, Zhixing; Lan, Yann-Wen; Jiao, Liying; Xu, Minxuan; Zhu, Xiaoyang; Zhang, Xiankun; Wu, Hualin; Qi, Junjie

2018-07-06

In this work, the vertical electrical transport behavior of bilayer MoS 2 under the coupling of force and light was explored by the use of conductive atomic force microscopy. We found that the current-voltage behavior across the tip-MoS 2 -Pt junction is a tunneling current that can be well fitted by a Simmons approximation. The transport behavior is direct tunneling at low bias and Fowler-Nordheim tunneling at high bias, and the transition voltage and tunnel barrier height are extracted. The effect of force and light on the effective band gap of the junction is investigated. Furthermore, the source-drain current drops surprisingly when we continually increase the force, and the dropping point is altered by the provided light. This mechanism is responsible for the tuning of tunneling barrier height and width by force and light. These results provide a new way to design devices that take advantage of ultrathin two-dimensional materials. Ultrashort channel length electronic components that possess tunneling current are important for establishing high-efficiency electronic and optoelectronic systems.

Artifacts in time-resolved Kelvin probe force microscopy

DOE PAGES

Sadewasser, Sascha; Nicoara, Nicoleta; Solares, Santiago D.

2018-04-24

Kelvin probe force microscopy (KPFM) has been used for the characterization of metals, insulators, and semiconducting materials on the nanometer scale. Especially in semiconductors, the charge dynamics are of high interest. Recently, several techniques for time-resolved measurements with time resolution down to picoseconds have been developed, many times using a modulated excitation signal, e.g. light modulation or bias modulation that induces changes in the charge carrier distribution. For fast modulation frequencies, the KPFM controller measures an average surface potential, which contains information about the involved charge carrier dynamics. Here, we show that such measurements are prone to artifacts due tomore » frequency mixing, by performing numerical dynamics simulations of the cantilever oscillation in KPFM subjected to a bias-modulated signal. For square bias pulses, the resulting time-dependent electrostatic forces are very complex and result in intricate mixing of frequencies that may, in some cases, have a component at the detection frequency, leading to falsified KPFM measurements. Additionally, we performed fast Fourier transform (FFT) analyses that match the results of the numerical dynamics simulations. Small differences are observed that can be attributed to transients and higher-order Fourier components, as a consequence of the intricate nature of the cantilever driving forces. These results are corroborated by experimental measurements on a model system. In the experimental case, additional artifacts are observed due to constructive or destructive interference of the bias modulation with the cantilever oscillation. Also, in the case of light modulation, we demonstrate artifacts due to unwanted illumination of the photodetector of the beam deflection detection system. Lastly, guidelines for avoiding such artifacts are given.« less

Artifacts in time-resolved Kelvin probe force microscopy

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

Sadewasser, Sascha; Nicoara, Nicoleta; Solares, Santiago D.

Kelvin probe force microscopy (KPFM) has been used for the characterization of metals, insulators, and semiconducting materials on the nanometer scale. Especially in semiconductors, the charge dynamics are of high interest. Recently, several techniques for time-resolved measurements with time resolution down to picoseconds have been developed, many times using a modulated excitation signal, e.g. light modulation or bias modulation that induces changes in the charge carrier distribution. For fast modulation frequencies, the KPFM controller measures an average surface potential, which contains information about the involved charge carrier dynamics. Here, we show that such measurements are prone to artifacts due tomore » frequency mixing, by performing numerical dynamics simulations of the cantilever oscillation in KPFM subjected to a bias-modulated signal. For square bias pulses, the resulting time-dependent electrostatic forces are very complex and result in intricate mixing of frequencies that may, in some cases, have a component at the detection frequency, leading to falsified KPFM measurements. Additionally, we performed fast Fourier transform (FFT) analyses that match the results of the numerical dynamics simulations. Small differences are observed that can be attributed to transients and higher-order Fourier components, as a consequence of the intricate nature of the cantilever driving forces. These results are corroborated by experimental measurements on a model system. In the experimental case, additional artifacts are observed due to constructive or destructive interference of the bias modulation with the cantilever oscillation. Also, in the case of light modulation, we demonstrate artifacts due to unwanted illumination of the photodetector of the beam deflection detection system. Lastly, guidelines for avoiding such artifacts are given.« less

A comparison of low back kinetic estimates obtained through posture matching, rigid link modeling and an EMG-assisted model.

PubMed

Parkinson, R J; Bezaire, M; Callaghan, J P

2011-07-01

This study examined errors introduced by a posture matching approach (3DMatch) relative to dynamic three-dimensional rigid link and EMG-assisted models. Eighty-eight lifting trials of various combinations of heights (floor, 0.67, 1.2 m), asymmetry (left, right and center) and mass (7.6 and 9.7 kg) were videotaped while spine postures, ground reaction forces, segment orientations and muscle activations were documented and used to estimate joint moments and forces (L5/S1). Posture matching over predicted peak and cumulative extension moment (p < 0.0001 for all variables). There was no difference between peak compression estimates obtained with posture matching or EMG-assisted approaches (p = 0.7987). Posture matching over predicted cumulative (p < 0.0001) compressive loading due to a bias in standing, however, individualized bias correction eliminated the differences. Therefore, posture matching provides a method to analyze industrial lifting exposures that will predict kinetic values similar to those of more sophisticated models, provided necessary corrections are applied. Copyright © 2010 Elsevier Ltd and The Ergonomics Society. All rights reserved.

EFM data mapped into 2D images of tip-sample contact potential difference and capacitance second derivative.

PubMed

Lilliu, S; Maragliano, C; Hampton, M; Elliott, M; Stefancich, M; Chiesa, M; Dahlem, M S; Macdonald, J E

2013-11-27

We report a simple technique for mapping Electrostatic Force Microscopy (EFM) bias sweep data into 2D images. The method allows simultaneous probing, in the same scanning area, of the contact potential difference and the second derivative of the capacitance between tip and sample, along with the height information. The only required equipment consists of a microscope with lift-mode EFM capable of phase shift detection. We designate this approach as Scanning Probe Potential Electrostatic Force Microscopy (SPP-EFM). An open-source MATLAB Graphical User Interface (GUI) for images acquisition, processing and analysis has been developed. The technique is tested with Indium Tin Oxide (ITO) and with poly(3-hexylthiophene) (P3HT) nanowires for organic transistor applications.

A variational technique for smoothing flight-test and accident data

NASA Technical Reports Server (NTRS)

Bach, R. E., Jr.

1980-01-01

The problem of determining aircraft motions along a trajectory is solved using a variational algorithm that generates unmeasured states and forcing functions, and estimates instrument bias and scale-factor errors. The problem is formulated as a nonlinear fixed-interval smoothing problem, and is solved as a sequence of linear two-point boundary value problems, using a sweep method. The algorithm has been implemented for use in flight-test and accident analysis. Aircraft motions are assumed to be governed by a six-degree-of-freedom kinematic model; forcing functions consist of body accelerations and winds, and the measurement model includes aerodynamic and radar data. Examples of the determination of aircraft motions from typical flight-test and accident data are presented.

A population comparison of participants and nonparticipants in a health survey.

PubMed Central

Klesges, R C; Williamson, J E; Somes, G W; Talcott, G W; Lando, H A; Haddock, C K

1999-01-01

OBJECTIVES: This study examined the characteristics of Air Force recruits willing to take part in a health survey vs those unwilling to participate. METHODS: US Air Force recruits undergoing basic military training (n = 32,144) were surveyed regarding demographic and health variables. RESULTS: Respondents indicating an unwillingness to participate in a health survey reported less healthy lifestyles than those willing to participate. Prediction equations modeling the characteristics of those engaging in 4 risky behaviors were nearly identical regardless of whether those refusing to participate were included. CONCLUSIONS: Results suggest that, despite some low estimates of health behaviors due to response bias, relationships between most risk factors are generally unaffected by those not responding to health surveys. PMID:10432911

Unanticipated ankle inversions are significantly different from anticipated ankle inversions during drop landings: overcoming anticipation bias.

PubMed

Dicus, Jeremy R; Seegmiller, Jeff G

2012-05-01

Few ankle inversion studies have taken anticipation bias into account or collected data with an experimental design that mimics actual injury mechanisms. Twenty-three participants performed randomized single-leg vertical drop landings from 20 cm. Subjects were blinded to the landing surface (a flat force plate or 30° inversion wedge on the force plate). After each trial, participants reported whether they anticipated the landing surface. Participant responses were validated with EMG data. The protocol was repeated until four anticipated and four unanticipated landings onto the inversion wedge were recorded. Results revealed a significant main effect for landing condition. Normalized vertical ground reaction force (% body weights), maximum ankle inversion (degrees), inversion velocity (degrees/second), and time from contact to peak muscle activation (seconds) were significantly greater in unanticipated landings, and the time from peak muscle activation to maximum VGRF (second) was shorter. Unanticipated landings presented different muscle activation patterns than landings onto anticipated surfaces, which calls into question the usefulness of clinical studies that have not controlled for anticipation bias.

Rightward biases in free-viewing visual bisection tasks: implications for leftward responses biases on similar tasks.

PubMed

Elias, Lorin J; Robinson, Brent; Saucier, Deborah M

2005-12-01

Neurologically normal individuals exhibit strong leftward response biases during free-viewing perceptual judgments of brightness, quantity, and size. When participants view two mirror-reversed objects and they are forced to choose which object appears darker, more numerous, or larger, the stimulus with the relevant feature on the left side is chosen 60-75% of the time. This effect could be influenced by inaccurate judgments of the true centre-point of the objects being compared. In order to test this possibility, 10 participants completed three visual bisection tasks on stimuli known to elicit strong leftward response biases. Participants were monitored using a remote eye-tracking device and instructed to stare at the subjective midpoint of objects presented on a computer screen. Although it was predicted that bisection errors would deviate to the left of centre (as is the case in the line bisection literature), the opposite effect was found. Significant rightward bisection errors were evident on two of the three tasks, and the leftward biases seen during forced-choice tasks could be the result of misjudgments to the right of centre on these same tasks.

Modelling cognitive affective biases in major depressive disorder using rodents

PubMed Central

Hales, Claire A; Stuart, Sarah A; Anderson, Michael H; Robinson, Emma S J

2014-01-01

Major depressive disorder (MDD) affects more than 10% of the population, although our understanding of the underlying aetiology of the disease and how antidepressant drugs act to remediate symptoms is limited. Major obstacles include the lack of availability of good animal models that replicate aspects of the phenotype and tests to assay depression-like behaviour in non-human species. To date, research in rodents has been dominated by two types of assays designed to test for depression-like behaviour: behavioural despair tests, such as the forced swim test, and measures of anhedonia, such as the sucrose preference test. These tests have shown relatively good predictive validity in terms of antidepressant efficacy, but have limited translational validity. Recent developments in clinical research have revealed that cognitive affective biases (CABs) are a key feature of MDD. Through the development of neuropsychological tests to provide objective measures of CAB in humans, we have the opportunity to use ‘reverse translation’ to develop and evaluate whether similar methods are suitable for research into MDD using animals. The first example of this approach was reported in 2004 where rodents in a putative negative affective state were shown to exhibit pessimistic choices in a judgement bias task. Subsequent work in both judgement bias tests and a novel affective bias task suggest that these types of assay may provide translational methods for studying MDD using animals. This review considers recent work in this area and the pharmacological and translational validity of these new animal models of CABs. Linked Articles This article is part of a themed section on Animal Models in Psychiatry Research. To view the other articles in this section visit http://dx.doi.org/10.1111/bph.2014.171.issue-20 PMID:24467454

In silico free energy predictions for ionic liquid-assisted exfoliation of a graphene bilayer into individual graphene nanosheets.

PubMed

Kamath, Ganesh; Baker, Gary A

2012-06-14

Free energies for graphene exfoliation from bilayer graphene using ionic liquids based on various cations paired with the bis(trifluoromethylsulfonyl)imide anion were determined from adaptive bias force-molecular dynamics (ABF-MD) simulation and fall in excellent qualitative agreement with experiment. This method has notable potential as an a priori screening tool for performance based rank order prediction of novel ionic liquids for the dispersion and exfoliation of various nanocarbons and inorganic graphene analogues.

Improvement in thrust force estimation of solenoid valve considering minor hysteresis loop

NASA Astrophysics Data System (ADS)

Yoon, Myung-Hwan; Choi, Yun-Yong; Hong, Jung-Pyo

2017-05-01

Solenoid valve is a very important hydraulic actuator for an automatic transmission in terms of shift quality. The same form of pressure for the clutch and the input current are required for an ideal control. However, the gap between a pressure and a current can occur which brings a delay in a transmission and a decrease in quality. This problem is caused by hysteresis phenomenon. As the ascending or descending magnetic field is applied to the solenoid, different thrust forces are generated. This paper suggests the calculation method of the thrust force considering the hysteresis phenomenon and consequently the accurate force can be obtained. Such hysteresis occurs in ferromagnetic materials, however the hysteresis phenomenon includes a minor hysteresis loop which begins with an initial magnetization curve and is generated by DC biased field density. As the core of the solenoid is ferromagnetic material, an accurate thrust force is obtained by applying the minor hysteresis loop compared to the force calculated by considering only the initial magnetization curve. An analytical background and the detailed explanation of measuring the minor hysteresis loop are presented. Furthermore experimental results and finite element analysis results are compared for the verification.

d'plus: A program to calculate accuracy and bias measures from detection and discrimination data.

PubMed

Macmillan, N A; Creelman, C D

1997-01-01

The program d'plus calculates accuracy (sensitivity) and response-bias parameters using Signal Detection Theory. Choice Theory, and 'nonparametric' models. is is appropriate for data from one-interval, two- and three-interval forced-choice, same different, ABX, and oddity experimental paradigms.

Improving the Accuracy of the AFWA-NASA (ANSA) Blended Snow-Cover Product over the Lower Great Lakes Region

NASA Technical Reports Server (NTRS)

Hall, Dorothy K.; Foster, James L.; Kumar, Sujay; Chien, Janety Y. L.; Riggs, George A.

2012-01-01

The Air Force Weather Agency (AFWA) -- NASA blended snow-cover product, called ANSA, utilizes Earth Observing System standard snow products from the Moderate- Resolution Imaging Spectroradiometer (MODIS) and the Advanced Microwave Scanning Radiometer for EOS (AMSR-E) to map daily snow cover and snow-water equivalent (SWE) globally. We have compared ANSA-derived SWE with SWE values calculated from snow depths reported at 1500 National Climatic Data Center (NCDC) co-op stations in the Lower Great Lakes Basin. Compared to station data, the ANSA significantly underestimates SWE in densely-forested areas. We use two methods to remove some of the bias observed in forested areas to reduce the root-mean-square error (RMSE) between the ANSA- and station-derived SWE. First, we calculated a 5- year mean ANSA-derived SWE for the winters of 2005-06 through 2009-10, and developed a five-year mean bias-corrected SWE map for each month. For most of the months studied during the five-year period, the 5-year bias correction improved the agreement between the ANSA-derived and station-derived SWE. However, anomalous months such as when there was very little snow on the ground compared to the 5-year mean, or months in which the snow was much greater than the 5-year mean, showed poorer results (as expected). We also used a 7-day running mean (7DRM) bias correction method using days just prior to the day in question to correct the ANSA data. This method was more effective in reducing the RMSE between the ANSA- and co-op-derived SWE values, and in capturing the effects of anomalous snow conditions.

Causes of the large warm bias in the Angola-Benguela Frontal Zone in the Norwegian Earth System Model

NASA Astrophysics Data System (ADS)

Koseki, Shunya; Keenlyside, Noel; Demissie, Teferi; Toniazzo, Thomas; Counillon, Francois; Bethke, Ingo; Ilicak, Mehmet; Shen, Mao-Lin

2018-06-01

We have investigated the causes of the sea surface temperature (SST) bias in the Angola-Benguela Frontal Zone (ABFZ) of the southeastern Atlantic Ocean simulated by the Norwegian Earth System Model (NorESM). Similar to other coupled-models, NorESM has a warm SST bias in the ABFZ of up to 8 °C in the annual mean. Our analysis of NorESM reveals that a cyclonic surface wind bias over the ABFZ drives a locally excessively strong southward (0.05 m/s (relative to observation)) Angola Current displacing the ABFZ southward. A series of uncoupled stand-alone atmosphere and ocean model simulations are performed to investigate the cause of the coupled model bias. The stand-alone atmosphere model driven with observed SST exhibits a similar cyclonic surface circulation bias; while the stand-alone ocean model forced with the reanalysis data produces a warm SST in the ABFZ with a magnitude approximately half of that in the coupled NorESM simulation. An additional uncoupled sensitivity experiment shows that the atmospheric model's local negative surface wind curl generates anomalously strong Angola Current at the ocean surface. Consequently, this contributes to the warm SST bias in the ABFZ by 2 °C (compared to the reanalysis forced simulation). There is no evidence that local air-sea feedbacks among wind stress curl, SST, and sea level pressure (SLP) affect the ABFZ SST bias. Turbulent surface heat flux differences between coupled and uncoupled experiments explain the remaining 2 °C warm SST bias in NorESM. Ocean circulation, upwelling and turbulent heat flux errors all modulate the intensity and the seasonality of the ABFZ errors.

Assessing Extratropical Influence on Tropical Climatology and Variability with Regional Coupled Data Assimilation

NASA Astrophysics Data System (ADS)

Lu, F.; Liu, Z.; Liu, Y.; Zhang, S.; Jacob, R. L.

2017-12-01

The Regional Coupled Data Assimilation (RCDA) method is introduced as a tool to study coupled climate dynamics and teleconnections. The RCDA method is built on an ensemble-based coupled data assimilation (CDA) system in a coupled general circulation model (CGCM). The RCDA method limits the data assimilation to the desired model components (e.g. atmosphere) and regions (e.g. the extratropics), and studies the ensemble-mean model response (e.g. tropical response to "observed" extratropical atmospheric variability). When applied to the extratropical influence on tropical climate, the RCDA method has shown some unique advantages, namely the combination of a fully coupled model, real-world observations and an ensemble approach. Tropical variability (e.g. El Niño-Southern Oscillation or ENSO) and climatology (e.g. asymmetric Inter-Tropical Convergence Zone or ITCZ) were initially thought to be determined mostly by local forcing and ocean-atmosphere interaction in the tropics. Since late 20th century, numerous studies have showed that extratropical forcing could affect, or even largely determine some aspects of the tropical climate. Due to the coupled nature of the climate system, however, the challenge of determining and further quantifying the causality of extratropical forcing on the tropical climate remains. Using the RCDA method, we have demonstrated significant control of extratropical atmospheric forcing on ENSO variability in a CGCM, both with model-generated and real-world observation datasets. The RCDA method has also shown robust extratropical impact on the tropical double-ITCZ bias in a CGCM. The RCDA method has provided the first systematic and quantitative assessment of extratropical influence on tropical climatology and variability by incorporating real world observations in a CGCM.

The unique contribution of manual chest compression-vibrations to airflow during physiotherapy in sedated, fully ventilated children.

PubMed

Gregson, Rachael K; Shannon, Harriet; Stocks, Janet; Cole, Tim J; Peters, Mark J; Main, Eleanor

2012-03-01

This study aimed to quantify the specific effects of manual lung inflations with chest compression-vibrations, commonly used to assist airway clearance in ventilated patients. The hypothesis was that force applied during the compressions made a significant additional contribution to increases in peak expiratory flow and expiratory to inspiratory flow ratio over and above that resulting from accompanying increases in inflation volume. Prospective observational study. Cardiac and general pediatric intensive care. Sedated, fully ventilated children. Customized force-sensing mats and a commercial respiratory monitor recorded force and respiration during physiotherapy. Percentage changes in peak expiratory flow, peak expiratory to inspiratory flow ratios, inflation volume, and peak inflation pressure between baseline and manual inflations with and without compression-vibrations were calculated. Analysis of covariance determined the relative contribution of changes in pressure, volume, and force to influence changes in peak expiratory flow and peak expiratory to inspiratory flow ratio. Data from 105 children were analyzed (median age, 1.3 yrs; range, 1 wk to 15.9 yrs). Force during compressions ranged from 15 to 179 N (median, 46 N). Peak expiratory flow increased on average by 76% during compressions compared with baseline ventilation. Increases in peak expiratory flow were significantly related to increases in inflation volume, peak inflation pressure, and force with peak expiratory flow increasing by, on average, 4% for every 10% increase in inflation volume (p < .001), 5% for every 10% increase in peak inflation pressure (p = .005), and 3% for each 10 N of applied force (p < .001). By contrast, increase in peak expiratory to inspiratory flow ratio was only related to applied force with a 4% increase for each 10 N of force (p < .001). These results provide evidence of the unique contribution of compression forces in increasing peak expiratory flow and peak expiratory to inspiratory flow ratio bias over and above that related to accompanying changes from manual hyperinflations. Force generated during compression-vibrations was the single significant factor in multivariable analysis to explain the increases in expiratory flow bias. Such increases in the expiratory bias provide theoretically optimal physiological conditions for cephalad mucus movement in fully ventilated children.

Impact of Childhood Maltreatment on the Recognition of Facial Expressions of Emotions.

PubMed

Ardizzi, Martina; Martini, Francesca; Umiltà, Maria Alessandra; Evangelista, Valentina; Ravera, Roberto; Gallese, Vittorio

2015-01-01

The development of the explicit recognition of facial expressions of emotions can be affected by childhood maltreatment experiences. A previous study demonstrated the existence of an explicit recognition bias for angry facial expressions among a population of adolescent Sierra Leonean street-boys exposed to high levels of maltreatment. In the present study, the recognition bias for angry facial expressions was investigated in a younger population of street-children and age-matched controls. Participants performed a forced-choice facial expressions recognition task. Recognition bias was measured as participants' tendency to over-attribute anger label to other negative facial expressions. Participants' heart rate was assessed and related to their behavioral performance, as index of their stress-related physiological responses. Results demonstrated the presence of a recognition bias for angry facial expressions among street-children, also pinpointing a similar, although significantly less pronounced, tendency among controls. Participants' performance was controlled for age, cognitive and educational levels and for naming skills. None of these variables influenced the recognition bias for angry facial expressions. Differently, a significant effect of heart rate on participants' tendency to use anger label was evidenced. Taken together, these results suggest that childhood exposure to maltreatment experiences amplifies children's "pre-existing bias" for anger labeling in forced-choice emotion recognition task. Moreover, they strengthen the thesis according to which the recognition bias for angry facial expressions is a manifestation of a functional adaptive mechanism that tunes victim's perceptive and attentive focus on salient environmental social stimuli.

How would publication bias distort the estimated effect size of prototypic antidepressants in the forced swim test?

PubMed

Ramos-Hryb, Ana B; Harris, Cari; Aighewi, Omorose; Lino-de-Oliveira, Cilene

2018-06-07

This commentary aims to discuss the impact of publication bias on the estimated effect of prototypic antidepressants in the forced swim test (FST). A systematic review and meta-analysis (SRMA) recently reported by Kara et al. (2018) showed that selected prototypic antidepressants reduced immobility time of mice in the FST across a variety of experimental designs. Despite differences in the procedures for SRMA, these results resemble the interim data collected by our research group according to a protocol deposited in the Systematic Review Facility and Open Science Framework (osf.io/9kxm4). Both studies detected a high amount of publications reporting statistically significant results and agreement with the primary hypothesis raising the possibility of publication bias in the field of FST. In our preliminary analysis, no evidence for publication bias was observed. However, the present work was limited to the effects of imipramine (doses ranging from 4 to 64 mg/kg) in different strains of mice. Therefore, more comprehensive studies are required to evaluate the risk of publication bias in the field of basic antidepressant research. We see the need to expand the current preliminary studies to evaluate the risk of publication bias within the preclinical research using the FST. Appraisal of the risk of publication bias may avoid misestimated effects of drugs in the FST providing better bases for the discovery of new antidepressants. Copyright © 2018. Published by Elsevier Ltd.

Side-effects of a bad attitude: How GNSS spacecraft orientation errors affect solar radiation pressure modelling

NASA Astrophysics Data System (ADS)

Dilssner, Florian; Springer, Tim; Schönemann, Erik; Zandbergen, Rene; Enderle, Werner

2015-04-01

Solar radiation pressure (SRP) is the largest non-gravitational perturbation for Global Navigation Satellite System (GNSS) satellites, and can therefore have substantial impact on their orbital dynamics. Various SRP force models have been developed over the past 30 years for the purpose of precise orbit determination. They all rely upon the assumption that the satellites continuously maintain a Sun-Nadir pointing attitude with the navigation antenna boresight (body-fixed z-axis) pointing towards Earth center, and the solar panel rotation axis (body-fixed y-axis) being normal to the Sun direction. However, in reality, this is not perfectly the case. Reasons for a non-nominal spacecraft attitude may be eclipse maneuvers, commanded attitude biases and Sun/horizon sensor measurement errors, for example due to mounting misalignment or incorrectly calibrated sensor electronics. In this work the effect of GNSS spacecraft orientation errors on SRP modelling is investigated. Simplified mathematical functions describing the SRP force acting on the solar arrays in the presence of yaw-, pitch- and roll-biases are derived. Special attention is paid to the yaw-bias and its relationship to the SRP dynamics, particular in direction of the spacecraft y-axis ("y-bias force"). Analytical and experimental results gathered from orbit and attitude analyses of GPS Block II/IIA/IIF satellites demonstrate how sensitive the SRP coefficients are to changes in yaw.

Assessment of Southern Ocean water mass circulation and characteristics in CMIP5 models: Historical bias and forcing response

NASA Astrophysics Data System (ADS)

Sallée, J.-B.; Shuckburgh, E.; Bruneau, N.; Meijers, A. J. S.; Bracegirdle, T. J.; Wang, Z.; Roy, T.

2013-04-01

The ability of the models contributing to the fifth Coupled Models Intercomparison Project (CMIP5) to represent the Southern Ocean hydrological properties and its overturning is investigated in a water mass framework. Models have a consistent warm and light bias spread over the entire water column. The greatest bias occurs in the ventilated layers, which are volumetrically dominated by mode and intermediate layers. The ventilated layers have been observed to have a strong fingerprint of climate change and to impact climate by sequestrating a significant amount of heat and carbon dioxide. The mode water layer is poorly represented in the models and both mode and intermediate water have a significant fresh bias. Under increased radiative forcing, models simulate a warming and lightening of the entire water column, which is again greatest in the ventilated layers, highlighting the importance of these layers for propagating the climate signal into the deep ocean. While the intensity of the water mass overturning is relatively consistent between models, when compared to observation-based reconstructions, they exhibit a slightly larger rate of overturning at shallow to intermediate depths, and a slower rate of overturning deeper in the water column. Under increased radiative forcing, atmospheric fluxes increase the rate of simulated upper cell overturning, but this increase is counterbalanced by diapycnal fluxes, including mixed-layer horizontal mixing, and mostly vanishes.

Association between mean and interannual equatorial Indian Ocean subsurface temperature bias in a coupled model

NASA Astrophysics Data System (ADS)

Srinivas, G.; Chowdary, Jasti S.; Gnanaseelan, C.; Prasad, K. V. S. R.; Karmakar, Ananya; Parekh, Anant

2018-03-01

In the present study the association between mean and interannual subsurface temperature bias over the equatorial Indian Ocean (EIO) is investigated during boreal summer (June through September; JJAS) in the National Centers for Environmental Prediction (NCEP) Climate Forecast System (CFSv2) hindcast. Anomalously high subsurface warm bias (greater than 3 °C) over the eastern EIO (EEIO) region is noted in CFSv2 during summer, which is higher compared to other parts of the tropical Indian Ocean. Prominent eastward current bias in the upper 100 m over the EIO region induced by anomalous westerly winds is primarily responsible for subsurface temperature bias. The eastward currents transport warm water to the EEIO and is pushed down to subsurface due to downwelling. Thus biases in both horizontal and vertical currents over the EIO region support subsurface warm bias. The evolution of systematic subsurface warm bias in the model shows strong interannual variability. These maximum subsurface warming episodes over the EEIO are mainly associated with La Niña like forcing. Strong convergence of low level winds over the EEIO and Maritime continent enhanced the westerly wind bias over the EIO during maximum warming years. This low level convergence of wind is induced by the bias in the gradient in the mean sea level pressure with positive bias over western EIO and negative bias over EEIO and parts of western Pacific. Consequently, changes in the atmospheric circulation associated with La Niña like conditions affected the ocean dynamics by modulating the current bias thereby enhancing the subsurface warm bias over the EEIO. It is identified that EEIO subsurface warming is stronger when La Niña co-occurred with negative Indian Ocean Dipole events as compared to La Niña only years in the model. Ocean general circulation model (OGCM) experiments forced with CFSv2 winds clearly support our hypothesis that ocean dynamics influenced by westerly winds bias is primarily responsible for the strong subsurface warm bias over the EEIO. This study advocates the importance of understanding the ability of the models in representing the large scale air-sea interactions over the tropics and their impact on ocean biases for better monsoon forecast.

[Childhood sexual behavior as an indicator of sexual abuse: professionals' criteria and biases].

PubMed

González Ortega, Eva; Orgaz Baz, Begoña; López Sánchez, Félix

2012-01-01

Some sexual behaviors are related to child sexual abuse experiences, but none unequivocally. Therefore, professionals might use non-empirical-based criteria and be biased when detecting and reporting victims. To check this hypothesis, we presented 974 Spanish and Latin American professionals from different fields (Psychology, Education, Health, Social Services, Justice, and Police Force) with hypothetical situations of child sexual behavior (varying the sex, age and behavior) by using an experimental vignette method based on Factorial Survey. Participants were asked to indicate whether such behaviors are a sign of abuse and whether they would report them. We also measured demographic, academic, professional and attitude factors. According to the analysis, professionals' suspicion of abuse is more affected by personal factors, whereas their reporting intention depends more on situational factors. The main criterion adopted is the type of sexual behavior, with professionals being more likely to suspect and report in response to aggressive sexual behavior and precocious sexual knowledge. Professionals' attitudes to sexuality seem to generate biases, as those who are erotophobic are more likely to suspect abuse. None of the sexual behaviors was seen as evidence of abuse.

Merging Station Observations with Large-Scale Gridded Data to Improve Hydrological Predictions over Chile

NASA Astrophysics Data System (ADS)

Peng, L.; Sheffield, J.; Verbist, K. M. J.

2016-12-01

Hydrological predictions at regional-to-global scales are often hampered by the lack of meteorological forcing data. The use of large-scale gridded meteorological data is able to overcome this limitation, but these data are subject to regional biases and unrealistic values at local scale. This is especially challenging in regions such as Chile, where climate exhibits high spatial heterogeneity as a result of long latitude span and dramatic elevation changes. However, regional station-based observational datasets are not fully exploited and have the potential of constraining biases and spatial patterns. This study aims at adjusting precipitation and temperature estimates from the Princeton University global meteorological forcing (PGF) gridded dataset to improve hydrological simulations over Chile, by assimilating 982 gauges from the Dirección General de Aguas (DGA). To merge station data with the gridded dataset, we use a state-space estimation method to produce optimal gridded estimates, considering both the error of the station measurements and the gridded PGF product. The PGF daily precipitation, maximum and minimum temperature at 0.25° spatial resolution are adjusted for the period of 1979-2010. Precipitation and temperature gauges with long and continuous records (>70% temporal coverage) are selected, while the remaining stations are used for validation. The leave-one-out cross validation verifies the robustness of this data assimilation approach. The merged dataset is then used to force the Variable Infiltration Capacity (VIC) hydrological model over Chile at daily time step which are compared to the observations of streamflow. Our initial results show that the station-merged PGF precipitation effectively captures drizzle and the spatial pattern of storms. Overall the merged dataset has significant improvements compared to the original PGF with reduced biases and stronger inter-annual variability. The invariant spatial pattern of errors between the station data and the gridded product opens up the possibility of merging real-time satellite and intermittent gauge observations to produce more accurate real-time hydrological predictions.

Full data acquisition in Kelvin Probe Force Microscopy: Mapping dynamic electric phenomena in real space

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

Balke, Nina; Kalinin, Sergei V.; Jesse, Stephen

Kelvin probe force microscopy (KPFM) has provided deep insights into the role local electronic, ionic and electrochemical processes play on the global functionality of materials and devices, even down to the atomic scale. Conventional KPFM utilizes heterodyne detection and bias feedback to measure the contact potential difference (CPD) between tip and sample. This measurement paradigm, however, permits only partial recovery of the information encoded in bias- and time-dependent electrostatic interactions between the tip and sample and effectively down-samples the cantilever response to a single measurement of CPD per pixel. This level of detail is insufficient for electroactive materials, devices, ormore » solid-liquid interfaces, where non-linear dielectrics are present or spurious electrostatic events are possible. Here, we simulate and experimentally validate a novel approach for spatially resolved KPFM capable of a full information transfer of the dynamic electric processes occurring between tip and sample. General acquisition mode, or G-Mode, adopts a big data approach utilising high speed detection, compression, and storage of the raw cantilever deflection signal in its entirety at high sampling rates (> 4 MHz), providing a permanent record of the tip trajectory. We develop a range of methodologies for analysing the resultant large multidimensional datasets involving classical, physics-based and information-based approaches. Physics-based analysis of G-Mode KPFM data recovers the parabolic bias dependence of the electrostatic force for each cycle of the excitation voltage, leading to a multidimensional dataset containing spatial and temporal dependence of the CPD and capacitance channels. We use multivariate statistical methods to reduce data volume and separate the complex multidimensional data sets into statistically significant components that can then be mapped onto separate physical mechanisms. Overall, G-Mode KPFM offers a new paradigm to study dynamic electric phenomena in electroactive interfaces as well as offer a promising approach to extend KPFM to solid-liquid interfaces.« less

The polar WRF downscaled historical and projected 21st century climate for the coast and foothills of Arctic Alaska

NASA Astrophysics Data System (ADS)

Cai, Lei; Alexeev, Vladimir A.; Arp, Christopher D.; Jones, Benjamin M.; Liljedahl, Anna K.; Gädeke, Anne

2018-01-01

Climate change is most pronounced in the northern high latitude region. Yet, climate observations are unable to fully capture regional-scale dynamics due to the sparse weather station coverage, which limits our ability to make reliable climate-based assessments. A set of simulated data products was therefore developed for the North Slope of Alaska through a dynamical downscaling approach. The polar-optimized Weather Research & Forecast (Polar WRF) model was forced by three sources: The ERA-interim reanalysis data (for 1979-2014), the Community Earth System Model 1.0 (CESM1.0) historical simulation (for 1950-2005), and the CESM1.0 projected (for 2006-2100) simulations in two Representative Concentration Pathways (RCP4.5 and RCP8.5) scenarios. Climatic variables were produced in a 10-km grid spacing and a 3-hour interval. The ERA-interim forced WRF (ERA-WRF) proves the value of dynamical downscaling, which yields more realistic topographical-induced precipitation and air temperature, as well as corrects underestimations in observed precipitation. In summary, dry and cold biases to the north of the Brooks Range are presented in ERA-WRF, while CESM forced WRF (CESM-WRF) holds wet and warm biases in its historical period. A linear scaling method allowed for an adjustment of the biases, while keeping the majority of the variability and extreme values of modeled precipitation and air temperature. CESM-WRF under RCP 4.5 scenario projects smaller increase in precipitation and air temperature than observed in the historical CESM-WRF product, while the CESM-WRF under RCP8.5 scenario shows larger changes. The fine spatial and temporal resolution, long temporal coverage, and multi-scenario projections jointly make the dataset appropriate to address a myriad of physical and biological changes occurring on the North Slope of Alaska.

Full data acquisition in Kelvin Probe Force Microscopy: Mapping dynamic electric phenomena in real space

DOE PAGES

Balke, Nina; Kalinin, Sergei V.; Jesse, Stephen; ...

2016-08-12

Kelvin probe force microscopy (KPFM) has provided deep insights into the role local electronic, ionic and electrochemical processes play on the global functionality of materials and devices, even down to the atomic scale. Conventional KPFM utilizes heterodyne detection and bias feedback to measure the contact potential difference (CPD) between tip and sample. This measurement paradigm, however, permits only partial recovery of the information encoded in bias- and time-dependent electrostatic interactions between the tip and sample and effectively down-samples the cantilever response to a single measurement of CPD per pixel. This level of detail is insufficient for electroactive materials, devices, ormore » solid-liquid interfaces, where non-linear dielectrics are present or spurious electrostatic events are possible. Here, we simulate and experimentally validate a novel approach for spatially resolved KPFM capable of a full information transfer of the dynamic electric processes occurring between tip and sample. General acquisition mode, or G-Mode, adopts a big data approach utilising high speed detection, compression, and storage of the raw cantilever deflection signal in its entirety at high sampling rates (> 4 MHz), providing a permanent record of the tip trajectory. We develop a range of methodologies for analysing the resultant large multidimensional datasets involving classical, physics-based and information-based approaches. Physics-based analysis of G-Mode KPFM data recovers the parabolic bias dependence of the electrostatic force for each cycle of the excitation voltage, leading to a multidimensional dataset containing spatial and temporal dependence of the CPD and capacitance channels. We use multivariate statistical methods to reduce data volume and separate the complex multidimensional data sets into statistically significant components that can then be mapped onto separate physical mechanisms. Overall, G-Mode KPFM offers a new paradigm to study dynamic electric phenomena in electroactive interfaces as well as offer a promising approach to extend KPFM to solid-liquid interfaces.« less

Three-dimensional profile extraction from CD-SEM image and top/bottom CD measurement by line-edge roughness analysis

NASA Astrophysics Data System (ADS)

Yamaguchi, Atsuko; Ohashi, Takeyoshi; Kawasaki, Takahiro; Inoue, Osamu; Kawada, Hiroki

2013-04-01

A new method for calculating critical dimension (CDs) at the top and bottom of three-dimensional (3D) pattern profiles from a critical-dimension scanning electron microscope (CD-SEM) image, called as "T-sigma method", is proposed and evaluated. Without preparing a library of database in advance, T-sigma can estimate a feature of a pattern sidewall. Furthermore, it supplies the optimum edge-definition (i.e., threshold level for determining edge position from a CDSEM signal) to detect the top and bottom of the pattern. This method consists of three steps. First, two components of line-edge roughness (LER); noise-induced bias (i.e., LER bias) and unbiased component (i.e., bias-free LER) are calculated with set threshold level. Second, these components are calculated with various threshold values, and the threshold-dependence of these two components, "T-sigma graph", is obtained. Finally, the optimum threshold value for the top and the bottom edge detection are given by the analysis of T-sigma graph. T-sigma was applied to CD-SEM images of three kinds of resist-pattern samples. In addition, reference metrology was performed with atomic force microscope (AFM) and scanning transmission electron microscope (STEM). Sensitivity of CD measured by T-sigma to the reference CD was higher than or equal to that measured by the conventional edge definition. Regarding the absolute measurement accuracy, T-sigma showed better results than the conventional definition. Furthermore, T-sigma graphs were calculated from CD-SEM images of two kinds of resist samples and compared with corresponding STEM observation results. Both bias-free LER and LER bias increased as the detected edge point moved from the bottom to the top of the pattern in the case that the pattern had a straight sidewall and a round top. On the other hand, they were almost constant in the case that the pattern had a re-entrant profile. T-sigma will be able to reveal a re-entrant feature. From these results, it is found that T-sigma method can provide rough cross-sectional pattern features and achieve quick, easy and accurate measurements of top and bottom CD.

Computation of free energy profiles with parallel adaptive dynamics

NASA Astrophysics Data System (ADS)

Lelièvre, Tony; Rousset, Mathias; Stoltz, Gabriel

2007-04-01

We propose a formulation of an adaptive computation of free energy differences, in the adaptive biasing force or nonequilibrium metadynamics spirit, using conditional distributions of samples of configurations which evolve in time. This allows us to present a truly unifying framework for these methods, and to prove convergence results for certain classes of algorithms. From a numerical viewpoint, a parallel implementation of these methods is very natural, the replicas interacting through the reconstructed free energy. We demonstrate how to improve this parallel implementation by resorting to some selection mechanism on the replicas. This is illustrated by computations on a model system of conformational changes.

Item Response Modeling of Forced-Choice Questionnaires

ERIC Educational Resources Information Center

Brown, Anna; Maydeu-Olivares, Alberto

2011-01-01

Multidimensional forced-choice formats can significantly reduce the impact of numerous response biases typically associated with rating scales. However, if scored with classical methodology, these questionnaires produce ipsative data, which lead to distorted scale relationships and make comparisons between individuals problematic. This research…

Force feedback delay affects perception of stiffness but not action, and the effect depends on the hand used but not on the handedness.

PubMed

Leib, Raz; Rubin, Inbar; Nisky, Ilana

2018-05-16

Interaction with an object often requires the estimation of its mechanical properties. We examined whether the hand that is used to interact with the object and their handedness affected people's estimation of these properties using stiffness estimation as a test case. We recorded participants' responses on a stiffness discrimination of a virtual elastic force field and the grip force applied on the robotic device during the interaction. In half of the trials, the robotic device delayed the participants' force feedback. Consistent with previous studies, delayed force feedback biased the perceived stiffness of the force field. Interestingly, in both left-handed and right-handed participants, for the delayed force field, there was even less perceived stiffness when participants used their left hand than their right hand. This result supports the idea that haptic processing is affected by laterality in the brain, not by handedness. Consistent with previous studies, participants adjusted their applied grip force according to the correct size and timing of the load force regardless of the hand that was used, the handedness, or the delay. This suggests that in all these conditions, participants were able to form an accurate internal representation of the anticipated trajectory of the load force (size and timing) and that this representation was used for accurate control of grip force independently of the perceptual bias. Thus, these results provide additional evidence for the dissociation between action and perception in the processing of delayed information.

Gender Bias in the Iranian High School EFL Textbooks

ERIC Educational Resources Information Center

Amini, Mohadeseh; Birjandi, Parviz

2012-01-01

Gender bias is unfortunately still present in many societies especially the developing countries. Such prejudice is in most cases in favor of males and against females. While females nowadays comprise a great majority of the work force all around the world, they are still being looked upon as the "weaker sex" associated with…

The fabrication of ordered arrays of exchange biased Ni/FeF2 nanostructures.

PubMed

Kovylina, M; Erekhinsky, M; Morales, R; Schuller, I K; Labarta, A; Batlle, X

2010-04-30

The fabrication of ordered arrays of exchange biased Ni/FeF(2) nanostructures by focused ion beam lithography is reported. High quality nano-elements, with controlled removal depth and no significant re-deposition, were carved using small ion beam currents (30 pA), moderate dwell times (1 micros) and repeated passages over the same area. Two types of nanostructures were fabricated: square arrays of circular dots with diameters from 125 +/- 8 to 500 +/- 12 nm and periodicities ranging from 200 +/- 8 to 1000 +/- 12 nm, and square arrays of square antidots (207 +/- 8 nm in edge length) with periodicities ranging from 300 +/- 8 to 1200 +/- 12 nm. The arrays were characterized using scanning ion and electron microscopy, and atomic force microscopy. The effect of the patterning on the exchange bias field (i.e., the shift in the hysteresis loop of ferromagnetic Ni due to proximity to antiferromagnetic FeF(2)) was studied using magneto-transport measurements. These high quality nanostructures offer a unique method to address some of the open questions regarding the microscopic origin of exchange bias. This is not only of major relevance in the fabrication and miniaturization of magnetic devices but it is also one of the important proximity phenomena in nanoscience and materials science.

Implementation of Coupled Skin Temperature Analysis and Bias Correction in a Global Atmospheric Data Assimilation System

NASA Technical Reports Server (NTRS)

Radakovich, Jon; Bosilovich, M.; Chern, Jiun-dar; daSilva, Arlindo

2004-01-01

The NASA/NCAR Finite Volume GCM (fvGCM) with the NCAR CLM (Community Land Model) version 2.0 was integrated into the NASA/GMAO Finite Volume Data Assimilation System (fvDAS). A new method was developed for coupled skin temperature assimilation and bias correction where the analysis increment and bias correction term is passed into the CLM2 and considered a forcing term in the solution to the energy balance. For our purposes, the fvDAS CLM2 was run at 1 deg. x 1.25 deg. horizontal resolution with 55 vertical levels. We assimilate the ISCCP-DX (30 km resolution) surface temperature product. The atmospheric analysis was performed 6-hourly, while the skin temperature analysis was performed 3-hourly. The bias correction term, which was updated at the analysis times, was added to the skin temperature tendency equation at every timestep. In this presentation, we focus on the validation of the surface energy budget at the in situ reference sites for the Coordinated Enhanced Observation Period (CEOP). We will concentrate on sites that include independent skin temperature measurements and complete energy budget observations for the month of July 2001. In addition, MODIS skin temperature will be used for validation. Several assimilations were conducted and preliminary results will be presented.

Calculation of the radial electric field with RF sheath boundary conditions in divertor geometry

NASA Astrophysics Data System (ADS)

Gui, B.; Xia, T. Y.; Xu, X. Q.; Myra, J. R.; Xiao, X. T.

2018-02-01

The equilibrium electric field that results from an imposed DC bias potential, such as that driven by a radio frequency (RF) sheath, is calculated using a new minimal two-field model in the BOUT++ framework. Biasing, using an RF-modified sheath boundary condition, is applied to an axisymmetric limiter, and a thermal sheath boundary is applied to the divertor plates. The penetration of the bias potential into the plasma is studied with a minimal self-consistent model that includes the physics of vorticity (charge balance), ion polarization currents, force balance with E× B , ion diamagnetic flow (ion pressure gradient) and parallel electron charge loss to the thermal and biased sheaths. It is found that a positive radial electric field forms in the scrape-off layer and it smoothly connects across the separatrix to the force-balanced radial electric field in the closed flux surface region. The results are in qualitative agreement with the experiments. Plasma convection related to the E× B net flow in front of the limiter is also obtained from the calculation.

Tackling force-field bias in protein folding simulations: folding of Villin HP35 and Pin WW domains in explicit water.

PubMed

Mittal, Jeetain; Best, Robert B

2010-08-04

The ability to fold proteins on a computer has highlighted the fact that existing force fields tend to be biased toward a particular type of secondary structure. Consequently, force fields for folding simulations are often chosen according to the native structure, implying that they are not truly "transferable." Here we show that, while the AMBER ff03 potential is known to favor helical structures, a simple correction to the backbone potential (ff03( *)) results in an unbiased energy function. We take as examples the 35-residue alpha-helical Villin HP35 and 37 residue beta-sheet Pin WW domains, which had not previously been folded with the same force field. Starting from unfolded configurations, simulations of both proteins in Amber ff03( *) in explicit solvent fold to within 2.0 A RMSD of the experimental structures. This demonstrates that a simple backbone correction results in a more transferable force field, an important requirement if simulations are to be used to interpret folding mechanism. 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Sources of method bias in social science research and recommendations on how to control it.

PubMed

Podsakoff, Philip M; MacKenzie, Scott B; Podsakoff, Nathan P

2012-01-01

Despite the concern that has been expressed about potential method biases, and the pervasiveness of research settings with the potential to produce them, there is disagreement about whether they really are a problem for researchers in the behavioral sciences. Therefore, the purpose of this review is to explore the current state of knowledge about method biases. First, we explore the meaning of the terms "method" and "method bias" and then we examine whether method biases influence all measures equally. Next, we review the evidence of the effects that method biases have on individual measures and on the covariation between different constructs. Following this, we evaluate the procedural and statistical remedies that have been used to control method biases and provide recommendations for minimizing method bias.

Endoscopes and robots for tight surgical spaces: use of precurved elastic elements to enhance curvature

NASA Astrophysics Data System (ADS)

Remirez, Andria A.; Webster, Robert J.

2016-03-01

Many applications in medicine require flexible surgical manipulators and endoscopes capable of reaching tight curvatures. The maximum curvature these devices can achieve is often restricted either by a strain limit, or by a maximum actuation force that the device's components can tolerate without risking mechanical failure. In this paper we propose the use of precurvature to "bias" the workspace of the device in one direction. Combined with axial shaft rotation, biasing increases the size of the device's workspace, enabling it to reach tighter curvatures than a comparable device without biasing can achieve, while still being able to fully straighten. To illustrate this effect, we describe several example prototype devices which use flexible nitinol strips that can be pushed and pulled to generate bending. We provide a statics model that relates the manipulator curvature to actuation force, and validate it experimentally.

Diagnosing causes of cloud parameterization deficiencies using ARM measurements over SGP site

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

Wu, W.; Liu, Y.; Betts, A. K.

2010-03-15

Decade-long continuous surface-based measurements at Great Southern Plains (SGP) collected by the US Department of Energy’s Atmospheric Radiation Measurement (ARM) Climate Research Facility are first used to evaluate the three major reanalyses (i.e., ERA-Interim, NCEP/NCAR Reanalysis I and NCEP/DOE Reanalysis II) to identify model biases in simulating surface shortwave cloud forcing and total cloud fraction. The results show large systematic lower biases in the modeled surface shortwave cloud forcing and cloud fraction from all the three reanalysis datasets. Then we focus on diagnosing the causes of these model biases using the Active Remote Sensing of Clouds (ARSCL) products (e.g., verticalmore » distribution of cloud fraction, cloud-base and cloud-top heights, and cloud optical depth) and meteorological measurements (temperature, humidity and stability). Efforts are made to couple cloud properties with boundary processes in the diagnosis.« less

CMIP5 Scientific Gaps and Recommendations for CMIP6

DOE PAGES

Stouffer, R. J.; Eyring, V.; Meehl, G. A.; ...

2017-01-23

The Coupled Model Intercomparison Project (CMIP) is an ongoing coordinated international activity of numerical experimentation of unprecedented scope and impact on climate science. Its most recent phase, the fifth phase (CMIP5), has created nearly 2 PB of output from dozens of experiments performed by dozens of comprehensive climate models available to the climate science research community. In so doing, it has greatly advanced climate science. While CMIP5 has given answers to important science questions, with the help of a community survey we identify and motivate three broad topics here that guided the scientific framework of the next phase of CMIP,more » that is, CMIP6: (1) How does the Earth system respond to changes in forcing? (2) What are the origins and consequences of systematic model biases? (3) How can we assess future climate changes given internal climate variability, predictability, and uncertainties in scenarios? CMIP has demonstrated the power of idealized experiments to better understand how the climate system works. We expect that these idealized approaches will continue to contribute to CMIP6. The quantification of radiative forcings and responses was poor, and thus it requires new methods and experiments to address this gap. There are a number of systematic model biases that appear in all phases of CMIP that remain a major climate modeling challenge. In conclusion, these biases need increased attention to better understand their origins and consequences through targeted experiments. Improving understanding of the mechanisms’ underlying internal climate variability for more skillful decadal climate predictions and long-term projections remains another challenge for CMIP6.« less

CMIP5 Scientific Gaps and Recommendations for CMIP6

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

Stouffer, R. J.; Eyring, V.; Meehl, G. A.

The Coupled Model Intercomparison Project (CMIP) is an ongoing coordinated international activity of numerical experimentation of unprecedented scope and impact on climate science. Its most recent phase, the fifth phase (CMIP5), has created nearly 2 PB of output from dozens of experiments performed by dozens of comprehensive climate models available to the climate science research community. In so doing, it has greatly advanced climate science. While CMIP5 has given answers to important science questions, with the help of a community survey we identify and motivate three broad topics here that guided the scientific framework of the next phase of CMIP,more » that is, CMIP6: (1) How does the Earth system respond to changes in forcing? (2) What are the origins and consequences of systematic model biases? (3) How can we assess future climate changes given internal climate variability, predictability, and uncertainties in scenarios? CMIP has demonstrated the power of idealized experiments to better understand how the climate system works. We expect that these idealized approaches will continue to contribute to CMIP6. The quantification of radiative forcings and responses was poor, and thus it requires new methods and experiments to address this gap. There are a number of systematic model biases that appear in all phases of CMIP that remain a major climate modeling challenge. In conclusion, these biases need increased attention to better understand their origins and consequences through targeted experiments. Improving understanding of the mechanisms’ underlying internal climate variability for more skillful decadal climate predictions and long-term projections remains another challenge for CMIP6.« less

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

Tournadre, Grégoire de, E-mail: gregoire.de-tournadre@univ-reims.fr; Reisdorffer, Frédéric; Simonetti, Olivier

A scanning surface potential measurement technique suited for thin-film devices operating under high voltages is reported. A commercial atomic force microscope has been customized to enable a feedback-controlled and secure surface potential measurement based on phase-shift detection under ambient conditions. Measurements of the local potential profile along the channel of bottom-gate organic thin-film transistors (TFTs) are shown to be useful to disentangle the contributions from the channel and contacts to the device performance. Intrinsic contact current-voltage characteristics have been measured on bottom-gate, top-contact (staggered) TFTs based on the small-molecule semiconductor dinaphtho[2,3-b:2′,3-f]thieno[3,2-b]thiophene (DNTT) and on bottom-gate, bottom-contact (coplanar) TFTs based onmore » the semiconducting polymer polytriarylamine (PTAA). Injection has been found to be linear in the staggered DNTT TFTs and nonlinear in the coplanar PTAA TFTs. In both types of TFT, the injection efficiency has been found to improve with increasing gate bias in the accumulation regime. Contact resistances as low as 130 Ω cm have been measured in the DNTT TFTs. A method that eliminates the influence of bias-stress-induced threshold-voltage shifts when measuring the local charge-carrier mobility in the channel is also introduced, and intrinsic channel mobilities of 1.5 cm{sup 2} V{sup −1} s{sup −1} and 1.1 × 10{sup −3} cm{sup 2} V{sup −1} s{sup −1} have been determined for DNTT and PTAA. In both semiconductors, the mobility has been found to be constant with respect to the gate bias. Despite its simplicity, the Kelvin probe force microscopy method reported here provides robust and accurate surface potential measurements on thin-film devices under operation and thus paves the way towards more extensive studies of particular interest in emerging fields of solid-state electronics.« less

Evaluation of regional climate simulations for air quality modelling purposes

NASA Astrophysics Data System (ADS)

Menut, Laurent; Tripathi, Om P.; Colette, Augustin; Vautard, Robert; Flaounas, Emmanouil; Bessagnet, Bertrand

2013-05-01

In order to evaluate the future potential benefits of emission regulation on regional air quality, while taking into account the effects of climate change, off-line air quality projection simulations are driven using weather forcing taken from regional climate models. These regional models are themselves driven by simulations carried out using global climate models (GCM) and economical scenarios. Uncertainties and biases in climate models introduce an additional "climate modeling" source of uncertainty that is to be added to all other types of uncertainties in air quality modeling for policy evaluation. In this article we evaluate the changes in air quality-related weather variables induced by replacing reanalyses-forced by GCM-forced regional climate simulations. As an example we use GCM simulations carried out in the framework of the ERA-interim programme and of the CMIP5 project using the Institut Pierre-Simon Laplace climate model (IPSLcm), driving regional simulations performed in the framework of the EURO-CORDEX programme. In summer, we found compensating deficiencies acting on photochemistry: an overestimation by GCM-driven weather due to a positive bias in short-wave radiation, a negative bias in wind speed, too many stagnant episodes, and a negative temperature bias. In winter, air quality is mostly driven by dispersion, and we could not identify significant differences in either wind or planetary boundary layer height statistics between GCM-driven and reanalyses-driven regional simulations. However, precipitation appears largely overestimated in GCM-driven simulations, which could significantly affect the simulation of aerosol concentrations. The identification of these biases will help interpreting results of future air quality simulations using these data. Despite these, we conclude that the identified differences should not lead to major difficulties in using GCM-driven regional climate simulations for air quality projections.

Exploring Local Electrostatic Effects with Scanning Probe Microscopy: Implications for Piezoresponse Force Microscopy and Triboelectricity

DOE PAGES

Balke, Nina; Maksymovych, Petro; Jesse, Stephen; ...

2014-09-25

The implementation of contact mode Kelvin probe force microscopy (KPFM) utilizes the electrostatic interactions between tip and sample when the tip and sample are in contact with each other. Surprisingly, the electrostatic forces in contact are large enough to be measured even with tips as stiff as 4.5 N/m. As for traditional non-contact KPFM, the signal depends strongly on electrical properties of the sample, such as the dielectric constant, and the tip-properties, such as the stiffness. Since the tip is in contact with the sample, bias-induced changes in the junction potential between tip and sample can be measured with highermore » lateral and temporal resolution compared to traditional non-contact KPFM. Significant and reproducible variations of tip-surface capacitance are observed and attributed to surface electrochemical phenomena. Lastly, observations of significant surface charge states at zero bias and strong hysteretic electromechanical responses at non-ferroelectric surface have significant implications for fields such as triboelectricity and piezoresponse force microscopy.« less

Dynamics of Permanent-Magnet Biased Active Magnetic Bearings

NASA Technical Reports Server (NTRS)

Fukata, Satoru; Yutani, Kazuyuki

1996-01-01

Active magnetic radial bearings are constructed with a combination of permanent magnets to provide bias forces and electromagnets to generate control forces for the reduction of cost and the operating energy consumption. Ring-shaped permanent magnets with axial magnetization are attached to a shaft and share their magnet stators with the electromagnets. The magnet cores are made of solid iron for simplicity. A simplified magnetic circuit of the combined magnet system is analyzed with linear circuit theory by approximating the characteristics of permanent magnets with a linear relation. A linearized dynamical model of the control force is presented with the first-order approximation of the effects of eddy currents. Frequency responses of the rotor motion to disturbance inputs and the motion for impulsive forces are tested in the non-rotating state. The frequency responses are compared with numerical results. The decay of rotor speed due to magnetic braking is examined. The experimental results and the presented linearized model are similar to those of the all-electromagnetic design.

A Comparison of Analytical and Experimental Data for a Magnetic Actuator

NASA Technical Reports Server (NTRS)

Groom, Nelson J.; Bloodgood, V. Dale, Jr.

2000-01-01

Theoretical and experimental force-displacement and force-current data are compared for two configurations of a simple horseshoe, or bipolar, magnetic actuator. One configuration utilizes permanent magnet wafers to provide a bias flux and the other configuration has no source of bias flux. The theoretical data are obtained from two analytical models of each configuration. One is an ideal analytical model which is developed under the following assumptions: (1) zero fringing and leakage flux, (2) zero actuator coil mmf loss, and (3) infinite permeability of the actuator core and suspended element flux return path. The other analytical model, called the extended model, is developed by adding loss and leakage factors to the ideal model. The values of the loss and leakage factors are calculated from experimental data. The experimental data are obtained from a magnetic actuator test fixture, which is described in detail. Results indicate that the ideal models for both configurations do not match the experimental data very well. However, except for the range around zero force, the extended models produce a good match. The best match is produced by the extended model of the configuration with permanent magnet flux bias.

Full data acquisition in Kelvin Probe Force Microscopy: Mapping dynamic electric phenomena in real space.

PubMed

Collins, Liam; Belianinov, Alex; Somnath, Suhas; Balke, Nina; Kalinin, Sergei V; Jesse, Stephen

2016-08-12

Kelvin probe force microscopy (KPFM) has provided deep insights into the local electronic, ionic and electrochemical functionalities in a broad range of materials and devices. In classical KPFM, which utilizes heterodyne detection and closed loop bias feedback, the cantilever response is down-sampled to a single measurement of the contact potential difference (CPD) per pixel. This level of detail, however, is insufficient for materials and devices involving bias and time dependent electrochemical events; or at solid-liquid interfaces, where non-linear or lossy dielectrics are present. Here, we demonstrate direct recovery of the bias dependence of the electrostatic force at high temporal resolution using General acquisition Mode (G-Mode) KPFM. G-Mode KPFM utilizes high speed detection, compression, and storage of the raw cantilever deflection signal in its entirety at high sampling rates. We show how G-Mode KPFM can be used to capture nanoscale CPD and capacitance information with a temporal resolution much faster than the cantilever bandwidth, determined by the modulation frequency of the AC voltage. In this way, G-Mode KPFM offers a new paradigm to study dynamic electric phenomena in electroactive interfaces as well as a promising route to extend KPFM to the solid-liquid interface.

Biased and flow driven Brownian motion in periodic channels

NASA Astrophysics Data System (ADS)

Martens, S.; Straube, A.; Schmid, G.; Schimansky-Geier, L.; Hänggi, P.

2012-02-01

In this talk we will present an expansion of the common Fick-Jacobs approximation to hydrodynamically as well as by external forces driven Brownian transport in two-dimensional channels exhibiting smoothly varying periodic cross-section. We employ an asymptotic analysis to the components of the flow field and to stationary probability density for finding the particles within the channel in a geometric parameter. We demonstrate that the problem of biased Brownian dynamics in a confined 2D geometry can be replaced by Brownian motion in an effective periodic one-dimensional potential ψ(x) which takes the external bias, the change of the local channel width, and the flow velocity component in longitudinal direction into account. In addition, we study the influence of the external force magnitude, respectively, the pressure drop of the fluid on the particle transport quantities like the averaged velocity and the effective diffusion coefficient. The critical ratio between the external force and pressure drop where the average velocity equals zero is identified and the dependence of the latter on the channel geometry is derived. Analytic findings are confirmed by numerical simulations of the particle dynamics in a reflection symmetric sinusoidal channel.

A comparative study of single-leg ground reaction forces in running lizards.

PubMed

McElroy, Eric J; Wilson, Robbie; Biknevicius, Audrone R; Reilly, Stephen M

2014-03-01

The role of different limbs in supporting and propelling the body has been studied in many species with animals appearing to have either similarity in limb function or differential limb function. Differential hindlimb versus forelimb function has been proposed as a general feature of running with a sprawling posture and as benefiting sprawled postured animals by enhancing maneuvering and minimizing joint moments. Yet only a few species have been studied and thus the generality of differential limb function in running animals with sprawled postures is unknown. We measured the limb lengths of seven species of lizard and their single-limb three-dimensional ground reaction forces during high-speed running. We found that all species relied on the hindlimb for producing accelerative forces. Braking forces were forelimb dominated in four species and equally distributed between limbs in the other three. Vertical forces were dominated by the hindlimb in three species and equally distributed between the forelimb and hindlimb in the other four. Medial forces were dominated by the hindlimb in four species and equally distributed in the other three, with all Iguanians exhibiting hindlimb-biased medial forces. Relative hindlimb to forelimb length of each species was related to variation in hindlimb versus forelimb medial forces; species with relatively longer hindlimbs compared with forelimbs exhibited medial forces that were more biased towards the hindlimbs. These results suggest that the function of individual limbs in lizards varies across species with only a single general pattern (hindlimb-dominated accelerative force) being present.

Valuing our differences. How to manage a culturally diverse work force.

PubMed

Veninga, R L

1994-12-01

How can we become aware of cultural blind spots that keep us from understanding one another? To adequately prepare for the new work force, healthcare organizations must establish work force diversity goals. Of course, goals by themselves will not empower minority workers. And if goals are perceived as "window dressing," resentment builds. Most organizations claim their hiring practices are not biased. One way to ensure that your hiring practices are unbiased is to ask important questions: Does the ethnic makeup of our work force resemble that of the community? If not, what can be done to strengthen our affirmative action programs? In a multicultural work force, misunderstandings are bound to arise because human behavior is conditioned by cultural factors. One way for an organization to identify problems that are culturally based is for supervisors and subordinates to meet informally to ensure that the organization is maximizing the minority worker's talents. Climate surveys and exit interviews are two other frequently used methods. Cultural diversity training programs can also make a difference in an organization. Some training programs help participants learn how culture influences the way we communicate. Knowledge of the cultural basis of how we interact is one factor in building bridges of understanding.

Hysteresis Bearingless Slice Motors with Homopolar Flux-biasing.

PubMed

Noh, Minkyun; Gruber, Wolfgang; Trumper, David L

2017-10-01

We present a new concept of bearingless slice motor that levitates and rotates a ring-shaped solid rotor. The rotor is made of a semi-hard magnetic material exhibiting magnetic hysteresis, such as D2 steel. The rotor is radially biased with a homopolar permanent-magnetic flux, on which the stator can superimpose 2-pole flux to generate suspension forces. By regulating the suspension forces based on position feedback, the two radial rotor degrees of freedom are actively stabilized. The two tilting degrees of freedom and the axial translation are passively stable due to the reluctance forces from the bias flux. In addition, the stator can generate a torque by superimposing 6- pole rotating flux, which drags the rotor via hysteresis coupling. This 6-pole flux does not generate radial forces in conjunction with the homopolar flux or 2-pole flux, and therefore the suspension force generation is in principle decoupled from the driving torque generation. We have developed a prototype system as a proof of concept. The stator has twelve teeth, each of which has a single phase winding that is individually driven by a linear transconductance power amplifier. The system has four reflective-type optical sensors to differentially measure the two radial degrees of freedom of the rotor. The suspension control loop is implemented such that the phase margin is 25 degrees at the cross-over frequency of 110 Hz. The prototype system can levitate the rotor and drive it up to about 1730 rpm. The maximum driving torque is about 2.7 mNm.

Improved estimates of biomass burning emissions in the southeast United States

NASA Astrophysics Data System (ADS)

Nowell, H.; Holmes, C.; Elsner, J.; Hiers, J. K.; Robertson, K.

2017-12-01

Biomass burning is a major source of gas and particle emissions that affects air quality, human health, and climate. Prescribed burns in the southeastern United States consume more biomass and cover a larger area than fires in the rest of the United States combined. Although fires can be detected remotely from thermal infrared emission and changes to surface reflectance, there are multiple issues that make satellite detections difficult in the eastern United States. These include small fire sizes, short duration, low intensity, canopy coverage, and rapid vegetation regrowth. Some attempts have been made to compensate for this bias, for example the small fire product in the Global Fire Emission Database (GFED4.1s) product. The accuracy of GFED and other remotely sensed global fire emission inventories are largely unknown, outside of a few field studies, mainly because there are few independent datasets of fire extent. The Florida Forest Service (FFS) has extensive records on fire type, size, location, and time for both prescribed and wild fires, which have not previously been used to evaluate fire area and emissions. For our study period of 2004 to 2016, we compared FFS burn authorization data against GFED4.1s burned area. When averaged across the state of Florida, there is 4 times more land burned than detected from satellite sensors. When comparing FFS data against high quality records from Apalachicola National Forest, Avon Park Air Force Range, Eglin Air Force Base, Tall Timbers Research Station, and Tyndall Air Force base, the areal discrepancy between these records and FFS reports are +/- 15%, well below the 4 times detection discrepancy between satellites and FFS reports. We have developed a method to statistically correct this satellite bias in fire detections. Treating the FFS burn authorizations as accurate, we have found this bias ratio can be predicted from fire size, land cover type, leaf area, and month. The regression model incorporating these factors can predict greater than 80% of variance in bias ratio across Florida during the summer months with correlations around 0.6 on average. This improved estimate of burned area in Florida will be used in global circulation models to determine the true contribution of prescribed wild fires in the southeast United States to gas and particle emissions.

The Absence of a Shape Bias in Children's Word Learning

ERIC Educational Resources Information Center

Cimpian, Andrei; Markman, Ellen M.

2005-01-01

There is debate about whether preschool-age children interpret words as referring to kinds or to classes defined by shape similarity. The authors argue that the shape bias reported in previous studies is a task-induced artifact rather than a genuine word-learning strategy. In particular, children were forced to extend an object's novel label to…

Psychopysics of Remembering: To Bias or Not to Bias?

ERIC Educational Resources Information Center

White, K. Geoffrey; Wixted, John T.

2010-01-01

Delayed matching to sample is typically a two-alternative forced-choice procedure with two sample stimuli. In this task the effects of varying the probability of reinforcers for correct choices and the resulting receiver operating characteristic are symmetrical. A version of the task where a sample is present on some trials and absent on others is…

Common method biases in behavioral research: a critical review of the literature and recommended remedies.

PubMed

Podsakoff, Philip M; MacKenzie, Scott B; Lee, Jeong-Yeon; Podsakoff, Nathan P

2003-10-01

Interest in the problem of method biases has a long history in the behavioral sciences. Despite this, a comprehensive summary of the potential sources of method biases and how to control for them does not exist. Therefore, the purpose of this article is to examine the extent to which method biases influence behavioral research results, identify potential sources of method biases, discuss the cognitive processes through which method biases influence responses to measures, evaluate the many different procedural and statistical techniques that can be used to control method biases, and provide recommendations for how to select appropriate procedural and statistical remedies for different types of research settings.

Enhanced conformational sampling of carbohydrates by Hamiltonian replica-exchange simulation.

PubMed

Mishra, Sushil Kumar; Kara, Mahmut; Zacharias, Martin; Koca, Jaroslav

2014-01-01

Knowledge of the structure and conformational flexibility of carbohydrates in an aqueous solvent is important to improving our understanding of how carbohydrates function in biological systems. In this study, we extend a variant of the Hamiltonian replica-exchange molecular dynamics (MD) simulation to improve the conformational sampling of saccharides in an explicit solvent. During the simulations, a biasing potential along the glycosidic-dihedral linkage between the saccharide monomer units in an oligomer is applied at various levels along the replica runs to enable effective transitions between various conformations. One reference replica runs under the control of the original force field. The method was tested on disaccharide structures and further validated on biologically relevant blood group B, Lewis X and Lewis A trisaccharides. The biasing potential-based replica-exchange molecular dynamics (BP-REMD) method provided a significantly improved sampling of relevant conformational states compared with standard continuous MD simulations, with modest computational costs. Thus, the proposed BP-REMD approach adds a new dimension to existing carbohydrate conformational sampling approaches by enhancing conformational sampling in the presence of solvent molecules explicitly at relatively low computational cost.

Gender fairness within the Force Concept Inventory

NASA Astrophysics Data System (ADS)

Traxler, Adrienne; Henderson, Rachel; Stewart, John; Stewart, Gay; Papak, Alexis; Lindell, Rebecca

2018-01-01

Research on the test structure of the Force Concept Inventory (FCI) has largely ignored gender, and research on FCI gender effects (often reported as "gender gaps") has seldom interrogated the structure of the test. These rarely crossed streams of research leave open the possibility that the FCI may not be structurally valid across genders, particularly since many reported results come from calculus-based courses where 75% or more of the students are men. We examine the FCI considering both psychometrics and gender disaggregation (while acknowledging this as a binary simplification), and find several problematic questions whose removal decreases the apparent gender gap. We analyze three samples (total Npre=5391 , Npost=5769 ) looking for gender asymmetries using classical test theory, item response theory, and differential item functioning. The combination of these methods highlights six items that appear substantially unfair to women and two items biased in favor of women. No single physical concept or prior experience unifies these questions, but they are broadly consistent with problematic items identified in previous research. Removing all significantly gender-unfair items halves the gender gap in the main sample in this study. We recommend that instructors using the FCI report the reduced-instrument score as well as the 30-item score, and that credit or other benefits to students not be assigned using the biased items.

Simultaneous Estimation of Electromechanical Modes and Forced Oscillations

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

Follum, Jim; Pierre, John W.; Martin, Russell

Over the past several years, great strides have been made in the effort to monitor the small-signal stability of power systems. These efforts focus on estimating electromechanical modes, which are a property of the system that dictate how generators in different parts of the system exchange energy. Though the algorithms designed for this task are powerful and important for reliable operation of the power system, they are susceptible to severe bias when forced oscillations are present in the system. Forced oscillations are fundamentally different from electromechanical oscillations in that they are the result of a rogue input to the system,more » rather than a property of the system itself. To address the presence of forced oscillations, the frequently used AutoRegressive Moving Average (ARMA) model is adapted to include sinusoidal inputs, resulting in the AutoRegressive Moving Average plus Sinusoid (ARMA+S) model. From this model, a new Two-Stage Least Squares algorithm is derived to incorporate the forced oscillations, thereby enabling the simultaneous estimation of the electromechanical modes and the amplitude and phase of the forced oscillations. The method is validated using simulated power system data as well as data obtained from the western North American power system (wNAPS) and Eastern Interconnection (EI).« less

Impact of Childhood Maltreatment on the Recognition of Facial Expressions of Emotions

PubMed Central

Ardizzi, Martina; Martini, Francesca; Umiltà, Maria Alessandra; Evangelista, Valentina; Ravera, Roberto; Gallese, Vittorio

2015-01-01

The development of the explicit recognition of facial expressions of emotions can be affected by childhood maltreatment experiences. A previous study demonstrated the existence of an explicit recognition bias for angry facial expressions among a population of adolescent Sierra Leonean street-boys exposed to high levels of maltreatment. In the present study, the recognition bias for angry facial expressions was investigated in a younger population of street-children and age-matched controls. Participants performed a forced-choice facial expressions recognition task. Recognition bias was measured as participants’ tendency to over-attribute anger label to other negative facial expressions. Participants’ heart rate was assessed and related to their behavioral performance, as index of their stress-related physiological responses. Results demonstrated the presence of a recognition bias for angry facial expressions among street-children, also pinpointing a similar, although significantly less pronounced, tendency among controls. Participants’ performance was controlled for age, cognitive and educational levels and for naming skills. None of these variables influenced the recognition bias for angry facial expressions. Differently, a significant effect of heart rate on participants’ tendency to use anger label was evidenced. Taken together, these results suggest that childhood exposure to maltreatment experiences amplifies children’s “pre-existing bias” for anger labeling in forced-choice emotion recognition task. Moreover, they strengthen the thesis according to which the recognition bias for angry facial expressions is a manifestation of a functional adaptive mechanism that tunes victim’s perceptive and attentive focus on salient environmental social stimuli. PMID:26509890

Toward an Enhanced Sampling Molecular Dynamics Method for Studying Ligand-Induced Conformational Changes in Proteins.

PubMed

Andersen, Ole Juul; Grouleff, Julie; Needham, Perri; Walker, Ross C; Jensen, Frank

2015-11-19

Current enhanced sampling molecular dynamics methods for studying large conformational changes in proteins suffer from certain limitations. These include, among others, the need for user defined collective variables, the prerequisite of both start and end point structures of the conformational change, and the need for a priori knowledge of the amount by which to boost specific parts of the potential. In this paper, a framework is proposed for a molecular dynamics method for studying ligand-induced conformational changes, in which the nonbonded interactions between the ligand and the protein are used to calculate a biasing force. The method requires only a single input structure, and does not entail the use of collective variables. We provide a proof-of-concept for accelerating conformational changes in three simple test molecules, as well as promising results for two proteins known to undergo domain closure upon ligand binding. For the ribose-binding protein, backbone root-mean-square deviations as low as 0.75 Å compared to the crystal structure of the closed conformation are obtained within 50 ns simulations, whereas no domain closures are observed in unbiased simulations. A skewed closed structure is obtained for the glutamine-binding protein at high bias values, indicating that specific protein-ligand interactions might suppress important protein-protein interactions.

Weighted divergence correction scheme and its fast implementation

NASA Astrophysics Data System (ADS)

Wang, ChengYue; Gao, Qi; Wei, RunJie; Li, Tian; Wang, JinJun

2017-05-01

Forcing the experimental volumetric velocity fields to satisfy mass conversation principles has been proved beneficial for improving the quality of measured data. A number of correction methods including the divergence correction scheme (DCS) have been proposed to remove divergence errors from measurement velocity fields. For tomographic particle image velocimetry (TPIV) data, the measurement uncertainty for the velocity component along the light thickness direction is typically much larger than for the other two components. Such biased measurement errors would weaken the performance of traditional correction methods. The paper proposes a variant for the existing DCS by adding weighting coefficients to the three velocity components, named as the weighting DCS (WDCS). The generalized cross validation (GCV) method is employed to choose the suitable weighting coefficients. A fast algorithm for DCS or WDCS is developed, making the correction process significantly low-cost to implement. WDCS has strong advantages when correcting velocity components with biased noise levels. Numerical tests validate the accuracy and efficiency of the fast algorithm, the effectiveness of GCV method, and the advantages of WDCS. Lastly, DCS and WDCS are employed to process experimental velocity fields from the TPIV measurement of a turbulent boundary layer. This shows that WDCS achieves a better performance than DCS in improving some flow statistics.

Design and performance test of a MEMS vibratory gyroscope with a novel AGC force rebalance control

NASA Astrophysics Data System (ADS)

Sung, Woon-Tahk; Sung, Sangkyung; Lee, Jang Gyu; Kang, Taesam

2007-10-01

In this paper, the development and performance test results of a laterally oscillating MEMS gyroscope using a novel force rebalance control strategy are presented. The micromachined structure and electrodes are fabricated using the deep reactive ion etching (DRIE) and anodic wafer bonding process. The high quality factor required for the resonance-based sensor is achieved using a vacuum-sealed device package. A systematic design approach of the force rebalance control is applied via a modified automatic gain control (AGC) method. The rebalance control design takes advantages of a novel AGC loop modification, which allows the approximation of the system's dynamics into a simple linear form. Using the proposed modification of AGC and the rebalance strategy that maintains a biased oscillation, a number of performance improvements including bandwidth extension and widened operating range were observed to be achieved. Finally, the experimental results of the gyroscope's practical application verify the feasibility and performance of the developed sensor.

Short-Term Retrospective Land Data Assimilation Schemes

NASA Technical Reports Server (NTRS)

Houser, P. R.; Cosgrove, B. A.; Entin, J. K.; Lettenmaier, D.; ODonnell, G.; Mitchell, K.; Marshall, C.; Lohmann, D.; Schaake, J. C.; Duan, Q.;

Objective classification of historical tropical cyclone intensity

NASA Astrophysics Data System (ADS)

Chenoweth, Michael

2007-03-01

Preinstrumental records of historical tropical cyclone activity require objective methods for accurately categorizing tropical cyclone intensity. Here wind force terms and damage reports from newspaper accounts in the Lesser Antilles and Jamaica for the period 1795-1879 are compared with wind speed estimates calculated from barometric pressure data. A total of 95 separate barometric pressure readings and colocated simultaneous wind force descriptors and wind-induced damage reports are compared. The wind speed estimates from barometric pressure data are taken as the most reliable and serve as a standard to compare against other data. Wind-induced damage reports are used to produce an estimated wind speed range using a modified Fujita scale. Wind force terms are compared with the barometric pressure data to determine if a gale, as used in the contemporary newspapers, is consistent with the modern definition of a gale. Results indicate that the modern definition of a gale (the threshold point separating the classification of a tropical depression from a tropical storm) is equivalent to that in contemporary newspaper accounts. Barometric pressure values are consistent with both reported wind force terms and wind damage on land when the location, speed and direction of movement of the tropical cyclone are determined. Damage reports and derived wind force estimates are consistent with other published results. Biases in ships' logbooks are confirmed and wind force terms of gale strength or greater are identified. These results offer a bridge between the earlier noninstrumental records of tropical cyclones and modern records thereby offering a method of consistently classifying storms in the Caribbean region into tropical depressions, tropical storms, nonmajor and major hurricanes.

Breaking the Time Barrier in Kelvin Probe Force Microscopy: Fast Free Force Reconstruction Using the G-Mode Platform

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

Collins, Liam; Ahmadi, Mahshid; Wu, Ting

The atomic force microscope (AFM) offers unparalleled insight into structure and material functionality across nanometer length scales. However, the spatial resolution afforded by the AFM tip is counterpoised by slow detection speeds compared to other common microscopy techniques (e.g. optical, scanning electron microscopy etc.). In this work, we develop an AFM imaging approach allowing ultrafast reconstruction of the tip-sample forces having ~2 orders of magnitude higher time resolution than standard detection methods. Fast free force recovery (F3R) overcomes the widely-viewed temporal bottleneck in AFM, i.e. the mechanical bandwidth of the cantilever, enabling time-resolved imaging at sub-bandwidth speeds. We demonstrate quantitativemore » recovery of electrostatic forces with ~10 µs temporal resolution, free from cantilever ring-down effects. We further apply the F3R method to Kelvin probe force microscopy (KPFM) measurements. F3R-KPFM is an open loop imaging approach (i.e. no bias feedback), allowing ultrafast surface potential measurements (e.g. < 20 µs) to be performed at regular KPFM scan speeds. F3R-KPFM is demonstrated for exploration of ion migration in organometallic halide perovskites materials and shown to allow spatio-temporal imaging of positively charged ion migration under applied electric field, as well as subsequent formation of accumulated charges at the perovskite/electrode interface. In this work we demonstrate quantitative F3R-KPFM measurements – however, we fully expect the F3R approach to be valid for all modes of non-contact AFM operation, including non-invasive probing of ultrafast electrical and magnetic dynamics.« less

Breaking the Time Barrier in Kelvin Probe Force Microscopy: Fast Free Force Reconstruction Using the G-Mode Platform

DOE PAGES

Collins, Liam; Ahmadi, Mahshid; Wu, Ting; ...

2017-08-06

The atomic force microscope (AFM) offers unparalleled insight into structure and material functionality across nanometer length scales. However, the spatial resolution afforded by the AFM tip is counterpoised by slow detection speeds compared to other common microscopy techniques (e.g. optical, scanning electron microscopy etc.). In this work, we develop an AFM imaging approach allowing ultrafast reconstruction of the tip-sample forces having ~2 orders of magnitude higher time resolution than standard detection methods. Fast free force recovery (F3R) overcomes the widely-viewed temporal bottleneck in AFM, i.e. the mechanical bandwidth of the cantilever, enabling time-resolved imaging at sub-bandwidth speeds. We demonstrate quantitativemore » recovery of electrostatic forces with ~10 µs temporal resolution, free from cantilever ring-down effects. We further apply the F3R method to Kelvin probe force microscopy (KPFM) measurements. F3R-KPFM is an open loop imaging approach (i.e. no bias feedback), allowing ultrafast surface potential measurements (e.g. < 20 µs) to be performed at regular KPFM scan speeds. F3R-KPFM is demonstrated for exploration of ion migration in organometallic halide perovskites materials and shown to allow spatio-temporal imaging of positively charged ion migration under applied electric field, as well as subsequent formation of accumulated charges at the perovskite/electrode interface. In this work we demonstrate quantitative F3R-KPFM measurements – however, we fully expect the F3R approach to be valid for all modes of non-contact AFM operation, including non-invasive probing of ultrafast electrical and magnetic dynamics.« less

Impact and Estimation of Balance Coordinate System Rotations and Translations in Wind-Tunnel Testing

NASA Technical Reports Server (NTRS)

Toro, Kenneth G.; Parker, Peter A.

2017-01-01

Discrepancies between the model and balance coordinate systems lead to biases in the aerodynamic measurements during wind-tunnel testing. The reference coordinate system relative to the calibration coordinate system at which the forces and moments are resolved is crucial to the overall accuracy of force measurements. This paper discusses sources of discrepancies and estimates of coordinate system rotation and translation due to machining and assembly differences. A methodology for numerically estimating the coordinate system biases will be discussed and developed. Two case studies are presented using this methodology to estimate the model alignment. Examples span from angle measurement system shifts on the calibration system to discrepancies in actual wind-tunnel data. The results from these case-studies will help aerodynamic researchers and force balance engineers to better the understand and identify potential differences in calibration systems due to coordinate system rotation and translation.

Dynamics and Control of a Biomimetic Vehicle Using Biased Wingbeat Forcing Functions: Part 1 - Aerodynamic Model (Postprint)

DTIC Science & Technology

2010-01-01

Experimental Biology, Vol. 46, 1967, pp. 431–443. 5Sane, S. P. and Dickenson , M. H., “The Control of Flight Force by a Flapping Wing: Lift and Drag Force...Production,” The Journal of Experimental Biology, Vol. 204, 2001, pp. 2607–2626. 6Sane, S. P. and Dickenson , M. H., “The aerodynamic effects of wing

The effect of changing wind forcing on Antarctic ice shelf melting in high-resolution, global sea ice-ocean simulations with the Accelerated Climate Model for Energy (ACME)

NASA Astrophysics Data System (ADS)

Asay-Davis, Xylar; Price, Stephen; Petersen, Mark; Wolfe, Jonathan

2017-04-01

The capability for simulating sub-ice shelf circulation and submarine melting and freezing has recently been added to the U.S. Department of Energy's Accelerated Climate Model for Energy (ACME). With this new capability, we use an eddy permitting ocean model to conduct two sets of simulations in the spirit of Spence et al. (GRL, 41, 2014), who demonstrate increased warm water upwelling along the Antarctic coast in response to poleward shifting and strengthening of Southern Ocean westerly winds. These characteristics, symptomatic of a positive Southern Annular Mode (SAM), are projected to continue into the 21st century under anthropogenic climate change (Fyfe et al., J. Clim., 20, 2007). In our first simulation, we force the climate model using the standard CORE interannual forcing dataset (Large and Yeager; Clim. Dyn., 33, 2009). In our second simulation, we force our climate model using an altered version of CORE interannual forcing, based on the latter half of the full time series, which we take as a proxy for a future climate state biased towards a positive SAM. We compare ocean model states and sub-ice shelf melt rates with observations, exploring sources of model biases as well as the effects of the two forcing scenarios.

Coupled Brownian motors: Anomalous hysteresis and zero-bias negative conductance

NASA Astrophysics Data System (ADS)

Reimann, P.; Kawai, R.; Van den Broeck, C.; Hänggi, P.

1999-03-01

We introduce a model of interacting Brownian particles in a symmetric, periodic potential that undergoes a noise-induced non-equilibrium phase transition. The associated spontaneous symmetry breaking entails a ratchet-like transport mechanism. In response to an external force we identify several novel features; among the most prominent being a zero-bias negative conductance and a prima facie counterintuitive, anomalous hysteresis.

Regional Climate Simulations over North America: Interaction of Local Processes with Improved Large-Scale Flow.

NASA Astrophysics Data System (ADS)

Miguez-Macho, Gonzalo; Stenchikov, Georgiy L.; Robock, Alan

2005-04-01

The reasons for biases in regional climate simulations were investigated in an attempt to discern whether they arise from deficiencies in the model parameterizations or are due to dynamical problems. Using the Regional Atmospheric Modeling System (RAMS) forced by the National Centers for Environmental Prediction-National Center for Atmospheric Research reanalysis, the detailed climate over North America at 50-km resolution for June 2000 was simulated. First, the RAMS equations were modified to make them applicable to a large region, and its turbulence parameterization was corrected. The initial simulations showed large biases in the location of precipitation patterns and surface air temperatures. By implementing higher-resolution soil data, soil moisture and soil temperature initialization, and corrections to the Kain-Fritch convective scheme, the temperature biases and precipitation amount errors could be removed, but the precipitation location errors remained. The precipitation location biases could only be improved by implementing spectral nudging of the large-scale (wavelength of 2500 km) dynamics in RAMS. This corrected for circulation errors produced by interactions and reflection of the internal domain dynamics with the lateral boundaries where the model was forced by the reanalysis.

Hamiltonian replica exchange combined with elastic network analysis to enhance global domain motions in atomistic molecular dynamics simulations.

PubMed

Ostermeir, Katja; Zacharias, Martin

2014-12-01

Coarse-grained elastic network models (ENM) of proteins offer a low-resolution representation of protein dynamics and directions of global mobility. A Hamiltonian-replica exchange molecular dynamics (H-REMD) approach has been developed that combines information extracted from an ENM analysis with atomistic explicit solvent MD simulations. Based on a set of centers representing rigid segments (centroids) of a protein, a distance-dependent biasing potential is constructed by means of an ENM analysis to promote and guide centroid/domain rearrangements. The biasing potentials are added with different magnitude to the force field description of the MD simulation along the replicas with one reference replica under the control of the original force field. The magnitude and the form of the biasing potentials are adapted during the simulation based on the average sampled conformation to reach a near constant biasing in each replica after equilibration. This allows for canonical sampling of conformational states in each replica. The application of the methodology to a two-domain segment of the glycoprotein 130 and to the protein cyanovirin-N indicates significantly enhanced global domain motions and improved conformational sampling compared with conventional MD simulations. © 2014 Wiley Periodicals, Inc.

Self-referential forces are sufficient to explain different dendritic morphologies

PubMed Central

Memelli, Heraldo; Torben-Nielsen, Benjamin; Kozloski, James

2013-01-01

Dendritic morphology constrains brain activity, as it determines first which neuronal circuits are possible and second which dendritic computations can be performed over a neuron's inputs. It is known that a range of chemical cues can influence the final shape of dendrites during development. Here, we investigate the extent to which self-referential influences, cues generated by the neuron itself, might influence morphology. To this end, we developed a phenomenological model and algorithm to generate virtual morphologies, which are then compared to experimentally reconstructed morphologies. In the model, branching probability follows a Galton–Watson process, while the geometry is determined by “homotypic forces” exerting influence on the direction of random growth in a constrained space. We model three such homotypic forces, namely an inertial force based on membrane stiffness, a soma-oriented tropism, and a force of self-avoidance, as directional biases in the growth algorithm. With computer simulations we explored how each bias shapes neuronal morphologies. We show that based on these principles, we can generate realistic morphologies of several distinct neuronal types. We discuss the extent to which homotypic forces might influence real dendritic morphologies, and speculate about the influence of other environmental cues on neuronal shape and circuitry. PMID:23386828

GneimoSim: A Modular Internal Coordinates Molecular Dynamics Simulation Package

PubMed Central

Larsen, Adrien B.; Wagner, Jeffrey R.; Kandel, Saugat; Salomon-Ferrer, Romelia; Vaidehi, Nagarajan; Jain, Abhinandan

2014-01-01

The Generalized Newton Euler Inverse Mass Operator (GNEIMO) method is an advanced method for internal coordinates molecular dynamics (ICMD). GNEIMO includes several theoretical and algorithmic advancements that address longstanding challenges with ICMD simulations. In this paper we describe the GneimoSim ICMD software package that implements the GNEIMO method. We believe that GneimoSim is the first software package to include advanced features such as the equipartition principle derived for internal coordinates, and a method for including the Fixman potential to eliminate systematic statistical biases introduced by the use of hard constraints. Moreover, by design, GneimoSim is extensible and can be easily interfaced with third party force field packages for ICMD simulations. Currently, GneimoSim includes interfaces to LAMMPS, OpenMM, Rosetta force field calculation packages. The availability of a comprehensive Python interface to the underlying C++ classes and their methods provides a powerful and versatile mechanism for users to develop simulation scripts to configure the simulation and control the simulation flow. GneimoSim has been used extensively for studying the dynamics of protein structures, refinement of protein homology models, and for simulating large scale protein conformational changes with enhanced sampling methods. GneimoSim is not limited to proteins and can also be used for the simulation of polymeric materials. PMID:25263538

GneimoSim: a modular internal coordinates molecular dynamics simulation package.

PubMed

Larsen, Adrien B; Wagner, Jeffrey R; Kandel, Saugat; Salomon-Ferrer, Romelia; Vaidehi, Nagarajan; Jain, Abhinandan

2014-12-05

The generalized Newton-Euler inverse mass operator (GNEIMO) method is an advanced method for internal coordinates molecular dynamics (ICMD). GNEIMO includes several theoretical and algorithmic advancements that address longstanding challenges with ICMD simulations. In this article, we describe the GneimoSim ICMD software package that implements the GNEIMO method. We believe that GneimoSim is the first software package to include advanced features such as the equipartition principle derived for internal coordinates, and a method for including the Fixman potential to eliminate systematic statistical biases introduced by the use of hard constraints. Moreover, by design, GneimoSim is extensible and can be easily interfaced with third party force field packages for ICMD simulations. Currently, GneimoSim includes interfaces to LAMMPS, OpenMM, and Rosetta force field calculation packages. The availability of a comprehensive Python interface to the underlying C++ classes and their methods provides a powerful and versatile mechanism for users to develop simulation scripts to configure the simulation and control the simulation flow. GneimoSim has been used extensively for studying the dynamics of protein structures, refinement of protein homology models, and for simulating large scale protein conformational changes with enhanced sampling methods. GneimoSim is not limited to proteins and can also be used for the simulation of polymeric materials. © 2014 Wiley Periodicals, Inc.

Test-to-Test Repeatability of Results From a Subsonic Wing-Body Configuration in the National Transonic Facility

NASA Technical Reports Server (NTRS)

Mineck, Raymond E.; Pendergraft, Odis C., Jr.

2000-01-01

Results from three wind tunnel tests in the National Transonic Facility of a model of an advanced-technology, subsonic-transport wing-body configuration have been analyzed to assess the test-to-test repeatability of several aerodynamic parameters. The scatter, as measured by the prediction interval, in the longitudinal force and moment coefficients increases as the Mach number increases. Residual errors with and without the ESP tubes installed suggest a bias leading to lower drag with the tubes installed. Residual errors as well as average values of the longitudinal force and moment coefficients show that there are small bias errors between the different tests.

Validation of the North American Land Data Assimilation System (NLDAS) retrospective forcing over the southern Great Plains

NASA Astrophysics Data System (ADS)

Luo, Lifeng; Robock, Alan; Mitchell, Kenneth E.; Houser, Paul R.; Wood, Eric F.; Schaake, John C.; Lohmann, Dag; Cosgrove, Brian; Wen, Fenghua; Sheffield, Justin; Duan, Qingyun; Higgins, R. Wayne; Pinker, Rachel T.; Tarpley, J. Dan

2003-11-01

Atmospheric forcing used by land surface models is a critical component of the North American Land Data Assimilation System (NLDAS) and its quality crucially affects the final product of NLDAS and our work on model improvement. A three-year (September 1996-September 1999) retrospective forcing data set was created from the Eta Data Assimilation System and observations and used to run the NLDAS land surface models for this period. We compared gridded NLDAS forcing with station observations obtained from networks including the Oklahoma Mesonet and Atmospheric Radiation Measurement/Cloud and Radiation Testbed at the southern Great Plains. Differences in all forcing variables except precipitation between the NLDAS forcing data set and station observations are small at all timescales. While precipitation data do not agree very well at an hourly timescale, they do agree better at longer timescales because of the way NLDAS precipitation forcing is generated. A small high bias in downward solar radiation and a low bias in downward longwave radiation exist in the retrospective forcing. To investigate the impact of these differences on land surface modeling we compared two sets of model simulations, one forced by the standard NLDAS product and one with station-observed meteorology. The differences in the resulting simulations of soil moisture and soil temperature for each model were small, much smaller than the differences between the models and between the models and observations. This indicates that NLDAS retrospective forcing provides an excellent state-of-the-art data set for land surface modeling, at least over the southern Great Plains region.

Optical and electrical properties of Cu-based all oxide semi-transparent photodetector

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

Kim, Hong-Sik; Patel, Malkeshkumar; Yadav, Pankaj

2016-09-05

Zero-bias operating Cu oxide-based photodetector was achieved by using large-scale available sputtering method. Cu oxide (Cu{sub 2}O or CuO) was used as p-type transparent layer to form a heterojunction by contacting n-type ZnO layer. All metal-oxide materials were employed to realize transparent device at room temperature and showed a high transparency (>75% at 600 nm) with excellent photoresponses. The structural, morphological, optical, and electrical properties of Cu oxides of CuO and Cu{sub 2}O are evaluated in depth by UV-visible spectrometer, X-ray diffraction, scanning electron microscopy, atomic force microscopy, Kelvin probe force microscopy, and Hall measurements. We may suggest a route ofmore » high-functional Cu oxide-based photoelectric devices for the applications in flexible and transparent electronics.« less

Concurrent validity of the Gyko inertial sensor system for the assessment of vertical jump height in female sub-elite youth soccer players.

PubMed

Lesinski, Melanie; Muehlbauer, Thomas; Granacher, Urs

2016-01-01

The aim of the present study was to verify concurrent validity of the Gyko inertial sensor system for the assessment of vertical jump height. Nineteen female sub-elite youth soccer players (mean age: 14.7 ± 0.6 years) performed three trials of countermovement (CMJ) and squat jumps (SJ), respectively. Maximal vertical jump height was simultaneously quantified with the Gyko system, a Kistler force-plate (i.e., gold standard), and another criterion device that is frequently used in the field, the Optojump system. Compared to the force-plate, the Gyko system determined significant systematic bias for mean CMJ (-0.66 cm, p  < 0.01, d  = 1.41) and mean SJ (-0.91 cm, p  < 0.01, d  = 1.69) height. Random bias was ± 3.2 cm for CMJ and ± 4.0 cm for SJ height and intraclass correlation coefficients (ICCs) were "excellent" (ICC = 0.87 for CMJ and 0.81 for SJ). Compared to the Optojump device, the Gyko system detected a significant systematic bias for mean CMJ (0.55 cm, p  < 0.05, d  = 0.94) but not for mean SJ (0.39 cm) height. Random bias was ± 3.3 cm for CMJ and ± 4.2 cm for SJ height and ICC values were "excellent" (ICC = 0.86 for CMJ and 0.82 for SJ). Consequently, apparatus specific regression equations were provided to estimate true vertical jump height for the Kistler force-plate and the Optojump device from Gyko-derived data. Our findings indicate that the Gyko system cannot be used interchangeably with a Kistler force-plate and the Optojump device in trained individuals. It is suggested that practitioners apply the correction equations to estimate vertical jump height for the force-plate and the Optojump system from Gyko-derived data.

Effect of temperature on residual force enhancement in single skeletal muscle fibers.

PubMed

Lee, Eun-Jeong; Herzog, Walter

2008-08-28

It is well accepted that the steady-state isometric force following active stretching of a muscle is greater than the steady-state isometric force obtained in a purely isometric contraction at the same length. This property of skeletal muscle has been called residual force enhancement (FE). Despite decades of research the mechanisms responsible for FE have remained largely unknown. Based on previous studies showing increases in FE in fibers in which cross-bridges were biased towards weakly bound states, we hypothesized that FE might be associated with a stretch-induced facilitation of transitioning from weakly to strongly bound cross-bridges. In order to test this hypothesis, single fibers (n=11) from the lumbrical muscles of frog (Rana pipiens) were used to determine FE at temperatures of 7 and 20 degrees C. At the cold temperature, cross-bridges are biased towards weakly bound states, therefore we expected FE to be greater at 7 degrees C compared to 20 degrees C. The average FE was significantly greater at 7 degrees C (11.5+/-1.1%) than at 20 degrees C (7.8+/-1.0%), as expected. The enhancement of force/stiffness was also significantly greater at the low (13.3+/-1.4%) compared to the high temperature (5.6+/-1.7%), indicating an increased conversion from weakly to strongly bound cross-bridges at the low temperature. We conclude from the results of this study that muscle preparations that are biased towards weakly bound cross-bridge states show increased FE for given stretch conditions, thereby supporting the idea that FE might be caused, in part, by a stretch-induced facilitation of the conversion of weakly to strongly bound cross-bridges.

Reversible Negative Resistive Switching in an Individual Fe@Al2O3 Hybrid Nanotube for Nonvolatile Memory.

PubMed

Ye, Yalong; Zhao, Jie; Xiao, Li; Cheng, Baochang; Xiao, Yanhe; Lei, Shuijin

2018-06-06

Hybrid nanostructures can show enormous potential in different areas because of their unique structural configurations. Herein, Fe@Al 2 O 3 hybrid nanotubes are constructed via a homogeneous coprecipitation method followed by subsequent annealing in a reducing atmosphere. The introduction of zero band gap Fe nanocrystals in the wall of ultrawide band gap Al 2 O 3 insulator nanotubes results in the formation of charge trap centers, and correspondingly a single hybrid nanotube-based two-terminal device can show reversible negative resistive switching (RS) characteristics with symmetrical negative differential resistance (NDR) at relatively high operation bias voltages. At a large bias voltage, holes and electrons can be injected into traps at two ends from electrodes, respectively, and then captured. The bias voltage dependence of asymmetrical filling of charges can lead to a reversible variation of built-in electromotive force, and therefore the symmetrical negative RS with NDR arises from two reversible back-to-back series bipolar RS. At a low readout voltage, the single Fe@Al 2 O 3 hybrid nanotube can show an excellent nonvolatile memory feature with a relatively large switching ratio of ∼30. The bias-governed reversible negative RS with superior stability, reversibility, nondestructive readout, and remarkable cycle performance makes it a potential candidate in next-generation erasable nonvolatile resistive random access memories.

PEST reduces bias in forced choice psychophysics.

PubMed

Taylor, M M; Forbes, S M; Creelman, C D

1983-11-01

Observers performed several different detection tasks using both the PEST adaptive psychophysical procedure and a fixed-level (method of constant stimuli) psychophysical procedure. In two experiments, PEST runs targeted at P (C) = 0.80 were immediately followed by fixed-level detection runs presented at the difficulty level resulting from the PEST run. The fixed-level runs yielded P (C) about 0.75. During the fixed-level runs, the probability of a correct response was greater when the preceding response was correct than when it was wrong. Observers, even highly trained ones, perform in a nonstationary manner. The sequential dependency data can be used to determine a lower bound for the observer's "true" capability when performing optimally; this lower bound is close to the PEST target, and well above the forced choice P (C). The observer's "true" capability is the measure used by most theories of detection performance. A further experiment compared psychometric functions obtained from a set of PEST runs using different targets with those obtained from blocks of fixed-level trials at different levels. PEST results were more stable across observers, performance at all but the highest signal levels was better with PEST, and the PEST psychometric functions had shallower slopes. We hypothesize that PEST permits the observer to keep track of what he is trying to detect, whereas in the fixed-level method performance is disrupted by memory failure. Some recently suggested "more virulent" versions of PEST may be subject to biases similar to those of the fixed-level procedures.(ABSTRACT TRUNCATED AT 250 WORDS)

Invited Commentary: The Need for Cognitive Science in Methodology.

PubMed

Greenland, Sander

2017-09-15

There is no complete solution for the problem of abuse of statistics, but methodological training needs to cover cognitive biases and other psychosocial factors affecting inferences. The present paper discusses 3 common cognitive distortions: 1) dichotomania, the compulsion to perceive quantities as dichotomous even when dichotomization is unnecessary and misleading, as in inferences based on whether a P value is "statistically significant"; 2) nullism, the tendency to privilege the hypothesis of no difference or no effect when there is no scientific basis for doing so, as when testing only the null hypothesis; and 3) statistical reification, treating hypothetical data distributions and statistical models as if they reflect known physical laws rather than speculative assumptions for thought experiments. As commonly misused, null-hypothesis significance testing combines these cognitive problems to produce highly distorted interpretation and reporting of study results. Interval estimation has so far proven to be an inadequate solution because it involves dichotomization, an avenue for nullism. Sensitivity and bias analyses have been proposed to address reproducibility problems (Am J Epidemiol. 2017;186(6):646-647); these methods can indeed address reification, but they can also introduce new distortions via misleading specifications for bias parameters. P values can be reframed to lessen distortions by presenting them without reference to a cutoff, providing them for relevant alternatives to the null, and recognizing their dependence on all assumptions used in their computation; they nonetheless require rescaling for measuring evidence. I conclude that methodological development and training should go beyond coverage of mechanistic biases (e.g., confounding, selection bias, measurement error) to cover distortions of conclusions produced by statistical methods and psychosocial forces. © The Author(s) 2017. Published by Oxford University Press on behalf of the Johns Hopkins Bloomberg School of Public Health. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Demonstration of asymmetric electron conduction in pseudosymmetrical photosynthetic reaction centre proteins in an electrical circuit

PubMed Central

Kamran, Muhammad; Friebe, Vincent M.; Delgado, Juan D.; Aartsma, Thijs J.; Frese, Raoul N.; Jones, Michael R.

2015-01-01

Photosynthetic reaction centres show promise for biomolecular electronics as nanoscale solar-powered batteries and molecular diodes that are amenable to atomic-level re-engineering. In this work the mechanism of electron conduction across the highly tractable Rhodobacter sphaeroides reaction centre is characterized by conductive atomic force microscopy. We find, using engineered proteins of known structure, that only one of the two cofactor wires connecting the positive and negative termini of this reaction centre is capable of conducting unidirectional current under a suitably oriented bias, irrespective of the magnitude of the bias or the applied force at the tunnelling junction. This behaviour, strong functional asymmetry in a largely symmetrical protein–cofactor matrix, recapitulates the strong functional asymmetry characteristic of natural photochemical charge separation, but it is surprising given that the stimulus for electron flow is simply an externally applied bias. Reasons for the electrical resistance displayed by the so-called B-wire of cofactors are explored. PMID:25751412

Demonstration of asymmetric electron conduction in pseudosymmetrical photosynthetic reaction centre proteins in an electrical circuit.

PubMed

Kamran, Muhammad; Friebe, Vincent M; Delgado, Juan D; Aartsma, Thijs J; Frese, Raoul N; Jones, Michael R

2015-03-09

Photosynthetic reaction centres show promise for biomolecular electronics as nanoscale solar-powered batteries and molecular diodes that are amenable to atomic-level re-engineering. In this work the mechanism of electron conduction across the highly tractable Rhodobacter sphaeroides reaction centre is characterized by conductive atomic force microscopy. We find, using engineered proteins of known structure, that only one of the two cofactor wires connecting the positive and negative termini of this reaction centre is capable of conducting unidirectional current under a suitably oriented bias, irrespective of the magnitude of the bias or the applied force at the tunnelling junction. This behaviour, strong functional asymmetry in a largely symmetrical protein-cofactor matrix, recapitulates the strong functional asymmetry characteristic of natural photochemical charge separation, but it is surprising given that the stimulus for electron flow is simply an externally applied bias. Reasons for the electrical resistance displayed by the so-called B-wire of cofactors are explored.

Confidence in Forced-Choice Recognition: What Underlies the Ratings?

ERIC Educational Resources Information Center

Zawadzka, Katarzyna; Higham, Philip A.; Hanczakowski, Maciej

2017-01-01

Two-alternative forced-choice recognition tests are commonly used to assess recognition accuracy that is uncontaminated by changes in bias. In such tests, participants are asked to endorse the studied item out of 2 presented alternatives. Participants may be further asked to provide confidence judgments for their recognition decisions. It is often…

The Revolutionary United Front and Child Soldiers during Sierra Leone’s Civil War

DTIC Science & Technology

2015-06-12

Armed Forces served as an ex post facto force during the internal conflict period between the APC and SLPP jockeying for the position of Prime Minister...civil war. Chapter 3, Research Methodology, addresses biases and the reliability of the study regarding the thesis findings. Chapter 4, Analysis

How IRT Can Solve Problems of Ipsative Data in Forced-Choice Questionnaires

ERIC Educational Resources Information Center

Brown, Anna; Maydeu-Olivares, Alberto

2013-01-01

In multidimensional forced-choice (MFC) questionnaires, items measuring different attributes are presented in blocks, and participants have to rank order the items within each block (fully or partially). Such comparative formats can reduce the impact of numerous response biases often affecting single-stimulus items (aka rating or Likert scales).…

Hypothesis Testing Using Factor Score Regression

PubMed Central

Devlieger, Ines; Mayer, Axel; Rosseel, Yves

2015-01-01

In this article, an overview is given of four methods to perform factor score regression (FSR), namely regression FSR, Bartlett FSR, the bias avoiding method of Skrondal and Laake, and the bias correcting method of Croon. The bias correcting method is extended to include a reliable standard error. The four methods are compared with each other and with structural equation modeling (SEM) by using analytic calculations and two Monte Carlo simulation studies to examine their finite sample characteristics. Several performance criteria are used, such as the bias using the unstandardized and standardized parameterization, efficiency, mean square error, standard error bias, type I error rate, and power. The results show that the bias correcting method, with the newly developed standard error, is the only suitable alternative for SEM. While it has a higher standard error bias than SEM, it has a comparable bias, efficiency, mean square error, power, and type I error rate. PMID:29795886

Mapping species distributions with MAXENT using a geographically biased sample of presence data: a performance assessment of methods for correcting sampling bias.

PubMed

Fourcade, Yoan; Engler, Jan O; Rödder, Dennis; Secondi, Jean

2014-01-01

MAXENT is now a common species distribution modeling (SDM) tool used by conservation practitioners for predicting the distribution of a species from a set of records and environmental predictors. However, datasets of species occurrence used to train the model are often biased in the geographical space because of unequal sampling effort across the study area. This bias may be a source of strong inaccuracy in the resulting model and could lead to incorrect predictions. Although a number of sampling bias correction methods have been proposed, there is no consensual guideline to account for it. We compared here the performance of five methods of bias correction on three datasets of species occurrence: one "virtual" derived from a land cover map, and two actual datasets for a turtle (Chrysemys picta) and a salamander (Plethodon cylindraceus). We subjected these datasets to four types of sampling biases corresponding to potential types of empirical biases. We applied five correction methods to the biased samples and compared the outputs of distribution models to unbiased datasets to assess the overall correction performance of each method. The results revealed that the ability of methods to correct the initial sampling bias varied greatly depending on bias type, bias intensity and species. However, the simple systematic sampling of records consistently ranked among the best performing across the range of conditions tested, whereas other methods performed more poorly in most cases. The strong effect of initial conditions on correction performance highlights the need for further research to develop a step-by-step guideline to account for sampling bias. However, this method seems to be the most efficient in correcting sampling bias and should be advised in most cases.

Mapping Species Distributions with MAXENT Using a Geographically Biased Sample of Presence Data: A Performance Assessment of Methods for Correcting Sampling Bias

PubMed Central

Fourcade, Yoan; Engler, Jan O.; Rödder, Dennis; Secondi, Jean

2014-01-01

MAXENT is now a common species distribution modeling (SDM) tool used by conservation practitioners for predicting the distribution of a species from a set of records and environmental predictors. However, datasets of species occurrence used to train the model are often biased in the geographical space because of unequal sampling effort across the study area. This bias may be a source of strong inaccuracy in the resulting model and could lead to incorrect predictions. Although a number of sampling bias correction methods have been proposed, there is no consensual guideline to account for it. We compared here the performance of five methods of bias correction on three datasets of species occurrence: one “virtual” derived from a land cover map, and two actual datasets for a turtle (Chrysemys picta) and a salamander (Plethodon cylindraceus). We subjected these datasets to four types of sampling biases corresponding to potential types of empirical biases. We applied five correction methods to the biased samples and compared the outputs of distribution models to unbiased datasets to assess the overall correction performance of each method. The results revealed that the ability of methods to correct the initial sampling bias varied greatly depending on bias type, bias intensity and species. However, the simple systematic sampling of records consistently ranked among the best performing across the range of conditions tested, whereas other methods performed more poorly in most cases. The strong effect of initial conditions on correction performance highlights the need for further research to develop a step-by-step guideline to account for sampling bias. However, this method seems to be the most efficient in correcting sampling bias and should be advised in most cases. PMID:24818607

Maximum likelihood estimation of protein kinetic parameters under weak assumptions from unfolding force spectroscopy experiments

NASA Astrophysics Data System (ADS)

Aioanei, Daniel; Samorì, Bruno; Brucale, Marco

2009-12-01

Single molecule force spectroscopy (SMFS) is extensively used to characterize the mechanical unfolding behavior of individual protein domains under applied force by pulling chimeric polyproteins consisting of identical tandem repeats. Constant velocity unfolding SMFS data can be employed to reconstruct the protein unfolding energy landscape and kinetics. The methods applied so far require the specification of a single stretching force increase function, either theoretically derived or experimentally inferred, which must then be assumed to accurately describe the entirety of the experimental data. The very existence of a suitable optimal force model, even in the context of a single experimental data set, is still questioned. Herein, we propose a maximum likelihood (ML) framework for the estimation of protein kinetic parameters which can accommodate all the established theoretical force increase models. Our framework does not presuppose the existence of a single force characteristic function. Rather, it can be used with a heterogeneous set of functions, each describing the protein behavior in the stretching time range leading to one rupture event. We propose a simple way of constructing such a set of functions via piecewise linear approximation of the SMFS force vs time data and we prove the suitability of the approach both with synthetic data and experimentally. Additionally, when the spontaneous unfolding rate is the only unknown parameter, we find a correction factor that eliminates the bias of the ML estimator while also reducing its variance. Finally, we investigate which of several time-constrained experiment designs leads to better estimators.

Do two and three year old children use an incremental first-NP-as-agent bias to process active transitive and passive sentences?: A permutation analysis

PubMed Central

Chang, Franklin; Rowland, Caroline; Ferguson, Heather; Pine, Julian

2017-01-01

We used eye-tracking to investigate if and when children show an incremental bias to assume that the first noun phrase in a sentence is the agent (first-NP-as-agent bias) while processing the meaning of English active and passive transitive sentences. We also investigated whether children can override this bias to successfully distinguish active from passive sentences, after processing the remainder of the sentence frame. For this second question we used eye-tracking (Study 1) and forced-choice pointing (Study 2). For both studies, we used a paradigm in which participants simultaneously saw two novel actions with reversed agent-patient relations while listening to active and passive sentences. We compared English-speaking 25-month-olds and 41-month-olds in between-subjects sentence structure conditions (Active Transitive Condition vs. Passive Condition). A permutation analysis found that both age groups showed a bias to incrementally map the first noun in a sentence onto an agent role. Regarding the second question, 25-month-olds showed some evidence of distinguishing the two structures in the eye-tracking study. However, the 25-month-olds did not distinguish active from passive sentences in the forced choice pointing task. In contrast, the 41-month-old children did reanalyse their initial first-NP-as-agent bias to the extent that they clearly distinguished between active and passive sentences both in the eye-tracking data and in the pointing task. The results are discussed in relation to the development of syntactic (re)parsing. PMID:29049390

Accuracy and precision of loadsol® insole force-sensors for the quantification of ground reaction force-based biomechanical running parameters.

PubMed

Seiberl, Wolfgang; Jensen, Elisabeth; Merker, Josephine; Leitel, Marco; Schwirtz, Ansgar

2018-05-29

Force plates represent the "gold standard" in measuring running kinetics to predict performance or to identify the sources of running-related injuries. As these measurements are generally limited to laboratory analyses, wireless high-quality sensors for measuring in the field are needed. This work analysed the accuracy and precision of a new wireless insole forcesensor for quantifying running-related kinetic parameters. Vertical ground reaction force (GRF) was simultaneously measured with pit-mounted force plates (1 kHz) and loadsol ® sensors (100 Hz) under unshod forefoot and rearfoot running-step conditions. GRF data collections were repeated four times, each separated by 30 min treadmill running, to test influence of extended use. A repeated-measures ANOVA was used to identify differences between measurement devices. Additionally, mean bias and Bland-Altman limits of agreement (LoA) were calculated. We found a significant difference (p < .05) in ground contact time, peak force, and force rate, while there was no difference in parameters impulse, time to peak, and negative force rate. There was no influence of time point of measurement. The mean bias of ground contact time, impulse, peak force, and time to peak ranged between 0.6% and 3.4%, demonstrating high accuracy of loadsol ® devices for these parameters. For these same parameters, the LoA analysis showed that 95% of all measurement differences between insole and force plate measurements were less than 12%, demonstrating high precision of the sensors. However, highly dynamic behaviour of GRF, such as force rate, is not yet sufficiently resolved by the insole devices, which is likely explained by the low sampling rate.

Development of a new physics-based internal coordinate mechanics force field and its application to protein loop modeling.

PubMed

Arnautova, Yelena A; Abagyan, Ruben A; Totrov, Maxim

2011-02-01

We report the development of internal coordinate mechanics force field (ICMFF), new force field parameterized using a combination of experimental data for crystals of small molecules and quantum mechanics calculations. The main features of ICMFF include: (a) parameterization for the dielectric constant relevant to the condensed state (ε = 2) instead of vacuum, (b) an improved description of hydrogen-bond interactions using duplicate sets of van der Waals parameters for heavy atom-hydrogen interactions, and (c) improved backbone covalent geometry and energetics achieved using novel backbone torsional potentials and inclusion of the bond angles at the C(α) atoms into the internal variable set. The performance of ICMFF was evaluated through loop modeling simulations for 4-13 residue loops. ICMFF was combined with a solvent-accessible surface area solvation model optimized using a large set of loop decoys. Conformational sampling was carried out using the biased probability Monte Carlo method. Average/median backbone root-mean-square deviations of the lowest energy conformations from the native structures were 0.25/0.21 Å for four residues loops, 0.84/0.46 Å for eight residue loops, and 1.16/0.73 Å for 12 residue loops. To our knowledge, these results are significantly better than or comparable with those reported to date for any loop modeling method that does not take crystal packing into account. Moreover, the accuracy of our method is on par with the best previously reported results obtained considering the crystal environment. We attribute this success to the high accuracy of the new ICM force field achieved by meticulous parameterization, to the optimized solvent model, and the efficiency of the search method. © 2010 Wiley-Liss, Inc.

Development of Spatiotemporal Bias-Correction Techniques for Downscaling GCM Predictions

NASA Astrophysics Data System (ADS)

Hwang, S.; Graham, W. D.; Geurink, J.; Adams, A.; Martinez, C. J.

2010-12-01

Accurately representing the spatial variability of precipitation is an important factor for predicting watershed response to climatic forcing, particularly in small, low-relief watersheds affected by convective storm systems. Although Global Circulation Models (GCMs) generally preserve spatial relationships between large-scale and local-scale mean precipitation trends, most GCM downscaling techniques focus on preserving only observed temporal variability on point by point basis, not spatial patterns of events. Downscaled GCM results (e.g., CMIP3 ensembles) have been widely used to predict hydrologic implications of climate variability and climate change in large snow-dominated river basins in the western United States (Diffenbaugh et al., 2008; Adam et al., 2009). However fewer applications to smaller rain-driven river basins in the southeastern US (where preserving spatial variability of rainfall patterns may be more important) have been reported. In this study a new method was developed to bias-correct GCMs to preserve both the long term temporal mean and variance of the precipitation data, and the spatial structure of daily precipitation fields. Forty-year retrospective simulations (1960-1999) from 16 GCMs were collected (IPCC, 2007; WCRP CMIP3 multi-model database: https://esg.llnl.gov:8443/), and the daily precipitation data at coarse resolution (i.e., 280km) were interpolated to 12km spatial resolution and bias corrected using gridded observations over the state of Florida (Maurer et al., 2002; Wood et al, 2002; Wood et al, 2004). In this method spatial random fields which preserved the observed spatial correlation structure of the historic gridded observations and the spatial mean corresponding to the coarse scale GCM daily rainfall were generated. The spatiotemporal variability of the spatio-temporally bias-corrected GCMs were evaluated against gridded observations, and compared to the original temporally bias-corrected and downscaled CMIP3 data for the central Florida. The hydrologic response of two southwest Florida watersheds to the gridded observation data, the original bias corrected CMIP3 data, and the new spatiotemporally corrected CMIP3 predictions was compared using an integrated surface-subsurface hydrologic model developed by Tampa Bay Water.

Sensitivity of the atmospheric water cycle to corrections of the sea surface temperature bias over southern Africa in a regional climate model

NASA Astrophysics Data System (ADS)

Weber, Torsten; Haensler, Andreas; Jacob, Daniela

2017-12-01

Regional climate models (RCMs) have been used to dynamically downscale global climate projections at high spatial and temporal resolution in order to analyse the atmospheric water cycle. In southern Africa, precipitation pattern were strongly affected by the moisture transport from the southeast Atlantic and southwest Indian Ocean and, consequently, by their sea surface temperatures (SSTs). However, global ocean models often have deficiencies in resolving regional to local scale ocean currents, e.g. in ocean areas offshore the South African continent. By downscaling global climate projections using RCMs, the biased SSTs from the global forcing data were introduced to the RCMs and affected the results of regional climate projections. In this work, the impact of the SST bias correction on precipitation, evaporation and moisture transport were analysed over southern Africa. For this analysis, several experiments were conducted with the regional climate model REMO using corrected and uncorrected SSTs. In these experiments, a global MPI-ESM-LR historical simulation was downscaled with the regional climate model REMO to a high spatial resolution of 50 × 50 km2 and of 25 × 25 km2 for southern Africa using a double-nesting method. The results showed a distinct impact of the corrected SST on the moisture transport, the meridional vertical circulation and on the precipitation pattern in southern Africa. Furthermore, it was found that the experiment with the corrected SST led to a reduction of the wet bias over southern Africa and to a better agreement with observations as without SST bias corrections.

Assimilation of ASCAT near-surface soil moisture into the SIM hydrological model over France

NASA Astrophysics Data System (ADS)

Draper, C.; Mahfouf, J.-F.; Calvet, J.-C.; Martin, E.; Wagner, W.

2011-12-01

This study examines whether the assimilation of remotely sensed near-surface soil moisture observations might benefit an operational hydrological model, specifically Météo-France's SAFRAN-ISBA-MODCOU (SIM) model. Soil moisture data derived from ASCAT backscatter observations are assimilated into SIM using a Simplified Extended Kalman Filter (SEKF) over 3.5 years. The benefit of the assimilation is tested by comparison to a delayed cut-off version of SIM, in which the land surface is forced with more accurate atmospheric analyses, due to the availability of additional atmospheric observations after the near-real time data cut-off. However, comparing the near-real time and delayed cut-off SIM models revealed that the main difference between them is a dry bias in the near-real time precipitation forcing, which resulted in a dry bias in the root-zone soil moisture and associated surface moisture flux forecasts. While assimilating the ASCAT data did reduce the root-zone soil moisture dry bias (by nearly 50%), this was more likely due to a bias within the SEKF, than due to the assimilation having accurately responded to the precipitation errors. Several improvements to the assimilation are identified to address this, and a bias-aware strategy is suggested for explicitly correcting the model bias. However, in this experiment the moisture added by the SEKF was quickly lost from the model surface due to the enhanced surface fluxes (particularly drainage) induced by the wetter soil moisture states. Consequently, by the end of each winter, during which frozen conditions prevent the ASCAT data from being assimilated, the model land surface had returned to its original (dry-biased) climate. This highlights that it would be more effective to address the precipitation bias directly, than to correct it by constraining the model soil moisture through data assimilation.

Seal assembly

DOEpatents

Johnson, Roger Neal; Longfritz, William David

2001-01-01

A seal assembly that seals a gap formed by a groove comprises a seal body, a biasing element, and a connection that connects the seal body to the biasing element to form the seal assembly. The seal assembly further comprises a concave-shaped center section and convex-shaped contact portions at each end of the seal body. The biasing element is formed from an elastic material and comprises a convex-shaped center section and concave-shaped biasing zones that are opposed to the convex-shaped contact portions. The biasing element is adapted to be compressed to change a width of the seal assembly from a first width to a second width that is smaller than the first width. In the compressed state, the seal assembly can be disposed in the groove. After release of the compressing force, the seal assembly expands. The contact portions will move toward a surface of the groove and the biasing zones will move into contact with another surface of the groove. The biasing zones will bias the contact portions of the seal body against the surface of the groove.

Codon usage bias in prokaryotic pyrimidine-ending codons is associated with the degeneracy of the encoded amino acids

PubMed Central

Wald, Naama; Alroy, Maya; Botzman, Maya; Margalit, Hanah

2012-01-01

Synonymous codons are unevenly distributed among genes, a phenomenon termed codon usage bias. Understanding the patterns of codon bias and the forces shaping them is a major step towards elucidating the adaptive advantage codon choice can confer at the level of individual genes and organisms. Here, we perform a large-scale analysis to assess codon usage bias pattern of pyrimidine-ending codons in highly expressed genes in prokaryotes. We find a bias pattern linked to the degeneracy of the encoded amino acid. Specifically, we show that codon-pairs that encode two- and three-fold degenerate amino acids are biased towards the C-ending codon while codons encoding four-fold degenerate amino acids are biased towards the U-ending codon. This codon usage pattern is widespread in prokaryotes, and its strength is correlated with translational selection both within and between organisms. We show that this bias is associated with an improved correspondence with the tRNA pool, avoidance of mis-incorporation errors during translation and moderate stability of codon–anticodon interaction, all consistent with more efficient translation. PMID:22581775

Does temperature nudging overwhelm aerosol radiative ...

EPA Pesticide Factsheets

For over two decades, data assimilation (popularly known as nudging) methods have been used for improving regional weather and climate simulations by reducing model biases in meteorological parameters and processes. Similar practice is also popular in many regional integrated meteorology-air quality models that include aerosol direct and indirect effects. However in such multi-modeling systems, temperature changes due to nudging can compete with temperature changes induced by radiatively active & hygroscopic short-lived tracers leading to interesting dilemmas: From weather and climate prediction’s (retrospective or future) point of view when nudging is continuously applied, is there any real added benefit of using such complex and computationally expensive regional integrated modeling systems? What are the relative sizes of these two competing forces? To address these intriguing questions, we convert temperature changes due to nudging into radiative fluxes (referred to as the pseudo radiative forcing, PRF) at the surface and troposphere, and compare the net PRF with the reported aerosol radiative forcing. Results indicate that the PRF at surface dominates PRF at top of the atmosphere (i.e., the net). Also, the net PRF is about 2-4 times larger than estimated aerosol radiative forcing at regional scales while it is significantly larger at local scales. These results also show large surface forcing errors at many polluted urban sites. Thus, operational c

First order reversal curve study of the dipolar interaction in Ni three-dimensional antidot arrays

NASA Astrophysics Data System (ADS)

Li, Bingqing; Chai, Xuzhao; Moeendarbari, Sina; Hao, Yaowu; Gilbert, Dustin A.; Liu, Kai; Zhang, Di; Feng, Gang; Han, Ping; Cheng, X. M.

2014-03-01

Three-dimensional antidot arrays (3DAAs) have attracted considerable attention due to potential applications in sensors, energy storage and transducers. Magnetic 3DAAs also provide an ideal system for studying the effect of dimensionality and morphology on magnetic properties. We report study of dipolar interactions in Ni 3DAAs using the first-order reversal curve (FORC) method. Ordered Ni 3DAAs were fabricated by electrochemical deposition into colloidal crystal templates of self-assembled polystyrene spheres. The samples have the same pore size of about 500 nm but different thicknesses, ranging from 0.3 μm to 1.2 μm, confirmed by scanning electron microscopy (SEM) and atomic force microscopy (AFM). FORCs of the samples with thicknesses of 0.3 μm, 0.8 μm, and 1.2 μm were measured by a vibrating sample magnetometer. The FORC diagram analysis reveals a demagnetizing magnetic dipolar interaction, and a decrease in the interaction strength with the increasing sample thickness, evidenced by a decrease in the spread of the irreversible peak in the bias distribution, as well as a decrease in the tilting of the FORC distribution from the local coercivity axis. Work at BMC and UCD is supported by NSF DMR-1207085 and DMR-1008791, respectively.

Hydrologic Implications of Dynamical and Statistical Approaches to Downscaling Climate Model Outputs

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

Wood, Andrew W; Leung, Lai R; Sridhar, V

Six approaches for downscaling climate model outputs for use in hydrologic simulation were evaluated, with particular emphasis on each method's ability to produce precipitation and other variables used to drive a macroscale hydrology model applied at much higher spatial resolution than the climate model. Comparisons were made on the basis of a twenty-year retrospective (1975–1995) climate simulation produced by the NCAR-DOE Parallel Climate Model (PCM), and the implications of the comparison for a future (2040–2060) PCM climate scenario were also explored. The six approaches were made up of three relatively simple statistical downscaling methods – linear interpolation (LI), spatial disaggregationmore » (SD), and bias-correction and spatial disaggregation (BCSD) – each applied to both PCM output directly (at T42 spatial resolution), and after dynamical downscaling via a Regional Climate Model (RCM – at ½-degree spatial resolution), for downscaling the climate model outputs to the 1/8-degree spatial resolution of the hydrological model. For the retrospective climate simulation, results were compared to an observed gridded climatology of temperature and precipitation, and gridded hydrologic variables resulting from forcing the hydrologic model with observations. The most significant findings are that the BCSD method was successful in reproducing the main features of the observed hydrometeorology from the retrospective climate simulation, when applied to both PCM and RCM outputs. Linear interpolation produced better results using RCM output than PCM output, but both methods (PCM-LI and RCM-LI) lead to unacceptably biased hydrologic simulations. Spatial disaggregation of the PCM output produced results similar to those achieved with the RCM interpolated output; nonetheless, neither PCM nor RCM output was useful for hydrologic simulation purposes without a bias-correction step. For the future climate scenario, only the BCSD-method (using PCM or RCM) was able to produce hydrologically plausible results. With the BCSD method, the RCM-derived hydrology was more sensitive to climate change than the PCM-derived hydrology.« less

Influence of certain forces on evolution of synonymous codon usage bias in certain species of three basal orders of aquatic insects.

PubMed

Selva Kumar, C; Nair, Rahul R; Sivaramakrishnan, K G; Ganesh, D; Janarthanan, S; Arunachalam, M; Sivaruban, T

2012-12-01

Forces that influence the evolution of synonymous codon usage bias are analyzed in six species of three basal orders of aquatic insects. The rationale behind choosing six species of aquatic insects (three from Ephemeroptera, one from Plecoptera, and two from Odonata) for the present analysis is based on phylogenetic position at the basal clades of the Order Insecta facilitating the understanding of the evolution of codon bias and of factors shaping codon usage patterns in primitive clades of insect lineages and their subtle differences in some of their ecological and environmental requirements in terms of habitat-microhabitat requirements, altitudinal preferences, temperature tolerance ranges, and consequent responses to climate change impacts. The present analysis focuses on open reading frames of the 13 protein-coding genes in the mitochondrial genome of six carefully chosen insect species to get a comprehensive picture of the evolutionary intricacies of codon bias. In all the six species, A and T contents are observed to be significantly higher than G and C, and are used roughly equally. Since transcription hypothesis on codon usage demands A richness and T poorness, it is quite likely that mutation pressure may be the key factor associated with synonymous codon usage (SCU) variations in these species because the mutation hypothesis predicts AT richness and GC poorness in the mitochondrial DNA. Thus, AT-biased mutation pressure seems to be an important factor in framing the SCU variation in all the selected species of aquatic insects, which in turn explains the predominance of A and T ending codons in these species. This study does not find any association between microhabitats and codon usage variations in the mitochondria of selected aquatic insects. However, this study has identified major forces, such as compositional constraints and mutation pressure, which shape patterns of codon usage in mitochondrial genes in the primitive clades of insect lineages.

Fore and aft elastic response characteristics of size 34x9.9, type 7, 14 ply-rated aircraft tires of bias ply, bias belted, and radial belted design. M.S. Thesis - George Washington Univ., Washington, D. C.

NASA Technical Reports Server (NTRS)

Tanner, J. A.

1973-01-01

An investigation was conducted to determine the fore-and-aft elastic response characteristics of aircraft tires of bias ply, bias-belted, and radial-belted design. The investigation consisted of: (1)static and rolling tests, (2)a statistical analysis which related the measured tire elastic characteristics to variations in the vertical load, inflation pressure, braking force and/or tire vertical deflection, and (3) a semi-empirical analysis which related the tire elastic behavior to measured wheel slippage during a steady-state braking. The results of this investigation indicate that the bias-belted tire has the largest spring constant value for most loading conditions and the radial-belted tire has the smallest spring constant value.

Forced-Choice Assessment of Work-Related Maladaptive Personality Traits: Preliminary Evidence From an Application of Thurstonian Item Response Modeling.

PubMed

Guenole, Nigel; Brown, Anna A; Cooper, Andrew J

2018-06-01

This article describes an investigation of whether Thurstonian item response modeling is a viable method for assessment of maladaptive traits. Forced-choice responses from 420 working adults to a broad-range personality inventory assessing six maladaptive traits were considered. The Thurstonian item response model's fit to the forced-choice data was adequate, while the fit of a counterpart item response model to responses to the same items but arranged in a single-stimulus design was poor. Monotrait heteromethod correlations indicated corresponding traits in the two formats overlapped substantially, although they did not measure equivalent constructs. A better goodness of fit and higher factor loadings for the Thurstonian item response model, coupled with a clearer conceptual alignment to the theoretical trait definitions, suggested that the single-stimulus item responses were influenced by biases that the independent clusters measurement model did not account for. Researchers may wish to consider forced-choice designs and appropriate item response modeling techniques such as Thurstonian item response modeling for personality questionnaire applications in industrial psychology, especially when assessing maladaptive traits. We recommend further investigation of this approach in actual selection situations and with different assessment instruments.

Novel Methods to Explore Building Energy Sensitivity to Climate and Heat Waves Using PNNL's BEND Model

NASA Astrophysics Data System (ADS)

Burleyson, C. D.; Voisin, N.; Taylor, T.; Xie, Y.; Kraucunas, I.

2017-12-01

The DOE's Pacific Northwest National Laboratory (PNNL) has been developing the Building ENergy Demand (BEND) model to simulate energy usage in residential and commercial buildings responding to changes in weather, climate, population, and building technologies. At its core, BEND is a mechanism to aggregate EnergyPlus simulations of a large number of individual buildings with a diversity of characteristics over large spatial scales. We have completed a series of experiments to explore methods to calibrate the BEND model, measure its ability to capture interannual variability in energy demand due to weather using simulations of two distinct weather years, and understand the sensitivity to the number and location of weather stations used to force the model. The use of weather from "representative cities" reduces computational costs, but often fails to capture spatial heterogeneity that may be important for simulations aimed at understanding how building stocks respond to a changing climate (Fig. 1). We quantify the potential reduction in temperature and load biases from using an increasing number of weather stations across the western U.S., ranging from 8 to roughly 150. Using 8 stations results in an average absolute summertime temperature bias of 4.0°C. The mean absolute bias drops to 1.5°C using all available stations. Temperature biases of this magnitude translate to absolute summertime mean simulated load biases as high as 13.8%. Additionally, using only 8 representative weather stations can lead to a 20-40% bias of peak building loads under heat wave or cold snap conditions, a significant error for capacity expansion planners who may rely on these types of simulations. This analysis suggests that using 4 stations per climate zone may be sufficient for most purposes. Our novel approach, which requires no new EnergyPlus simulations, could be useful to other researchers designing or calibrating aggregate building model simulations - particularly those looking at the impact of future climate scenarios. Fig. 1. An example of temperature bias that results from using 8 representative weather stations: (a) surface temperature from NLDAS on 5-July 2008 at 2000 UTC; (b) temperature from 8 representative stations at the same time mapped to all counties within a given IECC climate zone; (c) the difference between (a) and (b).

Exploring and accounting for publication bias in mental health: a brief overview of methods.

PubMed

Mavridis, Dimitris; Salanti, Georgia

2014-02-01

OBJECTIVE Publication bias undermines the integrity of published research. The aim of this paper is to present a synopsis of methods for exploring and accounting for publication bias. METHODS We discussed the main features of the following methods to assess publication bias: funnel plot analysis; trim-and-fill methods; regression techniques and selection models. We applied these methods to a well-known example of antidepressants trials that compared trials submitted to the Food and Drug Administration (FDA) for regulatory approval. RESULTS The funnel plot-related methods (visual inspection, trim-and-fill, regression models) revealed an association between effect size and SE. Contours of statistical significance showed that asymmetry in the funnel plot is probably due to publication bias. Selection model found a significant correlation between effect size and propensity for publication. CONCLUSIONS Researchers should always consider the possible impact of publication bias. Funnel plot-related methods should be seen as a means of examining for small-study effects and not be directly equated with publication bias. Possible causes for funnel plot asymmetry should be explored. Contours of statistical significance may help disentangle whether asymmetry in a funnel plot is caused by publication bias or not. Selection models, although underused, could be useful resource when publication bias and heterogeneity are suspected because they address directly the problem of publication bias and not that of small-study effects.

Consistent View of Protein Fluctuations from All-Atom Molecular Dynamics and Coarse-Grained Dynamics with Knowledge-Based Force-Field.

PubMed

Jamroz, Michal; Orozco, Modesto; Kolinski, Andrzej; Kmiecik, Sebastian

2013-01-08

It is widely recognized that atomistic Molecular Dynamics (MD), a classical simulation method, captures the essential physics of protein dynamics. That idea is supported by a theoretical study showing that various MD force-fields provide a consensus picture of protein fluctuations in aqueous solution [Rueda, M. et al. Proc. Natl. Acad. Sci. U.S.A. 2007, 104, 796-801]. However, atomistic MD cannot be applied to most biologically relevant processes due to its limitation to relatively short time scales. Much longer time scales can be accessed by properly designed coarse-grained models. We demonstrate that the aforementioned consensus view of protein dynamics from short (nanosecond) time scale MD simulations is fairly consistent with the dynamics of the coarse-grained protein model - the CABS model. The CABS model employs stochastic dynamics (a Monte Carlo method) and a knowledge-based force-field, which is not biased toward the native structure of a simulated protein. Since CABS-based dynamics allows for the simulation of entire folding (or multiple folding events) in a single run, integration of the CABS approach with all-atom MD promises a convenient (and computationally feasible) means for the long-time multiscale molecular modeling of protein systems with atomistic resolution.

Operational Data Reduction Procedure for Determining Density and Vertical Structure of the Martian Upper Atmosphere from Mars Global Surveyor Accelerometer Measurements

NASA Technical Reports Server (NTRS)

Cancro, George J.; Tolson, Robert H.; Keating, Gerald M.

1998-01-01

The success of aerobraking by the Mars Global Surveyor (MGS) spacecraft was partly due to the analysis of MGS accelerometer data. Accelerometer data was used to determine the effect of the atmosphere on each orbit, to characterize the nature of the atmosphere, and to predict the atmosphere for future orbits. To interpret the accelerometer data, a data reduction procedure was developed to produce density estimations utilizing inputs from the spacecraft, the Navigation Team, and pre-mission aerothermodynamic studies. This data reduction procedure was based on the calculation of aerodynamic forces from the accelerometer data by considering acceleration due to gravity gradient, solar pressure, angular motion of the MGS, instrument bias, thruster activity, and a vibration component due to the motion of the damaged solar array. Methods were developed to calculate all of the acceleration components including a 4 degree of freedom dynamics model used to gain a greater understanding of the damaged solar array. The total error inherent to the data reduction procedure was calculated as a function of altitude and density considering contributions from ephemeris errors, errors in force coefficient, and instrument errors due to bias and digitization. Comparing the results from this procedure to the data of other MGS Teams has demonstrated that this procedure can quickly and accurately describe the density and vertical structure of the Martian upper atmosphere.

Laryngeal Force Sensor: Quantifying Extralaryngeal Complications after Suspension Microlaryngoscopy.

PubMed

Feng, Allen L; Song, Phillip C

2018-04-01

Objectives To develop a novel sensor capable of dynamically analyzing the force exerted during suspension microlaryngoscopy and to examine the relationship between force and postoperative tongue complications. Study Design Prospective observational study. Setting Academic tertiary care center. Methods The laryngeal force sensor is a designed for use during microphonosurgery. Prospectively enrolled patients completed pre- and postoperative surveys to assess the development of tongue-related symptoms (dysgeusia, pain, paresthesia, and paresis) or dysphagia (10-item Eating Assessment Tool [EAT-10]). To prevent operator bias, surgeons were blinded to the force recordings during surgery. Results Fifty-six patients completed the study. Of these, 20 (36%) developed postoperative tongue symptoms, and 12 (21%) had abnormal EAT-10 scores. The mean maximum force across all procedures was 164.7 N (95% CI, 141.0-188.4; range, 48.5-402.6), while the mean suspension time was 34.3 minutes (95% CI, 27.4-41.2; range, 7.1-108.1). Multiple logistic regression showed maximum force (odds ratio, 1.15; 95% CI, 1.02-1.29; P = .019) and female sex (30.1%; 95% CI, 22.7%-37.5%; P < .001) as significant predictors for the development of tongue-related symptoms. The only significant predictor of an abnormal postoperative EAT-10 score was an increased maximum force (odds ratio, 1.03; 95% CI, 1.00-1.06; P = .045). Conclusions The laryngeal force sensor is capable of providing dynamic force measurements throughout suspension microlaryngoscopy. An increase in maximum force during surgery may be a significant predictor for the development of tongue-related symptoms and an abnormal EAT-10 score. Female patients may also be at greater risk for developing postoperative tongue symptoms.

Use of the forced-oscillation technique to estimate spirometry values.

PubMed

Yamamoto, Shoichiro; Miyoshi, Seigo; Katayama, Hitoshi; Okazaki, Mikio; Shigematsu, Hisayuki; Sano, Yoshifumi; Matsubara, Minoru; Hamaguchi, Naohiko; Okura, Takafumi; Higaki, Jitsuo

2017-01-01

Spirometry is sometimes difficult to perform in elderly patients and in those with severe respiratory distress. The forced-oscillation technique (FOT) is a simple and noninvasive method of measuring respiratory impedance. The aim of this study was to determine if FOT data reflect spirometric indices. Patients underwent both FOT and spirometry procedures prior to inclusion in development (n=1,089) and validation (n=552) studies. Multivariate linear regression analysis was performed to identify FOT parameters predictive of vital capacity (VC), forced VC (FVC), and forced expiratory volume in 1 second (FEV 1 ). A regression equation was used to calculate estimated VC, FVC, and FEV 1 . We then determined whether the estimated data reflected spirometric indices. Agreement between actual and estimated spirometry data was assessed by Bland-Altman analysis. Significant correlations were observed between actual and estimated VC, FVC, and FEV 1 values (all r >0.8 and P <0.001). These results were deemed robust by a separate validation study (all r >0.8 and P <0.001). Bias between the actual data and estimated data for VC, FVC, and FEV 1 in the development study was 0.007 L (95% limits of agreement [LOA] 0.907 and -0.893 L), -0.064 L (95% LOA 0.843 and -0.971 L), and -0.039 L (95% LOA 0.735 and -0.814 L), respectively. On the other hand, bias between the actual data and estimated data for VC, FVC, and FEV 1 in the validation study was -0.201 L (95% LOA 0.62 and -1.022 L), -0.262 L (95% LOA 0.582 and -1.106 L), and -0.174 L (95% LOA 0.576 and -0.923 L), respectively, suggesting that the estimated data in the validation study did not have high accuracy. Further studies are needed to generate more accurate regression equations for spirometric indices based on FOT measurements.

A simple and effective solution to the constrained QM/MM simulations

NASA Astrophysics Data System (ADS)

Takahashi, Hideaki; Kambe, Hiroyuki; Morita, Akihiro

2018-04-01

It is a promising extension of the quantum mechanical/molecular mechanical (QM/MM) approach to incorporate the solvent molecules surrounding the QM solute into the QM region to ensure the adequate description of the electronic polarization of the solute. However, the solvent molecules in the QM region inevitably diffuse into the MM bulk during the QM/MM simulation. In this article, we developed a simple and efficient method, referred to as the "boundary constraint with correction (BCC)," to prevent the diffusion of the solvent water molecules by means of a constraint potential. The point of the BCC method is to compensate the error in a statistical property due to the bias potential by adding a correction term obtained through a set of QM/MM simulations. The BCC method is designed so that the effect of the bias potential completely vanishes when the QM solvent is identical with the MM solvent. Furthermore, the desirable conditions, that is, the continuities of energy and force and the conservations of energy and momentum, are fulfilled in principle. We applied the QM/MM-BCC method to a hydronium ion(H3O+) in aqueous solution to construct the radial distribution function (RDF) of the solvent around the solute. It was demonstrated that the correction term fairly compensated the error and led the RDF in good agreement with the result given by an ab initio molecular dynamics simulation.

Seal for fluid forming tools

DOEpatents

Golovashchenko, Sergey Fedorovich [Beverly Hills, MI; Bonnen, John Joseph Francis [Milford, MI

2012-03-20

An electro-hydraulic forming tool for forming a sheet metal blank in a one-sided die has first and second rigid rings that engage opposite sides of a sheet metal blank. The rigid rings are contained within slots on a die portion and a hydraulic force applicator portion of the forming tool. The seals are either resiliently biased by an elastomeric member or inherently resiliently biased into contact with the blank.

Improving US Theater Nuclear Doctrine. A Critical Analysis,

DTIC Science & Technology

1983-01-01

the Armed Forces Staff College. In addition to these monographs, the NDU Press publishes the National Security Essay Series, books , issue pa- pers... secondhand or thirdhand. He then lacks responsiveness to deal with changes there. 11 US Doctrine Has a Defensive Bias. The defensive bias of US nuclear...security. The research results, normally published in monographs, issue papers, or books , are made available to cognizant Government officials and

RACORO Continental Boundary Layer Cloud Investigations: 3. Separation of Parameterization Biases in Single-Column Model CAM5 Simulations of Shallow Cumulus

NASA Technical Reports Server (NTRS)

Lin, Wuyin; Liu, Yangang; Vogelmann, Andrew M.; Fridlind, Ann; Endo, Satoshi; Song, Hua; Feng, Sha; Toto, Tami; Li, Zhijin; Zhang, Minghua

2015-01-01

Climatically important low-level clouds are commonly misrepresented in climate models. The FAst-physics System TEstbed and Research (FASTER) Project has constructed case studies from the Atmospheric Radiation Measurement Climate Research Facility's Southern Great Plain site during the RACORO aircraft campaign to facilitate research on model representation of boundary-layer clouds. This paper focuses on using the single-column Community Atmosphere Model version 5 (SCAM5) simulations of a multi-day continental shallow cumulus case to identify specific parameterization causes of low-cloud biases. Consistent model biases among the simulations driven by a set of alternative forcings suggest that uncertainty in the forcing plays only a relatively minor role. In-depth analysis reveals that the model's shallow cumulus convection scheme tends to significantly under-produce clouds during the times when shallow cumuli exist in the observations, while the deep convective and stratiform cloud schemes significantly over-produce low-level clouds throughout the day. The links between model biases and the underlying assumptions of the shallow cumulus scheme are further diagnosed with the aid of large-eddy simulations and aircraft measurements, and by suppressing the triggering of the deep convection scheme. It is found that the weak boundary layer turbulence simulated is directly responsible for the weak cumulus activity and the simulated boundary layer stratiform clouds. Increased vertical and temporal resolutions are shown to lead to stronger boundary layer turbulence and reduction of low-cloud biases.

RACORO continental boundary layer cloud investigations. 3. Separation of parameterization biases in single-column model CAM5 simulations of shallow cumulus

DOE PAGES

Lin, Wuyin; Liu, Yangang; Vogelmann, Andrew M.; ...

2015-06-19

Climatically important low-level clouds are commonly misrepresented in climate models. The FAst-physics System TEstbed and Research (FASTER) project has constructed case studies from the Atmospheric Radiation Measurement (ARM) Climate Research Facility's Southern Great Plain site during the RACORO aircraft campaign to facilitate research on model representation of boundary-layer clouds. This paper focuses on using the single-column Community Atmosphere Model version 5 (SCAM5) simulations of a multi-day continental shallow cumulus case to identify specific parameterization causes of low-cloud biases. Consistent model biases among the simulations driven by a set of alternative forcings suggest that uncertainty in the forcing plays only amore » relatively minor role. In-depth analysis reveals that the model's shallow cumulus convection scheme tends to significantly under-produce clouds during the times when shallow cumuli exist in the observations, while the deep convective and stratiform cloud schemes significantly over-produce low-level clouds throughout the day. The links between model biases and the underlying assumptions of the shallow cumulus scheme are further diagnosed with the aid of large-eddy simulations and aircraft measurements, and by suppressing the triggering of the deep convection scheme. It is found that the weak boundary layer turbulence simulated is directly responsible for the weak cumulus activity and the simulated boundary layer stratiform clouds. Increased vertical and temporal resolutions are shown to lead to stronger boundary layer turbulence and reduction of low-cloud biases.« less

Optimal updating magnitude in adaptive flat-distribution sampling

NASA Astrophysics Data System (ADS)

Zhang, Cheng; Drake, Justin A.; Ma, Jianpeng; Pettitt, B. Montgomery

2017-11-01

We present a study on the optimization of the updating magnitude for a class of free energy methods based on flat-distribution sampling, including the Wang-Landau (WL) algorithm and metadynamics. These methods rely on adaptive construction of a bias potential that offsets the potential of mean force by histogram-based updates. The convergence of the bias potential can be improved by decreasing the updating magnitude with an optimal schedule. We show that while the asymptotically optimal schedule for the single-bin updating scheme (commonly used in the WL algorithm) is given by the known inverse-time formula, that for the Gaussian updating scheme (commonly used in metadynamics) is often more complex. We further show that the single-bin updating scheme is optimal for very long simulations, and it can be generalized to a class of bandpass updating schemes that are similarly optimal. These bandpass updating schemes target only a few long-range distribution modes and their optimal schedule is also given by the inverse-time formula. Constructed from orthogonal polynomials, the bandpass updating schemes generalize the WL and Langfeld-Lucini-Rago algorithms as an automatic parameter tuning scheme for umbrella sampling.

Optimal updating magnitude in adaptive flat-distribution sampling.

PubMed

Zhang, Cheng; Drake, Justin A; Ma, Jianpeng; Pettitt, B Montgomery

2017-11-07

We present a study on the optimization of the updating magnitude for a class of free energy methods based on flat-distribution sampling, including the Wang-Landau (WL) algorithm and metadynamics. These methods rely on adaptive construction of a bias potential that offsets the potential of mean force by histogram-based updates. The convergence of the bias potential can be improved by decreasing the updating magnitude with an optimal schedule. We show that while the asymptotically optimal schedule for the single-bin updating scheme (commonly used in the WL algorithm) is given by the known inverse-time formula, that for the Gaussian updating scheme (commonly used in metadynamics) is often more complex. We further show that the single-bin updating scheme is optimal for very long simulations, and it can be generalized to a class of bandpass updating schemes that are similarly optimal. These bandpass updating schemes target only a few long-range distribution modes and their optimal schedule is also given by the inverse-time formula. Constructed from orthogonal polynomials, the bandpass updating schemes generalize the WL and Langfeld-Lucini-Rago algorithms as an automatic parameter tuning scheme for umbrella sampling.

System Dynamic Analysis of a Wind Tunnel Model with Applications to Improve Aerodynamic Data Quality

NASA Technical Reports Server (NTRS)

Buehrle, Ralph David

1997-01-01

The research investigates the effect of wind tunnel model system dynamics on measured aerodynamic data. During wind tunnel tests designed to obtain lift and drag data, the required aerodynamic measurements are the steady-state balance forces and moments, pressures, and model attitude. However, the wind tunnel model system can be subjected to unsteady aerodynamic and inertial loads which result in oscillatory translations and angular rotations. The steady-state force balance and inertial model attitude measurements are obtained by filtering and averaging data taken during conditions of high model vibrations. The main goals of this research are to characterize the effects of model system dynamics on the measured steady-state aerodynamic data and develop a correction technique to compensate for dynamically induced errors. Equations of motion are formulated for the dynamic response of the model system subjected to arbitrary aerodynamic and inertial inputs. The resulting modal model is examined to study the effects of the model system dynamic response on the aerodynamic data. In particular, the equations of motion are used to describe the effect of dynamics on the inertial model attitude, or angle of attack, measurement system that is used routinely at the NASA Langley Research Center and other wind tunnel facilities throughout the world. This activity was prompted by the inertial model attitude sensor response observed during high levels of model vibration while testing in the National Transonic Facility at the NASA Langley Research Center. The inertial attitude sensor cannot distinguish between the gravitational acceleration and centrifugal accelerations associated with wind tunnel model system vibration, which results in a model attitude measurement bias error. Bias errors over an order of magnitude greater than the required device accuracy were found in the inertial model attitude measurements during dynamic testing of two model systems. Based on a theoretical modal approach, a method using measured vibration amplitudes and measured or calculated modal characteristics of the model system is developed to correct for dynamic bias errors in the model attitude measurements. The correction method is verified through dynamic response tests on two model systems and actual wind tunnel test data.

Assimilation of ASCAT near-surface soil moisture into the French SIM hydrological model

NASA Astrophysics Data System (ADS)

Draper, C.; Mahfouf, J.-F.; Calvet, J.-C.; Martin, E.; Wagner, W.

2011-06-01

The impact of assimilating near-surface soil moisture into the SAFRAN-ISBA-MODCOU (SIM) hydrological model over France is examined. Specifically, the root-zone soil moisture in the ISBA land surface model is constrained over three and a half years, by assimilating the ASCAT-derived surface degree of saturation product, using a Simplified Extended Kalman Filter. In this experiment ISBA is forced with the near-real time SAFRAN analysis, which analyses the variables required to force ISBA from relevant observations available before the real time data cut-off. The assimilation results are tested against ISBA forecasts generated with a higher quality delayed cut-off SAFRAN analysis. Ideally, assimilating the ASCAT data will constrain the ISBA surface state to correct for errors in the near-real time SAFRAN forcing, the most significant of which was a substantial dry bias caused by a dry precipitation bias. The assimilation successfully reduced the mean root-zone soil moisture bias, relative to the delayed cut-off forecasts, by close to 50 % of the open-loop value. The improved soil moisture in the model then led to significant improvements in the forecast hydrological cycle, reducing the drainage, runoff, and evapotranspiration biases (by 17 %, 11 %, and 70 %, respectively). When coupled to the MODCOU hydrogeological model, the ASCAT assimilation also led to improved streamflow forecasts, increasing the mean discharge ratio, relative to the delayed cut off forecasts, from 0.68 to 0.76. These results demonstrate that assimilating near-surface soil moisture observations can effectively constrain the SIM model hydrology, while also confirming the accuracy of the ASCAT surface degree of saturation product. This latter point highlights how assimilation experiments can contribute towards the difficult issue of validating remotely sensed land surface observations over large spatial scales.

Evaluation of high-level clouds in cloud resolving model simulations with ARM and KWAJEX observations

DOE PAGES

Liu, Zheng; Muhlbauer, Andreas; Ackerman, Thomas

2015-11-05

In this paper, we evaluate high-level clouds in a cloud resolving model during two convective cases, ARM9707 and KWAJEX. The simulated joint histograms of cloud occurrence and radar reflectivity compare well with cloud radar and satellite observations when using a two-moment microphysics scheme. However, simulations performed with a single moment microphysical scheme exhibit low biases of approximately 20 dB. During convective events, two-moment microphysical overestimate the amount of high-level cloud and one-moment microphysics precipitate too readily and underestimate the amount and height of high-level cloud. For ARM9707, persistent large positive biases in high-level cloud are found, which are not sensitivemore » to changes in ice particle fall velocity and ice nuclei number concentration in the two-moment microphysics. These biases are caused by biases in large-scale forcing and maintained by the periodic lateral boundary conditions. The combined effects include significant biases in high-level cloud amount, radiation, and high sensitivity of cloud amount to nudging time scale in both convective cases. The high sensitivity of high-level cloud amount to the thermodynamic nudging time scale suggests that thermodynamic nudging can be a powerful ‘‘tuning’’ parameter for the simulated cloud and radiation but should be applied with caution. The role of the periodic lateral boundary conditions in reinforcing the biases in cloud and radiation suggests that reducing the uncertainty in the large-scale forcing in high levels is important for similar convective cases and has far reaching implications for simulating high-level clouds in super-parameterized global climate models such as the multiscale modeling framework.« less

How does dynamical downscaling affect model biases and future projections of explosive extratropical cyclones along North America's Atlantic coast?

NASA Astrophysics Data System (ADS)

Seiler, C.; Zwiers, F. W.; Hodges, K. I.; Scinocca, J. F.

2018-01-01

Explosive extratropical cyclones (EETCs) are rapidly intensifying low pressure systems that generate severe weather along North America's Atlantic coast. Global climate models (GCMs) tend to simulate too few EETCs, perhaps partly due to their coarse horizontal resolution and poorly resolved moist diabatic processes. This study explores whether dynamical downscaling can reduce EETC frequency biases, and whether this affects future projections of storms along North America's Atlantic coast. A regional climate model (CanRCM4) is forced with the CanESM2 GCM for the periods 1981 to 2000 and 2081 to 2100. EETCs are tracked from relative vorticity using an objective feature tracking algorithm. CanESM2 simulates 38% fewer EETC tracks compared to reanalysis data, which is consistent with a negative Eady growth rate bias (-0.1 day^{-1}). Downscaling CanESM2 with CanRCM4 increases EETC frequency by one third, which reduces the frequency bias to -22%, and increases maximum EETC precipitation by 22%. Anthropogenic greenhouse gas forcing is projected to decrease EETC frequency (-15%, -18%) and Eady growth rate (-0.2 day^{-1}, -0.2 day^{-1}), and increase maximum EETC precipitation (46%, 52%) in CanESM2 and CanRCM4, respectively. The limited effect of dynamical downscaling on EETC frequency projections is consistent with the lack of impact on the maximum Eady growth rate. The coarse spatial resolution of GCMs presents an important limitation for simulating extreme ETCs, but Eady growth rate biases are likely just as relevant. Further bias reductions could be achieved by addressing processes that lead to an underestimation of lower tropospheric meridional temperature gradients.

Representativeness of wind measurements in moderately complex terrain

NASA Astrophysics Data System (ADS)

van den Bossche, Michael; De Wekker, Stephan F. J.

2018-02-01

We investigated the representativeness of 10-m wind measurements in a 4 km × 2 km area of modest relief by comparing observations at a central site with those at four satellite sites located in the same area. Using a combination of established and new methods to quantify and visualize representativeness, we found significant differences in wind speed and direction between the four satellite sites and the central site. The representativeness of the central site wind measurements depended strongly on surface wind speed and direction, and atmospheric stability. Through closer inspection of the observations at one of the satellite sites, we concluded that terrain-forced flows combined with thermally driven downslope winds caused large biases in wind direction and speed. We used these biases to generate a basic model, showing that terrain-related differences in wind observations can to a large extent be predicted. Such a model is a cost-effective way to enhance an area's wind field determination and to improve the outcome of pollutant dispersion and weather forecasting models.

Aligning Spinoza with Descartes: An informed Cartesian account of the truth bias.

PubMed

Street, Chris N H; Kingstone, Alan

2017-08-01

There is a bias towards believing information is true rather than false. The Spinozan account claims there is an early, automatic bias towards believing. Only afterwards can people engage in an effortful re-evaluation and disbelieve the information. Supporting this account, there is a greater bias towards believing information is true when under cognitive load. However, developing on the Adaptive Lie Detector (ALIED) theory, the informed Cartesian can equally explain this data. The account claims the bias under load is not evidence of automatic belief; rather, people are undecided, but if forced to guess they can rely on context information to make an informed judgement. The account predicts, and we found, that if people can explicitly indicate their uncertainty, there should be no bias towards believing because they are no longer required to guess. Thus, we conclude that belief formation can be better explained by an informed Cartesian account - an attempt to make an informed judgment under uncertainty. © 2016 The British Psychological Society.

A query theory account of the effect of memory retrieval on the sunk cost bias.

PubMed

Ting, Hsuchi; Wallsten, Thomas S

2011-08-01

The sunk cost bias occurs when individuals continue to invest in the same option when better alternatives are available. Many researchers believe that this bias is due to overemphasizing the past investment over the (missed) opportunities offered by alternatives. As an alternative or complement to this view, we show that memory retrieval and attention play important roles in the sunk cost bias. In two experiments, individuals generated more reasons for pursuing the invested option than for an alternative; they generated those reasons earlier in a sequence of reasons; and these effects increased as the individuals made progress toward attaining the reward yielded by the invested option. Associated with these effects, individuals perceived an increasingly wide gap in value between the invested and alternative options as they progressed toward the goal, thereby creating the sunk cost bias. Forcing individuals to reverse the order in which they generated reasons for the invested and alternative options reduced the bias. [corrected

Individual Biases, Cultural Evolution, and the Statistical Nature of Language Universals: The Case of Colour Naming Systems

PubMed Central

Baronchelli, Andrea; Loreto, Vittorio; Puglisi, Andrea

2015-01-01

Language universals have long been attributed to an innate Universal Grammar. An alternative explanation states that linguistic universals emerged independently in every language in response to shared cognitive or perceptual biases. A computational model has recently shown how this could be the case, focusing on the paradigmatic example of the universal properties of colour naming patterns, and producing results in quantitative agreement with the experimental data. Here we investigate the role of an individual perceptual bias in the framework of the model. We study how, and to what extent, the structure of the bias influences the corresponding linguistic universal patterns. We show that the cultural history of a group of speakers introduces population-specific constraints that act against the pressure for uniformity arising from the individual bias, and we clarify the interplay between these two forces. PMID:26018391

The Impact of Parameterized Convection on Climatological Precipitation in Atmospheric Global Climate Models

NASA Astrophysics Data System (ADS)

Maher, Penelope; Vallis, Geoffrey K.; Sherwood, Steven C.; Webb, Mark J.; Sansom, Philip G.

2018-04-01

Convective parameterizations are widely believed to be essential for realistic simulations of the atmosphere. However, their deficiencies also result in model biases. The role of convection schemes in modern atmospheric models is examined using Selected Process On/Off Klima Intercomparison Experiment simulations without parameterized convection and forced with observed sea surface temperatures. Convection schemes are not required for reasonable climatological precipitation. However, they are essential for reasonable daily precipitation and constraining extreme daily precipitation that otherwise develops. Systematic effects on lapse rate and humidity are likewise modest compared with the intermodel spread. Without parameterized convection Kelvin waves are more realistic. An unexpectedly large moist Southern Hemisphere storm track bias is identified. This storm track bias persists without convection schemes, as does the double Intertropical Convergence Zone and excessive ocean precipitation biases. This suggests that model biases originate from processes other than convection or that convection schemes are missing key processes.

Exploring RNA structure and dynamics through enhanced sampling simulations.

PubMed

Mlýnský, Vojtěch; Bussi, Giovanni

2018-04-01

RNA function is intimately related to its structural dynamics. Molecular dynamics simulations are useful for exploring biomolecular flexibility but are severely limited by the accessible timescale. Enhanced sampling methods allow this timescale to be effectively extended in order to probe biologically relevant conformational changes and chemical reactions. Here, we review the role of enhanced sampling techniques in the study of RNA systems. We discuss the challenges and promises associated with the application of these methods to force-field validation, exploration of conformational landscapes and ion/ligand-RNA interactions, as well as catalytic pathways. Important technical aspects of these methods, such as the choice of the biased collective variables and the analysis of multi-replica simulations, are examined in detail. Finally, a perspective on the role of these methods in the characterization of RNA dynamics is provided. Copyright © 2018 Elsevier Ltd. All rights reserved.

Our Families, Our Children: The Lesbian and Gay Child Care Task Force Report on Quality Child Care.

ERIC Educational Resources Information Center

Dispenza, Mary

The Lesbian and Gay Child Care Task Force documented anecdotal evidence of homophobia in child care and school age communities, including: (1) refusal to accept children from lesbian, gay, bisexual, and transgender (LGBT) families into child care; (2) biased attitudes expressed to children when they speak about their families; and (3) demonstrated…

Good practices for quantitative bias analysis.

PubMed

Lash, Timothy L; Fox, Matthew P; MacLehose, Richard F; Maldonado, George; McCandless, Lawrence C; Greenland, Sander

2014-12-01

Quantitative bias analysis serves several objectives in epidemiological research. First, it provides a quantitative estimate of the direction, magnitude and uncertainty arising from systematic errors. Second, the acts of identifying sources of systematic error, writing down models to quantify them, assigning values to the bias parameters and interpreting the results combat the human tendency towards overconfidence in research results, syntheses and critiques and the inferences that rest upon them. Finally, by suggesting aspects that dominate uncertainty in a particular research result or topic area, bias analysis can guide efficient allocation of sparse research resources. The fundamental methods of bias analyses have been known for decades, and there have been calls for more widespread use for nearly as long. There was a time when some believed that bias analyses were rarely undertaken because the methods were not widely known and because automated computing tools were not readily available to implement the methods. These shortcomings have been largely resolved. We must, therefore, contemplate other barriers to implementation. One possibility is that practitioners avoid the analyses because they lack confidence in the practice of bias analysis. The purpose of this paper is therefore to describe what we view as good practices for applying quantitative bias analysis to epidemiological data, directed towards those familiar with the methods. We focus on answering questions often posed to those of us who advocate incorporation of bias analysis methods into teaching and research. These include the following. When is bias analysis practical and productive? How does one select the biases that ought to be addressed? How does one select a method to model biases? How does one assign values to the parameters of a bias model? How does one present and interpret a bias analysis?. We hope that our guide to good practices for conducting and presenting bias analyses will encourage more widespread use of bias analysis to estimate the potential magnitude and direction of biases, as well as the uncertainty in estimates potentially influenced by the biases. © The Author 2014; all rights reserved. Published by Oxford University Press on behalf of the International Epidemiological Association.

A new method to measure galaxy bias by combining the density and weak lensing fields

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

Pujol, Arnau; Chang, Chihway; Gaztañaga, Enrique

We present a new method to measure redshift-dependent galaxy bias by combining information from the galaxy density field and the weak lensing field. This method is based on the work of Amara et al., who use the galaxy density field to construct a bias-weighted convergence field κg. The main difference between Amara et al.'s work and our new implementation is that here we present another way to measure galaxy bias, using tomography instead of bias parametrizations. The correlation between κg and the true lensing field κ allows us to measure galaxy bias using different zero-lag correlations, such as / ormore » /. Our method measures the linear bias factor on linear scales, under the assumption of no stochasticity between galaxies and matter. We use the Marenostrum Institut de Ciències de l'Espai (MICE) simulation to measure the linear galaxy bias for a flux-limited sample (i < 22.5) in tomographic redshift bins using this method. This article is the first that studies the accuracy and systematic uncertainties associated with the implementation of the method and the regime in which it is consistent with the linear galaxy bias defined by projected two-point correlation functions (2PCF). We find that our method is consistent with a linear bias at the per cent level for scales larger than 30 arcmin, while non-linearities appear at smaller scales. This measurement is a good complement to other measurements of bias, since it does not depend strongly on σ8 as do the 2PCF measurements. We will apply this method to the Dark Energy Survey Science Verification data in a follow-up article.« less

An Evaluation of Attitude-Independent Magnetometer-Bias Determination Methods

NASA Technical Reports Server (NTRS)

Hashmall, J. A.; Deutschmann, Julie

1996-01-01

Although several algorithms now exist for determining three-axis magnetometer (TAM) biases without the use of attitude data, there are few studies on the effectiveness of these methods, especially in comparison with attitude dependent methods. This paper presents the results of a comparison of three attitude independent methods and an attitude dependent method for computing TAM biases. The comparisons are based on in-flight data from the Extreme Ultraviolet Explorer (EUVE), the Upper Atmosphere Research Satellite (UARS), and the Compton Gamma Ray Observatory (GRO). The effectiveness of an algorithm is measured by the accuracy of attitudes computed using biases determined with that algorithm. The attitude accuracies are determined by comparison with known, extremely accurate, star-tracker-based attitudes. In addition, the effect of knowledge of calibration parameters other than the biases on the effectiveness of all bias determination methods is examined.

Magnetic force driven magnetoelectric effect in bi-cantilever composites

NASA Astrophysics Data System (ADS)

Zhang, Ru; Wu, Gaojian; Zhang, Ning

2017-12-01

The magnetic force driven magnetoelectric (ME) effect in bi-cantilever Mn-Zn-Ferrite /PZT composites is presented. Compared with single cantilever, the ME voltage coefficient in bi-cantilever composite is a little lower and the resonance frequency is higher, but the bi-cantilever structure is advantageous for integration. When the magnetic gap is 3 mm, the ME voltage coefficient can achieve 6.2 Vcm-1Oe-1 at resonance under optimum bias field Hm=1030 Oe; when the magnetic gap is 1.5 mm, the ME voltage coefficient can get the value as high as 4.4 Vcm-1Oe-1 under much lower bias field H=340 Oe. The stable ME effect in bi-cantilever composites has important potential application in the design of new type ME device.

Improvement of suspended sediment concentration estimation for the Yarlung Zangbo river

NASA Astrophysics Data System (ADS)

Zeng, C.; Zhang, F.

2017-12-01

Suspended sediment load of a river represents integrated results of soil erosion, ecosystem variation and landform change occurring within basin over a specified period. Accurate estimation of suspended sediment concentration is important for calculating suspended sediment load, therefore is helpful for evaluating the impact of natural and anthropogenic factors on earth system processes under the background of global climate change. However, long-term observation of suspended sediment concentration usually very difficult in harsh condition areas e.g. rivers on the Tibet Plateau. This study proposed two sediment rating curve subdivision methods, the flood rank method and suspended sediment concentration stages method, to improve the estimations of daily suspended sediment concentration of the Yarlung Zangbo river during 2007 to 2009. The flood rank method, hypothesized that the higher water flow with larger erosive power can mobilize sediment sources not available during lower flows, suitable for application where sediments were mainly transported by first few flood events. The suspended sediment concentration stages method, assumed that precipitation is the dominating driving force of sediment erosion and transport processes during the flooding periods, suitable for application where soil erosion was closely related to precipitation events. Compared to traditional sediment rating curve and subdivision methods, results showed that the proposed methods can improve suspended sediment concentration and subsequent suspended sediment load estimations in the middle reach of the Yarlung Zangbo river with higher coefficients of determination (R2) and Nash-Sutcliffe efficiency coefficients (NSE), and yielded smaller bias (BIAS) and root-mean-square errors (RMSE). This study can provide guidelines for regional ecological and environmental management.

Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method.

PubMed

Molloy, Kevin; Shehu, Amarda

2013-01-01

Many proteins tune their biological function by transitioning between different functional states, effectively acting as dynamic molecular machines. Detailed structural characterization of transition trajectories is central to understanding the relationship between protein dynamics and function. Computational approaches that build on the Molecular Dynamics framework are in principle able to model transition trajectories at great detail but also at considerable computational cost. Methods that delay consideration of dynamics and focus instead on elucidating energetically-credible conformational paths connecting two functionally-relevant structures provide a complementary approach. Effective sampling-based path planning methods originating in robotics have been recently proposed to produce conformational paths. These methods largely model short peptides or address large proteins by simplifying conformational space. We propose a robotics-inspired method that connects two given structures of a protein by sampling conformational paths. The method focuses on small- to medium-size proteins, efficiently modeling structural deformations through the use of the molecular fragment replacement technique. In particular, the method grows a tree in conformational space rooted at the start structure, steering the tree to a goal region defined around the goal structure. We investigate various bias schemes over a progress coordinate for balance between coverage of conformational space and progress towards the goal. A geometric projection layer promotes path diversity. A reactive temperature scheme allows sampling of rare paths that cross energy barriers. Experiments are conducted on small- to medium-size proteins of length up to 214 amino acids and with multiple known functionally-relevant states, some of which are more than 13Å apart of each-other. Analysis reveals that the method effectively obtains conformational paths connecting structural states that are significantly different. A detailed analysis on the depth and breadth of the tree suggests that a soft global bias over the progress coordinate enhances sampling and results in higher path diversity. The explicit geometric projection layer that biases the exploration away from over-sampled regions further increases coverage, often improving proximity to the goal by forcing the exploration to find new paths. The reactive temperature scheme is shown effective in increasing path diversity, particularly in difficult structural transitions with known high-energy barriers.

The impact of emotion on perception: bias or enhanced processing?

PubMed

Zeelenberg, René; Wagenmakers, Eric-Jan; Rotteveel, Mark

2006-04-01

Recent studies have shown that emotionally significant stimuli are often better identified than neutral stimuli. It is not clear, however, whether these results are due to enhanced perceptual processing or to a bias favoring the identification of emotionally significant stimuli over neutral stimuli. The present study used a two-alternative forced-choice perceptual identification task to disentangle the effects of bias and enhanced processing. We found that emotionally significant targets were better identified than neutral targets. In contrast, the emotional significance of the foil alternative had no effect on performance. The present results support the hypothesis that perceptual encoding of emotionally significant stimuli is enhanced.

Size-dependent selective mechanisms on males and females and the evolution of sexual size dimorphism in frogs.

PubMed

Nali, Renato C; Zamudio, Kelly R; Haddad, Célio F B; Prado, Cynthia P A

2014-12-01

Sexual size dimorphism (SSD) varies in animals from male biased to female biased. The evolution of SSD is potentially influenced by a number of factors, such as territoriality, fecundity, and temporal breeding patterns (explosive vs. prolonged). In general, frogs show female-biased SSD with broad variance among species. Using comparative methods, we examine how different selective forces affect male and female sizes, and we test hypotheses about size-dependent mechanisms shaping SSD in frogs. Male size was weakly associated with SSD in all size classes, and we found no significant association among SSD, male size, temporal breeding pattern, and male territoriality. In contrast, female size best explained SSD variation across all size classes but especially for small-bodied species. We found a stronger evolutionary association between female body size and fecundity, and this fecundity advantage was highest in explosively breeding species. Our data indicate that the fecundity advantage associated with female body size may not be linear, such that intermediate and large females benefit less with body size increases. Therefore, size-dependent selection in females associated with fecundity and breeding patterns is an important mechanism driving SSD evolution in frogs. Our study underscores the fact that lineage-specific ecology and behavior should be incorporated in comparative analyses of animal SSD.

Intercomparison of shortwave radiative transfer schemes in global aerosol modeling: results from the AeroCom Radiative Transfer Experiment

NASA Astrophysics Data System (ADS)

Randles, C. A.; Kinne, S.; Myhre, G.; Schulz, M.; Stier, P.; Fischer, J.; Doppler, L.; Highwood, E.; Ryder, C.; Harris, B.; Huttunen, J.; Ma, Y.; Pinker, R. T.; Mayer, B.; Neubauer, D.; Hitzenberger, R.; Oreopoulos, L.; Lee, D.; Pitari, G.; Di Genova, G.; Quaas, J.; Rose, Fred G.; Kato, S.; Rumbold, S. T.; Vardavas, I.; Hatzianastassiou, N.; Matsoukas, C.; Yu, H.; Zhang, F.; Zhang, H.; Lu, P.

2012-12-01

In this study we examine the performance of 31 global model radiative transfer schemes in cloud-free conditions with prescribed gaseous absorbers and no aerosols (Rayleigh atmosphere), with prescribed scattering-only aerosols, and with more absorbing aerosols. Results are compared to benchmark results from high-resolution, multi-angular line-by-line radiation models. For purely scattering aerosols, model bias relative to the line-by-line models in the top-of-the atmosphere aerosol radiative forcing ranges from roughly -10 to 20%, with over- and underestimates of radiative cooling at higher and lower sun elevation, respectively. Inter-model diversity (relative standard deviation) increases from ~10 to 15% as sun elevation increases. Inter-model diversity in atmospheric and surface forcing decreases with increased aerosol absorption, indicating that the treatment of multiple-scattering is more variable than aerosol absorption in the models considered. Aerosol radiative forcing results from multi-stream models are generally in better agreement with the line-by-line results than the simpler two-stream schemes. Considering radiative fluxes, model performance is generally the same or slightly better than results from previous radiation scheme intercomparisons. However, the inter-model diversity in aerosol radiative forcing remains large, primarily as a result of the treatment of multiple-scattering. Results indicate that global models that estimate aerosol radiative forcing with two-stream radiation schemes may be subject to persistent biases introduced by these schemes, particularly for regional aerosol forcing.

Intercomparison of shortwave radiative transfer schemes in global aerosol modeling: results from the AeroCom Radiative Transfer Experiment

NASA Astrophysics Data System (ADS)

Randles, C. A.; Kinne, S.; Myhre, G.; Schulz, M.; Stier, P.; Fischer, J.; Doppler, L.; Highwood, E.; Ryder, C.; Harris, B.; Huttunen, J.; Ma, Y.; Pinker, R. T.; Mayer, B.; Neubauer, D.; Hitzenberger, R.; Oreopoulos, L.; Lee, D.; Pitari, G.; Di Genova, G.; Quaas, J.; Rose, F. G.; Kato, S.; Rumbold, S. T.; Vardavas, I.; Hatzianastassiou, N.; Matsoukas, C.; Yu, H.; Zhang, F.; Zhang, H.; Lu, P.

2013-03-01

In this study we examine the performance of 31 global model radiative transfer schemes in cloud-free conditions with prescribed gaseous absorbers and no aerosols (Rayleigh atmosphere), with prescribed scattering-only aerosols, and with more absorbing aerosols. Results are compared to benchmark results from high-resolution, multi-angular line-by-line radiation models. For purely scattering aerosols, model bias relative to the line-by-line models in the top-of-the atmosphere aerosol radiative forcing ranges from roughly -10 to 20%, with over- and underestimates of radiative cooling at lower and higher solar zenith angle, respectively. Inter-model diversity (relative standard deviation) increases from ~10 to 15% as solar zenith angle decreases. Inter-model diversity in atmospheric and surface forcing decreases with increased aerosol absorption, indicating that the treatment of multiple-scattering is more variable than aerosol absorption in the models considered. Aerosol radiative forcing results from multi-stream models are generally in better agreement with the line-by-line results than the simpler two-stream schemes. Considering radiative fluxes, model performance is generally the same or slightly better than results from previous radiation scheme intercomparisons. However, the inter-model diversity in aerosol radiative forcing remains large, primarily as a result of the treatment of multiple-scattering. Results indicate that global models that estimate aerosol radiative forcing with two-stream radiation schemes may be subject to persistent biases introduced by these schemes, particularly for regional aerosol forcing.

A new insight into diffusional escape from a biased cylindrical trap

NASA Astrophysics Data System (ADS)

Berezhkovskii, Alexander M.; Dagdug, Leonardo; Bezrukov, Sergey M.

2017-09-01

Recent experiments with single biological nanopores, as well as single-molecule fluorescence spectroscopy and pulling studies of protein and nucleic acid folding raised a number of questions that stimulated theoretical and computational investigations of barrier crossing dynamics. The present paper addresses a closely related problem focusing on trajectories of Brownian particles that escape from a cylindrical trap in the presence of a force F parallel to the cylinder axis. To gain new insights into the escape dynamics, we analyze the "fine structure" of these trajectories. Specifically, we divide trajectories into two segments: a looping segment, when a particle unsuccessfully tries to escape returning to the trap bottom again and again, and a direct-transit segment, when it finally escapes moving without touching the bottom. Analytical expressions are derived for the Laplace transforms of the probability densities of the durations of the two segments. These expressions are used to find the mean looping and direct-transit times as functions of the biasing force F. It turns out that the force-dependences of the two mean times are qualitatively different. The mean looping time monotonically increases as F decreases, approaching exponential F-dependence at large negative forces pushing the particle towards the trap bottom. In contrast to this intuitively appealing behavior, the mean direct-transit time shows rather counterintuitive behavior: it decreases as the force magnitude, |F|, increases independently of whether the force pushes the particles to the trap bottom or to the exit from the trap, having a maximum at F = 0.

Reproducibility of precipitation distributions over extratropical continental regions in the CMIP5

NASA Astrophysics Data System (ADS)

Hirota, Nagio; Takayabu, Yukari

2013-04-01

Reproducibility of precipitation distributions over extratropical continental regions in the CMIP5 Nagio Hirota1,2 and Yukari N. Takayabu2 (1) National Institute of Polar Research (NIPR) (2) Atmosphere and Ocean Research Institute (AORI), the University of Tokyo Reproducibility of precipitation distributions over extratropical continental regions by CMIP5 climate models in their historical runs are evaluated, in comparison with GPCP(V2.2), CMAP(V0911), daily gridded gauge data APHRODITE. Surface temperature, cloud radiative forcing, and atmospheric circulations are also compared with observations of CRU-UEA, CERES, and ERA-interim/ERA40/JRA reanalysis data. It is shown that many CMIP5 models underestimate and overestimate summer precipitation over West and East Eurasia, respectively. These precipitation biases correspond to moisture transport associated with a cyclonic circulation bias over the whole continent of Eurasia. Meanwhile, many models underestimate cloud over the Eurasian continent, and associated shortwave cloud radiative forcing result in a significant warm bias. Evaporation feedback amplify the warm bias over West Eurasia. These processes consistently explain the precipitation biases over the Erasian continent in summer. We also examined reproducibility of winter precipitation, but robust results are not obtained yet due to the large uncertainty in observation associated with the adjustment of snow measurement in windy condition. Better observational data sets are necessary for further model validation. Acknowledgment: This study is supported by the PMM RA of JAXA, Green Network of Excellence (GRENE) Program by the Ministry of Education, Culture, Sports, Science and Technology, Japan, and Environment Research and Technology Development Fund (A-1201) of the Ministry of the Environment, Japan.

On the impact of the resolution on the surface and subsurface Eastern Tropical Atlantic warm bias

NASA Astrophysics Data System (ADS)

Martín-Rey, Marta; Lazar, Alban

2016-04-01

The tropical variability has a great importance for the climate of adjacent areas. Its sea surface temperature anomalies (SSTA) affect in particular the Brazilian Nordeste and the Sahelian region, as well as the tropical Pacific or the Euro-Atlantic sector. Nevertheless, the state-of the art climate models exhibits very large systematic errors in reproducing the seasonal cycle and inter-annual variability in the equatorial and coastal Africa upwelling zones (up to several °C for SST). Theses biases exist already, in smaller proportions though, in forced ocean models (several 1/10th of °C), and affect not only the mixed layer but also the whole thermocline. Here, we present an analysis of the impact of horizontal and vertical resolution changes on these biases. Three different DRAKKAR NEMO OGCM simulations have been analysed, associated to the same forcing set (DFS4.4) with different grid resolutions: "REF" for reference (1/4°, 46 vertical levels), "HH" with a finer horizontal grid (1/12°, 46 v.l.) and "HV" with a finer vertical grid (1/4°, 75 v.l.). At the surface, a more realistic seasonal SST cycle is produced in HH in the three upwellings, where the warm bias decreases (by 10% - 20%) during boreal spring and summer. A notable result is that increasing vertical resolution in HV causes a shift (in advance) of the upwelling SST seasonal cycles. In order to better understand these results, we estimate the three upwelling subsurface temperature errors, using various in-situ datasets, and provide thus a three-dimensional view of the biases.

Adjusting for partial verification or workup bias in meta-analyses of diagnostic accuracy studies.

PubMed

de Groot, Joris A H; Dendukuri, Nandini; Janssen, Kristel J M; Reitsma, Johannes B; Brophy, James; Joseph, Lawrence; Bossuyt, Patrick M M; Moons, Karel G M

2012-04-15

A key requirement in the design of diagnostic accuracy studies is that all study participants receive both the test under evaluation and the reference standard test. For a variety of practical and ethical reasons, sometimes only a proportion of patients receive the reference standard, which can bias the accuracy estimates. Numerous methods have been described for correcting this partial verification bias or workup bias in individual studies. In this article, the authors describe a Bayesian method for obtaining adjusted results from a diagnostic meta-analysis when partial verification or workup bias is present in a subset of the primary studies. The method corrects for verification bias without having to exclude primary studies with verification bias, thus preserving the main advantages of a meta-analysis: increased precision and better generalizability. The results of this method are compared with the existing methods for dealing with verification bias in diagnostic meta-analyses. For illustration, the authors use empirical data from a systematic review of studies of the accuracy of the immunohistochemistry test for diagnosis of human epidermal growth factor receptor 2 status in breast cancer patients.

A universal approach to determine footfall timings from kinematics of a single foot marker in hoofed animals

PubMed Central

Clayton, Hilary M.

2015-01-01

The study of animal movement commonly requires the segmentation of continuous data streams into individual strides. The use of forceplates and foot-mounted accelerometers readily allows the detection of the foot-on and foot-off events that define a stride. However, when relying on optical methods such as motion capture, there is lack of validated robust, universally applicable stride event detection methods. To date, no method has been validated for movement on a circle, while algorithms are commonly specific to front/hind limbs or gait. In this study, we aimed to develop and validate kinematic stride segmentation methods applicable to movement on straight line and circle at walk and trot, which exclusively rely on a single, dorsal hoof marker. The advantage of such marker placement is the robustness to marker loss and occlusion. Eight horses walked and trotted on a straight line and in a circle over an array of multiple forceplates. Kinetic events were detected based on the vertical force profile and used as the reference values. Kinematic events were detected based on displacement, velocity or acceleration signals of the dorsal hoof marker depending on the algorithm using (i) defined thresholds associated with derived movement signals and (ii) specific events in the derived movement signals. Method comparison was performed by calculating limits of agreement, accuracy, between-horse precision and within-horse precision based on differences between kinetic and kinematic event. In addition, we examined the effect of force thresholds ranging from 50 to 150 N on the timings of kinetic events. The two approaches resulted in very good and comparable performance: of the 3,074 processed footfall events, 95% of individual foot on and foot off events differed by no more than 26 ms from the kinetic event, with average accuracy between −11 and 10 ms and average within- and between horse precision ≤8 ms. While the event-based method may be less likely to suffer from scaling effects, on soft ground the threshold-based method may prove more valuable. While we found that use of velocity thresholds for foot on detection results in biased event estimates for the foot on the inside of the circle at trot, adjusting thresholds for this condition negated the effect. For the final four algorithms, we found no noteworthy bias between conditions or between front- and hind-foot timings. Different force thresholds in the range of 50 to 150 N had the greatest systematic effect on foot-off estimates in the hind limbs (up to on average 16 ms per condition), being greater than the effect on foot-on estimates or foot-off estimates in the forelimbs (up to on average ±7 ms per condition). PMID:26157641

Investigating the Stability of Four Methods for Estimating Item Bias.

ERIC Educational Resources Information Center

Perlman, Carole L.; And Others

The reliability of item bias estimates was studied for four methods: (1) the transformed delta method; (2) Shepard's modified delta method; (3) Rasch's one-parameter residual analysis; and (4) the Mantel-Haenszel procedure. Bias statistics were computed for each sample using all methods. Data were from administration of multiple-choice items from…

Estimation of the uncertainty of a climate model using an ensemble simulation

NASA Astrophysics Data System (ADS)

Barth, A.; Mathiot, P.; Goosse, H.

2012-04-01

The atmospheric forcings play an important role in the study of the ocean and sea-ice dynamics of the Southern Ocean. Error in the atmospheric forcings will inevitably result in uncertain model results. The sensitivity of the model results to errors in the atmospheric forcings are studied with ensemble simulations using multivariate perturbations of the atmospheric forcing fields. The numerical ocean model used is the NEMO-LIM in a global configuration with an horizontal resolution of 2°. NCEP reanalyses are used to provide air temperature and wind data to force the ocean model over the last 50 years. A climatological mean is used to prescribe relative humidity, cloud cover and precipitation. In a first step, the model results is compared with OSTIA SST and OSI SAF sea ice concentration of the southern hemisphere. The seasonal behavior of the RMS difference and bias in SST and ice concentration is highlighted as well as the regions with relatively high RMS errors and biases such as the Antarctic Circumpolar Current and near the ice-edge. Ensemble simulations are performed to statistically characterize the model error due to uncertainties in the atmospheric forcings. Such information is a crucial element for future data assimilation experiments. Ensemble simulations are performed with perturbed air temperature and wind forcings. A Fourier decomposition of the NCEP wind vectors and air temperature for 2007 is used to generate ensemble perturbations. The perturbations are scaled such that the resulting ensemble spread matches approximately the RMS differences between the satellite SST and sea ice concentration. The ensemble spread and covariance are analyzed for the minimum and maximum sea ice extent. It is shown that errors in the atmospheric forcings can extend to several hundred meters in depth near the Antarctic Circumpolar Current.

The application of musculoskeletal modeling to investigate gender bias in non-contact ACL injury rate during single-leg landings.

PubMed

Ali, Nicholas; Andersen, Michael Skipper; Rasmussen, John; Robertson, D Gordon E; Rouhi, Gholamreza

2014-01-01

The central tenet of this study was to develop, validate and apply various individualised 3D musculoskeletal models of the human body for application to single-leg landings over increasing vertical heights and horizontal distances. While contributing to an understanding of whether gender differences explain the higher rate of non-contact anterior cruciate ligament (ACL) injuries among females, this study also correlated various musculoskeletal variables significantly impacted by gender, height and/or distance and their interactions with two ACL injury-risk predictor variables; peak vertical ground reaction force (VGRF) and peak proximal tibia anterior shear force (PTASF). Kinematic, kinetic and electromyography data of three male and three female subjects were measured. Results revealed no significant gender differences in the musculoskeletal variables tested except peak VGRF (p = 0.039) and hip axial compressive force (p = 0.032). The quadriceps and the gastrocnemius muscle forces had significant correlations with peak PTASF (r = 0.85, p < 0.05 and r = - 0.88, p < 0.05, respectively). Furthermore, hamstring muscle force was significantly correlated with peak VGRF (r = - 0.90, p < 0.05). The ankle flexion angle was significantly correlated with peak PTASF (r = - 0.82, p < 0.05). Our findings indicate that compared to males, females did not exhibit significantly different muscle forces, or ankle, knee and hip flexion angles during single-leg landings that would explain the gender bias in non-contact ACL injury rate. Our results also suggest that higher quadriceps muscle force increases the risk, while higher hamstring and gastrocnemius muscle forces as well as ankle flexion angle reduce the risk of non-contact ACL injury.

Secondary Structure of Rat and Human Amylin across Force Fields

PubMed Central

Hoffmann, Kyle Quynn; McGovern, Michael; Chiu, Chi-cheng; de Pablo, Juan J.

2015-01-01

The aggregation of human amylin has been strongly implicated in the progression of Type II diabetes. This 37-residue peptide forms a variety of secondary structures, including random coils, α-helices, and β-hairpins. The balance between these structures depends on the chemical environment, making amylin an ideal candidate to examine inherent biases in force fields. Rat amylin differs from human amylin by only 6 residues; however, it does not form fibrils. Therefore it provides a useful complement to human amylin in studies of the key events along the aggregation pathway. In this work, the free energy of rat and human amylin was determined as a function of α-helix and β-hairpin content for the Gromos96 53a6, OPLS-AA/L, CHARMM22/CMAP, CHARMM22*, Amberff99sb*-ILDN, and Amberff03w force fields using advanced sampling techniques, specifically bias exchange metadynamics. This work represents a first systematic attempt to evaluate the conformations and the corresponding free energy of a large, clinically relevant disordered peptide in solution across force fields. The NMR chemical shifts of rIAPP were calculated for each of the force fields using their respective free energy maps, allowing us to quantitatively assess their predictions. We show that the predicted distribution of secondary structures is sensitive to the choice of force-field: Gromos53a6 is biased towards β-hairpins, while CHARMM22/CMAP predicts structures that are overly α-helical. OPLS-AA/L favors disordered structures. Amberff99sb*-ILDN, AmberFF03w and CHARMM22* provide the balance between secondary structures that is most consistent with available experimental data. In contrast to previous reports, our findings suggest that the equilibrium conformations of human and rat amylin are remarkably similar, but that subtle differences arise in transient alpha-helical and beta-strand containing structures that the human peptide can more readily adopt. We hypothesize that these transient states enable dynamic pathways that facilitate the formation of aggregates and, eventually, amyloid fibrils. PMID:26221949

Secondary structure of rat and human amylin across force fields

DOE PAGES

Hoffmann, Kyle Quynn; McGovern, Michael; Chiu, Chi -cheng; ...

2015-07-29

The aggregation of human amylin has been strongly implicated in the progression of Type II diabetes. This 37-residue peptide forms a variety of secondary structures, including random coils, α-helices, and β-hairpins. The balance between these structures depends on the chemical environment, making amylin an ideal candidate to examine inherent biases in force fields. Rat amylin differs from human amylin by only 6 residues; however, it does not form fibrils. Therefore it provides a useful complement to human amylin in studies of the key events along the aggregation pathway. In this work, the free energy of rat and human amylin wasmore » determined as a function of α-helix and β-hairpin content for the Gromos96 53a6, OPLS-AA/L, CHARMM22/CMAP, CHARMM22*, Amberff99sb*-ILDN, and Amberff03w force fields using advanced sampling techniques, specifically bias exchange metadynamics. This work represents a first systematic attempt to evaluate the conformations and the corresponding free energy of a large, clinically relevant disordered peptide in solution across force fields. The NMR chemical shifts of rIAPP were calculated for each of the force fields using their respective free energy maps, allowing us to quantitatively assess their predictions. We show that the predicted distribution of secondary structures is sensitive to the choice of force-field: Gromos53a6 is biased towards β-hairpins, while CHARMM22/CMAP predicts structures that are overly α-helical. OPLS-AA/L favors disordered structures. Amberff99sb*-ILDN, AmberFF03w and CHARMM22* provide the balance between secondary structures that is most consistent with available experimental data. In contrast to previous reports, our findings suggest that the equilibrium conformations of human and rat amylin are remarkably similar, but that subtle differences arise in transient alpha-helical and beta-strand containing structures that the human peptide can more readily adopt. We hypothesize that these transient states enable dynamic pathways that facilitate the formation of aggregates and, eventually, amyloid fibrils.« less

Assessing the Regional/Diurnal Bias between Satellite Retrievals and GEOS-5/MERRA Model Estimates of Land Surface Temperature

NASA Astrophysics Data System (ADS)

Scarino, B. R.; Smith, W. L., Jr.; Minnis, P.; Bedka, K. M.

2017-12-01

Atmospheric models rely on high-accuracy, high-resolution initial radiometric and surface conditions for better short-term meteorological forecasts, as well as improved evaluation of global climate models. Continuous remote sensing of the Earth's energy budget, as conducted by the Clouds and Earth's Radiant Energy System (CERES) project, allows for near-realtime evaluation of cloud and surface radiation properties. It is unfortunately common for there to be bias between atmospheric/surface radiation models and Earth-observations. For example, satellite-observed surface skin temperature (Ts), an important parameter for characterizing the energy exchange at the ground/water-atmosphere interface, can be biased due to atmospheric adjustment assumptions and anisotropy effects. Similarly, models are potentially biased by errors in initial conditions and regional forcing assumptions, which can be mitigated through assimilation with true measurements. As such, when frequent, broad-coverage, and accurate retrievals of satellite Ts are available, important insights into model estimates of Ts can be gained. The Satellite ClOud and Radiation Property retrieval System (SatCORPS) employs a single-channel thermal-infrared method to produce anisotropy-corrected Ts over clear-sky land and ocean surfaces from data taken by geostationary Earth orbit (GEO) satellite imagers. Regional and diurnal changes in model land surface temperature (LST) performance can be assessed owing to the somewhat continuous measurements of the LST offered by GEO satellites - measurements which are accurate to within 0.2 K. A seasonal, hourly comparison of satellite-observed LST with the NASA Goddard Earth Observing System Version 5 (GEOS-5) and the Modern-Era Retrospective Analysis for Research and Applications (MERRA) LST estimates is conducted to reveal regional and diurnal biases. This assessment is an important first step for evaluating the effectiveness of Ts assimilation, as well for determining the impact anisotropy correction has on observation - model bias, and is of critical importance for CERES.

Specificity of interpretation and judgemental biases in social phobia versus depression.

PubMed

Voncken, M J; Bögels, S M; Peeters, F

2007-09-01

A body of studies shows that social phobia is characterized by content specific interpretation and judgmental biases. That is, they show bias in social situations but not in non-social situations. Comorbid depression, one of the major comorbid disorders in social phobia, might account for these biases in social phobia since depression also is characterized by cognitive distortions in social situations. This study hypothesized that, despite comorbid depression, patients with social phobia would suffer from contentspecific biases. Participants filled out the Interpretation and Judgmental Questionnaire (IJQ) to assess interpretation bias (using open-ended responses and forced-interpretations) and judgmental bias in social and non-social situations. Four groups participated: social phobic patients with high (N=38) and low (N=47) depressive symptoms, depressed patients (N=22) and normal controls (N=33). We found both social phobic groups to interpret social situations more negatively and judge social situations as more threatening than non-social situations relative to depressed patients and normal controls. As expected, depressive symptoms related to increased general interpretation and judgmental biases across social and non-social situations. In contrast to expectations, we did not find these patterns for the open-ended measure of interpretation bias. The content-specific biases for social situations distinguished social phobic patients from depressive patients. This speaks for the importance of establishing the primary diagnosis in patients with mixed depression and social anxiety complaints.

Bias extension test on a bi-axial non-crimp fabric powdered with a non-reactive binder system

NASA Astrophysics Data System (ADS)

Pourtier, Jean; Duchamp, Boris; Kowalski, Maxime; Legrand, Xavier; Wang, Peng; Soulat, Damien

2018-05-01

In this communication, we investigated the effects of a chemical non-reactive binder system (powder) on the formability of NCF. Those influences are evaluated for two different of bi-axial NCF structures tested in a range of temperature [20°C - 140°] during bias extension tests (Fig. 1). This analyze is based on the study of force in function of deformation modes (slipping effects and shear angle field).

Hypothesis Testing Using Factor Score Regression: A Comparison of Four Methods

ERIC Educational Resources Information Center

Devlieger, Ines; Mayer, Axel; Rosseel, Yves

2016-01-01

In this article, an overview is given of four methods to perform factor score regression (FSR), namely regression FSR, Bartlett FSR, the bias avoiding method of Skrondal and Laake, and the bias correcting method of Croon. The bias correcting method is extended to include a reliable standard error. The four methods are compared with each other and…

Spring loaded thermocouple module

DOEpatents

McKelvey, T.E.; Guarnieri, J.J.

1984-03-13

A thermocouple arrangement is provided for mounting in a blind hole of a specimen. The thermocouple arrangement includes a cup-like holder member, which receives an elongated thermal insulator, one end of which is seated at an end wall of the holder. A pair of thermocouple wires, threaded through passageways in the insulator, extend beyond the insulator member, terminating in free ends which are joined together in a spherical weld bead. A spring, held captive within the holder, applies a bias force to the weld bead, through the insulator member. The outside surface of the holder is threaded for engagement with the blind hole of the specimen. When the thermocouple is installed in the specimen, the spherical contact surface of the weld bead is held in contact with the end wall of the blind hole, with a predetermined bias force.

Spring loaded thermocouple module

DOEpatents

McKelvey, Thomas E.; Guarnieri, Joseph J.

1985-01-01

A thermocouple arrangement is provided for mounting in a blind hole of a specimen. The thermocouple arrangement includes a cup-like holder member, which receives an elongated thermal insulator, one end of which is seated at an end wall of the holder. A pair of thermocouple wires, threaded through passageways in the insulator, extend beyond the insulator member, terminating in free ends which are joined together in a spherical weld bead. A spring, held captive within the holder, applies a bias force to the weld bead, through the insulator member. The outside surface of the holder is threaded for engagement with the blind hole of the specimen. When the thermocouple is installed in the specimen, the spherical contact surface of the weld bead is held in contact with the end wall of the blind hole, with a predetermined bias force.

North Tropical Atlantic Climate Variability and Model Biases

NASA Astrophysics Data System (ADS)

Yang, Y.

2017-12-01

Remote forcing from El Niño-Southern Oscillation (ENSO) and local ocean-atmosphere feedback are important for climate variability over the North Tropical Atlantic. These two factors are extracted by the ensemble mean and inter-member difference of a 10-member Pacific Ocean-Global Atmosphere (POGA) experiment, in which sea surface temperatures (SSTs) are restored to the observed anomalies over the tropical Pacific but fully coupled to the atmosphere elsewhere. POGA reasonably captures main features of observed North Tropical Atlantic variability. ENSO forced and local North Tropical Atlantic modes (NTAMs) develop with wind-evaporation-SST feedback, explaining one third and two thirds of total variance respectively. Notable biases, however, exist. The seasonality of the simulated NTAM is delayed by one month, due to the late development of the North Atlantic Oscillation (NAO) in the model. A spurious band of enhanced sea surface temperature (SST) variance (SBEV) is identified over the northern equatorial Atlantic in POGA and 14 out of 23 CMIP5 models. The SBEV is especially pronounced in boreal spring and due to the combined effect of both anomalous atmospheric thermal forcing and oceanic vertical upwelling. While the tropical North Atlantic variability is only weakly correlated with the Atlantic Zonal Mode (AZM) in observations, the SBEV in CMIP5 produces conditions that drive and intensify the AZM variability via triggering the Bjerknes feedback. This partially explains why AZM is strong in some CMIP5 models even though the equatorial cold tongue and easterly trades are biased low.

Electrostatically Biased Binding of Kinesin to Microtubules

PubMed Central

Zheng, Wenjun; Alonso, Maria; Huber, Gary; Dlugosz, Maciej; McCammon, J. Andrew; Cross, Robert A.

2011-01-01

The minimum motor domain of kinesin-1 is a single head. Recent evidence suggests that such minimal motor domains generate force by a biased binding mechanism, in which they preferentially select binding sites on the microtubule that lie ahead in the progress direction of the motor. A specific molecular mechanism for biased binding has, however, so far been lacking. Here we use atomistic Brownian dynamics simulations combined with experimental mutagenesis to show that incoming kinesin heads undergo electrostatically guided diffusion-to-capture by microtubules, and that this produces directionally biased binding. Kinesin-1 heads are initially rotated by the electrostatic field so that their tubulin-binding sites face inwards, and then steered towards a plus-endwards binding site. In tethered kinesin dimers, this bias is amplified. A 3-residue sequence (RAK) in kinesin helix alpha-6 is predicted to be important for electrostatic guidance. Real-world mutagenesis of this sequence powerfully influences kinesin-driven microtubule sliding, with one mutant producing a 5-fold acceleration over wild type. We conclude that electrostatic interactions play an important role in the kinesin stepping mechanism, by biasing the diffusional association of kinesin with microtubules. PMID:22140358

Fore and aft elastic response characteristics of 34 x 9.9, type 7, 14 ply-rating aircraft tires of bias-ply, bias-belted, and radial-belted design. M.S. Thesis - George Washington Univ., May 1973; [static and rolling tests on dry concrete pavements

NASA Technical Reports Server (NTRS)

Tanner, J. A.

1974-01-01

An investigation was conducted to determine the fore-and-aft elastic response characteristics of 34 x 9.9, type VII, 14 ply-rating aircraft tires of bias-ply, bias-belted, and radial-belted design. The investigation consisted of static and rolling tests on dry concrete pavements at the Langley aircraft landing loads and traction facility; statistical techniques which related the measured tire elastic characteristics to variations in the vertical load, inflation pressure, braking force and/or tire vertical deflection; and a semiempirical analysis which related the tire elastic behavior to measured wheel slippage during steady-state braking. The bias-belted tire developed the largest spring constant value for most loading conditions; the radial-belted tire, the smallest. The elastic response of the tire free periphery to static braking included both tread stretch and carcass torsional wind-up about the axle for the bias-ply and bias-belted tires and carcass wind-up alone for the radial-belted tire.

Preference bias of head orientation in choosing between two non-durables.

PubMed

Funaya, Hiroyuki; Shibata, Tomohiro

2015-01-01

The goal of this study is to investigate how customers' gaze, head and body orientations reflect their choices. Although the relationship between human choice and gaze behavior has been well-studied, other behaviors such as head and body are unknown. We conducted a two-alternatives-forced-choice task to examine (1) whether preference bias, i.e., a positional bias in gaze, head and body toward the item that was later chosen, exists in choice, (2) when preference bias is observed and when prediction of the resulting choice becomes possible (3) whether human choice is affected when the body orientations are manipulated. We used real non-durable products (cheap snacks and clothing) on a shopping shelf. The results showed that there was a significant preference bias in head orientation at the beginning 1 s when the subjects stood straight toward the shelf, and that the head orientation was more biased toward the selected item than the gaze and the center of pressure at the ending 1 s. Manipulating body orientation did not affect the result of choice. The preference bias detected by observing the head orientation would be useful in marketing science for predicting customers' choice.

FRAME (Force Review Automation Environment): MATLAB-based AFM data processor.

PubMed

Partola, Kostyantyn R; Lykotrafitis, George

2016-05-03

Data processing of force-displacement curves generated by atomic force microscopes (AFMs) for elastic moduli and unbinding event measurements is very time consuming and susceptible to user error or bias. There is an evident need for consistent, dependable, and easy-to-use AFM data processing software. We have developed an open-source software application, the force review automation environment (or FRAME), that provides users with an intuitive graphical user interface, automating data processing, and tools for expediting manual processing. We did not observe a significant difference between manually processed and automatically processed results from the same data sets. Copyright © 2016 Elsevier Ltd. All rights reserved.

On the performance of satellite precipitation products in riverine flood modeling: A review

NASA Astrophysics Data System (ADS)

Maggioni, Viviana; Massari, Christian

2018-03-01

This work is meant to summarize lessons learned on using satellite precipitation products for riverine flood modeling and to propose future directions in this field of research. Firstly, the most common satellite precipitation products (SPPs) during the Tropical Rainfall Measuring Mission (TRMM) and Global Precipitation Mission (GPM) eras are reviewed. Secondly, we discuss the main errors and uncertainty sources in these datasets that have the potential to affect streamflow and runoff model simulations. Thirdly, past studies that focused on using SPPs for predicting streamflow and runoff are analyzed. As the impact of floods depends not only on the characteristics of the flood itself, but also on the characteristics of the region (population density, land use, geophysical and climatic factors), a regional analysis is required to assess the performance of hydrologic models in monitoring and predicting floods. The performance of SPP-forced hydrological models was shown to largely depend on several factors, including precipitation type, seasonality, hydrological model formulation, topography. Across several basins around the world, the bias in SPPs was recognized as a major issue and bias correction methods of different complexity were shown to significantly reduce streamflow errors. Model re-calibration was also raised as a viable option to improve SPP-forced streamflow simulations, but caution is necessary when recalibrating models with SPP, which may result in unrealistic parameter values. From a general standpoint, there is significant potential for using satellite observations in flood forecasting, but the performance of SPP in hydrological modeling is still inadequate for operational purposes.

Handwriting analysis indicates spontaneous dyskinesias in neuroleptic naïve adolescents at high risk for psychosis.

PubMed

Dean, Derek J; Teulings, Hans-Leo; Caligiuri, Michael; Mittal, Vijay A

2013-11-21

Growing evidence suggests that movement abnormalities are a core feature of psychosis. One marker of movement abnormality, dyskinesia, is a result of impaired neuromodulation of dopamine in fronto-striatal pathways. The traditional methods for identifying movement abnormalities include observer-based reports and force stability gauges. The drawbacks of these methods are long training times for raters, experimenter bias, large site differences in instrumental apparatus, and suboptimal reliability. Taking these drawbacks into account has guided the development of better standardized and more efficient procedures to examine movement abnormalities through handwriting analysis software and tablet. Individuals at risk for psychosis showed significantly more dysfluent pen movements (a proximal measure for dyskinesia) in a handwriting task. Handwriting kinematics offers a great advance over previous methods of assessing dyskinesia, which could clearly be beneficial for understanding the etiology of psychosis.

Class-modelling in food analytical chemistry: Development, sampling, optimisation and validation issues - A tutorial.

PubMed

Oliveri, Paolo

2017-08-22

Qualitative data modelling is a fundamental branch of pattern recognition, with many applications in analytical chemistry, and embraces two main families: discriminant and class-modelling methods. The first strategy is appropriate when at least two classes are meaningfully defined in the problem under study, while the second strategy is the right choice when the focus is on a single class. For this reason, class-modelling methods are also referred to as one-class classifiers. Although, in the food analytical field, most of the issues would be properly addressed by class-modelling strategies, the use of such techniques is rather limited and, in many cases, discriminant methods are forcedly used for one-class problems, introducing a bias in the outcomes. Key aspects related to the development, optimisation and validation of suitable class models for the characterisation of food products are critically analysed and discussed. Copyright © 2017 Elsevier B.V. All rights reserved.

Handwriting Analysis Indicates Spontaneous Dyskinesias in Neuroleptic Naïve Adolescents at High Risk for Psychosis

PubMed Central

Dean, Derek J.; Teulings, Hans-Leo; Caligiuri, Michael; Mittal, Vijay A.

2013-01-01

Growing evidence suggests that movement abnormalities are a core feature of psychosis. One marker of movement abnormality, dyskinesia, is a result of impaired neuromodulation of dopamine in fronto-striatal pathways. The traditional methods for identifying movement abnormalities include observer-based reports and force stability gauges. The drawbacks of these methods are long training times for raters, experimenter bias, large site differences in instrumental apparatus, and suboptimal reliability. Taking these drawbacks into account has guided the development of better standardized and more efficient procedures to examine movement abnormalities through handwriting analysis software and tablet. Individuals at risk for psychosis showed significantly more dysfluent pen movements (a proximal measure for dyskinesia) in a handwriting task. Handwriting kinematics offers a great advance over previous methods of assessing dyskinesia, which could clearly be beneficial for understanding the etiology of psychosis. PMID:24300590

Correction of gene expression data: Performance-dependency on inter-replicate and inter-treatment biases.

PubMed

Darbani, Behrooz; Stewart, C Neal; Noeparvar, Shahin; Borg, Søren

2014-10-20

This report investigates for the first time the potential inter-treatment bias source of cell number for gene expression studies. Cell-number bias can affect gene expression analysis when comparing samples with unequal total cellular RNA content or with different RNA extraction efficiencies. For maximal reliability of analysis, therefore, comparisons should be performed at the cellular level. This could be accomplished using an appropriate correction method that can detect and remove the inter-treatment bias for cell-number. Based on inter-treatment variations of reference genes, we introduce an analytical approach to examine the suitability of correction methods by considering the inter-treatment bias as well as the inter-replicate variance, which allows use of the best correction method with minimum residual bias. Analyses of RNA sequencing and microarray data showed that the efficiencies of correction methods are influenced by the inter-treatment bias as well as the inter-replicate variance. Therefore, we recommend inspecting both of the bias sources in order to apply the most efficient correction method. As an alternative correction strategy, sequential application of different correction approaches is also advised. Copyright © 2014 Elsevier B.V. All rights reserved.

A method for the quantification of biased signalling at constitutively active receptors.

PubMed

Hall, David A; Giraldo, Jesús

2018-06-01

Biased agonism, the ability of an agonist to differentially activate one of several signal transduction pathways when acting at a given receptor, is an increasingly recognized phenomenon at many receptors. The Black and Leff operational model lacks a way to describe constitutive receptor activity and hence inverse agonism. Thus, it is impossible to analyse the biased signalling of inverse agonists using this model. In this theoretical work, we develop and illustrate methods for the analysis of biased inverse agonism. Methods were derived for quantifying biased signalling in systems that demonstrate constitutive activity using the modified operational model proposed by Slack and Hall. The methods were illustrated using Monte Carlo simulations. The Monte Carlo simulations demonstrated that, with an appropriate experimental design, the model parameters are 'identifiable'. The method is consistent with methods based on the measurement of intrinsic relative activity (RA i ) (ΔΔlogR or ΔΔlog(τ/K a )) proposed by Ehlert and Kenakin and their co-workers but has some advantages. In particular, it allows the quantification of ligand bias independently of 'system bias' removing the requirement to normalize to a standard ligand. In systems with constitutive activity, the Slack and Hall model provides methods for quantifying the absolute bias of agonists and inverse agonists. This provides an alternative to methods based on RA i and is complementary to the ΔΔlog(τ/K a ) method of Kenakin et al. in systems where use of that method is inappropriate due to the presence of constitutive activity. © 2018 The British Pharmacological Society.

Kinetic and kinematic follow‐up gait analysis in Doberman Pinschers with cervical spondylomyelopathy treated medically and surgically

PubMed Central

Smith, Rebecca L.; da Costa, Ronaldo C.

2018-01-01

Background The efficacy of treatment of dogs with cervical spondylomyelopathy (CSM) is commonly based on the owner's and clinician's perception of the gait, which is highly subjective and suffers from observer bias. Hypothesis/Objectives To compare selected kinetic and kinematic parameters before and after treatments and to correlate the findings of gait analysis to clinical outcome. Animals Eight Doberman Pinschers with CSM confirmed by magnetic resonsance imaging. Methods Patients were prospectively studied and treated with either medical management (n = 5) or surgery (n = 3). Force plate analysis and 3‐D kinematic motion capture were performed at initial presentation and approximately 8 weeks later. Force plate parameters evaluated included peak vertical force (PVF). Kinematic parameters measured included number of pelvic limb strides, stifle flexion and extension, maximum and minimum thoracic limb distance, truncal sway, and thoracic limb stride duration. Results Kinematic analysis showed that deviation of the spine to the right (truncal sway) was significantly smaller (P < .001) and the degree of right stifle flexion was significantly larger (P = .029) after treatment. Force plate analysis indicated that PVF was significantly different after treatment (P = .049) and the difference of the PVF also was significantly larger (P = .027). However, no correlation was found with either method of gait analysis and clinical recovery. Conclusions and Clinical Importance Kinetic and kinematic gait analysis were able to detect differences in dogs with CSM before and after treatment. A correlation of gait analysis to clinical improvement could not be determined. PMID:29572944

Are we using the right fuel to drive hydrological models? A climate impact study in the Upper Blue Nile

NASA Astrophysics Data System (ADS)

Liersch, Stefan; Tecklenburg, Julia; Rust, Henning; Dobler, Andreas; Fischer, Madlen; Kruschke, Tim; Koch, Hagen; Fokko Hattermann, Fred

2018-04-01

Climate simulations are the fuel to drive hydrological models that are used to assess the impacts of climate change and variability on hydrological parameters, such as river discharges, soil moisture, and evapotranspiration. Unlike with cars, where we know which fuel the engine requires, we never know in advance what unexpected side effects might be caused by the fuel we feed our models with. Sometimes we increase the fuel's octane number (bias correction) to achieve better performance and find out that the model behaves differently but not always as was expected or desired. This study investigates the impacts of projected climate change on the hydrology of the Upper Blue Nile catchment using two model ensembles consisting of five global CMIP5 Earth system models and 10 regional climate models (CORDEX Africa). WATCH forcing data were used to calibrate an eco-hydrological model and to bias-correct both model ensembles using slightly differing approaches. On the one hand it was found that the bias correction methods considerably improved the performance of average rainfall characteristics in the reference period (1970-1999) in most of the cases. This also holds true for non-extreme discharge conditions between Q20 and Q80. On the other hand, bias-corrected simulations tend to overemphasize magnitudes of projected change signals and extremes. A general weakness of both uncorrected and bias-corrected simulations is the rather poor representation of high and low flows and their extremes, which were often deteriorated by bias correction. This inaccuracy is a crucial deficiency for regional impact studies dealing with water management issues and it is therefore important to analyse model performance and characteristics and the effect of bias correction, and eventually to exclude some climate models from the ensemble. However, the multi-model means of all ensembles project increasing average annual discharges in the Upper Blue Nile catchment and a shift in seasonal patterns, with decreasing discharges in June and July and increasing discharges from August to November.

Power tong torque control

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

Buck, D.A.; James, R.N.

1987-10-20

Torque controlled powered pipe tongs, are described the apparatus comprises: (a) a power tong powered by a fluid motor; (b) a fluid power source connected to the motor; (c) a force conducting element attached to the power tong, situated to oppose reaction torque from the tongs when torque is applied to pipe; (d) force sensing means operatively associated with the force conducting element situated to sense at least part of the force experienced by the force conducting element, arranged to produce a pressure signal proportional to force sensed; and (e) a fluid by-pass valve, adjustably biased toward a closed position,more » responsive to the signal to tend to move toward an open position, the by-pass valve connected between the fluid power source and the motor.« less

Radiative Forcing by Well-Mixed Greenhouse Gases: Estimates from Climate Models in the Intergovernmental Panel on Climate Change (IPCC) Fourth Assessment Report (AR4)

NASA Technical Reports Server (NTRS)

Collins, W. D.; Ramaswamy, V.; Schwarzkopf, M. D.; Sun, Y.; Portmann, R. W.; Fu, Q.; Casanova, S. E. B.; Dufresne, J.-L.; Fillmore, D. W.; Forster, P. M. D.;

Evolutionary Thinking in Microeconomic Models: Prestige Bias and Market Bubbles

PubMed Central

Bell, Adrian Viliami

2013-01-01

Evolutionary models broadly support a number of social learning strategies likely important in economic behavior. Using a simple model of price dynamics, I show how prestige bias, or copying of famed (and likely successful) individuals, influences price equilibria and investor disposition in a way that exacerbates or creates market bubbles. I discuss how integrating the social learning and demographic forces important in cultural evolution with economic models provides a fruitful line of inquiry into real-world behavior. PMID:23544100

Air and Space Power Journal. Volume 30, Number 2, Summer 2016

DTIC Science & Technology

2016-01-01

Nicholas J. Thomas, USAF, PE Features Thinking beyond the Books ❙ 15 Sociological Biases of Our Military Institutions Ben Zweibelson Institutional ...Retired Editor, Strategic Studies Quarterly Air Force Research Institute Dr. Grant T. Hammond USAF Center for Strategy and Technology Dr. Dale L...Hayden Air Force Research Institute Col S. Clinton Hinote Military Fellow Council on Foreign Relations Dr. Thomas Hughes USAF School of Advanced Air and

Detecting and removing multiplicative spatial bias in high-throughput screening technologies.

PubMed

Caraus, Iurie; Mazoure, Bogdan; Nadon, Robert; Makarenkov, Vladimir

2017-10-15

Considerable attention has been paid recently to improve data quality in high-throughput screening (HTS) and high-content screening (HCS) technologies widely used in drug development and chemical toxicity research. However, several environmentally- and procedurally-induced spatial biases in experimental HTS and HCS screens decrease measurement accuracy, leading to increased numbers of false positives and false negatives in hit selection. Although effective bias correction methods and software have been developed over the past decades, almost all of these tools have been designed to reduce the effect of additive bias only. Here, we address the case of multiplicative spatial bias. We introduce three new statistical methods meant to reduce multiplicative spatial bias in screening technologies. We assess the performance of the methods with synthetic and real data affected by multiplicative spatial bias, including comparisons with current bias correction methods. We also describe a wider data correction protocol that integrates methods for removing both assay and plate-specific spatial biases, which can be either additive or multiplicative. The methods for removing multiplicative spatial bias and the data correction protocol are effective in detecting and cleaning experimental data generated by screening technologies. As our protocol is of a general nature, it can be used by researchers analyzing current or next-generation high-throughput screens. The AssayCorrector program, implemented in R, is available on CRAN. makarenkov.vladimir@uqam.ca. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

General purpose force doctrine

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

Weltman, J.J.

In contemporary American strategic parlance, the general purpose forces have come to mean those forces intended for conflict situations other than nuclear war with the Soviet Union. As with all military forces, the general purpose forces are powerfully determined by prevailing conceptions of the problems they must meet and by institutional biases as to the proper way to deal with those problems. This paper deals with the strategic problems these forces are intended to meet, the various and often conflicting doctrines and organizational structures which have been generated in order to meet those problems, and the factors which will influencemore » general purpose doctrine and structure in the future. This paper does not attempt to prescribe technological solutions to the needs of the general purpose forces. Rather, it attempts to display the doctrinal and institutional context within which new technologies must operate, and which will largely determine whether these technologies are accepted into the force structure or not.« less

Switches in Genomic GC Content Drive Shifts of Optimal Codons under Sustained Selection on Synonymous Sites

PubMed Central

Sun, Yu; Tamarit, Daniel

2017-01-01

Abstract The major codon preference model suggests that codons read by tRNAs in high concentrations are preferentially utilized in highly expressed genes. However, the identity of the optimal codons differs between species although the forces driving such changes are poorly understood. We suggest that these questions can be tackled by placing codon usage studies in a phylogenetic framework and that bacterial genomes with extreme nucleotide composition biases provide informative model systems. Switches in the background substitution biases from GC to AT have occurred in Gardnerella vaginalis (GC = 32%), and from AT to GC in Lactobacillus delbrueckii (GC = 62%) and Lactobacillus fermentum (GC = 63%). We show that despite the large effects on codon usage patterns by these switches, all three species evolve under selection on synonymous sites. In G. vaginalis, the dramatic codon frequency changes coincide with shifts of optimal codons. In contrast, the optimal codons have not shifted in the two Lactobacillus genomes despite an increased fraction of GC-ending codons. We suggest that all three species are in different phases of an on-going shift of optimal codons, and attribute the difference to a stronger background substitution bias and/or longer time since the switch in G. vaginalis. We show that comparative and correlative methods for optimal codon identification yield conflicting results for genomes in flux and discuss possible reasons for the mispredictions. We conclude that switches in the direction of the background substitution biases can drive major shifts in codon preference patterns even under sustained selection on synonymous codon sites. PMID:27540085

Effects of biases in domain wall network evolution. II. Quantitative analysis

NASA Astrophysics Data System (ADS)

Correia, J. R. C. C. C.; Leite, I. S. C. R.; Martins, C. J. A. P.

2018-04-01

Domain walls form at phase transitions which break discrete symmetries. In a cosmological context, they often overclose the Universe (contrary to observational evidence), although one may prevent this by introducing biases or forcing anisotropic evolution of the walls. In a previous work [Correia et al., Phys. Rev. D 90, 023521 (2014), 10.1103/PhysRevD.90.023521], we numerically studied the evolution of various types of biased domain wall networks in the early Universe, confirming that anisotropic networks ultimately reach scaling while those with a biased potential or biased initial conditions decay. We also found that the analytic decay law obtained by Hindmarsh was in good agreement with simulations of biased potentials, but not of biased initial conditions, and suggested that the difference was related to the Gaussian approximation underlying the analytic law. Here, we extend our previous work in several ways. For the cases of biased potential and biased initial conditions, we study in detail the field distributions in the simulations, confirming that the validity (or not) of the Gaussian approximation is the key difference between the two cases. For anisotropic walls, we carry out a more extensive set of numerical simulations and compare them to the canonical velocity-dependent one-scale model for domain walls, finding that the model accurately predicts the linear scaling regime after isotropization. Overall, our analysis provides a quantitative description of the cosmological evolution of these networks.

Detrended partial cross-correlation analysis of two nonstationary time series influenced by common external forces

NASA Astrophysics Data System (ADS)

Qian, Xi-Yuan; Liu, Ya-Min; Jiang, Zhi-Qiang; Podobnik, Boris; Zhou, Wei-Xing; Stanley, H. Eugene

2015-06-01

When common factors strongly influence two power-law cross-correlated time series recorded in complex natural or social systems, using detrended cross-correlation analysis (DCCA) without considering these common factors will bias the results. We use detrended partial cross-correlation analysis (DPXA) to uncover the intrinsic power-law cross correlations between two simultaneously recorded time series in the presence of nonstationarity after removing the effects of other time series acting as common forces. The DPXA method is a generalization of the detrended cross-correlation analysis that takes into account partial correlation analysis. We demonstrate the method by using bivariate fractional Brownian motions contaminated with a fractional Brownian motion. We find that the DPXA is able to recover the analytical cross Hurst indices, and thus the multiscale DPXA coefficients are a viable alternative to the conventional cross-correlation coefficient. We demonstrate the advantage of the DPXA coefficients over the DCCA coefficients by analyzing contaminated bivariate fractional Brownian motions. We calculate the DPXA coefficients and use them to extract the intrinsic cross correlation between crude oil and gold futures by taking into consideration the impact of the U.S. dollar index. We develop the multifractal DPXA (MF-DPXA) method in order to generalize the DPXA method and investigate multifractal time series. We analyze multifractal binomial measures masked with strong white noises and find that the MF-DPXA method quantifies the hidden multifractal nature while the multifractal DCCA method fails.

Following Easy Slope Paths on a Free Energy Landscape: The Case Study of the Trp-Cage Folding Mechanism

PubMed Central

Marinelli, Fabrizio

2013-01-01

In this work a new method for the automatic exploration and calculation of multidimensional free energy landscapes is proposed. Inspired by metadynamics, it uses several collective variables that are relevant for the investigated process and a bias potential that discourages the sampling of already visited configurations. The latter potential allows escaping a local free energy minimum following the direction of slow motions. This is different from metadynamics in which there is no specific direction of the biasing force and the computational effort increases significantly with the number of collective variables. The method is tested on the Ace-Ala3-Nme peptide, and then it is applied to investigate the Trp-cage folding mechanism. For this protein, within a few hundreds of nanoseconds, a broad range of conformations is explored, including nearly native ones, initiating the simulation from a completely unfolded conformation. Finally, several folding/unfolding trajectories give a systematic description of the Trp-cage folding pathways, leading to a unified view for the folding mechanisms of this protein. The proposed mechanism is consistent with NMR chemical shift data at increasing temperature and recent experimental observations pointing to a pivotal role of secondary structure elements in directing the folding process toward the native state. PMID:24010667

Study of aerosol direct and indirect effects and auto-conversion processes over the West African monsoon region using a regional climate model

NASA Astrophysics Data System (ADS)

Salah, Zeinab; Shalaby, Ahmed; Steiner, Allison L.; Zakey, Ashraf S.; Gautam, Ritesh; Abdel Wahab, Mohamed M.

2018-02-01

This study assesses the direct and indirect effects of natural and anthropogenic aerosols (e.g., black carbon and sulfate) over West and Central Africa during the West African monsoon (WAM) period (June-July-August). We investigate the impacts of aerosols on the amount of cloudiness, the influences on the precipitation efficiency of clouds, and the associated radiative forcing (direct and indirect). Our study includes the implementation of three new formulations of auto-conversion parameterization [namely, the Beheng (BH), Tripoli and Cotton (TC) and Liu and Daum (R6) schemes] in RegCM4.4.1, besides the default model's auto-conversion scheme (Kessler). Among the new schemes, BH reduces the precipitation wet bias by more than 50% over West Africa and achieves a bias reduction of around 25% over Central Africa. Results from detailed sensitivity experiments suggest a significant path forward in terms of addressing the long-standing issue of the characteristic wet bias in RegCM. In terms of aerosol-induced radiative forcing, the impact of the various schemes is found to vary considerably (ranging from -5 to -25 W m-2).

GPS-Based Reduced Dynamic Orbit Determination Using Accelerometer Data

NASA Technical Reports Server (NTRS)

VanHelleputte, Tom; Visser, Pieter

2007-01-01

Currently two gravity field satellite missions, CHAMP and GRACE, are equipped with high sensitivity electrostatic accelerometers, measuring the non-conservative forces acting on the spacecraft in three orthogonal directions. During the gravity field recovery these measurements help to separate gravitational and non-gravitational contributions in the observed orbit perturbations. For precise orbit determination purposes all these missions have a dual-frequency GPS receiver on board. The reduced dynamic technique combines the dense and accurate GPS observations with physical models of the forces acting on the spacecraft, complemented by empirical accelerations, which are stochastic parameters adjusted in the orbit determination process. When the spacecraft carries an accelerometer, these measured accelerations can be used to replace the models of the non-conservative forces, such as air drag and solar radiation pressure. This approach is implemented in a batch least-squares estimator of the GPS High Precision Orbit Determination Software Tools (GHOST), developed at DLR/GSOC and DEOS. It is extensively tested with data of the CHAMP and GRACE satellites. As accelerometer observations typically can be affected by an unknown scale factor and bias in each measurement direction, they require calibration during processing. Therefore the estimated state vector is augmented with six parameters: a scale and bias factor for the three axes. In order to converge efficiently to a good solution, reasonable a priori values for the bias factor are necessary. These are calculated by combining the mean value of the accelerometer observations with the mean value of the non-conservative force models and empirical accelerations, estimated when using these models. When replacing the non-conservative force models with accelerometer observations and still estimating empirical accelerations, a good orbit precision is achieved. 100 days of GRACE B data processing results in a mean orbit fit of a few centimeters with respect to high-quality JPL reference orbits. This shows a slightly better consistency compared to the case when using force models. A purely dynamic orbit, without estimating empirical accelerations thus only adjusting six state parameters and the bias and scale factors, gives an orbit fit for the GRACE B test case below the decimeter level. The in orbit calibrated accelerometer observations can be used to validate the modelled accelerations and estimated empirical accelerations computed with the GHOST tools. In along track direction they show the best resemblance, with a mean correlation coefficient of 93% for the same period. In radial and normal direction the correlation is smaller. During days of high solar activity the benefit of using accelerometer observations is clearly visible. The observations during these days show fluctuations which the modelled and empirical accelerations can not follow.

Bias correction of risk estimates in vaccine safety studies with rare adverse events using a self-controlled case series design.

PubMed

Zeng, Chan; Newcomer, Sophia R; Glanz, Jason M; Shoup, Jo Ann; Daley, Matthew F; Hambidge, Simon J; Xu, Stanley

2013-12-15

The self-controlled case series (SCCS) method is often used to examine the temporal association between vaccination and adverse events using only data from patients who experienced such events. Conditional Poisson regression models are used to estimate incidence rate ratios, and these models perform well with large or medium-sized case samples. However, in some vaccine safety studies, the adverse events studied are rare and the maximum likelihood estimates may be biased. Several bias correction methods have been examined in case-control studies using conditional logistic regression, but none of these methods have been evaluated in studies using the SCCS design. In this study, we used simulations to evaluate 2 bias correction approaches-the Firth penalized maximum likelihood method and Cordeiro and McCullagh's bias reduction after maximum likelihood estimation-with small sample sizes in studies using the SCCS design. The simulations showed that the bias under the SCCS design with a small number of cases can be large and is also sensitive to a short risk period. The Firth correction method provides finite and less biased estimates than the maximum likelihood method and Cordeiro and McCullagh's method. However, limitations still exist when the risk period in the SCCS design is short relative to the entire observation period.

Measurement errors when estimating the vertical jump height with flight time using photocell devices: the example of Optojump.

PubMed

Attia, A; Dhahbi, W; Chaouachi, A; Padulo, J; Wong, D P; Chamari, K

2017-03-01

Common methods to estimate vertical jump height (VJH) are based on the measurements of flight time (FT) or vertical reaction force. This study aimed to assess the measurement errors when estimating the VJH with flight time using photocell devices in comparison with the gold standard jump height measured by a force plate (FP). The second purpose was to determine the intrinsic reliability of the Optojump photoelectric cells in estimating VJH. For this aim, 20 subjects (age: 22.50±1.24 years) performed maximal vertical jumps in three modalities in randomized order: the squat jump (SJ), counter-movement jump (CMJ), and CMJ with arm swing (CMJarm). Each trial was simultaneously recorded by the FP and Optojump devices. High intra-class correlation coefficients (ICCs) for validity (0.98-0.99) and low limits of agreement (less than 1.4 cm) were found; even a systematic difference in jump height was consistently observed between FT and double integration of force methods (-31% to -27%; p<0.001) and a large effect size (Cohen's d >1.2). Intra-session reliability of Optojump was excellent, with ICCs ranging from 0.98 to 0.99, low coefficients of variation (3.98%), and low standard errors of measurement (0.8 cm). It was concluded that there was a high correlation between the two methods to estimate the vertical jump height, but the FT method cannot replace the gold standard, due to the large systematic bias. According to our results, the equations of each of the three jump modalities were presented in order to obtain a better estimation of the jump height.

Measurement errors when estimating the vertical jump height with flight time using photocell devices: the example of Optojump

PubMed Central

Attia, A; Chaouachi, A; Padulo, J; Wong, DP; Chamari, K

2016-01-01

Common methods to estimate vertical jump height (VJH) are based on the measurements of flight time (FT) or vertical reaction force. This study aimed to assess the measurement errors when estimating the VJH with flight time using photocell devices in comparison with the gold standard jump height measured by a force plate (FP). The second purpose was to determine the intrinsic reliability of the Optojump photoelectric cells in estimating VJH. For this aim, 20 subjects (age: 22.50±1.24 years) performed maximal vertical jumps in three modalities in randomized order: the squat jump (SJ), counter-movement jump (CMJ), and CMJ with arm swing (CMJarm). Each trial was simultaneously recorded by the FP and Optojump devices. High intra-class correlation coefficients (ICCs) for validity (0.98-0.99) and low limits of agreement (less than 1.4 cm) were found; even a systematic difference in jump height was consistently observed between FT and double integration of force methods (-31% to -27%; p<0.001) and a large effect size (Cohen’s d>1.2). Intra-session reliability of Optojump was excellent, with ICCs ranging from 0.98 to 0.99, low coefficients of variation (3.98%), and low standard errors of measurement (0.8 cm). It was concluded that there was a high correlation between the two methods to estimate the vertical jump height, but the FT method cannot replace the gold standard, due to the large systematic bias. According to our results, the equations of each of the three jump modalities were presented in order to obtain a better estimation of the jump height. PMID:28416900

How does bias correction of RCM precipitation affect modelled runoff?

NASA Astrophysics Data System (ADS)

Teng, J.; Potter, N. J.; Chiew, F. H. S.; Zhang, L.; Vaze, J.; Evans, J. P.

2014-09-01

Many studies bias correct daily precipitation from climate models to match the observed precipitation statistics, and the bias corrected data are then used for various modelling applications. This paper presents a review of recent methods used to bias correct precipitation from regional climate models (RCMs). The paper then assesses four bias correction methods applied to the weather research and forecasting (WRF) model simulated precipitation, and the follow-on impact on modelled runoff for eight catchments in southeast Australia. Overall, the best results are produced by either quantile mapping or a newly proposed two-state gamma distribution mapping method. However, the difference between the tested methods is small in the modelling experiments here (and as reported in the literature), mainly because of the substantial corrections required and inconsistent errors over time (non-stationarity). The errors remaining in bias corrected precipitation are typically amplified in modelled runoff. The tested methods cannot overcome limitation of RCM in simulating precipitation sequence, which affects runoff generation. Results further show that whereas bias correction does not seem to alter change signals in precipitation means, it can introduce additional uncertainty to change signals in high precipitation amounts and, consequently, in runoff. Future climate change impact studies need to take this into account when deciding whether to use raw or bias corrected RCM results. Nevertheless, RCMs will continue to improve and will become increasingly useful for hydrological applications as the bias in RCM simulations reduces.

Anthropometry of Brazilian Air Force pilots.

PubMed

da Silva, Gilvan V; Halpern, Manny; Gordon, Claire C

2017-10-01

Anthropometric data are essential for the design of military equipment including sizing of aircraft cockpits and personal gear. Currently, there are no anthropometric databases specific to Brazilian military personnel. The aim of this study was to create a Brazilian anthropometric database of Air Force pilots. The methods, protocols, descriptions, definitions, landmarks, tools and measurements procedures followed the instructions outlined in Measurer's Handbook: US Army and Marine Corps Anthropometric Surveys, 2010-2011 - NATICK/TR-11/017. The participants were measured countrywide, in all five Brazilian Geographical Regions. Thirty-nine anthropometric measurements related to cockpit design were selected. The results of 2133 males and 206 females aged 16-52 years constitute a set of basic data for cockpit design, space arrangement issues and adjustments, protective gear and equipment design, as well as for digital human modelling. Another important implication is that this study can be considered a starting point for reducing gender bias in women's career as pilots. Practitioner Summary: This paper describes the first large-scale anthropometric survey of the Brazilian Air Force pilots and the development of the related database. This study provides critical data for improving aircraft cockpit design for ergonomics and comprehensive pilot accommodation, protective gear and uniform design, as well as digital human modelling.

Conformational sampling enhancement of replica exchange molecular dynamics simulations using swarm particle intelligence

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

Kamberaj, Hiqmet, E-mail: hkamberaj@ibu.edu.mk

In this paper, we present a new method based on swarm particle social intelligence for use in replica exchange molecular dynamics simulations. In this method, the replicas (representing the different system configurations) are allowed communicating with each other through the individual and social knowledge, in additional to considering them as a collection of real particles interacting through the Newtonian forces. The new method is based on the modification of the equations of motion in such way that the replicas are driven towards the global energy minimum. The method was tested for the Lennard-Jones clusters of N = 4,  5, andmore » 6 atoms. Our results showed that the new method is more efficient than the conventional replica exchange method under the same practical conditions. In particular, the new method performed better on optimizing the distribution of the replicas among the thermostats with time and, in addition, ergodic convergence is observed to be faster. We also introduce a weighted histogram analysis method allowing analyzing the data from simulations by combining data from all of the replicas and rigorously removing the inserted bias.« less

Conformational sampling enhancement of replica exchange molecular dynamics simulations using swarm particle intelligence

NASA Astrophysics Data System (ADS)

Kamberaj, Hiqmet

2015-09-01

In this paper, we present a new method based on swarm particle social intelligence for use in replica exchange molecular dynamics simulations. In this method, the replicas (representing the different system configurations) are allowed communicating with each other through the individual and social knowledge, in additional to considering them as a collection of real particles interacting through the Newtonian forces. The new method is based on the modification of the equations of motion in such way that the replicas are driven towards the global energy minimum. The method was tested for the Lennard-Jones clusters of N = 4, 5, and 6 atoms. Our results showed that the new method is more efficient than the conventional replica exchange method under the same practical conditions. In particular, the new method performed better on optimizing the distribution of the replicas among the thermostats with time and, in addition, ergodic convergence is observed to be faster. We also introduce a weighted histogram analysis method allowing analyzing the data from simulations by combining data from all of the replicas and rigorously removing the inserted bias.

Biases in medication prescribing: the case of second-generation antipsychotics.

PubMed

Makhinson, Michael

2010-01-01

The shift from first-generation antipsychotic medications to second-generation antipsychotic medications initially caused a wave of excitement about the potential for improved and broader efficacy of these medications concurrent with an improved side-effect profile. Recent data from high-quality research analyses have subsequently raised significant questions about these claims. This research evidence has, however, not altered prescribing behavior in a way that would be expected from fully rational evaluation of the evidence. Prescribing decisions represent poorly understood, complex behaviors influenced by a number of external and internal forces, some of which may be elucidated by advances in social and cognitive psychology. In this article, the decision to prescribe first- versus second-generation antipsychotic medications is examined, and specific social psychological biases and individual cognitive biases are hypothesized to be significant influences on clinicians. These biases may perpetuate disparity between research evidence and clinical practice.

Priming in implicit memory tasks: prior study causes enhanced discriminability, not only bias.

PubMed

Zeelenberg, René; Wagenmakers, Eric-Jan M; Raaijmakers, Jeroen G W

2002-03-01

R. Ratcliff and G. McKoon (1995, 1996, 1997; R. Ratcliff, D. Allbritton, & G. McKoon, 1997) have argued that repetition priming effects are solely due to bias. They showed that prior study of the target resulted in a benefit in a later implicit memory task. However, prior study of a stimulus similar to the target resulted in a cost. The present study, using a 2-alternative forced-choice procedure, investigated the effect of prior study in an unbiased condition: Both alternatives were studied prior to their presentation in an implicit memory task. Contrary to a pure bias interpretation of priming, consistent evidence was obtained in 3 implicit memory tasks (word fragment completion, auditory word identification, and picture identification) that performance was better when both alternatives were studied than when neither alternative was studied. These results show that prior study results in enhanced discriminability, not only bias.

Language use and stereotyping: the role of approach and avoidance motivation goals.

PubMed

Gil de Montes, Lorena; Ortiz, Garbiñe; Valencia, José F; Larrañaga, Maider; Agirrezabal, Arrate

2012-11-01

The use of more abstract language to describe expected behaviors as opposed to unexpected behaviors has traditionally been considered a way of stereotype maintenance. This tendency is known as linguistic expectancy bias. Two experiments examined the influence of approach and avoidance motivational orientations on the production of this linguistic expectancy bias. It was predicted that approach strategic orientation is likely to describe expectancy consistent behaviors at a higher level of linguistic abstraction than expectancy inconsistent behaviors. In contrast, avoidance strategic orientation is likely to describe both expectancy consistent behaviors and expectancy inconsistent behaviors at a lower level of linguistic abstraction, thus facilitating the disappearance of linguistic expectancy bias. Two experiments confirmed these expectations, using strategic orientation manipulations based either on communication goals or on motor action, and measuring linguistic abstraction either on forced-choice answer format or on free descriptions. Implications for the generalisation of linguistic expectancy bias are discussed.

Large-Scale Genomic Analysis of Codon Usage in Dengue Virus and Evaluation of Its Phylogenetic Dependence

PubMed Central

Lara-Ramírez, Edgar E.; Salazar, Ma Isabel; López-López, María de Jesús; Salas-Benito, Juan Santiago; Sánchez-Varela, Alejandro

2014-01-01

The increasing number of dengue virus (DENV) genome sequences available allows identifying the contributing factors to DENV evolution. In the present study, the codon usage in serotypes 1–4 (DENV1–4) has been explored for 3047 sequenced genomes using different statistics methods. The correlation analysis of total GC content (GC) with GC content at the three nucleotide positions of codons (GC1, GC2, and GC3) as well as the effective number of codons (ENC, ENCp) versus GC3 plots revealed mutational bias and purifying selection pressures as the major forces influencing the codon usage, but with distinct pressure on specific nucleotide position in the codon. The correspondence analysis (CA) and clustering analysis on relative synonymous codon usage (RSCU) within each serotype showed similar clustering patterns to the phylogenetic analysis of nucleotide sequences for DENV1–4. These clustering patterns are strongly related to the virus geographic origin. The phylogenetic dependence analysis also suggests that stabilizing selection acts on the codon usage bias. Our analysis of a large scale reveals new feature on DENV genomic evolution. PMID:25136631

Counterintuitive electron localisation from density-functional theory with polarisable solvent models

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

Dale, Stephen G., E-mail: sdale@ucmerced.edu; Johnson, Erin R., E-mail: erin.johnson@dal.ca

2015-11-14

Exploration of the solvated electron phenomena using density-functional theory (DFT) generally results in prediction of a localised electron within an induced solvent cavity. However, it is well known that DFT favours highly delocalised charges, rendering the localisation of a solvated electron unexpected. We explore the origins of this counterintuitive behaviour using a model Kevan-structure system. When a polarisable-continuum solvent model is included, it forces electron localisation by introducing a strong energetic bias that favours integer charges. This results in the formation of a large energetic barrier for charge-hopping and can cause the self-consistent field to become trapped in local minimamore » thus converging to stable solutions that are higher in energy than the ground electronic state. Finally, since the bias towards integer charges is caused by the polarisable continuum, these findings will also apply to other classical polarisation corrections, as in combined quantum mechanics and molecular mechanics (QM/MM) methods. The implications for systems beyond the solvated electron, including cationic DNA bases, are discussed.« less

Surface-induced effects in fluctuation-based measurements of single-polymer elasticity: A direct probe of the radius of gyration

NASA Astrophysics Data System (ADS)

Innes-Gold, Sarah N.; Morgan, Ian L.; Saleh, Omar A.

2018-03-01

Single-molecule measurements of polymer elasticity are powerful, direct probes of both biomolecular structure and principles of polymer physics. Recent work has revealed low-force regimes in which biopolymer elasticity is understood through blob-based scaling models. However, the small tensions required to observe these regimes have the potential to create measurement biases, particularly due to the increased interactions of the polymer chain with tethering surfaces. Here, we examine one experimentally observed bias, in which fluctuation-based estimates of elasticity report an unexpectedly low chain compliance. We show that the effect is in good agreement with predictions based on quantifying the exclusion effect of the surface through an image-method calculation of available polymer configurations. The analysis indicates that the effect occurs at an external tension inversely proportional to the polymer's zero-tension radius of gyration. We exploit this to demonstrate a self-consistent scheme for estimating the radius of gyration of the tethered polymer. This is shown in measurements of both hyaluronic acid and poly(ethylene glycol) chains.

RELIC: a novel dye-bias correction method for Illumina Methylation BeadChip.

PubMed

Xu, Zongli; Langie, Sabine A S; De Boever, Patrick; Taylor, Jack A; Niu, Liang

2017-01-03

The Illumina Infinium HumanMethylation450 BeadChip and its successor, Infinium MethylationEPIC BeadChip, have been extensively utilized in epigenome-wide association studies. Both arrays use two fluorescent dyes (Cy3-green/Cy5-red) to measure methylation level at CpG sites. However, performance difference between dyes can result in biased estimates of methylation levels. Here we describe a novel method, called REgression on Logarithm of Internal Control probes (RELIC) to correct for dye bias on whole array by utilizing the intensity values of paired internal control probes that monitor the two color channels. We evaluate the method in several datasets against other widely used dye-bias correction methods. Results on data quality improvement showed that RELIC correction statistically significantly outperforms alternative dye-bias correction methods. We incorporated the method into the R package ENmix, which is freely available from the Bioconductor website ( https://www.bioconductor.org/packages/release/bioc/html/ENmix.html ). RELIC is an efficient and robust method to correct for dye-bias in Illumina Methylation BeadChip data. It outperforms other alternative methods and conveniently implemented in R package ENmix to facilitate DNA methylation studies.

An open-access CMIP5 pattern library for temperature and precipitation: Description and methodology

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

Lynch, Cary D.; Hartin, Corinne A.; Bond-Lamberty, Benjamin

Pattern scaling is used to efficiently emulate general circulation models and explore uncertainty in climate projections under multiple forcing scenarios. Pattern scaling methods assume that local climate changes scale with a global mean temperature increase, allowing for spatial patterns to be generated for multiple models for any future emission scenario. For uncertainty quantification and probabilistic statistical analysis, a library of patterns with descriptive statistics for each file would be beneficial, but such a library does not presently exist. Of the possible techniques used to generate patterns, the two most prominent are the delta and least squared regression methods. We exploremore » the differences and statistical significance between patterns generated by each method and assess performance of the generated patterns across methods and scenarios. Differences in patterns across seasons between methods and epochs were largest in high latitudes (60-90°N/S). Bias and mean errors between modeled and pattern predicted output from the linear regression method were smaller than patterns generated by the delta method. Across scenarios, differences in the linear regression method patterns were more statistically significant, especially at high latitudes. We found that pattern generation methodologies were able to approximate the forced signal of change to within ≤ 0.5°C, but choice of pattern generation methodology for pattern scaling purposes should be informed by user goals and criteria. As a result, this paper describes our library of least squared regression patterns from all CMIP5 models for temperature and precipitation on an annual and sub-annual basis, along with the code used to generate these patterns.« less

An open-access CMIP5 pattern library for temperature and precipitation: Description and methodology

DOE PAGES

Lynch, Cary D.; Hartin, Corinne A.; Bond-Lamberty, Benjamin; ...

2017-05-15

Pattern scaling is used to efficiently emulate general circulation models and explore uncertainty in climate projections under multiple forcing scenarios. Pattern scaling methods assume that local climate changes scale with a global mean temperature increase, allowing for spatial patterns to be generated for multiple models for any future emission scenario. For uncertainty quantification and probabilistic statistical analysis, a library of patterns with descriptive statistics for each file would be beneficial, but such a library does not presently exist. Of the possible techniques used to generate patterns, the two most prominent are the delta and least squared regression methods. We exploremore » the differences and statistical significance between patterns generated by each method and assess performance of the generated patterns across methods and scenarios. Differences in patterns across seasons between methods and epochs were largest in high latitudes (60-90°N/S). Bias and mean errors between modeled and pattern predicted output from the linear regression method were smaller than patterns generated by the delta method. Across scenarios, differences in the linear regression method patterns were more statistically significant, especially at high latitudes. We found that pattern generation methodologies were able to approximate the forced signal of change to within ≤ 0.5°C, but choice of pattern generation methodology for pattern scaling purposes should be informed by user goals and criteria. As a result, this paper describes our library of least squared regression patterns from all CMIP5 models for temperature and precipitation on an annual and sub-annual basis, along with the code used to generate these patterns.« less

Intervendor consistency and reproducibility of left ventricular 2D global and regional strain with two different high-end ultrasound systems.

PubMed

Shiino, Kenji; Yamada, Akira; Ischenko, Matthew; Khandheria, Bijoy K; Hudaverdi, Mahala; Speranza, Vicki; Harten, Mary; Benjamin, Anthony; Hamilton-Craig, Christian R; Platts, David G; Burstow, Darryl J; Scalia, Gregory M; Chan, Jonathan

2017-06-01

We aimed to assess intervendor agreement of global (GLS) and regional longitudinal strain by vendor-specific software after EACVI/ASE Industry Task Force Standardization Initiatives for Deformation Imaging. Fifty-five patients underwent prospective dataset acquisitions on the same day by the same operator using two commercially available cardiac ultrasound systems (GE Vivid E9 and Philips iE33). GLS and regional peak longitudinal strain were analyzed offline using corresponding vendor-specific software (EchoPAC BT13 and QLAB version 10.3). Absolute mean GLS measurements were similar between the two vendors (GE -17.5 ± 5.2% vs. Philips -18.9 ± 5.1%, P = 0.15). There was excellent intervendor correlation of GLS by the same observer [r = 0.94, P < 0.0001; bias -1.3%, 95% CI limits of agreement (LOA) -4.8 to 2.2%). Intervendor comparison for regional longitudinal strain by coronary artery territories distribution were: LAD: r = 0.85, P < 0.0001; bias 0.5%, LOA -5.3 to 6.4%; RCA: r = 0.88, P < 0.0001; bias -2.4%, LOA -8.6 to 3.7%; LCX: r = 0.76, P < 0.0001; bias -5.3%, LOA -10.6 to 2.0%. Intervendor comparison for regional longitudinal strain by LV levels were: basal: r = 0.86, P < 0.0001; bias -3.6%, LOA -9.9 to 2.0%; mid: r = 0.90, P < 0.0001; bias -2.6%, LOA -7.8 to 2.6%; apical: r = 0.74; P < 0.0001; bias -1.3%, LOA -9.4 to 6.8%. Intervendor agreement in GLS and regional strain measurements have significantly improved after the EACVI/ASE Task Force Strain Standardization Initiatives. However, significant wide LOA still exist, especially for regional strain measurements, which remains relevant when considering vendor-specific software for serial measurements. Published on behalf of the European Society of Cardiology. All rights reserved. © The Author 2016. For permissions please email: journals.permissions@oup.com.

Elucidating the ensemble of functionally-relevant transitions in protein systems with a robotics-inspired method

PubMed Central

2013-01-01

Background Many proteins tune their biological function by transitioning between different functional states, effectively acting as dynamic molecular machines. Detailed structural characterization of transition trajectories is central to understanding the relationship between protein dynamics and function. Computational approaches that build on the Molecular Dynamics framework are in principle able to model transition trajectories at great detail but also at considerable computational cost. Methods that delay consideration of dynamics and focus instead on elucidating energetically-credible conformational paths connecting two functionally-relevant structures provide a complementary approach. Effective sampling-based path planning methods originating in robotics have been recently proposed to produce conformational paths. These methods largely model short peptides or address large proteins by simplifying conformational space. Methods We propose a robotics-inspired method that connects two given structures of a protein by sampling conformational paths. The method focuses on small- to medium-size proteins, efficiently modeling structural deformations through the use of the molecular fragment replacement technique. In particular, the method grows a tree in conformational space rooted at the start structure, steering the tree to a goal region defined around the goal structure. We investigate various bias schemes over a progress coordinate for balance between coverage of conformational space and progress towards the goal. A geometric projection layer promotes path diversity. A reactive temperature scheme allows sampling of rare paths that cross energy barriers. Results and conclusions Experiments are conducted on small- to medium-size proteins of length up to 214 amino acids and with multiple known functionally-relevant states, some of which are more than 13Å apart of each-other. Analysis reveals that the method effectively obtains conformational paths connecting structural states that are significantly different. A detailed analysis on the depth and breadth of the tree suggests that a soft global bias over the progress coordinate enhances sampling and results in higher path diversity. The explicit geometric projection layer that biases the exploration away from over-sampled regions further increases coverage, often improving proximity to the goal by forcing the exploration to find new paths. The reactive temperature scheme is shown effective in increasing path diversity, particularly in difficult structural transitions with known high-energy barriers. PMID:24565158

Evaluating the impact of method bias in health behaviour research: a meta-analytic examination of studies utilising the theories of reasoned action and planned behaviour.

PubMed

McDermott, Máirtín S; Sharma, Rajeev

2017-12-01

The methods employed to measure behaviour in research testing the theories of reasoned action/planned behaviour (TRA/TPB) within the context of health behaviours have the potential to significantly bias findings. One bias yet to be examined in that literature is that due to common method variance (CMV). CMV introduces a variance in scores attributable to the method used to measure a construct, rather than the construct it represents. The primary aim of this study was to evaluate the impact of method bias on the associations of health behaviours with TRA/TPB variables. Data were sourced from four meta-analyses (177 studies). The method used to measure behaviour for each effect size was coded for susceptibility to bias. The moderating impact of method type was assessed using meta-regression. Method type significantly moderated the associations of intentions, attitudes and social norms with behaviour, but not that between perceived behavioural control and behaviour. The magnitude of the moderating effect of method type appeared consistent between cross-sectional and prospective studies, but varied across behaviours. The current findings strongly suggest that method bias significantly inflates associations in TRA/TPB research, and poses a potentially serious validity threat to the cumulative findings reported in that field.

Essential slow degrees of freedom in protein-surface simulations: A metadynamics investigation.

PubMed

Prakash, Arushi; Sprenger, K G; Pfaendtner, Jim

2018-03-29

Many proteins exhibit strong binding affinities to surfaces, with binding energies much greater than thermal fluctuations. When modelling these protein-surface systems with classical molecular dynamics (MD) simulations, the large forces that exist at the protein/surface interface generally confine the system to a single free energy minimum. Exploring the full conformational space of the protein, especially finding other stable structures, becomes prohibitively expensive. Coupling MD simulations with metadynamics (enhanced sampling) has fast become a common method for sampling the adsorption of such proteins. In this paper, we compare three different flavors of metadynamics, specifically well-tempered, parallel-bias, and parallel-tempering in the well-tempered ensemble, to exhaustively sample the conformational surface-binding landscape of model peptide GGKGG. We investigate the effect of mobile ions and ion charge, as well as the choice of collective variable (CV), on the binding free energy of the peptide. We make the case for explicitly biasing ions to sample the true binding free energy of biomolecules when the ion concentration is high and the binding free energies of the solute and ions are similar. We also make the case for choosing CVs that apply bias to all atoms of the solute to speed up calculations and obtain the maximum possible amount of information about the system. Copyright © 2017 Elsevier Inc. All rights reserved.

Effectiveness of Low-Level Laser Therapy in Reducing Orthodontic Pain: A Systematic Review and Meta-Analysis

PubMed Central

Deana, Naira Figueiredo; Zaror, Carlos; Sandoval, Paulo

2017-01-01

Objectives To assess the effectiveness of low-level laser therapy (LLLT) in reducing orthodontic pain after the application of orthodontic force (OF). Methods A systematic search was conducted in the MEDLINE, EMBASE, Scopus, Cochrane Library, Web of Science, and EBSCOhost databases. The study included randomized clinical trials (RCT) which analysed the effectiveness of LLLT in reducing orthodontic pain assessed at 24 and 72 hrs after the application of OF. The risk of bias of the eligible trials was assessed using the Cochrane Collaboration's risk of bias tool. Standard mean difference was calculated and pooled by meta-analysis using random effect models. Results Of 467 identified articles, 20 RCT were finally included. In the risk of bias assessments, 13 studies presented a high risk, 5 an unclear risk, and 2 a low risk. The meta-analysis showed that in patients treated with laser versus placebo there was a difference in favour of LLLT in spontaneous pain 24 and 72 hrs after the installation of light archwires and spontaneous pain and chewing pain 24 and 72 hrs after the installation of elastomeric separators. Conclusions LLLT proved to be effective in promoting a reduction in spontaneous and chewing pain after the application of OF; however, the poor quality of the evidence requires these results to be treated with caution. PMID:29089818

A nu-space for image correlation spectroscopy: characterization and application to measure protein transport in live cells

NASA Astrophysics Data System (ADS)

Potvin-Trottier, Laurent; Chen, Lingfeng; Horwitz, Alan Rick; Wiseman, Paul W.

2013-08-01

We introduce a new generalized theoretical framework for image correlation spectroscopy (ICS). Using this framework, we extend the ICS method in time-frequency (ν, nu) space to map molecular flow of fluorescently tagged proteins in individual living cells. Even in the presence of a dominant immobile population of fluorescent molecules, nu-space ICS (nICS) provides an unbiased velocity measurement, as well as the diffusion coefficient of the flow, without requiring filtering. We also develop and characterize a tunable frequency-filter for spatio-temporal ICS (STICS) that allows quantification of the density, the diffusion coefficient and the velocity of biased diffusion. We show that the techniques are accurate over a wide range of parameter space in computer simulation. We then characterize the retrograde flow of adhesion proteins (α6- and αLβ2-GFP integrins and mCherry-paxillin) in CHO.B2 cells plated on laminin and intercellular adhesion molecule 1 (ICAM-1) ligands respectively. STICS with a tunable frequency filter, in conjunction with nICS, measures two new transport parameters, the density and transport bias coefficient (a measure of the diffusive character of a flow/biased diffusion), showing that molecular flow in this cell system has a significant diffusive component. Our results suggest that the integrin-ligand interaction, along with the internal myosin-motor generated force, varies for different integrin-ligand pairs, consistent with previous results.

The Midlatitude Continental Convective Clouds Experiment (MC3E) sounding network: operations, processing and analysis

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

Jensen, M. P.; Toto, T.; Troyan, D.

2015-01-01

The Midlatitude Continental Convective Clouds Experiment (MC3E) took place during the spring of 2011 centered in north-central Oklahoma, USA. The main goal of this field campaign was to capture the dynamical and microphysical characteristics of precipitating convective systems in the US Central Plains. A major component of the campaign was a six-site radiosonde array designed to capture the large-scale variability of the atmospheric state with the intent of deriving model forcing data sets. Over the course of the 46-day MC3E campaign, a total of 1362 radiosondes were launched from the enhanced sonde network. This manuscript provides details on the instrumentationmore » used as part of the sounding array, the data processing activities including quality checks and humidity bias corrections and an analysis of the impacts of bias correction and algorithm assumptions on the determination of convective levels and indices. It is found that corrections for known radiosonde humidity biases and assumptions regarding the characteristics of the surface convective parcel result in significant differences in the derived values of convective levels and indices in many soundings. In addition, the impact of including the humidity corrections and quality controls on the thermodynamic profiles that are used in the derivation of a large-scale model forcing data set are investigated. The results show a significant impact on the derived large-scale vertical velocity field illustrating the importance of addressing these humidity biases.« less

The Midlatitude Continental Convective Clouds Experiment (MC3E) sounding network: operations, processing and analysis

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

Jensen, M. P.; Toto, T.; Troyan, D.

2015-01-27

The Midlatitude Continental Convective Clouds Experiment (MC3E) took place during the spring of 2011 centered in north-central Oklahoma, USA. The main goal of this field campaign was to capture the dynamical and microphysical characteristics of precipitating convective systems in the US Central Plains. A major component of the campaign was a six-site radiosonde array designed to capture the large-scale variability of the atmospheric state with the intent of deriving model forcing data sets. Over the course of the 46-day MC3E campaign, a total of 1362 radiosondes were launched from the enhanced sonde network. This manuscript provides details on the instrumentationmore » used as part of the sounding array, the data processing activities including quality checks and humidity bias corrections and an analysis of the impacts of bias correction and algorithm assumptions on the determination of convective levels and indices. It is found that corrections for known radiosonde humidity biases and assumptions regarding the characteristics of the surface convective parcel result in significant differences in the derived values of convective levels and indices in many soundings. In addition, the impact of including the humidity corrections and quality controls on the thermodynamic profiles that are used in the derivation of a large-scale model forcing data set are investigated. The results show a significant impact on the derived large-scale vertical velocity field illustrating the importance of addressing these humidity biases.« less

Enhanced cell trapping throughput using DC-biased AC electric field in a dielectrophoresis-based fluidic device with densely packed silica beads.

PubMed

Lewpiriyawong, Nuttawut; Xu, Guolin; Yang, Chun

2018-03-01

This paper presents the use of DC-biased AC electric field for enhancing cell trapping throughput in an insulator-based dielectrophoretic (iDEP) fluidic device with densely packed silica beads. Cell suspension is carried through the iDEP device by a pressure-driven flow. Under an applied DC-biased AC electric field, DEP trapping force is produced as a result of non-uniform electric field induced by the gap of electrically insulating silica beads packed between two mesh electrodes that allow both fluid and cells to pass through. While the AC component is mainly to control the magnitude of DEP trapping force, the DC component generates local electroosmotic (EO) flow in the cavity between the beads and the EO flow can be set to move along or against the main pressure-driven flow. Our experimental and simulation results show that desirable trapping is achieved when the EO flow direction is along (not against) the main flow direction. Using our proposed DC-biased AC field, the device can enhance the trapping throughput (in terms of the flowrate of cell suspension) up to five times while yielding almost the same cell capture rates as compared to the pure AC field case. Additionally, the device was demonstrated to selectively trap dead yeast cells from a mixture of flowing live and dead yeast cells. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Publication bias in dermatology systematic reviews and meta-analyses.

PubMed

Atakpo, Paul; Vassar, Matt

2016-05-01

Systematic reviews and meta-analyses in dermatology provide high-level evidence for clinicians and policy makers that influence clinical decision making and treatment guidelines. One methodological problem with systematic reviews is the under representation of unpublished studies. This problem is due in part to publication bias. Omission of statistically non-significant data from meta-analyses may result in overestimation of treatment effect sizes which may lead to clinical consequences. Our goal was to assess whether systematic reviewers in dermatology evaluate and report publication bias. Further, we wanted to conduct our own evaluation of publication bias on meta-analyses that failed to do so. Our study considered systematic reviews and meta-analyses from ten dermatology journals from 2006 to 2016. A PubMed search was conducted, and all full-text articles that met our inclusion criteria were retrieved and coded by the primary author. 293 articles were included in our analysis. Additionally, we formally evaluated publication bias in meta-analyses that failed to do so using trim and fill and cumulative meta-analysis by precision methods. Publication bias was mentioned in 107 articles (36.5%) and was formally evaluated in 64 articles (21.8%). Visual inspection of a funnel plot was the most common method of evaluating publication bias. Publication bias was present in 45 articles (15.3%), not present in 57 articles (19.5%) and not determined in 191 articles (65.2%). Using the trim and fill method, 7 meta-analyses (33.33%) showed evidence of publication bias. Although the trim and fill method only found evidence of publication bias in 7 meta-analyses, the cumulative meta-analysis by precision method found evidence of publication bias in 15 meta-analyses (71.4%). Many of the reviews in our study did not mention or evaluate publication bias. Further, of the 42 articles that stated following PRISMA reporting guidelines, 19 (45.2%) evaluated for publication bias. In comparison to other studies, we found that systematic reviews in dermatology were less likely to evaluate for publication bias. Evaluating and reporting the likelihood of publication bias should be standard practice in systematic reviews when appropriate. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Driven Metadynamics: Reconstructing Equilibrium Free Energies from Driven Adaptive-Bias Simulations

PubMed Central

2013-01-01

We present a novel free-energy calculation method that constructively integrates two distinct classes of nonequilibrium sampling techniques, namely, driven (e.g., steered molecular dynamics) and adaptive-bias (e.g., metadynamics) methods. By employing nonequilibrium work relations, we design a biasing protocol with an explicitly time- and history-dependent bias that uses on-the-fly work measurements to gradually flatten the free-energy surface. The asymptotic convergence of the method is discussed, and several relations are derived for free-energy reconstruction and error estimation. Isomerization reaction of an atomistic polyproline peptide model is used to numerically illustrate the superior efficiency and faster convergence of the method compared with its adaptive-bias and driven components in isolation. PMID:23795244

Can quantile mapping improve precipitation extremes from regional climate models?

NASA Astrophysics Data System (ADS)

Tani, Satyanarayana; Gobiet, Andreas

2015-04-01

The ability of quantile mapping to accurately bias correct regard to precipitation extremes is investigated in this study. We developed new methods by extending standard quantile mapping (QMα) to improve the quality of bias corrected extreme precipitation events as simulated by regional climate model (RCM) output. The new QM version (QMβ) was developed by combining parametric and nonparametric bias correction methods. The new nonparametric method is tested with and without a controlling shape parameter (Qmβ1 and Qmβ0, respectively). Bias corrections are applied on hindcast simulations for a small ensemble of RCMs at six different locations over Europe. We examined the quality of the extremes through split sample and cross validation approaches of these three bias correction methods. This split-sample approach mimics the application to future climate scenarios. A cross validation framework with particular focus on new extremes was developed. Error characteristics, q-q plots and Mean Absolute Error (MAEx) skill scores are used for evaluation. We demonstrate the unstable behaviour of correction function at higher quantiles with QMα, whereas the correction functions with for QMβ0 and QMβ1 are smoother, with QMβ1 providing the most reasonable correction values. The result from q-q plots demonstrates that, all bias correction methods are capable of producing new extremes but QMβ1 reproduces new extremes with low biases in all seasons compared to QMα, QMβ0. Our results clearly demonstrate the inherent limitations of empirical bias correction methods employed for extremes, particularly new extremes, and our findings reveals that the new bias correction method (Qmß1) produces more reliable climate scenarios for new extremes. These findings present a methodology that can better capture future extreme precipitation events, which is necessary to improve regional climate change impact studies.

Moment and maximum likelihood estimators for Weibull distributions under length- and area-biased sampling

Treesearch

Jeffrey H. Gove

2003-01-01

Many of the most popular sampling schemes used in forestry are probability proportional to size methods. These methods are also referred to as size biased because sampling is actually from a weighted form of the underlying population distribution. Length- and area-biased sampling are special cases of size-biased sampling where the probability weighting comes from a...

Bias Correction for the Maximum Likelihood Estimate of Ability. Research Report. ETS RR-05-15

ERIC Educational Resources Information Center

Zhang, Jinming

2005-01-01

Lord's bias function and the weighted likelihood estimation method are effective in reducing the bias of the maximum likelihood estimate of an examinee's ability under the assumption that the true item parameters are known. This paper presents simulation studies to determine the effectiveness of these two methods in reducing the bias when the item…

Pneumatic tube system transport does not alter platelet function in optical and whole blood aggregometry, prothrombin time, activated partial thromboplastin time, platelet count and fibrinogen in patients on anti-platelet drug therapy

PubMed Central

Enko, Dietmar; Mangge, Harald; Münch, Andreas; Niedrist, Tobias; Mahla, Elisabeth; Metzler, Helfried; Prüller, Florian

2017-01-01

Introduction The aim of this study was to assess pneumatic tube system (PTS) alteration on platelet function by the light transmission aggregometry (LTA) and whole blood aggregometry (WBA) method, and on the results of platelet count, prothrombin time (PT), activated partial thromboplastin time (APTT), and fibrinogen. Materials and methods Venous blood was collected into six 4.5 mL VACUETTE® 9NC coagulation sodium citrate 3.8% tubes (Greiner Bio-One International GmbH, Kremsmünster, Austria) from 49 intensive care unit (ICU) patients on dual anti-platelet therapy and immediately hand carried to the central laboratory. Blood samples were divided into 2 Groups: Group 1 samples (N = 49) underwent PTS (4 m/s) transport from the central laboratory to the distant laboratory and back to the central laboratory, whereas Group 2 samples (N = 49) were excluded from PTS forces. In both groups, LTA and WBA stimulated with collagen, adenosine-5’-diphosphate (ADP), arachidonic acid (AA) and thrombin-receptor-activated-peptide 6 (TRAP-6) as well as platelet count, PT, APTT, and fibrinogen were performed. Results No statistically significant differences were observed between blood samples with (Group 1) and without (Group 2) PTS transport (P values from 0.064 – 0.968). The AA-induced LTA (bias: 68.57%) exceeded the bias acceptance limit of ≤ 25%. Conclusions Blood sample transportation with computer controlled PTS in our hospital had no statistically significant effects on platelet aggregation determined in patients with anti-platelet therapy. Although AA induced LTA showed a significant bias, the diagnostic accuracy was not influenced. PMID:28392742

A Novel Method for Estimating Shortwave Direct Radiative Effect of Above-Cloud Aerosols Using CALIOP and MODIS Data

NASA Technical Reports Server (NTRS)

Zhang, Zhibo; Meyer, Kerry G.; Platnick, Steven; Oreopoulos, Lazaros; Lee, Dongmin; Yu, Hongbin

2014-01-01

This paper describes an efficient and unique method for computing the shortwave direct radiative effect (DRE) of aerosol residing above low-level liquid-phase clouds using CALIOP and MODIS data. It addresses the overlap of aerosol and cloud rigorously by utilizing the joint histogram of cloud optical depth and cloud top pressure while also accounting for subgrid-scale variations of aerosols. The method is computationally efficient because of its use of grid-level cloud and aerosol statistics, instead of pixel-level products, and a pre-computed look-up table based on radiative transfer calculations. We verify that for smoke over the southeast Atlantic Ocean the method yields a seasonal mean instantaneous (approximately 1:30PM local time) shortwave DRE of above cloud aerosol (ACA) that generally agrees with more rigorous pixel-level computation within 4 percent. We also estimate the impact of potential CALIOP aerosol optical depth (AOD) retrieval bias of ACA on DRE. We find that the regional and seasonal mean instantaneous DRE of ACA over southeast Atlantic Ocean would increase, from the original value of 6.4 W m(-2) based on operational CALIOP AOD to 9.6 W m(-2) if CALIOP AOD retrieval are biased low by a factor of 1.5 (Meyer et al., 2013) and further to 30.9 W m(-2) if CALIOP AOD retrieval are biased low by a factor of 5 as suggested in (Jethva et al., 2014). In contrast, the instantaneous ACA radiative forcing efficiency (RFE) remains relatively invariant in all cases at about 53 W m(-2) AOD(-1), suggesting a near linear relation between the instantaneous RFE and AOD. We also compute the annual mean instantaneous shortwave DRE of light-absorbing aerosols (i.e., smoke and polluted dust) over global oceans based on 4 years of CALIOP and MODIS data. We find that the variability of the annual mean shortwave DRE of above-cloud light-absorbing aerosol is mainly driven by the optical depth of the underlying clouds. While we demonstrate our method using CALIOP and MODIS data, it can also be extended to other satellite data sets, as well as climate model outputs.

How does bias correction of regional climate model precipitation affect modelled runoff?

NASA Astrophysics Data System (ADS)

Teng, J.; Potter, N. J.; Chiew, F. H. S.; Zhang, L.; Wang, B.; Vaze, J.; Evans, J. P.

2015-02-01

Many studies bias correct daily precipitation from climate models to match the observed precipitation statistics, and the bias corrected data are then used for various modelling applications. This paper presents a review of recent methods used to bias correct precipitation from regional climate models (RCMs). The paper then assesses four bias correction methods applied to the weather research and forecasting (WRF) model simulated precipitation, and the follow-on impact on modelled runoff for eight catchments in southeast Australia. Overall, the best results are produced by either quantile mapping or a newly proposed two-state gamma distribution mapping method. However, the differences between the methods are small in the modelling experiments here (and as reported in the literature), mainly due to the substantial corrections required and inconsistent errors over time (non-stationarity). The errors in bias corrected precipitation are typically amplified in modelled runoff. The tested methods cannot overcome limitations of the RCM in simulating precipitation sequence, which affects runoff generation. Results further show that whereas bias correction does not seem to alter change signals in precipitation means, it can introduce additional uncertainty to change signals in high precipitation amounts and, consequently, in runoff. Future climate change impact studies need to take this into account when deciding whether to use raw or bias corrected RCM results. Nevertheless, RCMs will continue to improve and will become increasingly useful for hydrological applications as the bias in RCM simulations reduces.

Information bias in health research: definition, pitfalls, and adjustment methods

PubMed Central

Althubaiti, Alaa

2016-01-01

As with other fields, medical sciences are subject to different sources of bias. While understanding sources of bias is a key element for drawing valid conclusions, bias in health research continues to be a very sensitive issue that can affect the focus and outcome of investigations. Information bias, otherwise known as misclassification, is one of the most common sources of bias that affects the validity of health research. It originates from the approach that is utilized to obtain or confirm study measurements. This paper seeks to raise awareness of information bias in observational and experimental research study designs as well as to enrich discussions concerning bias problems. Specifying the types of bias can be essential to limit its effects and, the use of adjustment methods might serve to improve clinical evaluation and health care practice. PMID:27217764

Racial bias in judgments of physical size and formidability: From size to threat.

PubMed

Wilson, John Paul; Hugenberg, Kurt; Rule, Nicholas O

2017-07-01

Black men tend to be stereotyped as threatening and, as a result, may be disproportionately targeted by police even when unarmed. Here, we found evidence that biased perceptions of young Black men's physical size may play a role in this process. The results of 7 studies showed that people have a bias to perceive young Black men as bigger (taller, heavier, more muscular) and more physically threatening (stronger, more capable of harm) than young White men. Both bottom-up cues of racial prototypicality and top-down information about race supported these misperceptions. Furthermore, this racial bias persisted even among a target sample from whom upper-body strength was controlled (suggesting that racial differences in formidability judgments are a product of bias rather than accuracy). Biased formidability judgments in turn promoted participants' justifications of hypothetical use of force against Black suspects of crime. Thus, perceivers appear to integrate multiple pieces of information to ultimately conclude that young Black men are more physically threatening than young White men, believing that they must therefore be controlled using more aggressive measures. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Controlled growth of aligned carbon nanotube using pulsed glow barrier discharge

NASA Astrophysics Data System (ADS)

Nozaki, Tomohiro; Kimura, Yoshihito; Okazaki, Ken

2002-10-01

We first achieved a catalytic growth of aligned carbon nanotube (CNT) using atmospheric pressure pulsed glow barrier discharge combined with DC bias (1000 V). Aligned CNT can grow with the directional electric field, and this is a big challenge in barrier discharges since dielectric barrier does not allow DC bias and forces to use AC voltage to maintain stable plasma conditions. To overcome this, we developed a power source generating Gaussian-shape pulses at 20 kpps with 4% duty, and DC bias was applied to the GND electrode where Ni-, Fe-coated substrate existed. With positive pulse, i.e. substrate was the cathode, random growth of CNT was observed at about 10^9 cm-2. Growth rate significantly reduced when applied negative pulse; Negative glow formation near substrate is essential for sufficient supply of radical species to the catalyst. If -DC was biased, aligned CNT with 20 nm was synthesized because negative bias enhanced negative glow formation. Interestingly, 2 to 3 CNTs stuck each other with +DC bias, resulting in 50-70 nm and non-aligned CNT. Atmospheric pressure glow barrier discharges can be highly controlled and be a potential alternative to vacuum plasmas for CVD, micro-scale, nano-scale fabrication.

Final Sampling Bias in Haptic Judgments: How Final Touch Affects Decision-Making.

PubMed

Mitsuda, Takashi; Yoshioka, Yuichi

2018-01-01

When people make a choice between multiple items, they usually evaluate each item one after the other repeatedly. The effect of the order and number of evaluating items on one's choices is essential to understanding the decision-making process. Previous studies have shown that when people choose a favorable item from two items, they tend to choose the item that they evaluated last. This tendency has been observed regardless of sensory modalities. This study investigated the origin of this bias by using three experiments involving two-alternative forced-choice tasks using handkerchiefs. First, the bias appeared in a smoothness discrimination task, which indicates that the bias was not based on judgments of preference. Second, the handkerchief that was touched more often tended to be chosen more frequently in the preference task, but not in the smoothness discrimination task, indicating that a mere exposure effect enhanced the bias. Third, in the condition where the number of touches did not differ between handkerchiefs, the bias appeared when people touched a handkerchief they wanted to touch last, but not when people touched the handkerchief that was predetermined. This finding suggests a direct coupling between final voluntary touching and judgment.

Seasonally Distinct Reconstructions of Northern Alaskan Temperature Variability Since the Last Glacial Maximum

NASA Astrophysics Data System (ADS)

Longo, W. M.; Crowther, J.; Daniels, W.; Russell, J. M.; Giblin, A. E.; Morrill, C.; Zhang, X.; Wang, X.; Huang, Y.

2015-12-01

Paleoclimate reconstructions have provided little consensus on how continental temperatures in Eastern Beringia changed from the Last Glacial Maximum (LGM) to the present. Reconstructions show regional differences in LGM severity, the timing of deglacial warming, and Holocene temperature variability. Currently, arctic temperatures are increasing at the fastest rates on the planet, highlighting the need to identify the sensitivities of arctic systems to various climate forcings. This cannot be done without resolving the complex climate history of Eastern Beringia. Here, we present two new organic geochemical temperature reconstructions from Lake E5, north central Alaska that span the LGM, last glacial termination and Holocene. The proxies (alkenones and brGDGTs) record seasonally distinct temperatures, allowing for the attribution of different forcings to each proxy. The alkenone-based UK37 reconstruction records spring/early summer lake temperatures and indicates a 4 oC abrupt warming at 13.1 ka and a relatively warm late Holocene, which peaks at 2.4 ka and exhibits a cooling trend from 2.4 to 0.1 ka. The brGDGT reconstruction is calibrated to mean annual air temperature and interpreted here as exhibiting a strong warm season bias. BrGDGTs show an abrupt 4.5 oC warming at 14 ka, and show evidence for an early Holocene Thermal Maximum (HTM), which cools by 3 oC after 8.4 ka. Because UK37 temperatures do not exhibit an early HTM, we hypothesize that summer insolation had a minimal effect on spring/early summer lake temperatures. Instead, the UK37 reconstruction agrees with sea ice and sea surface temperature reconstructions from the Beaufort and Chukchi Seas and northeast Pacific Ocean. We hypothesize that forcings associated with sea ice concentration and changes in atmospheric circulation had stronger affects on spring/early summer lake temperatures and we present modern observational data in support of this hypothesis. By contrast, the summer-biased brGDGT reconstruction suggests a strong and relatively direct temperature response to summer insolation forcing. Together, these records suggest that both internal and external forcings significantly affected LGM to present temperature variability in Eastern Beringia, with different seasonal biases.

Harnessing Macroscopic Forces in Catalysis

DTIC Science & Technology

2009-11-09

Figure 1. Schematic representation of biasing reaction selectivity via mechanocatalysis. A catalyst, “ mcat ”, is embedded in an elastomeric support...Deformation of the elastomeric support transfers mechanical stress to mcat . Under stress-free conditions, mcat catalyzes the transformation of reactant

Why Choose Teaching?

ERIC Educational Resources Information Center

Vocke, David E.; Foran, James V.

2017-01-01

With the teaching profession under attack from political, social, and economic forces, what is attracting individuals to seek out careers in education? Sort out the facts from the biases with evidence to guide your informed, thoughtful decision about teaching as a viable career option.

Why Home Economics Should Be Morally Biased.

ERIC Educational Resources Information Center

Leach, Mary S.; Page, Ralph C.

1987-01-01

The authors argue that the home economics curriculum should be designed to help students deal with the conflicting values of family and career, which the authors see as a major force behind gender discrimination and inequality of the sexes. (CH)

Neuroanatomy of intergroup bias: A white matter microstructure study of individual differences.

PubMed

Baumgartner, Thomas; Nash, Kyle; Hill, Christopher; Knoch, Daria

2015-11-15

Intergroup bias-the tendency to behave more positively toward an ingroup member than an outgroup member-is a powerful social force, for good and ill. Although it is widely demonstrated, intergroup bias is not universal, as it is characterized by significant individual differences. Recently, attention has begun to turn to whether neuroanatomy might explain these individual differences in intergroup bias. However, no research to date has examined whether white matter microstructure could help determine differences in behavior toward ingroup and outgroup members. In the current research, we examine intergroup bias with the third-party punishment paradigm and white matter integrity and connectivity strength as determined by diffusion tensor imaging (DTI). We found that both increased white matter integrity at the right temporal-parietal junction (TPJ) and connectivity strength between the right TPJ and the dorsomedial prefrontal cortex (DMPFC) were associated with increased impartiality in the third-party punishment paradigm, i.e., reduced intergroup bias. Further, consistent with the role that these brain regions play in the mentalizing network, we found that these effects were mediated by mentalizing processes. Participants with greater white matter integrity at the right TPJ and connectivity strength between the right TPJ and the DMPFC employed mentalizing processes more equally for ingroup and outgroup members, and this non-biased use of mentalizing was associated with increased impartiality. The current results help shed light on the mechanisms of bias and, potentially, on interventions that promote impartiality over intergroup bias. Copyright © 2015 Elsevier Inc. All rights reserved.

The Roles of Convection Parameterization in the Formation of Double ITCZ Syndrome in the NCAR CESM: I. Atmospheric Processes

NASA Astrophysics Data System (ADS)

Song, Xiaoliang; Zhang, Guang J.

2018-03-01

Several improvements are implemented in the Zhang-McFarlane (ZM) convection scheme to investigate the roles of convection parameterization in the formation of double intertropical convergence zone (ITCZ) bias in the NCAR CESM1.2.1. It is shown that the prominent double ITCZ biases of precipitation, sea surface temperature (SST), and wind stress in the standard CESM1.2.1 are largely eliminated in all seasons with the use of these improvements in convection scheme. This study for the first time demonstrates that the modifications of convection scheme can eliminate the double ITCZ biases in all seasons, including boreal winter and spring. Further analysis shows that the elimination of the double ITCZ bias is achieved not by improving other possible contributors, such as stratus cloud bias off the west coast of South America and cloud/radiation biases over the Southern Ocean, but by modifying the convection scheme itself. This study demonstrates that convection scheme is the primary contributor to the double ITCZ bias in the CESM1.2.1, and provides a possible solution to the long-standing double ITCZ problem. The atmospheric model simulations forced by observed SST show that the original ZM convection scheme tends to produce double ITCZ bias in high SST scenario, while the modified convection scheme does not. The impact of changes in each core component of convection scheme on the double ITCZ bias in atmospheric model is identified and further investigated.

A propensity score approach to correction for bias due to population stratification using genetic and non-genetic factors.

PubMed

Zhao, Huaqing; Rebbeck, Timothy R; Mitra, Nandita

2009-12-01

Confounding due to population stratification (PS) arises when differences in both allele and disease frequencies exist in a population of mixed racial/ethnic subpopulations. Genomic control, structured association, principal components analysis (PCA), and multidimensional scaling (MDS) approaches have been proposed to address this bias using genetic markers. However, confounding due to PS can also be due to non-genetic factors. Propensity scores are widely used to address confounding in observational studies but have not been adapted to deal with PS in genetic association studies. We propose a genomic propensity score (GPS) approach to correct for bias due to PS that considers both genetic and non-genetic factors. We compare the GPS method with PCA and MDS using simulation studies. Our results show that GPS can adequately adjust and consistently correct for bias due to PS. Under no/mild, moderate, and severe PS, GPS yielded estimated with bias close to 0 (mean=-0.0044, standard error=0.0087). Under moderate or severe PS, the GPS method consistently outperforms the PCA method in terms of bias, coverage probability (CP), and type I error. Under moderate PS, the GPS method consistently outperforms the MDS method in terms of CP. PCA maintains relatively high power compared to both MDS and GPS methods under the simulated situations. GPS and MDS are comparable in terms of statistical properties such as bias, type I error, and power. The GPS method provides a novel and robust tool for obtaining less-biased estimates of genetic associations that can consider both genetic and non-genetic factors. 2009 Wiley-Liss, Inc.

Comparison of Relative Bias, Precision, and Efficiency of Sampling Methods for Natural Enemies of Soybean Aphid (Hemiptera: Aphididae).

PubMed

Bannerman, J A; Costamagna, A C; McCornack, B P; Ragsdale, D W

2015-06-01

Generalist natural enemies play an important role in controlling soybean aphid, Aphis glycines (Hemiptera: Aphididae), in North America. Several sampling methods are used to monitor natural enemy populations in soybean, but there has been little work investigating their relative bias, precision, and efficiency. We compare five sampling methods: quadrats, whole-plant counts, sweep-netting, walking transects, and yellow sticky cards to determine the most practical methods for sampling the three most prominent species, which included Harmonia axyridis (Pallas), Coccinella septempunctata L. (Coleoptera: Coccinellidae), and Orius insidiosus (Say) (Hemiptera: Anthocoridae). We show an important time by sampling method interaction indicated by diverging community similarities within and between sampling methods as the growing season progressed. Similarly, correlations between sampling methods for the three most abundant species over multiple time periods indicated differences in relative bias between sampling methods and suggests that bias is not consistent throughout the growing season, particularly for sticky cards and whole-plant samples. Furthermore, we show that sticky cards produce strongly biased capture rates relative to the other four sampling methods. Precision and efficiency differed between sampling methods and sticky cards produced the most precise (but highly biased) results for adult natural enemies, while walking transects and whole-plant counts were the most efficient methods for detecting coccinellids and O. insidiosus, respectively. Based on bias, precision, and efficiency considerations, the most practical sampling methods for monitoring in soybean include walking transects for coccinellid detection and whole-plant counts for detection of small predators like O. insidiosus. Sweep-netting and quadrat samples are also useful for some applications, when efficiency is not paramount. © The Authors 2015. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Impacts of correcting the inter-variable correlation of climate model outputs on hydrological modeling

NASA Astrophysics Data System (ADS)

Chen, Jie; Li, Chao; Brissette, François P.; Chen, Hua; Wang, Mingna; Essou, Gilles R. C.

2018-05-01

Bias correction is usually implemented prior to using climate model outputs for impact studies. However, bias correction methods that are commonly used treat climate variables independently and often ignore inter-variable dependencies. The effects of ignoring such dependencies on impact studies need to be investigated. This study aims to assess the impacts of correcting the inter-variable correlation of climate model outputs on hydrological modeling. To this end, a joint bias correction (JBC) method which corrects the joint distribution of two variables as a whole is compared with an independent bias correction (IBC) method; this is considered in terms of correcting simulations of precipitation and temperature from 26 climate models for hydrological modeling over 12 watersheds located in various climate regimes. The results show that the simulated precipitation and temperature are considerably biased not only in the individual distributions, but also in their correlations, which in turn result in biased hydrological simulations. In addition to reducing the biases of the individual characteristics of precipitation and temperature, the JBC method can also reduce the bias in precipitation-temperature (P-T) correlations. In terms of hydrological modeling, the JBC method performs significantly better than the IBC method for 11 out of the 12 watersheds over the calibration period. For the validation period, the advantages of the JBC method are greatly reduced as the performance becomes dependent on the watershed, GCM and hydrological metric considered. For arid/tropical and snowfall-rainfall-mixed watersheds, JBC performs better than IBC. For snowfall- or rainfall-dominated watersheds, however, the two methods behave similarly, with IBC performing somewhat better than JBC. Overall, the results emphasize the advantages of correcting the P-T correlation when using climate model-simulated precipitation and temperature to assess the impact of climate change on watershed hydrology. However, a thorough validation and a comparison with other methods are recommended before using the JBC method, since it may perform worse than the IBC method for some cases due to bias nonstationarity of climate model outputs.

Estimating Gravity Biases with Wavelets in Support of a 1-cm Accurate Geoid Model

NASA Astrophysics Data System (ADS)

Ahlgren, K.; Li, X.

2017-12-01

Systematic errors that reside in surface gravity datasets are one of the major hurdles in constructing a high-accuracy geoid model at high resolutions. The National Oceanic and Atmospheric Administration's (NOAA) National Geodetic Survey (NGS) has an extensive historical surface gravity dataset consisting of approximately 10 million gravity points that are known to have systematic biases at the mGal level (Saleh et al. 2013). As most relevant metadata is absent, estimating and removing these errors to be consistent with a global geopotential model and airborne data in the corresponding wavelength is quite a difficult endeavor. However, this is crucial to support a 1-cm accurate geoid model for the United States. With recently available independent gravity information from GRACE/GOCE and airborne gravity from the NGS Gravity for the Redefinition of the American Vertical Datum (GRAV-D) project, several different methods of bias estimation are investigated which utilize radial basis functions and wavelet decomposition. We estimate a surface gravity value by incorporating a satellite gravity model, airborne gravity data, and forward-modeled topography at wavelet levels according to each dataset's spatial wavelength. Considering the estimated gravity values over an entire gravity survey, an estimate of the bias and/or correction for the entire survey can be found and applied. In order to assess the accuracy of each bias estimation method, two techniques are used. First, each bias estimation method is used to predict the bias for two high-quality (unbiased and high accuracy) geoid slope validation surveys (GSVS) (Smith et al. 2013 & Wang et al. 2017). Since these surveys are unbiased, the various bias estimation methods should reflect that and provide an absolute accuracy metric for each of the bias estimation methods. Secondly, the corrected gravity datasets from each of the bias estimation methods are used to build a geoid model. The accuracy of each geoid model provides an additional metric to assess the performance of each bias estimation method. The geoid model accuracies are assessed using the two GSVS lines and GPS-leveling data across the United States.

The halo Boltzmann equation

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

Biagetti, Matteo; Desjacques, Vincent; Kehagias, Alex

2016-04-01

Dark matter halos are the building blocks of the universe as they host galaxies and clusters. The knowledge of the clustering properties of halos is therefore essential for the understanding of the galaxy statistical properties. We derive an effective halo Boltzmann equation which can be used to describe the halo clustering statistics. In particular, we show how the halo Boltzmann equation encodes a statistically biased gravitational force which generates a bias in the peculiar velocities of virialized halos with respect to the underlying dark matter, as recently observed in N-body simulations.

Electron tunneling through atomically flat and ultrathin hexagonal boron nitride

NASA Astrophysics Data System (ADS)

Lee, Gwan-Hyoung; Yu, Young-Jun; Lee, Changgu; Dean, Cory; Shepard, Kenneth L.; Kim, Philip; Hone, James

2011-12-01

Electron tunneling through atomically flat and ultrathin hexagonal boron nitride (h-BN) on gold-coated mica was investigated using conductive atomic force microscopy. Low-bias direct tunneling was observed in mono-, bi-, and tri-layer h-BN. For all thicknesses, Fowler-Nordheim tunneling (FNT) occurred at high bias, showing an increase of breakdown voltage with thickness. Based on the FNT model, the barrier height for tunneling (3.07 eV) and dielectric strength (7.94 MV/cm) of h-BN are obtained; these values are comparable to those of SiO2.

Adhesion Warfare: US Army Combat Forces Face an Enemy who is Capable of Negating their Doctrinal Stand-off Firepower Advantage in Afghanistan, with Deadly Consequences

DTIC Science & Technology

2008-12-12

those who assist who make the difference. I am indebted to all for the wonderful, professional and candid support. I dedicate this work to the...same spirit as his forefathers did at places like the Marne, Luzon, Chosin and Hill 875. All the Way! vi TABLE OF CONTENTS Page MASTER OF...scope and bias. All effort was made to mitigate bias and present various views on the information researched. The core material is pre-Global War on

Eastern equatorial Pacific sea surface temperature annual cycle in the Kiel climate model: simulation benefits from enhancing atmospheric resolution

NASA Astrophysics Data System (ADS)

Wengel, C.; Latif, M.; Park, W.; Harlaß, J.; Bayr, T.

2018-05-01

A long-standing difficulty of climate models is to capture the annual cycle (AC) of eastern equatorial Pacific (EEP) sea surface temperature (SST). In this study, we first examine the EEP SST AC in a set of integrations of the coupled Kiel Climate Model, in which only atmosphere model resolution differs. When employing coarse horizontal and vertical atmospheric resolution, significant biases in the EEP SST AC are observed. These are reflected in an erroneous timing of the cold tongue's onset and termination as well as in an underestimation of the boreal spring warming amplitude. A large portion of these biases are linked to a wrong simulation of zonal surface winds, which can be traced back to precipitation biases on both sides of the equator and an erroneous low-level atmospheric circulation over land. Part of the SST biases also is related to shortwave radiation biases related to cloud cover biases. Both wind and cloud cover biases are inherent to the atmospheric component, as shown by companion uncoupled atmosphere model integrations forced by observed SSTs. Enhancing atmosphere model resolution, horizontal and vertical, markedly reduces zonal wind and cloud cover biases in coupled as well as uncoupled mode and generally improves simulation of the EEP SST AC. Enhanced atmospheric resolution reduces convection biases and improves simulation of surface winds over land. Analysis of a subset of models from the Coupled Model Intercomparison Project phase 5 (CMIP5) reveals that in these models, very similar mechanisms are at work in driving EEP SST AC biases.

Structural Uncertainty in Antarctic sea ice simulations

NASA Astrophysics Data System (ADS)

Schneider, D. P.

2016-12-01

The inability of the vast majority of historical climate model simulations to reproduce the observed increase in Antarctic sea ice has motivated many studies about the quality of the observational record, the role of natural variability versus forced changes, and the possibility of missing or inadequate forcings in the models (such as freshwater discharge from thinning ice shelves or an inadequate magnitude of stratospheric ozone depletion). In this presentation I will highlight another source of uncertainty that has received comparatively little attention: Structural uncertainty, that is, the systematic uncertainty in simulated sea ice trends that arises from model physics and mean-state biases. Using two large ensembles of experiments from the Community Earth System Model (CESM), I will show that the model is predisposed towards producing negative Antarctic sea ice trends during 1979-present, and that this outcome is not simply because the model's decadal variability is out-of-synch with that in nature. In the "Tropical Pacific Pacemaker" ensemble, in which observed tropical Pacific SST anomalies are prescribed, the model produces very realistic atmospheric circulation trends over the Southern Ocean, yet the sea ice trend is negative in every ensemble member. However, if the ensemble-mean trend (commonly interpreted as the forced response) is removed, some ensemble members show a sea ice increase that is very similar to the observed. While this results does confirm the important role of natural variability, it also suggests a strong bias in the forced response. I will discuss the reasons for this systematic bias and explore possible remedies. This an important problem to solve because projections of 21st -Century changes in the Antarctic climate system (including ice sheet surface mass balance changes and related changes in the sea level budget) have a strong dependence on the mean state of and changes in the Antarctic sea ice cover. This problem is not unique to CESM, but is pervasive across CMIP5-class models.

Selective forces and mutational biases drive stop codon usage in the human genome: a comparison with sense codon usage.

PubMed

Trotta, Edoardo

2016-05-17

The three stop codons UAA, UAG, and UGA signal the termination of mRNA translation. As a result of a mechanism that is not adequately understood, they are normally used with unequal frequencies. In this work, we showed that selective forces and mutational biases drive stop codon usage in the human genome. We found that, in respect to sense codons, stop codon usage was affected by stronger selective forces but was less influenced by neutral mutational biases. UGA is the most frequent termination codon in human genome. However, UAA was the preferred stop codon in genes with high breadth of expression, high level of expression, AT-rich coding sequences, housekeeping functions, and in gene ontology categories with the largest deviation from expected stop codon usage. Selective forces associated with the breadth and the level of expression favoured AT-rich sequences in the mRNA region including the stop site and its proximal 3'-UTR, but acted with scarce effects on sense codons, generating two regions, upstream and downstream of the stop codon, with strongly different base composition. By favouring low levels of GC-content, selection promoted labile local secondary structures at the stop site and its proximal 3'-UTR. The compositional and structural context favoured by selection was surprisingly emphasized in the class of ribosomal proteins and was consistent with sequence elements that increase the efficiency of translational termination. Stop codons were also heterogeneously distributed among chromosomes by a mechanism that was strongly correlated with the GC-content of coding sequences. In human genome, the nucleotide composition and the thermodynamic stability of stop codon site and its proximal 3'-UTR are correlated with the GC-content of coding sequences and with the breadth and the level of gene expression. In highly expressed genes stop codon usage is compositionally and structurally consistent with highly efficient translation termination signals.

Robust Tracking of Small Displacements with a Bayesian Estimator

PubMed Central

Dumont, Douglas M.; Byram, Brett C.

2016-01-01

Radiation-force-based elasticity imaging describes a group of techniques that use acoustic radiation force (ARF) to displace tissue in order to obtain qualitative or quantitative measurements of tissue properties. Because ARF-induced displacements are on the order of micrometers, tracking these displacements in vivo can be challenging. Previously, it has been shown that Bayesian-based estimation can overcome some of the limitations of a traditional displacement estimator like normalized cross-correlation (NCC). In this work, we describe a Bayesian framework that combines a generalized Gaussian-Markov random field (GGMRF) prior with an automated method for selecting the prior’s width. We then evaluate its performance in the context of tracking the micrometer-order displacements encountered in an ARF-based method like acoustic radiation force impulse (ARFI) imaging. The results show that bias, variance, and mean-square error performance vary with prior shape and width, and that an almost one order-of-magnitude reduction in mean-square error can be achieved by the estimator at the automatically-selected prior width. Lesion simulations show that the proposed estimator has a higher contrast-to-noise ratio but lower contrast than NCC, median-filtered NCC, and the previous Bayesian estimator, with a non-Gaussian prior shape having better lesion-edge resolution than a Gaussian prior. In vivo results from a cardiac, radiofrequency ablation ARFI imaging dataset show quantitative improvements in lesion contrast-to-noise ratio over NCC as well as the previous Bayesian estimator. PMID:26529761

50 ways to trace your veteran: increasing response rates can be cheap and effective

PubMed Central

Fear, Nicola Townsend; Van Staden, Lauren; Iversen, Amy; Hall, John; Wessely, Simon

2010-01-01

Background while low response rates need not introduce bias into research, having a lower percentage of responders does increase the potential for this to occur. This is of particular concern given the decline that has been occurring in response rates since the 1950s. However, there are various methods that can be incorporated into the study design, which can assist in increasing levels of participation. Objective To outline the methods used by the King's Centre for Military Health Research (KCMHR) when conducting a recent telephone survey of serving and ex-Service military personnel. Design Using participants who had already taken part in a questionnaire-based study on the health effects of serving in the UK Armed Forces (n=10,272), a subsample was selected for an in-depth telephone interview-based follow-up study. The subsample consisted of 1,105 participants, selected on the basis of their mental health status. An adjusted response rate of 76% was achieved (n=821). Results Various methods of contact were used in this study to ensure an adequate response rate was achieved. Conclusions Simple research strategies increase response rates and are likely to reduce bias. Use of multiple simultaneous tracing methods and customisation of the approach to the target population increases rapport between participants, ensuring that those who take part feel valued as members of the study. In the current climate of decreasing participation in studies, research teams need to engage with their study population and devise innovative strategies to keep participants involved in the research being undertaken. PMID:22893795

Model selection on solid ground: Rigorous comparison of nine ways to evaluate Bayesian model evidence

PubMed Central

Schöniger, Anneli; Wöhling, Thomas; Samaniego, Luis; Nowak, Wolfgang

2014-01-01

Bayesian model selection or averaging objectively ranks a number of plausible, competing conceptual models based on Bayes' theorem. It implicitly performs an optimal trade-off between performance in fitting available data and minimum model complexity. The procedure requires determining Bayesian model evidence (BME), which is the likelihood of the observed data integrated over each model's parameter space. The computation of this integral is highly challenging because it is as high-dimensional as the number of model parameters. Three classes of techniques to compute BME are available, each with its own challenges and limitations: (1) Exact and fast analytical solutions are limited by strong assumptions. (2) Numerical evaluation quickly becomes unfeasible for expensive models. (3) Approximations known as information criteria (ICs) such as the AIC, BIC, or KIC (Akaike, Bayesian, or Kashyap information criterion, respectively) yield contradicting results with regard to model ranking. Our study features a theory-based intercomparison of these techniques. We further assess their accuracy in a simplistic synthetic example where for some scenarios an exact analytical solution exists. In more challenging scenarios, we use a brute-force Monte Carlo integration method as reference. We continue this analysis with a real-world application of hydrological model selection. This is a first-time benchmarking of the various methods for BME evaluation against true solutions. Results show that BME values from ICs are often heavily biased and that the choice of approximation method substantially influences the accuracy of model ranking. For reliable model selection, bias-free numerical methods should be preferred over ICs whenever computationally feasible. PMID:25745272

Normal and anomalous transport phenomena in two-dimensional NaCl, MoS2 and honeycomb surfaces

NASA Astrophysics Data System (ADS)

Mbemmo, A. M. Fopossi; Kenmoé, G. Djuidjé; Kofané, T. C.

2018-04-01

Understanding the effects of anisotropy and substrate shape on the stochastic processes is critically needed for the improvement of the quality of the transport information. The effect of biharmonic force on the transport phenomena of a particle in two-dimensional is investigated in the framework of three representative substrate lattices: NaCl, MoS2 and honeycomb. We focus on the particles drift velocity, to characterize the transport properties in the system. Normal and anomalous transport are identified for a particular set of the system parameters such as the biharmonic parameter, the bias force, the phase-lag of two signals, as well as the noise amplitude. According to the direction ψ where the bias force is applied, we determine the biharmonic parameter ɛ for the presence of anomalous transport and show that for the NaCl surface, the anomalous transport is observed for 2 < ɛ < 10. For the MoS2 surface, it appears at monochromatic driven (ɛ = 0) and for 3 < ɛ < 9. In particular for the honeycomb surface anomalous transport is generated for 0 ⩽ ɛ < 6 only when ψ > 30 °.

Multiple vaccinations, health, and recall bias within UK armed forces deployed to Iraq: cohort study.

PubMed

Murphy, Dominic; Hotopf, Matthew; Wessely, Simon

2008-06-30

To assess the relation between self reported number of vaccinations received and health, and between numbers of vaccinations recorded from individuals' medical records and health. First phase of a cohort study. UK armed forces personnel. 4882 randomly selected military personnel deployed to Iraq since 2003 and a subset of 378 whose vaccination records were accessed. Psychological distress, fatigue, symptoms of post-traumatic stress disorder, health perception, and multiple physical symptoms. Personnel who reported receiving two or more vaccinations on a single day were more likely to report symptoms of fatigue (adjusted risk ratio 1.17, 95% confidence interval 1.05 to 1.30), show caseness according to the general health questionnaire (1.31, 1.13 to 1.53), and have multiple physical symptoms (1.32, 1.08 to 1.60). These associations were no longer significant when number of vaccinations recorded in individuals' medical records was used as the independent variable. Multiple vaccinations given to personnel in the UK armed forces in preparation for deployment to Iraq are not associated with adverse health consequences when vaccinations are recorded objectively from medical records. Adverse health consequences associated with self reported multiple vaccinations could be explained by recall bias.

Directionally compliant legs influence the intrinsic pitch behaviour of a trotting quadruped

PubMed Central

Lee, David V; Meek, Sanford G

2005-01-01

Limb design is well conserved among quadrupeds, notably, the knees point forward (i.e. cranial inclination of femora) and the elbows point back (i.e. caudal inclination of humeri). This study was undertaken to examine the effects of joint orientation on individual leg forces and centre of mass dynamics. Steady-speed trotting was simulated in two quadrupedal models. Model I had the knee and elbow orientation of a quadruped and model II had a reversed leg configuration in which knees point back and elbows point forward. The model's legs showed directional compliance determined by the orientation of the knee/elbow. In both models, forward pointing knees/elbows produced a propulsive force bias, while rearward pointing knees/elbows produced a braking force bias. Hence, model I showed the same pattern of hind-leg propulsion and fore-leg braking observed in trotting animals. Simulations revealed minimal pitch oscillations during steady-speed trotting of model I, but substantially greater and more irregular pitch oscillations of model II. The reduced pitch oscillation of model I was a result of fore-leg and hind-leg forces that reduced pitching moments during early and late stance, respectively. This passive mechanism for reducing pitch oscillations was an emergent property of directionally compliant legs with the fore–hind configuration of model I. Such intrinsic stability resulting from mechanical design can simplify control tasks and lead to more robust running machines. PMID:15817430

The right side? Under time pressure, approach motivation leads to right-oriented bias.

PubMed

Roskes, Marieke; Sligte, Daniel; Shalvi, Shaul; De Dreu, Carsten K W

2011-11-01

Approach motivation, a focus on achieving positive outcomes, is related to relative left-hemispheric brain activation, which translates to a variety of right-oriented behavioral biases. In two studies, we found that approach-motivated individuals display a right-oriented bias, but only when they are forced to act quickly. In a task in which they had to divide lines into two equal parts, approach-motivated individuals bisected the line at a point farther to the right than avoidance-motivated individuals did, but only when they worked under high time pressure. In our analysis of all Fédération Internationale de Football Association (FIFA) World Cup penalty shoot-outs, we found that goalkeepers were two times more likely to dive to the right than to the left when their team was behind, a situation that we conjecture induces approach motivation. Because penalty takers shot toward the two sides of the goal equally often, the goalkeepers' right-oriented bias was dysfunctional, allowing more goals to be scored. Directional biases may facilitate group coordination but prove maladaptive in individual settings and interpersonal competition.

A study of electrostatic spring softening for dual-axis micromirror

NASA Astrophysics Data System (ADS)

Zhao, Yi; E H Tay, Francis; Zhou, Guangya; Siong Chau, Fook

2006-08-01

Electrostatic spring softening is an important characteristic of electrostatically actuated dual-axis micromirror, since it lowers the resonant frequencies. This paper presents an approach based on approximating the electrostatic forces by the first-order Taylor's series expansion to investigate this characteristic. The dual-axis micromirror studied in this paper has three motion modes, two torsional (about x- and y-axis, respectively) and one translational (about z-axis). The stiffnesses of all these modes are softened by a DC bias voltage applied to the mirror plate. The resonant frequencies are lowered with the increment of the bias voltage. The relationship of the bias voltage and the resonant frequencies of all the motion modes is derived. The analytical results show that the resonant frequency curves are affected by the capacitor geometries, i.e. the gap between the mirror plate and the electrodes and the electrodes size. The lowering curves drop slowly when the bias voltage is small. While for large bias voltage, the lowering curves drop rapidly. The experiment results are consistent with those obtained by the analytical approach.

Timing of nest vegetation measurement may obscure adaptive significance of nest-site characteristics: A simulation study.

PubMed

McConnell, Mark D; Monroe, Adrian P; Burger, Loren Wes; Martin, James A

2017-02-01

Advances in understanding avian nesting ecology are hindered by a prevalent lack of agreement between nest-site characteristics and fitness metrics such as nest success. We posit this is a result of inconsistent and improper timing of nest-site vegetation measurements. Therefore, we evaluated how the timing of nest vegetation measurement influences the estimated effects of vegetation structure on nest survival. We simulated phenological changes in nest-site vegetation growth over a typical nesting season and modeled how the timing of measuring that vegetation, relative to nest fate, creates bias in conclusions regarding its influence on nest survival. We modeled the bias associated with four methods of measuring nest-site vegetation: Method 1-measuring at nest initiation, Method 2-measuring at nest termination regardless of fate, Method 3-measuring at nest termination for successful nests and at estimated completion for unsuccessful nests, and Method 4-measuring at nest termination regardless of fate while also accounting for initiation date. We quantified and compared bias for each method for varying simulated effects, ranked models for each method using AIC, and calculated the proportion of simulations in which each model (measurement method) was selected as the best model. Our results indicate that the risk of drawing an erroneous or spurious conclusion was present in all methods but greater with Method 2 which is the most common method reported in the literature. Methods 1 and 3 were similarly less biased. Method 4 provided no additional value as bias was similar to Method 2 for all scenarios. While Method 1 is seldom practical to collect in the field, Method 3 is logistically practical and minimizes inherent bias. Implementation of Method 3 will facilitate estimating the effect of nest-site vegetation on survival, in the least biased way, and allow reliable conclusions to be drawn.

The effectiveness of adhesives on the retention of mandibular free end saddle partial dentures: An in vitro study.

PubMed

Quiney, Daniel; Nishio Ayre, Wayne; Milward, Paul

2017-07-01

Existing in vitro methods for testing denture adhesives do not fully replicate the complex oral geometries and environment; and in vivo methods are qualitative, prone to bias and not easily reproducible. The purpose of this study was to develop a novel, quantitative and more accurate model to test the effect of adhesives on the retentive force of mandibular free end saddle partial dentures. An in vitro model was developed based on an anatomically accurate cast of a clinical case. Experimentally, the amount of adhesive was varied (0.2g-1g) and the tensile force required for displacement was measured. Different commercially available adhesives were then tested at the optimum volume using the in vitro model. A 3D finite element model of the denture was used to assess how the forces to induce denture displacement varied according to the position of the force along the saddle length. The mass of adhesive was found to significantly alter retention forces, with 0.4-0.7g being the optimum range for this particular scenario. Use of adhesives significantly improved mandibular free end saddle partial denture retention with the worst performing adhesive increasing retention nine-fold whilst the best performing adhesive increased retention twenty three-fold. The finite element model revealed that 77% more force was required to displace the denture by positioning forces towards the mesial end of the saddle compared to the distal end. An in vitro denture adhesive model was developed, which demonstrated that mass of adhesive plays a significant role in enhancing denture retention and supported the design principle of placing as few teeth as clinically necessary on the distal end of the free end saddles. Limiting the position of teeth on free end saddles to the mesial and mid portion of the saddle will reduce displacements caused by mastication. The movement of mandibular free end saddle partial dentures can be restricted with the use of denture adhesives. Altering the mass of adhesive used can further improve the retention of mandibular free end saddle partial dentures for patients. Copyright © 2017 Elsevier Ltd. All rights reserved.

Concurrent validity and reliability of using ground reaction force and center of pressure parameters in the determination of leg movement initiation during single leg lift.

PubMed

Aldabe, Daniela; de Castro, Marcelo Peduzzi; Milosavljevic, Stephan; Bussey, Melanie Dawn

2016-09-01

Postural adjustment evaluations during single leg lift requires the initiation of heel lift (T1) identification. T1 measured by means of motion analyses system is the most reliable approach. However, this method involves considerable workspace, expensive cameras, and time processing data and setting up laboratory. The use of ground reaction forces (GRF) and centre of pressure (COP) data is an alternative method as its data processing and setting up is less time consuming. Further, kinetic data is normally collected using frequency samples higher than 1000Hz whereas kinematic data are commonly captured using 50-200Hz. This study describes the concurrent-validity and reliability of GRF and COP measurements in determining T1, using a motion analysis system as reference standard. Kinematic and kinetic data during single leg lift were collected from ten participants. GRF and COP data were collected using one and two force plates. Displacement of a single heel marker was captured by means of ten Vicon(©) cameras. Kinetic and kinematic data were collected using a sample frequency of 1000Hz. Data were analysed in two stages: identification of key events in the kinetic data, and assessing concurrent validity of T1 based on the chosen key events with T1 provided by the kinematic data. The key event presenting the least systematic bias, along with a narrow 95% CI and limits of agreement against the reference standard T1, was the Baseline COPy event. Baseline COPy event was obtained using one force plate and presented excellent between-tester reliability. Copyright © 2016 Elsevier B.V. All rights reserved.

Methods to Quantify Cell Signaling and GPCR Receptor Ligand Bias: Characterization of Drugs that Target the Endocannabinoid Receptors in Huntington's Disease.

PubMed

Bagher, Amina M; Laprairie, Robert B; Kelly, Melanie E M; Denovan-Wright, Eileen M

2018-01-01

G protein-coupled receptors (GPCRs) interact with multiple intracellular effector proteins such that different ligands may preferentially activate one signal pathway over others, a phenomenon known as signaling bias. Signaling bias can be quantified to optimize drug selection for preclinical research. Here, we describe moderate-throughput methods to quantify signaling bias of known and novel compounds. In the example provided, we describe a method to define cannabinoid-signaling bias in a cell culture model of Huntington's disease (HD). Decreasing type 1 cannabinoid receptor (CB 1 ) levels is correlated with chorea and cognitive deficits in HD. There is evidence that elevating CB 1 levels and/or signaling may be beneficial for HD patients while decreasing CB 1 levels and/or signaling may be detrimental. Recent studies have found that Gα i/o -biased CB 1 agonists activate extracellular signal-regulated kinase (ERK), increase CB 1 protein levels, and improve viability of cells expressing mutant huntingtin. In contrast, CB 1 agonists that are β-arrestin1-biased were found to reduce CB 1 protein levels and cell viability. Measuring agonist bias of known and novel CB 1 agonists will provide important data that predict CB 1 -specific agonists that might be beneficial in animal models of HD and, following animal testing, in HD patients. This method can also be applied to study signaling bias for other GPCRs.

Monitoring and forecasting the 2009-2010 severe drought in Southwest China

NASA Astrophysics Data System (ADS)

Zhang, X.; Tang, Q.; Liu, X.; Leng, G.; Li, Z.; Cui, H.

2015-12-01

From the fall of 2009 to the spring of 2010, an unprecedented drought swept across southwest China (SW) and led to a severe shortage in drinking water and a huge loss to regional economy. Monitoring and predicting the severe drought with several months in advance is of critical importance for such hydrological disaster assessment, preparation and mitigation. In this study, we attempted to carry out a model-based hydrological monitoring and seasonal forecasting framework, and assessed its skill in capturing the evolution of the SW drought in 2009-2010. Using the satellite-based meteorological forcings and the Variable Infiltration Capacity (VIC) hydrologic model, the drought conditions were assessed in a near-real-time manner based on a 62-year (1952-2013) retrospective simulation, wherein the satellite data was adjusted by a gauge-based forcing to remove systematic biases. Bias-corrected seasonal forecasting outputs from the National Centers for Environmental Prediction (NCEP) Climate Forecast System Version 2 (CFSv2) was tentatively applied for a seasonal hydrologic prediction and its predictive skill was overall evaluated relative to a traditional Ensemble Streamflow Prediction (ESP) method with lead time varying from 1 to 6 months. The results show that the climate model-driven hydrologic predictability is generally limited to 1-month lead time and exhibits negligible skill improvement relative to ESP during this drought event, suggesting the initial hydrologic conditions (IHCs) play a dominant role in forecasting performance. The research highlights the value of the framework in providing accurate IHCs in a real-time manner which will greatly benefit drought early-warning.

Study of high-power GaAs-based laser diodes operation and failure by cross-sectional electrostatic force microscopy

NASA Astrophysics Data System (ADS)

Ankudinov, A.; Titkov, A. N.; Evtikhiev, Vadim P.; Kotelnikov, Eugeny Y.; Bazhenov, N.; Zegrya, Georgy G.; Huhtinen, H.; Laiho, R.

2003-06-01

One of the important factors that restricts the power limit of semiconductor lasers is a catastrophic optical mirror damage. This process is significantly suppressed through decreasing the optical power density due to its redistribution over the broad transverse waveguide (BW). Recently it was shown that record-breaking values of the quasicontinuous and continuous-wave (QWC and CW) output power for 100-μm-wide-aperture devices can be achieved by incorporating a broad transverse waveguide into 0.97 μm emitting Al-free InGaAs(P)/InGaP/GaAs and Al-containing InGaAs/AlGaAs/GaAs separate confinement heterostructure quantum-well lasers (SCH-QWL). Another important factor limiting the CW output power is the Joule overheating of a laser diode due to an extra serial resistance. Traditionally, a decrease in the resistance is achieved by development of the contacts, whereas a voltage distribution across the device structure is not analyzed properly. At high operating currents the applied voltage can drop not only across the n-p-junction, but also at certain additional regions of the laser structure depending on a particular design of the device. Electrostatic force microscopy (EFM) provides a very promising method to study the voltage distribution across an operating device with a nanometer space resolution. An application of EFM for diagnostics of III-V laser diodes without and under applied biases have been recently demonstrated. However, the most interesting range of the biases, the lazing regime, has not been studied yet.

Neural Network and Nearest Neighbor Algorithms for Enhancing Sampling of Molecular Dynamics.

PubMed

Galvelis, Raimondas; Sugita, Yuji

2017-06-13

The free energy calculations of complex chemical and biological systems with molecular dynamics (MD) are inefficient due to multiple local minima separated by high-energy barriers. The minima can be escaped using an enhanced sampling method such as metadynamics, which apply bias (i.e., importance sampling) along a set of collective variables (CV), but the maximum number of CVs (or dimensions) is severely limited. We propose a high-dimensional bias potential method (NN2B) based on two machine learning algorithms: the nearest neighbor density estimator (NNDE) and the artificial neural network (ANN) for the bias potential approximation. The bias potential is constructed iteratively from short biased MD simulations accounting for correlation among CVs. Our method is capable of achieving ergodic sampling and calculating free energy of polypeptides with up to 8-dimensional bias potential.

Bias correction of temperature produced by the Community Climate System Model using Artificial Neural Networks

NASA Astrophysics Data System (ADS)

Moghim, S.; Hsu, K.; Bras, R. L.

2013-12-01

General Circulation Models (GCMs) are used to predict circulation and energy transfers between the atmosphere and the land. It is known that these models produce biased results that will have impact on their uses. This work proposes a new method for bias correction: the equidistant cumulative distribution function-artificial neural network (EDCDFANN) procedure. The method uses artificial neural networks (ANNs) as a surrogate model to estimate bias-corrected temperature, given an identification of the system derived from GCM models output variables. A two-layer feed forward neural network is trained with observations during a historical period and then the adjusted network can be used to predict bias-corrected temperature for future periods. To capture the extreme values this method is combined with the equidistant CDF matching method (EDCDF, Li et al. 2010). The proposed method is tested with the Community Climate System Model (CCSM3) outputs using air and skin temperature, specific humidity, shortwave and longwave radiation as inputs to the ANN. This method decreases the mean square error and increases the spatial correlation between the modeled temperature and the observed one. The results indicate the EDCDFANN has potential to remove the biases of the model outputs.

Magnetic charge distribution and stray field landscape of asymmetric néel walls in a magnetically patterned exchange bias layer system

NASA Astrophysics Data System (ADS)

Zingsem, Norbert; Ahrend, Florian; Vock, Silvia; Gottlob, Daniel; Krug, Ingo; Doganay, Hatice; Holzinger, Dennis; Neu, Volker; Ehresmann, Arno

2017-12-01

The 3D stray field landscape above an exchange bias layer system with engineered domain walls has been fully characterized by quantitative magnetic force microscopy (qMFM) measurements. This method is based on a complete quantification of the MFM tip’s imaging properties and the subtraction of its contribution from the measured MFM data by deconvolution in Fourier space. The magnetically patterned Ir17Mn83/Co70Fe30-exchange-bias-multilayers have been designed to contain asymmetric head-to-head (hh)/tail-to-tail (tt) Néel walls between domains of different magnetic anisotropies for potential use in guided particle transport. In the current application, qMFM reveals the effective magnetic charge profile on the surface of the sample—with high spatial resolution and in an absolute quantitative manner. These data enable to calculate the magnetostatic potential and the full stray field landscape above the sample surface. It has been successfully tested against: (i) micromagnetic simulations of the magnetization structure of a comparable exchange-bias layer system, (ii) measurements of the magnetization profile across the domain boundary with x-ray photoemission electron microscopy, and (iii) direct stray field measurements obtained by scanning Hall probe microscopy at elevated scan heights. This approach results in a quantitative determination of the stray field landscape at close distances to the sample surface, which will be of importance for remote magnetic particle transport applications in lab-on-a-chip devices. Furthermore, the highly resolving and quantitative MFM approach reveals details of the domain transition across the artificially structured phase boundary, which have to be attributed to a continuous change in the materials parameters across this boundary, rather than an abrupt one.

Vertical Jump Height Estimation Algorithm Based on Takeoff and Landing Identification Via Foot-Worn Inertial Sensing.

PubMed

Wang, Jianren; Xu, Junkai; Shull, Peter B

2018-03-01

Vertical jump height is widely used for assessing motor development, functional ability, and motor capacity. Traditional methods for estimating vertical jump height rely on force plates or optical marker-based motion capture systems limiting assessment to people with access to specialized laboratories. Current wearable designs need to be attached to the skin or strapped to an appendage which can potentially be uncomfortable and inconvenient to use. This paper presents a novel algorithm for estimating vertical jump height based on foot-worn inertial sensors. Twenty healthy subjects performed countermovement jumping trials and maximum jump height was determined via inertial sensors located above the toe and under the heel and was compared with the gold standard maximum jump height estimation via optical marker-based motion capture. Average vertical jump height estimation errors from inertial sensing at the toe and heel were -2.2±2.1 cm and -0.4±3.8 cm, respectively. Vertical jump height estimation with the presented algorithm via inertial sensing showed excellent reliability at the toe (ICC(2,1)=0.98) and heel (ICC(2,1)=0.97). There was no significant bias in the inertial sensing at the toe, but proportional bias (b=1.22) and fixed bias (a=-10.23cm) were detected in inertial sensing at the heel. These results indicate that the presented algorithm could be applied to foot-worn inertial sensors to estimate maximum jump height enabling assessment outside of traditional laboratory settings, and to avoid bias errors, the toe may be a more suitable location for inertial sensor placement than the heel.

Improvement in the electrical performance and bias-stress stability of dual-active-layered silicon zinc oxide/zinc oxide thin-film transistor

NASA Astrophysics Data System (ADS)

Liu, Yu-Rong; Zhao, Gao-Wei; Lai, Pai-To; Yao, Ruo-He

2016-08-01

Si-doped zinc oxide (SZO) thin films are deposited by using a co-sputtering method, and used as the channel active layers of ZnO-based TFTs with single and dual active layer structures. The effects of silicon content on the optical transmittance of the SZO thin film and electrical properties of the SZO TFT are investigated. Moreover, the electrical performances and bias-stress stabilities of the single- and dual-active-layer TFTs are investigated and compared to reveal the effects of the Si doping and dual-active-layer structure. The average transmittances of all the SZO films are about 90% in the visible light region of 400 nm-800 nm, and the optical band gap of the SZO film gradually increases with increasing Si content. The Si-doping can effectively suppress the grain growth of ZnO, revealed by atomic force microscope analysis. Compared with that of the undoped ZnO TFT, the off-state current of the SZO TFT is reduced by more than two orders of magnitude and it is 1.5 × 10-12 A, and thus the on/off current ratio is increased by more than two orders of magnitude. In summary, the SZO/ZnO TFT with dual-active-layer structure exhibits a high on/off current ratio of 4.0 × 106 and superior stability under gate-bias and drain-bias stress. Projected supported by the National Natural Science Foundation of China (Grant Nos. 61076113 and 61274085), the Natural Science Foundation of Guangdong Province (Grant No. 2016A030313474), and the University Development Fund (Nanotechnology Research Institute, Grant No. 00600009) of the University of Hong Kong, China.

The Effectiveness of Using Limited Gauge Measurements for Bias Adjustment of Satellite-Based Precipitation Estimation over Saudi Arabia

NASA Astrophysics Data System (ADS)

Alharbi, Raied; Hsu, Kuolin; Sorooshian, Soroosh; Braithwaite, Dan

2018-01-01

Precipitation is a key input variable for hydrological and climate studies. Rain gauges are capable of providing reliable precipitation measurements at point scale. However, the uncertainty of rain measurements increases when the rain gauge network is sparse. Satellite -based precipitation estimations appear to be an alternative source of precipitation measurements, but they are influenced by systematic bias. In this study, a method for removing the bias from the Precipitation Estimation from Remotely Sensed Information using Artificial Neural Networks-Cloud Classification System (PERSIANN-CCS) over a region where the rain gauge is sparse is investigated. The method consists of monthly empirical quantile mapping, climate classification, and inverse-weighted distance method. Daily PERSIANN-CCS is selected to test the capability of the method for removing the bias over Saudi Arabia during the period of 2010 to 2016. The first six years (2010 - 2015) are calibrated years and 2016 is used for validation. The results show that the yearly correlation coefficient was enhanced by 12%, the yearly mean bias was reduced by 93% during validated year. Root mean square error was reduced by 73% during validated year. The correlation coefficient, the mean bias, and the root mean square error show that the proposed method removes the bias on PERSIANN-CCS effectively that the method can be applied to other regions where the rain gauge network is sparse.

Model-Based Control of Observer Bias for the Analysis of Presence-Only Data in Ecology

PubMed Central

Warton, David I.; Renner, Ian W.; Ramp, Daniel

2013-01-01

Presence-only data, where information is available concerning species presence but not species absence, are subject to bias due to observers being more likely to visit and record sightings at some locations than others (hereafter “observer bias”). In this paper, we describe and evaluate a model-based approach to accounting for observer bias directly – by modelling presence locations as a function of known observer bias variables (such as accessibility variables) in addition to environmental variables, then conditioning on a common level of bias to make predictions of species occurrence free of such observer bias. We implement this idea using point process models with a LASSO penalty, a new presence-only method related to maximum entropy modelling, that implicitly addresses the “pseudo-absence problem” of where to locate pseudo-absences (and how many). The proposed method of bias-correction is evaluated using systematically collected presence/absence data for 62 plant species endemic to the Blue Mountains near Sydney, Australia. It is shown that modelling and controlling for observer bias significantly improves the accuracy of predictions made using presence-only data, and usually improves predictions as compared to pseudo-absence or “inventory” methods of bias correction based on absences from non-target species. Future research will consider the potential for improving the proposed bias-correction approach by estimating the observer bias simultaneously across multiple species. PMID:24260167

Causes of Cool-Season Precipitation Bias in the East South Central U.S.

NASA Astrophysics Data System (ADS)

Bukovsky, M. S.; McCrary, R. R.; Rendfrey, T. S.; Schroeder, A. D.; Mearns, L.

2017-12-01

A climatological maximum in cool-season precipitation, secondary to that in the Pacific Northwest, exists in the East South Central U.S. region (ESC). Many regional climate simulations have difficulty reproducing this maximum, whether forced with a reanalysis or global climate model (GCM). This problem exists in some, but not all, of the simulations completed for the North American component of CORDEX (Coordinated Regional Downscaling Experiment) and NARCCAP (North American Regional Climate Change Assessment Program). We use both of these ensembles of regional climate model (RCM) simulations to examine precipitation and some of the factors that govern its climatology in this region to develop a better understanding of why some simulations perform better than others. The ESC roughly encompasses the Lower Mississippi, western South Atlantic, southern Ohio and Tennessee hydrologic regions. Cool-season precipitation (November-April) in the ESC is often convective in nature and strongly forced. In this presentation, we will examine some of the potential causes of the climatological precipitation bias for this region, including bias in: sea-surface temperature, moisture flux, El Nino-Southern Oscillation teleconnections, and the climatology of extratropical cyclones. We will also examine simulation configurations to identify any common threads between the simulations that perform better and those that perform worse.

Codon Usage Bias and Determining Forces in Taenia solium Genome.

PubMed

Yang, Xing; Ma, Xusheng; Luo, Xuenong; Ling, Houjun; Zhang, Xichen; Cai, Xuepeng

2015-12-01

The tapeworm Taenia solium is an important human zoonotic parasite that causes great economic loss and also endangers public health. At present, an effective vaccine that will prevent infection and chemotherapy without any side effect remains to be developed. In this study, codon usage patterns in the T. solium genome were examined through 8,484 protein-coding genes. Neutrality analysis showed that T. solium had a narrow GC distribution, and a significant correlation was observed between GC12 and GC3. Examination of an NC (ENC vs GC3s)-plot showed a few genes on or close to the expected curve, but the majority of points with low-ENC (the effective number of codons) values were detected below the expected curve, suggesting that mutational bias plays a major role in shaping codon usage. The Parity Rule 2 plot (PR2) analysis showed that GC and AT were not used proportionally. We also identified 26 optimal codons in the T. solium genome, all of which ended with either a G or C residue. These optimal codons in the T. solium genome are likely consistent with tRNAs that are highly expressed in the cell, suggesting that mutational and translational selection forces are probably driving factors of codon usage bias in the T. solium genome.

Geologic constraints on the macroevolutionary history of marine animals

PubMed Central

Peters, Shanan E.

2005-01-01

The causes of mass extinctions and the nature of taxonomic radiations are central questions in paleobiology. Several episodes of taxonomic turnover in the fossil record, particularly the major mass extinctions, are generally thought to transcend known biases in the geologic record and are widely interpreted as distinct macroevolutionary phenomena that require unique forcing mechanisms. Here, by using a previously undescribed compilation of the durations of sedimentary rock sequences, I compare the rates of expansion and truncation of preserved marine sedimentary basins to rates of origination and extinction among Phanerozoic marine animal genera. Many features of the highly variable record of taxonomic first and last occurrences in the marine animal fossil record, including the major mass extinctions, the frequency distribution of genus longevities, and short- and long-term patterns of genus diversity, can be predicted on the basis of the temporal continuity and quantity of preserved sedimentary rock. Although these results suggest that geologically mediated sampling biases have distorted macroevolutionary patterns in the fossil record, preservation biases alone cannot easily explain the extent to which the sedimentary record duplicates paleobiological patterns. Instead, these results suggest that the processes responsible for producing variability in the sedimentary rock record, such as plate tectonics and sea-level change, may have been dominant and consistent macroevolutionary forces throughout the Phanerozoic. PMID:16105949

Linear Regression Quantile Mapping (RQM) - A new approach to bias correction with consistent quantile trends

NASA Astrophysics Data System (ADS)

Passow, Christian; Donner, Reik

2017-04-01

Quantile mapping (QM) is an established concept that allows to correct systematic biases in multiple quantiles of the distribution of a climatic observable. It shows remarkable results in correcting biases in historical simulations through observational data and outperforms simpler correction methods which relate only to the mean or variance. Since it has been shown that bias correction of future predictions or scenario runs with basic QM can result in misleading trends in the projection, adjusted, trend preserving, versions of QM were introduced in the form of detrended quantile mapping (DQM) and quantile delta mapping (QDM) (Cannon, 2015, 2016). Still, all previous versions and applications of QM based bias correction rely on the assumption of time-independent quantiles over the investigated period, which can be misleading in the context of a changing climate. Here, we propose a novel combination of linear quantile regression (QR) with the classical QM method to introduce a consistent, time-dependent and trend preserving approach of bias correction for historical and future projections. Since QR is a regression method, it is possible to estimate quantiles in the same resolution as the given data and include trends or other dependencies. We demonstrate the performance of the new method of linear regression quantile mapping (RQM) in correcting biases of temperature and precipitation products from historical runs (1959 - 2005) of the COSMO model in climate mode (CCLM) from the Euro-CORDEX ensemble relative to gridded E-OBS data of the same spatial and temporal resolution. A thorough comparison with established bias correction methods highlights the strengths and potential weaknesses of the new RQM approach. References: A.J. Cannon, S.R. Sorbie, T.Q. Murdock: Bias Correction of GCM Precipitation by Quantile Mapping - How Well Do Methods Preserve Changes in Quantiles and Extremes? Journal of Climate, 28, 6038, 2015 A.J. Cannon: Multivariate Bias Correction of Climate Model Outputs - Matching Marginal Distributions and Inter-variable Dependence Structure. Journal of Climate, 29, 7045, 2016

Understanding electric field-enhanced transport for the measurement of nanoparticles and their assembly on surfaces

NASA Astrophysics Data System (ADS)

Tsai, De-Hao

The goal of this dissertation is to understand the synthesis, characterization, and integration of nanoparticles and nanoparticle-based devices by electric field-enhanced transport of nanoparticles. Chapter I describes the factors used for determining particle trajectories and found that electric fields provide the directional electrostatic force to overcome other non-directional influences on particle trajectories. This idea is widely applied in the nanoparticle classification, characterization, and assembly onto substrate surfaces as investigated in the following chapters. Chapter 2 presents a new assembly method to position metal nanoparticles delivered from the gas phase onto surfaces using the electrostatic force generated by biased p-n junction patterned substrates. Aligned deposition patterns of metal nanoparticles were observed, and the patterning selectivity quantified. A simple model accounting for the generated electric field, and the electrostatic, van der Waals, and image forces was used to explain the observed results. Chapter 2.2 describes a data set for particle size resolved deposition, from which a Brownian dynamics model for the process can be evaluated. Brownian motion and fluid convection of nanoparticles, as well as the interactions between the charged nanoparticles and the patterned substrate, including electrostatic force, image force and van der Waals force, are accounted for in the simulation. Using both experiment and simulation the effects of the particle size, electric field intensity, and the convective flow on coverage selectivity have been investigated. Coverage selectivity is most sensitive to electric field, which is controlled by the applied reverse bias voltage across the p-n junction. A non-dimensional analysis of the competition between the electrostatic and diffusion force is found to provide a means to collapse a wide range of process operating conditions and an effective indicator or process performance. Directed assembly of size-selected nanoparticles has been applied in the study of nanoparticle enhanced fluorescence (NEF) bio-sensing devices. Chapter 3 presents results of a systematic examination of funct onalized gold nanoparticles by electrospray-differential mobility analysis (ES-DMA). Formation of selfassembled monolayers (SAMs) of alkylthiol molecules and singly stranded DNA (ssDNA) on the Au-NP surface was detected from a change in particle mobility, which could be modeled to extract the surface packing density. A gas-phase temperature-programmed desorption (TPD) kinetic study of SAMs on the Au-NP found the data to be consistent with a second order Arrhenius based rate law, yielding an Arrhenius-factor of 1x1011s -1 and an activation energy ˜105 kJ/mol. This study suggests that the ES-DMA can be added to the tool set of characterization methods being employed and developed to study the structure and properties of coated nanoparticles. Chapter 3.2 demonstrates this ES-DMA as a new method to investigate colloidal aggregation and the parameters that govern it. Nanoparticle suspensions were characterized by sampling a Au nanoparticle (Au-NP) colloidal solution via electrospray (ES), followed by differential ion-mobility analysis (DMA) to determine the mobility distribution, and thus the aggregate distribution. By sampling at various times, the degree of flocculation and the flocculation rate are determined and found to be inversely proportional to the ionic strength and proportional to the residence time. A stability ratio at different ionic strengths, the critical concentration, and surface potential or surface charge density of Au-NPs are obtained from these data. This method should be a generically useful tool to probe the early stages of colloidal aggregation. Study of ES-DMA is extended to include the characterizations of a variety of materials. Biologically interested materials such as viruses and antibodies could also be characterized. These results show ES-DMA provides a general way to characterize the colloidal materials as well as aerosolized particles.

Data assimilation in integrated hydrological modelling in the presence of observation bias

NASA Astrophysics Data System (ADS)

Rasmussen, J.; Madsen, H.; Jensen, K. H.; Refsgaard, J. C.

2015-08-01

The use of bias-aware Kalman filters for estimating and correcting observation bias in groundwater head observations is evaluated using both synthetic and real observations. In the synthetic test, groundwater head observations with a constant bias and unbiased stream discharge observations are assimilated in a catchment scale integrated hydrological model with the aim of updating stream discharge and groundwater head, as well as several model parameters relating to both stream flow and groundwater modeling. The Colored Noise Kalman filter (ColKF) and the Separate bias Kalman filter (SepKF) are tested and evaluated for correcting the observation biases. The study found that both methods were able to estimate most of the biases and that using any of the two bias estimation methods resulted in significant improvements over using a bias-unaware Kalman Filter. While the convergence of the ColKF was significantly faster than the convergence of the SepKF, a much larger ensemble size was required as the estimation of biases would otherwise fail. Real observations of groundwater head and stream discharge were also assimilated, resulting in improved stream flow modeling in terms of an increased Nash-Sutcliffe coefficient while no clear improvement in groundwater head modeling was observed. Both the ColKF and the SepKF tended to underestimate the biases, which resulted in drifting model behavior and sub-optimal parameter estimation, but both methods provided better state updating and parameter estimation than using a bias-unaware filter.

Data assimilation in integrated hydrological modelling in the presence of observation bias

NASA Astrophysics Data System (ADS)

Rasmussen, Jørn; Madsen, Henrik; Høgh Jensen, Karsten; Refsgaard, Jens Christian

2016-05-01

The use of bias-aware Kalman filters for estimating and correcting observation bias in groundwater head observations is evaluated using both synthetic and real observations. In the synthetic test, groundwater head observations with a constant bias and unbiased stream discharge observations are assimilated in a catchment-scale integrated hydrological model with the aim of updating stream discharge and groundwater head, as well as several model parameters relating to both streamflow and groundwater modelling. The coloured noise Kalman filter (ColKF) and the separate-bias Kalman filter (SepKF) are tested and evaluated for correcting the observation biases. The study found that both methods were able to estimate most of the biases and that using any of the two bias estimation methods resulted in significant improvements over using a bias-unaware Kalman filter. While the convergence of the ColKF was significantly faster than the convergence of the SepKF, a much larger ensemble size was required as the estimation of biases would otherwise fail. Real observations of groundwater head and stream discharge were also assimilated, resulting in improved streamflow modelling in terms of an increased Nash-Sutcliffe coefficient while no clear improvement in groundwater head modelling was observed. Both the ColKF and the SepKF tended to underestimate the biases, which resulted in drifting model behaviour and sub-optimal parameter estimation, but both methods provided better state updating and parameter estimation than using a bias-unaware filter.

Method for revealing biases in precision mass measurements

NASA Astrophysics Data System (ADS)

Vabson, V.; Vendt, R.; Kübarsepp, T.; Noorma, M.

2013-02-01

A practical method for the quantification of systematic errors of large-scale automatic comparators is presented. This method is based on a comparison of the performance of two different comparators. First, the differences of 16 equal partial loads of 1 kg are measured with a high-resolution mass comparator featuring insignificant bias and 1 kg maximum load. At the second stage, a large-scale comparator is tested by using combined loads with known mass differences. Comparing the different results, the biases of any comparator can be easily revealed. These large-scale comparator biases are determined over a 16-month period, and for the 1 kg loads, a typical pattern of biases in the range of ±0.4 mg is observed. The temperature differences recorded inside the comparator concurrently with mass measurements are found to remain within a range of ±30 mK, which obviously has a minor effect on the detected biases. Seasonal variations imply that the biases likely arise mainly due to the functioning of the environmental control at the measurement location.

Comparison of meteorological forcing (WFDEI, AGRI4CAST) to in-situ observations in a semi arid catchment. The case of Merguellil in Tunisia.

NASA Astrophysics Data System (ADS)

Le Page, Michel; Gosset, Cindy; Oueslati, Ines; Calvez, Roger; Zribi, Mehrez; Lilli Chabaane, Zohra

2015-04-01

Meteorological forcing is essential to hydrological and hydro-geological modeling. In the case of the semi-arid catchment of Merguellil in Tunisia, long term time series are only available in the plain for a SYNOP station. Other meteorological stations have been installed since 2010. Therefore, this study aims at qualifying the reliability of the meteorological forcing necessary for an integrated model conception. We compare the meteorological data from 7 stations (sources: WMO and our own station), inside and around the Merguellil catchment, with daily gridded data at 25*25 km from AGRI4CAST and 50*50km from WFDEI. AGRI4CAST (Biaveti et al, 2008) is an interpolated dataset based on actual weather stations produced by the Joint Research Centre (JRC) for the Monitoring Agricultural Resources Unit (MARS). The WFDEI second version dataset (Weedon et al, 2014) has been generated using the same methodology as the widely used WATCH Forcing Data (WFD) by making use of the ERA-Interim reanalysis data. The studied meteorological variables are Rs, Tmoy, U2, P, RH and ET0, with the scores RMSE, bias and R pearson. Regarding the AGRI4CAST dataset, the scores are established over different periods according to variables based on stepping between the observed and interpolated data. The scores show good correlations between the observed temperatures, but with a spatial variability bound to the stations elevations. The moderate and interpolated radiations also show a good concordance indicating a good reliability. The R pearson score obtained for the values of relative humidity show a good correlation between the observations and the interpolations, however, the short periods of comparisons do not allow obtaining significant information and the RMSE and bias are important. Wind speed has an important negative bias for a majority of stations (positively for only one). Only one station shows concordances between the data. The study of the data indicates that we shall have to adjust the wind speeds and the relative humidity of the air for the implementation of a model. Finally the reference evapotranspiration seems relatively coherent, in spite of the dispersal observed during the meteorological measures, but with biases rather high and RMSE also rather high (> 1.3 mm). After revised the parameter U2 and RH, AGRI4CAST can possibly be corrected by ancillary ground stations. The analysis of the WFDEI dataset is currently under evaluation. (1) Biavetti, I., Karetsos, S., Ceglar, A., Toreti, A., Panagos P. (2014), European meteorological data: contribution to research, development and policy support, Proc. of SPIE Vol. 9229 922907-1 (2) Weedon, G. P., G. Balsamo, N. Bellouin, S. Gomes, M. J. Best, and P. Viterbo (2014), The WFDEI meteorological forcing data set: WATCH Forcing Data methodology applied to ERA-Interim reanalysis data, Water Resour. Res., 50, 7505-7514, doi:10.1002/ 2014WR015638.

Identification of flame transfer functions in the presence of intrinsic thermoacoustic feedback and noise

NASA Astrophysics Data System (ADS)

Jaensch, Stefan; Merk, Malte; Emmert, Thomas; Polifke, Wolfgang

2018-05-01

The Large Eddy Simulation/System Identification (LES/SI) approach is a general and efficient numerical method for deducing a Flame Transfer Function (FTF) from the LES of turbulent reacting flow. The method may be summarised as follows: a simulated flame is forced with a broadband excitation signal. The resulting fluctuations of the reference velocity and of the global heat release rate are post-processed via SI techniques in order to estimate a low-order model of the flame dynamics. The FTF is readily deduced from the low-order model. The SI method most frequently applied in aero- and thermo-acoustics has been Wiener-Hopf Inversion (WHI). This method is known to yield biased estimates in situations with feedback, thus it was assumed that non-reflective boundary conditions are required to generate accurate results with the LES/SI approach. Recent research has shown that the FTF is part of the so-called Intrinsic ThermoAcoustic (ITA) feedback loop. Hence, identifying an FTF from a compressible LES is always a closed-loop problem, and consequently one should expect that the WHI would yield biased results. However, several studies proved that WHI results compare favourably with validation data. To resolve this apparent contradiction, a variety of identification methods are compared against each other, including models designed for closed-loop identification. In agreement with theory, we show that the estimate given by WHI does not converge to the actual FTF. Fortunately, the error made is small if excitation amplitudes can be set such that the signal-to-noise ratio is large, but not large enough to trigger nonlinear flame dynamics. Furthermore, we conclude that non-reflective boundary conditions are not essentially necessary to apply the LES/SI approach.

Effect of NiFeCr seed and capping layers on exchange bias and planar Hall voltage response of NiFe/Au/IrMn trilayer structures

NASA Astrophysics Data System (ADS)

Talantsev, Artem; Elzwawy, Amir; Kim, CheolGi

2018-05-01

Thin films and cross junctions, based on NiFe/Au/IrMn structures, were grown on Ta and NiFeCr seed layers by magnetron sputtering. The effects of substitution of Ta with NiFeCr in seed and capping layers on an exchange bias field are studied. A threefold improvement of the exchange bias value in the structures, grown with NiFeCr seed and capping layers, is demonstrated. The reasons for this effect are discussed. Formation of clusters in the NiFeCr capping layer is proved by atomic force microscopy technique. Ta replacement on NiFeCr in the capping layer results in the enhancement of magnetoresistive response and a reduction of noise.

Modification and optimization of the united-residue (UNRES) potential-energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins

PubMed Central

Liwo, Adam; Khalili, Mey; Czaplewski, Cezary; Kalinowski, Sebastian; Ołdziej, Stanisław; Wachucik, Katarzyna; Scheraga, Harold A.

2011-01-01

We report the modification and parameterization of the united-residue (UNRES) force field for energy-based protein-structure prediction and protein-folding simulations. We tested the approach on three training proteins separately: 1E0L (β), 1GAB (α), and 1E0G (α + β). Heretofore, the UNRES force field had been designed and parameterized to locate native-like structures of proteins as global minima of their effective potential-energy surfaces, which largely neglected the conformational entropy because decoys composed of only lowest-energy conformations were used to optimize the force field. Recently, we developed a mesoscopic dynamics procedure for UNRES, and applied it with success to simulate protein folding pathways. How ever, the force field turned out to be largely biased towards α-helical structures in canonical simulations because the conformational entropy had been neglected in the parameterization. We applied the hierarchical optimization method developed in our earlier work to optimize the force field, in which the conformational space of a training protein is divided into levels each corresponding to a certain degree of native-likeness. The levels are ordered according to increasing native-likeness; level 0 corresponds to structures with no native-like elements and the highest level corresponds to the fully native-like structures. The aim of optimization is to achieve the order of the free energies of levels, decreasing as their native-likeness increases. The procedure is iterative, and decoys of the training protein(s) generated with the energy-function parameters of the preceding iteration are used to optimize the force field in a current iteration. We applied the multiplexing replica exchange molecular dynamics (MREMD) method, recently implemented in UNRES, to generate decoys; with this modification, conformational entropy is taken into account. Moreover, we optimized the free-energy gaps between levels at temperatures corresponding to a predominance of folded or unfolded structures, as well as to structures at the putative folding-transition temperature, changing the sign of the gaps at the transition temperature. This enabled us to obtain force fields characterized by a single peak in the heat capacity at the transition temperature. Furthermore, we introduced temperature dependence to the UNRES force field; this is consistent with the fact that it is a free-energy and not a potential-energy function. PMID:17201450

Estimating Bias Error Distributions

NASA Technical Reports Server (NTRS)

Liu, Tian-Shu; Finley, Tom D.

2001-01-01

This paper formulates the general methodology for estimating the bias error distribution of a device in a measuring domain from less accurate measurements when a minimal number of standard values (typically two values) are available. A new perspective is that the bias error distribution can be found as a solution of an intrinsic functional equation in a domain. Based on this theory, the scaling- and translation-based methods for determining the bias error distribution arc developed. These methods are virtually applicable to any device as long as the bias error distribution of the device can be sufficiently described by a power series (a polynomial) or a Fourier series in a domain. These methods have been validated through computational simulations and laboratory calibration experiments for a number of different devices.

The L0 Regularized Mumford-Shah Model for Bias Correction and Segmentation of Medical Images.

PubMed

Duan, Yuping; Chang, Huibin; Huang, Weimin; Zhou, Jiayin; Lu, Zhongkang; Wu, Chunlin

2015-11-01

We propose a new variant of the Mumford-Shah model for simultaneous bias correction and segmentation of images with intensity inhomogeneity. First, based on the model of images with intensity inhomogeneity, we introduce an L0 gradient regularizer to model the true intensity and a smooth regularizer to model the bias field. In addition, we derive a new data fidelity using the local intensity properties to allow the bias field to be influenced by its neighborhood. Second, we use a two-stage segmentation method, where the fast alternating direction method is implemented in the first stage for the recovery of true intensity and bias field and a simple thresholding is used in the second stage for segmentation. Different from most of the existing methods for simultaneous bias correction and segmentation, we estimate the bias field and true intensity without fixing either the number of the regions or their values in advance. Our method has been validated on medical images of various modalities with intensity inhomogeneity. Compared with the state-of-art approaches and the well-known brain software tools, our model is fast, accurate, and robust with initializations.

Constructing a multidimensional free energy surface like a spider weaving a web.

PubMed

Chen, Changjun

2017-10-15

Complete free energy surface in the collective variable space provides important information of the reaction mechanisms of the molecules. But, sufficient sampling in the collective variable space is not easy. The space expands quickly with the number of the collective variables. To solve the problem, many methods utilize artificial biasing potentials to flatten out the original free energy surface of the molecule in the simulation. Their performances are sensitive to the definitions of the biasing potentials. Fast-growing biasing potential accelerates the sampling speed but decreases the accuracy of the free energy result. Slow-growing biasing potential gives an optimized result but needs more simulation time. In this article, we propose an alternative method. It adds the biasing potential to a representative point of the molecule in the collective variable space to improve the conformational sampling. And the free energy surface is calculated from the free energy gradient in the constrained simulation, not given by the negative of the biasing potential as previous methods. So the presented method does not require the biasing potential to remove all the barriers and basins on the free energy surface exactly. Practical applications show that the method in this work is able to produce the accurate free energy surfaces for different molecules in a short time period. The free energy errors are small in the cases of various biasing potentials. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Powering a burnt bridges Brownian ratchet: a model for an extracellular motor driven by proteolysis of collagen.

PubMed

Saffarian, Saveez; Qian, Hong; Collier, Ivan; Elson, Elliot; Goldberg, Gregory

2006-04-01

Biased diffusion of collagenase on collagen fibrils may represent the first observed adenosine triphosphate-independent extracellular molecular motor. The magnitude of force generated by the enzyme remains unclear. We propose a propulsion mechanism based on a burnt bridges Brownian ratchet model with a varying degree of coupling of the free energy from collagen proteolysis to the enzyme motion. When constrained by experimental observations, our model predicts 0.1 pN stall force for individual collagenase molecules. A dimer, surprisingly, can generate a force in the range of 5 pN, suggesting that the motor can be of biological significance.

Using Propensity Scores to Reduce Selection Bias in Mathematics Education Research

ERIC Educational Resources Information Center

Graham, Suzanne E.

2010-01-01

Selection bias is a problem for mathematics education researchers interested in using observational rather than experimental data to make causal inferences about the effects of different instructional methods in mathematics on student outcomes. Propensity score methods represent 1 approach to dealing with such selection bias. This article…

Correction of stream quality trends for the effects of laboratory measurement bias

USGS Publications Warehouse

Alexander, Richard B.; Smith, Richard A.; Schwarz, Gregory E.

1993-01-01

We present a statistical model relating measurements of water quality to associated errors in laboratory methods. Estimation of the model allows us to correct trends in water quality for long-term and short-term variations in laboratory measurement errors. An illustration of the bias correction method for a large national set of stream water quality and quality assurance data shows that reductions in the bias of estimates of water quality trend slopes are achieved at the expense of increases in the variance of these estimates. Slight improvements occur in the precision of estimates of trend in bias by using correlative information on bias and water quality to estimate random variations in measurement bias. The results of this investigation stress the need for reliable, long-term quality assurance data and efficient statistical methods to assess the effects of measurement errors on the detection of water quality trends.

Bias correction for magnetic resonance images via joint entropy regularization.

PubMed

Wang, Shanshan; Xia, Yong; Dong, Pei; Luo, Jianhua; Huang, Qiu; Feng, Dagan; Li, Yuanxiang

2014-01-01

Due to the imperfections of the radio frequency (RF) coil or object-dependent electrodynamic interactions, magnetic resonance (MR) images often suffer from a smooth and biologically meaningless bias field, which causes severe troubles for subsequent processing and quantitative analysis. To effectively restore the original signal, this paper simultaneously exploits the spatial and gradient features of the corrupted MR images for bias correction via the joint entropy regularization. With both isotropic and anisotropic total variation (TV) considered, two nonparametric bias correction algorithms have been proposed, namely IsoTVBiasC and AniTVBiasC. These two methods have been applied to simulated images under various noise levels and bias field corruption and also tested on real MR data. The test results show that the proposed two methods can effectively remove the bias field and also present comparable performance compared to the state-of-the-art methods.

Effects of inductive bias on computational evaluations of ligand-based modeling and on drug discovery

NASA Astrophysics Data System (ADS)

Cleves, Ann E.; Jain, Ajay N.

2008-03-01

Inductive bias is the set of assumptions that a person or procedure makes in making a prediction based on data. Different methods for ligand-based predictive modeling have different inductive biases, with a particularly sharp contrast between 2D and 3D similarity methods. A unique aspect of ligand design is that the data that exist to test methodology have been largely man-made, and that this process of design involves prediction. By analyzing the molecular similarities of known drugs, we show that the inductive bias of the historic drug discovery process has a very strong 2D bias. In studying the performance of ligand-based modeling methods, it is critical to account for this issue in dataset preparation, use of computational controls, and in the interpretation of results. We propose specific strategies to explicitly address the problems posed by inductive bias considerations.

Investigating possible ethnicity and sex bias in clinical examiners: an analysis of data from the MRCP(UK) PACES and nPACES examinations.

PubMed

McManus, I C; Elder, Andrew T; Dacre, Jane

2013-07-30

Bias of clinical examiners against some types of candidate, based on characteristics such as sex or ethnicity, would represent a threat to the validity of an examination, since sex or ethnicity are 'construct-irrelevant' characteristics. In this paper we report a novel method for assessing sex and ethnic bias in over 2000 examiners who had taken part in the PACES and nPACES (new PACES) examinations of the MRCP(UK). PACES and nPACES are clinical skills examinations that have two examiners at each station who mark candidates independently. Differences between examiners cannot be due to differences in performance of a candidate because that is the same for the two examiners, and hence may result from bias or unreliability on the part of the examiners. By comparing each examiner against a 'basket' of all of their co-examiners, it is possible to identify examiners whose behaviour is anomalous. The method assessed hawkishness-doveishness, sex bias, ethnic bias and, as a control condition to assess the statistical method, 'even-number bias' (i.e. treating candidates with odd and even exam numbers differently). Significance levels were Bonferroni corrected because of the large number of examiners being considered. The results of 26 diets of PACES and six diets of nPACES were examined statistically to assess the extent of hawkishness, as well as sex bias and ethnicity bias in individual examiners. The control (odd-number) condition suggested that about 5% of examiners were significant at an (uncorrected) 5% level, and that the method therefore worked as expected. As in a previous study (BMC Medical Education, 2006, 6:42), some examiners were hawkish or doveish relative to their peers. No examiners showed significant sex bias, and only a single examiner showed evidence consistent with ethnic bias. A re-analysis of the data considering only one examiner per station, as would be the case for many clinical examinations, showed that analysis with a single examiner runs a serious risk of false positive identifications probably due to differences in case-mix and content-specificity. In examinations where there are two independent examiners at a station, our method can assess the extent of bias against candidates with particular characteristics. The method would be far less sensitive in examinations with only a single examiner per station as examiner variance would be confounded with candidate performance variance. The method however works well when there is more than one examiner at a station and in the case of the current MRCP(UK) clinical examination, nPACES, found possible sex bias in no examiners and possible ethnic bias in only one.

Comparison of phonomyography with balloon pressure mechanomyography to measure contractile force at the corrugator supercilii muscle.

PubMed

Hemmerling, Thomas M; Michaud, Guillaume; Babin, Denis; Trager, Guillaume; Donati, François

2004-02-01

Phonomyography is based on the creation of low frequency sounds during muscle contraction, which can be recorded and used for neuromuscular monitoring. In this study, balloon pressure mechanomyography, a novel method to measure the force of contraction via pressure changes in an air-filled balloon, was compared with phonomyography to determine neuromuscular blockade at the corrugator supercilii muscle. After approval of the Ethics Committee and informed consent, 15 patients were studied. A small condenser microphone was taped to the area just above the eyebrow for phonomyography; an air-filled balloon was taped to the area just above the opposite eyebrow. After induction of anesthesia using remifentanil and propofol, a laryngeal mask airway was inserted without the aid of neuromuscular blocking agents. The facial nerve was stimulated supramaximally with single-twitch stimulation (0.1 Hz) using superficial electrodes placed on both temporal areas for onset and train-of-four stimulation every 12 sec during offset of neuromuscular blockade produced by mivacurium 0.1 mg.kg(-1). Onset and recovery measured by the two methods were compared using the t test and agreement between phonomyography and balloon pressure mechanomyography was examined using the Bland-Altman method. Onset, peak effect, and time to reach 25%, 75%, and 90% of control twitch response for phonomyography vs balloon pressure method were 83 +/- 16 sec vs 81 +/- 15 sec, 80 +/- 15% vs 82 +/- 17%, 7.7 +/- 2.3 min vs 7.5 +/- 2.4 min, 9.9 +/- 4.1 min vs 10.5 +/- 4 min, and 12.6 +/- 4.3 min vs 13.1 +/- 4.5 min respectively without being significantly different. Mean bias was 1% with limits of agreement of -9 and +9% of twitch height (T1). We applied a balloon pressure method to measure the force at the corrugator supercilii. Phonomyography at the corrugator supercilii shows good agreement with this modified version of mechanomyography.

Breast density quantification using magnetic resonance imaging (MRI) with bias field correction: A postmortem study

PubMed Central

Ding, Huanjun; Johnson, Travis; Lin, Muqing; Le, Huy Q.; Ducote, Justin L.; Su, Min-Ying; Molloi, Sabee

2013-01-01

Purpose: Quantification of breast density based on three-dimensional breast MRI may provide useful information for the early detection of breast cancer. However, the field inhomogeneity can severely challenge the computerized image segmentation process. In this work, the effect of the bias field in breast density quantification has been investigated with a postmortem study. Methods: T1-weighted images of 20 pairs of postmortem breasts were acquired on a 1.5 T breast MRI scanner. Two computer-assisted algorithms were used to quantify the volumetric breast density. First, standard fuzzy c-means (FCM) clustering was used on raw images with the bias field present. Then, the coherent local intensity clustering (CLIC) method estimated and corrected the bias field during the iterative tissue segmentation process. Finally, FCM clustering was performed on the bias-field-corrected images produced by CLIC method. The left–right correlation for breasts in the same pair was studied for both segmentation algorithms to evaluate the precision of the tissue classification. Finally, the breast densities measured with the three methods were compared to the gold standard tissue compositions obtained from chemical analysis. The linear correlation coefficient, Pearson's r, was used to evaluate the two image segmentation algorithms and the effect of bias field. Results: The CLIC method successfully corrected the intensity inhomogeneity induced by the bias field. In left–right comparisons, the CLIC method significantly improved the slope and the correlation coefficient of the linear fitting for the glandular volume estimation. The left–right breast density correlation was also increased from 0.93 to 0.98. When compared with the percent fibroglandular volume (%FGV) from chemical analysis, results after bias field correction from both the CLIC the FCM algorithms showed improved linear correlation. As a result, the Pearson's r increased from 0.86 to 0.92 with the bias field correction. Conclusions: The investigated CLIC method significantly increased the precision and accuracy of breast density quantification using breast MRI images by effectively correcting the bias field. It is expected that a fully automated computerized algorithm for breast density quantification may have great potential in clinical MRI applications. PMID:24320536

The Corporate View. A Multicultural Workforce Can Be a Competitive Advantage.

ERIC Educational Resources Information Center

Wilcox, John

1991-01-01

Work force diversity programs are designed to protect the company's return on investment by bringing to the surface the subtle discomforts, fears, and biases most people experience when they find themselves working with people who are different from themselves. (Author)

A microprocessor-based table lookup approach for magnetic bearing linearization

NASA Technical Reports Server (NTRS)

Groom, N. J.; Miller, J. B.

1981-01-01

An approach for producing a linear transfer characteristic between force command and force output of a magnetic bearing actuator without flux biasing is presented. The approach is microprocessor based and uses a table lookup to generate drive signals for the magnetic bearing power driver. An experimental test setup used to demonstrate the feasibility of the approach is described, and test results are presented. The test setup contains bearing elements similar to those used in a laboratory model annular momentum control device.

An open-access CMIP5 pattern library for temperature and precipitation: description and methodology

NASA Astrophysics Data System (ADS)

Lynch, Cary; Hartin, Corinne; Bond-Lamberty, Ben; Kravitz, Ben

2017-05-01

Pattern scaling is used to efficiently emulate general circulation models and explore uncertainty in climate projections under multiple forcing scenarios. Pattern scaling methods assume that local climate changes scale with a global mean temperature increase, allowing for spatial patterns to be generated for multiple models for any future emission scenario. For uncertainty quantification and probabilistic statistical analysis, a library of patterns with descriptive statistics for each file would be beneficial, but such a library does not presently exist. Of the possible techniques used to generate patterns, the two most prominent are the delta and least squares regression methods. We explore the differences and statistical significance between patterns generated by each method and assess performance of the generated patterns across methods and scenarios. Differences in patterns across seasons between methods and epochs were largest in high latitudes (60-90° N/S). Bias and mean errors between modeled and pattern-predicted output from the linear regression method were smaller than patterns generated by the delta method. Across scenarios, differences in the linear regression method patterns were more statistically significant, especially at high latitudes. We found that pattern generation methodologies were able to approximate the forced signal of change to within ≤ 0.5 °C, but the choice of pattern generation methodology for pattern scaling purposes should be informed by user goals and criteria. This paper describes our library of least squares regression patterns from all CMIP5 models for temperature and precipitation on an annual and sub-annual basis, along with the code used to generate these patterns. The dataset and netCDF data generation code are available at doi:10.5281/zenodo.495632.

All-atom calculation of protein free-energy profiles

NASA Astrophysics Data System (ADS)

Orioli, S.; Ianeselli, A.; Spagnolli, G.; Faccioli, P.

2017-10-01

The Bias Functional (BF) approach is a variational method which enables one to efficiently generate ensembles of reactive trajectories for complex biomolecular transitions, using ordinary computer clusters. For example, this scheme was applied to simulate in atomistic detail the folding of proteins consisting of several hundreds of amino acids and with experimental folding time of several minutes. A drawback of the BF approach is that it produces trajectories which do not satisfy microscopic reversibility. Consequently, this method cannot be used to directly compute equilibrium observables, such as free energy landscapes or equilibrium constants. In this work, we develop a statistical analysis which permits us to compute the potential of mean-force (PMF) along an arbitrary collective coordinate, by exploiting the information contained in the reactive trajectories calculated with the BF approach. We assess the accuracy and computational efficiency of this scheme by comparing its results with the PMF obtained for a small protein by means of plain molecular dynamics.

Controlling bias and inflation in epigenome- and transcriptome-wide association studies using the empirical null distribution.

PubMed

van Iterson, Maarten; van Zwet, Erik W; Heijmans, Bastiaan T

2017-01-27

We show that epigenome- and transcriptome-wide association studies (EWAS and TWAS) are prone to significant inflation and bias of test statistics, an unrecognized phenomenon introducing spurious findings if left unaddressed. Neither GWAS-based methodology nor state-of-the-art confounder adjustment methods completely remove bias and inflation. We propose a Bayesian method to control bias and inflation in EWAS and TWAS based on estimation of the empirical null distribution. Using simulations and real data, we demonstrate that our method maximizes power while properly controlling the false positive rate. We illustrate the utility of our method in large-scale EWAS and TWAS meta-analyses of age and smoking.

Investigations of a voltage-biased microwave cavity for quantum measurements of nanomechanical resonators

NASA Astrophysics Data System (ADS)

Rouxinol, Francisco; Hao, Hugo; Lahaye, Matt

2015-03-01

Quantum electromechanical systems incorporating superconducting qubits have received extensive interest in recent years due to their promising prospects for studying fundamental topics of quantum mechanics such as quantum measurement, entanglement and decoherence in new macroscopic limits, also for their potential as elements in technological applications in quantum information network and weak force detector, to name a few. In this presentation we will discuss ours efforts toward to devise an electromechanical circuit to strongly couple a nanomechanical resonator to a superconductor qubit, where a high voltage dc-bias is required, to study quantum behavior of a mechanical resonator. Preliminary results of our latest generation of devices integrating a superconductor qubit into a high-Q voltage biased microwave cavities are presented. Developments in the circuit design to couple a mechanical resonator to a qubit in the high-Q voltage bias CPW cavity is discussed as well prospects of achieving single-phonon measurement resolution. National Science Foundation under Grant No. DMR-1056423 and Grant No. DMR-1312421.

Force measurements of a magnetic micro actuator proposed for a microvalve array

NASA Astrophysics Data System (ADS)

Chang, Pauline J.; Chang, Frank W.; Yuen, Michelle C.; Otillar, Robert; Horsley, David A.

2014-03-01

Low-cost, easily-fabricated and power-efficient microvalves are necessary for many microfluidic lab-on-a-chip applications. In this study, we present a simple, low-power, scalable, CMOS-compatible magnetic actuator for microvalve applications composed of a paramagnetic bead as the ball valve over a picoliter reaction well etched into a silicon substrate. The paramagnetic bead, composed of either pure FeSi or magnetite in a SiO2 matrix, is actuated by the local magnetic field gradient generated by a microcoil in an aqueous environment, and the reaction well is situated at the microcoil center. A permanent magnet beneath the microvalve device provides an external magnetic biasing field that magnetizes the bead, enabling bidirectional actuation and reducing the current required to actuate the bead to a level below 10 mA. The vertical and radial magnetic forces exerted on the bead by the microcoil were measured for both pure FeSi and composite beads and agree well with the predictions of 2D axisymmetric finite element method models. Vertical forces were within a range of 13-80 nN, and radial forces were 11-60 nN depending on the bead type. The threshold current required to initiate bead actuation was measured as a function of bead diameter and is found to scale inversely with volume for small beads, as expected based on the magnetic force model. To provide an estimate of the stiction force acting between the bead and the passivation layer on the substrate, repeated actuation trials were used to study the bead throw distance for substrates coated with silicon dioxide, Parylene-C, and photoresist. The stiction observed was lowest for a photoresist-coated substrate, while silicon dioxide and Parylene-C coated substrates exhibited similar levels of stiction.

A Model of Gravity Vector Measurement Noise for Estimating Accelerometer Bias in Gravity Disturbance Compensation.

PubMed

Tie, Junbo; Cao, Juliang; Chang, Lubing; Cai, Shaokun; Wu, Meiping; Lian, Junxiang

2018-03-16

Compensation of gravity disturbance can improve the precision of inertial navigation, but the effect of compensation will decrease due to the accelerometer bias, and estimation of the accelerometer bias is a crucial issue in gravity disturbance compensation. This paper first investigates the effect of accelerometer bias on gravity disturbance compensation, and the situation in which the accelerometer bias should be estimated is established. The accelerometer bias is estimated from the gravity vector measurement, and a model of measurement noise in gravity vector measurement is built. Based on this model, accelerometer bias is separated from the gravity vector measurement error by the method of least squares. Horizontal gravity disturbances are calculated through EGM2008 spherical harmonic model to build the simulation scene, and the simulation results indicate that precise estimations of the accelerometer bias can be obtained with the proposed method.

A Model of Gravity Vector Measurement Noise for Estimating Accelerometer Bias in Gravity Disturbance Compensation

PubMed Central

Cao, Juliang; Cai, Shaokun; Wu, Meiping; Lian, Junxiang

2018-01-01

Compensation of gravity disturbance can improve the precision of inertial navigation, but the effect of compensation will decrease due to the accelerometer bias, and estimation of the accelerometer bias is a crucial issue in gravity disturbance compensation. This paper first investigates the effect of accelerometer bias on gravity disturbance compensation, and the situation in which the accelerometer bias should be estimated is established. The accelerometer bias is estimated from the gravity vector measurement, and a model of measurement noise in gravity vector measurement is built. Based on this model, accelerometer bias is separated from the gravity vector measurement error by the method of least squares. Horizontal gravity disturbances are calculated through EGM2008 spherical harmonic model to build the simulation scene, and the simulation results indicate that precise estimations of the accelerometer bias can be obtained with the proposed method. PMID:29547552

A machine learning model with human cognitive biases capable of learning from small and biased datasets.

PubMed

Taniguchi, Hidetaka; Sato, Hiroshi; Shirakawa, Tomohiro

2018-05-09

Human learners can generalize a new concept from a small number of samples. In contrast, conventional machine learning methods require large amounts of data to address the same types of problems. Humans have cognitive biases that promote fast learning. Here, we developed a method to reduce the gap between human beings and machines in this type of inference by utilizing cognitive biases. We implemented a human cognitive model into machine learning algorithms and compared their performance with the currently most popular methods, naïve Bayes, support vector machine, neural networks, logistic regression and random forests. We focused on the task of spam classification, which has been studied for a long time in the field of machine learning and often requires a large amount of data to obtain high accuracy. Our models achieved superior performance with small and biased samples in comparison with other representative machine learning methods.

A systematic review of health promotion intervention studies in the police force: study characteristics, intervention design and impacts on health.

PubMed

MacMillan, Freya; Karamacoska, Diana; El Masri, Aymen; McBride, Kate A; Steiner, Genevieve Z; Cook, Amelia; Kolt, Gregory S; Klupp, Nerida; George, Emma S

2017-12-01

To systematically review studies of health promotion intervention in the police force. Four databases were searched for articles reporting on prepost single and multigroup studies in police officers and trainees. Data were extracted and bias assessed to evaluate study characteristics, intervention design and the impact of interventions on health. Database searching identified 25 articles reporting on 21 studies relevant to the aims of this review. Few studies (n=3) were of long duration (≥6 months). Nine of 21 studies evaluated structured physical activity and/or diet programmes only, 5 studies used education and behaviour change support-only interventions, 5 combined structured programmes with education and behaviour change support, and 2 studies used computer prompts to minimise sedentary behaviour. A wide array of lifestyle behaviour and health outcomes was measured, with 11/13 multigroup and 8/8 single-group studies reporting beneficial impacts on outcomes. High risk of bias was evident across most studies. In those with the lowest risk of bias (n=2), a large effect on blood pressure and small effects on diet, sleep quality, stress and tobacco use, were reported. Health promotion interventions can impact beneficially on health of the police force, particularly blood pressure, diet, sleep, stress and tobacco use. Limited reporting made comparison of findings challenging. Combined structured programmes with education and behaviour change support and programmes including peer support resulted in the most impact on health-related outcomes. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

FGOALS-s2 simulation of upper-level jet streams over East Asia: Mean state bias and synoptic-scale transient eddy activity

NASA Astrophysics Data System (ADS)

Song, Fengfei; Zhou, Tianjun

2013-05-01

Upper-level jet streams over East Asia simulated by the LASG/IAP coupled climate system model FGOALS-s2 were assessed, and the mean state bias explained in terms of synoptic-scale transient eddy activity (STEA). The results showed that the spatial distribution of the seasonal mean jet stream was reproduced well by the model, except that following a weaker meridional temperature gradient (MTG), the intensity of the jet stream was weaker than in National Centers for Environment Prediction (NCEP)/Department of Energy Atmospheric Model Inter-comparison Project II reanalysis data (NCEP2). Based on daily mean data, the jet core number was counted to identify the geographical border between the East Asian Subtropical Jet (EASJ) and the East Asian Polar-front Jet (EAPJ). The border is located over the Tibetan Plateau according to NCEP2 data, but was not evident in FGOALS-s2 simulations. The seasonal cycles of the jet streams were found to be reasonably reproduced, except that they shifted northward relative to reanalysis data in boreal summer owing to the northward shift of negative MTGs. To identify the reasons for mean state bias, the dynamical and thermal forcings of STEA on mean flow were examined with a focus on boreal winter. The dynamical and thermal forcings were estimated by extended Eliassen-Palm flux ( E) and transient heat flux, respectively. The results showed that the failure to reproduce the tripolar-pattern of the divergence of E over the jet regions led to an unsuccessful separation of the EASJ and EAPJ, while dynamical forcing contributed less to the weaker EASJ. In contrast, the weaker transient heat flux partly explained the weaker EASJ over the ocean.

Application of Degenerately Doped Metal Oxides in the Study of Photoinduced Interfacial Electron Transfer.

PubMed

Farnum, Byron H; Morseth, Zachary A; Brennaman, M Kyle; Papanikolas, John M; Meyer, Thomas J

2015-06-18

Degenerately doped In2O3:Sn semiconductor nanoparticles (nanoITO) have been used to study the photoinduced interfacial electron-transfer reactivity of surface-bound [Ru(II)(bpy)2(4,4'-(PO3H2)2-bpy)](2+) (RuP(2+)) molecules as a function of driving force over a range of 1.8 eV. The metallic properties of the ITO nanoparticles, present within an interconnected mesoporous film, allowed for the driving force to be tuned by controlling their Fermi level with an external bias while their optical transparency allowed for transient absorption spectroscopy to be used to monitor electron-transfer kinetics. Photoinduced electron transfer from excited-state -RuP(2+*) molecules to nanoITO was found to be dependent on applied bias and competitive with nonradiative energy transfer to nanoITO. Back electron transfer from nanoITO to oxidized -RuP(3+) was also dependent on the applied bias but without complication from inter- or intraparticle electron diffusion in the oxide nanoparticles. Analysis of the electron injection kinetics as a function of driving force using Marcus-Gerischer theory resulted in an experimental estimate of the reorganization energy for the excited-state -RuP(3+/2+*) redox couple of λ* = 0.83 eV and an electronic coupling matrix element, arising from electronic wave function overlap between the donor orbital in the molecule and the acceptor orbital(s) in the nanoITO electrode, of Hab = 20-45 cm(-1). Similar analysis of the back electron-transfer kinetics yielded λ = 0.56 eV for the ground-state -RuP(3+/2+) redox couple and Hab = 2-4 cm(-1). The use of these wide band gap, degenerately doped materials provides a unique experimental approach for investigating single-site electron transfer at the surface of oxide nanoparticles.

GOTHiC, a probabilistic model to resolve complex biases and to identify real interactions in Hi-C data.

PubMed

Mifsud, Borbala; Martincorena, Inigo; Darbo, Elodie; Sugar, Robert; Schoenfelder, Stefan; Fraser, Peter; Luscombe, Nicholas M

2017-01-01

Hi-C is one of the main methods for investigating spatial co-localisation of DNA in the nucleus. However, the raw sequencing data obtained from Hi-C experiments suffer from large biases and spurious contacts, making it difficult to identify true interactions. Existing methods use complex models to account for biases and do not provide a significance threshold for detecting interactions. Here we introduce a simple binomial probabilistic model that resolves complex biases and distinguishes between true and false interactions. The model corrects biases of known and unknown origin and yields a p-value for each interaction, providing a reliable threshold based on significance. We demonstrate this experimentally by testing the method against a random ligation dataset. Our method outperforms previous methods and provides a statistical framework for further data analysis, such as comparisons of Hi-C interactions between different conditions. GOTHiC is available as a BioConductor package (http://www.bioconductor.org/packages/release/bioc/html/GOTHiC.html).

Interpopulation Comparison of Sex-Biased Mortality and Sexual Size Dimorphism in Sea-Run Masu Salmon, Oncorhynchus masou.

PubMed

Tamate, Tsuyoshi

2015-08-01

Evolutionary ecologists often expect that natural and sexual selection result in systematic co-occurrence patterns of sex-biased mortality and sexual size dimorphism (SSD) within animal species. However, whether such patterns actually occur in wild animals is poorly examined. The following expectation, the larger sex suffers higher mortality, was primarily tested here for apparently native sea-run masu salmon (Oncorhynchus masou) in three populations in Hokkaido, Japan. Field surveys on sex ratios, body sizes, and ages of smolts and returning adults revealed that two of the three populations exhibited an expected pattern, a female-biased marine mortality and SSD, but one population demonstrated an unexpected co-occurrence of male-biased marine mortality and female-biased SSD. These female-biased SSDs were attributed to faster marine growth of females because of no sex difference in smolt body size. It has been previously suggested that breeding selection favoring large size generally act more strongly in females than in males in Japanese anadromous masu, as there is a weak sexual selection on adult males but universally intensive natural selection on adult females. Thus, this hypothesis explains female-biased SSDs well in all study populations. Interpopulation variation in sex-biased mortality found here might result from differences in marine predation and/or fishing pressures, given that selection driving female-biased SSD makes females forage more aggressively than males during the marine phase. Taken together, these results raise the possibility that evolutionary forces have shaped adaptive sex-specific foraging strategies under relationships between growth and mortality, resulting in co-occurrence patterns of sex-biased mortality and SSD within animal species.

Simulated building energy demand biases resulting from the use of representative weather stations

DOE PAGES

Burleyson, Casey D.; Voisin, Nathalie; Taylor, Z. Todd; ...

2017-11-06

Numerical building models are typically forced with weather data from a limited number of “representative cities” or weather stations representing different climate regions. The use of representative weather stations reduces computational costs, but often fails to capture spatial heterogeneity in weather that may be important for simulations aimed at understanding how building stocks respond to a changing climate. Here, we quantify the potential reduction in temperature and load biases from using an increasing number of weather stations over the western U.S. Our novel approach is based on deriving temperature and load time series using incrementally more weather stations, ranging frommore » 8 to roughly 150, to evaluate the ability to capture weather patterns across different seasons. Using 8 stations across the western U.S., one from each IECC climate zone, results in an average absolute summertime temperature bias of ~4.0 °C with respect to a high-resolution gridded dataset. The mean absolute bias drops to ~1.5 °C using all available weather stations. Temperature biases of this magnitude could translate to absolute summertime mean simulated load biases as high as 13.5%. Increasing the size of the domain over which biases are calculated reduces their magnitude as positive and negative biases may cancel out. Using 8 representative weather stations can lead to a 20–40% bias of peak building loads during both summer and winter, a significant error for capacity expansion planners who may use these types of simulations. Using weather stations close to population centers reduces both mean and peak load biases. Our approach could be used by others designing aggregate building simulations to understand the sensitivity to their choice of weather stations used to drive the models.« less

Simulated building energy demand biases resulting from the use of representative weather stations

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

Burleyson, Casey D.; Voisin, Nathalie; Taylor, Z. Todd

Numerical building models are typically forced with weather data from a limited number of “representative cities” or weather stations representing different climate regions. The use of representative weather stations reduces computational costs, but often fails to capture spatial heterogeneity in weather that may be important for simulations aimed at understanding how building stocks respond to a changing climate. Here, we quantify the potential reduction in temperature and load biases from using an increasing number of weather stations over the western U.S. Our novel approach is based on deriving temperature and load time series using incrementally more weather stations, ranging frommore » 8 to roughly 150, to evaluate the ability to capture weather patterns across different seasons. Using 8 stations across the western U.S., one from each IECC climate zone, results in an average absolute summertime temperature bias of ~4.0 °C with respect to a high-resolution gridded dataset. The mean absolute bias drops to ~1.5 °C using all available weather stations. Temperature biases of this magnitude could translate to absolute summertime mean simulated load biases as high as 13.5%. Increasing the size of the domain over which biases are calculated reduces their magnitude as positive and negative biases may cancel out. Using 8 representative weather stations can lead to a 20–40% bias of peak building loads during both summer and winter, a significant error for capacity expansion planners who may use these types of simulations. Using weather stations close to population centers reduces both mean and peak load biases. Our approach could be used by others designing aggregate building simulations to understand the sensitivity to their choice of weather stations used to drive the models.« less

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.

Estimation of the auto frequency response function at unexcited points using dummy masses

NASA Astrophysics Data System (ADS)

Hosoya, Naoki; Yaginuma, Shinji; Onodera, Hiroshi; Yoshimura, Takuya

2015-02-01

If structures with complex shapes have space limitations, vibration tests using an exciter or impact hammer for the excitation are difficult. Although measuring the auto frequency response function at an unexcited point may not be practical via a vibration test, it can be obtained by assuming that the inertia acting on a dummy mass is an external force on the target structure upon exciting a different excitation point. We propose a method to estimate the auto frequency response functions at unexcited points by attaching a small mass (dummy mass), which is comparable to the accelerometer mass. The validity of the proposed method is demonstrated by comparing the auto frequency response functions estimated at unexcited points in a beam structure to those obtained from numerical simulations. We also consider random measurement errors by finite element analysis and vibration tests, but not bias errors. Additionally, the applicability of the proposed method is demonstrated by applying it to estimate the auto frequency response function of the lower arm in a car suspension.

Integration of sensory force feedback is disturbed in CRPS-related dystonia.

PubMed

Mugge, Winfred; van der Helm, Frans C T; Schouten, Alfred C

2013-01-01

Complex regional pain syndrome (CRPS) is characterized by pain and disturbed blood flow, temperature regulation and motor control. Approximately 25% of cases develop fixed dystonia. The origin of this movement disorder is poorly understood, although recent insights suggest involvement of disturbed force feedback. Assessment of sensorimotor integration may provide insight into the pathophysiology of fixed dystonia. Sensory weighting is the process of integrating and weighting sensory feedback channels in the central nervous system to improve the state estimate. It was hypothesized that patients with CRPS-related dystonia bias sensory weighting of force and position toward position due to the unreliability of force feedback. The current study provides experimental evidence for dysfunctional sensory integration in fixed dystonia, showing that CRPS-patients with fixed dystonia weight force and position feedback differently than controls do. The study shows reduced force feedback weights in CRPS-patients with fixed dystonia, making it the first to demonstrate disturbed integration of force feedback in fixed dystonia, an important step towards understanding the pathophysiology of fixed dystonia.

Efficient global biopolymer sampling with end-transfer configurational bias Monte Carlo

NASA Astrophysics Data System (ADS)

Arya, Gaurav; Schlick, Tamar

2007-01-01

We develop an "end-transfer configurational bias Monte Carlo" method for efficient thermodynamic sampling of complex biopolymers and assess its performance on a mesoscale model of chromatin (oligonucleosome) at different salt conditions compared to other Monte Carlo moves. Our method extends traditional configurational bias by deleting a repeating motif (monomer) from one end of the biopolymer and regrowing it at the opposite end using the standard Rosenbluth scheme. The method's sampling efficiency compared to local moves, pivot rotations, and standard configurational bias is assessed by parameters relating to translational, rotational, and internal degrees of freedom of the oligonucleosome. Our results show that the end-transfer method is superior in sampling every degree of freedom of the oligonucleosomes over other methods at high salt concentrations (weak electrostatics) but worse than the pivot rotations in terms of sampling internal and rotational sampling at low-to-moderate salt concentrations (strong electrostatics). Under all conditions investigated, however, the end-transfer method is several orders of magnitude more efficient than the standard configurational bias approach. This is because the characteristic sampling time of the innermost oligonucleosome motif scales quadratically with the length of the oligonucleosomes for the end-transfer method while it scales exponentially for the traditional configurational-bias method. Thus, the method we propose can significantly improve performance for global biomolecular applications, especially in condensed systems with weak nonbonded interactions and may be combined with local enhancements to improve local sampling.

Propagation of Satelite Rainfall Products uncertainties in hydrological applications : Examples in West-Africa in the framework of the Megha-Tropiques Satellite Mission

NASA Astrophysics Data System (ADS)

Casse, C.; Gosset, M.; Peugeot, C.; Boone, A.; Pedinotti, V.

2013-12-01

The use of satellite based rainfall in research or operational Hydrological application is becoming more and more frequent. This is specially true in the Tropics where ground based gauge (or radar) network are generally scarce and often degrading. Member of the GPM constellation, the new French-Indian satellite Mission Megha-Tropiques (MT) dedicated to the water and energy budget in the tropical atmosphere contributes to a better monitoring of rainfall in the inter-tropical zone. As part of this mission, research is developed on the use of MT rainfall products for hydrological research or operational application such as flood monitoring. A key issue for such applications is how to account for rainfall products biases and uncertainties, and how to propagate them in the end user models ? Another important question is how to choose the best space-time resolution for the rainfall forcing, given that both model performances and rain-product uncertainties are resolution dependent. This talk will present on going investigations and perspectives on this subject, with examples from the Megha_tropiques Ground validation sites in West Africa. The CNRM model Surfex-ISBA/TRIP has been set up to simulate the hydrological behavior of the Niger River. This modeling set up is being used to study the predictability of Niger Floods events in the city of Niamey and the performances of satellite rainfall products as forcing for such predictions. One of the interesting feature of the Niger outflow in Niamey is its double peak : a first peak attributed to 'local' rainfall falling in small to medium size basins situated in the region of Niamey, and a second peak linked to the rainfall falling in the upper par of the river, and slowly propagating through the river towards Niamey. The performances of rainfall products are found to differ between the wetter/upper part of the basin, and the local/sahelian areas. Both academic tests with artificially biased or 'perturbed' rainfield and actual rainfall products are carried out. A simple method based on probability matching is applied to correct the RT products from their main biases. Several sensitivity studies have also been carried out in the Oueme Basin in Benin, West Africa, one of the instrumented basin used for MT products direct and hydrological validation. The tests highlight the fact that not only total biases but also the distribution of rain rates are key players for explaining the hydrological model sensitivity. (a) TMPAv7 total rainfall in 2010 in West Africa. Solid gray line delimits Niger river catchment, and dotted lines delimit Niger right bank tributary catchments. (b) Observed and simulated discharge at Niamey station. Preliminary results using the SURFEX hydrological model over Niger catchment and different satellite rainfall products as forcing.

The contrasting climate response to tropical and extratropical energy perturbations

NASA Astrophysics Data System (ADS)

Hawcroft, Matt; Haywood, Jim M.; Collins, Mat; Jones, Andy

2018-01-01

The link between cross-equatorial energy transport, the double-intertropical convergence zone (DI) problem and biases in tropical and extratropical albedo and energy budgets in climate models have been investigated in multiple studies, though DI biases persist in many models. Here, a coupled climate model, HadGEM2-ES, is used to investigate the response to idealised energy perturbations in the tropics and extratropics, in both the northern and southern hemispheres, through the imposition of stratospheric aerosols that reflect incoming radiation. The impact on the tropical climate of high and low latitude forcing strongly contrasts, with large changes in tropical precipitation and modulation of the DI bias when the tropics are cooled as precipitation moves away from the cooled hemisphere. These responses are muted when the extratropics are cooled, as the meridional energy transport anomalies that are excited by these energy budget anomalies are partitioned between the atmosphere and ocean. The results here highlight the persistence of the DI bias in HadGEM2-ES, indicating why little progress has been made in rectifying these problems through many generations of climate models. A highly linear relationship between cross-equatorial atmospheric energy transport, tropical precipitation asymmetry and tropical sea surface temperature biases is also demonstrated, giving some suggestion as to where improvements in these large scale, persistent biases may be achieved.

The CHESS method of forensic opinion formulation: striving to checkmate bias.

PubMed

Wills, Cheryl D

2008-01-01

Expert witnesses use various methods to render dispassionate opinions. Some forensic psychiatrists acknowledge bias up front; other experts use principles endorsed by the American Academy of Psychiatry and the Law or other professional organizations. This article introduces CHESS, a systematic method for reducing bias in expert opinions. The CHESS method involves identifying a Claim or preliminary opinion; developing a Hierarchy of supporting evidence; examining the evidence for weaknesses or areas of Exposure; Studying and revising the claim and supporting evidence; and Synthesizing a revised opinion. Case examples illustrate how the CHESS method may help experts reduce bias while strengthening opinions. The method also helps experts prepare for court by reminding them to anticipate questions that may be asked during cross-examination. The CHESS method provides a framework for formulating, revising, and identifying limitations of opinions, which allows experts to incorporate neutrality into forensic opinions.

Streamflow forecasting and data assimilation: bias in precipitation, soil moisture states, and groundwater fluxes.

NASA Astrophysics Data System (ADS)

McCreight, J. L.; Gochis, D. J.; Hoar, T.; Dugger, A. L.; Yu, W.

2014-12-01

Uncertainty in precipitation forcing, soil moisture states, and model groundwater fluxes are first-order sources of error in streamflow forecasting. While near-surface estimates of soil moisture are now available from satellite, very few soil moisture observations below 5 cm depth or groundwater discharge estimates are available for operational forecasting. Radar precipitation estimates are subject to large biases, particularly during extreme events (e.g. Steiner et al., 2010) and their correction is not typically available in real-time. Streamflow data, however, are readily available in near-real-time and can be assimilated operationally to help constrain uncertainty in these uncertain states and improve streamflow forecasts. We examine the ability of streamflow observations to diagnose bias in the three most uncertain variables: precipitation forcing, soil moisture states, and groundwater fluxes. We investigate strategies for their subsequent bias correction. These include spinup and calibration strategies with and without the use of data assimilation and the determination of the proper spinup timescales. Global and spatially distributed multipliers on the uncertain states included in the assimilation state vector (e.g. Seo et al., 2003) will also be evaluated. We examine real cases and observing system simulation experiments for both normal and extreme rainfall events. One of our test cases considers the Colorado Front Range flood of September 2013 where the range of disagreement amongst five precipitation estimates spanned a factor of five with only one exhibiting appreciable positive bias (Gochis et al, submitted). Our experiments are conducted using the WRF-Hydro model with the NoahMP land surface component and the data assimilation research testbed (DART). A variety of ensemble data assimilation approaches (filters) are considered. ReferencesGochis, DJ, et al. "The Great Colorado Flood of September 2013" BAMS (Submitted 4-7-14). Seo, DJ, V Koren, and N Cajina. "Real-time variational assimilation of hydrologic and hydrometeorological data into operational hydrologic forecasting." J Hydromet (2003). Steiner, Matthias, JA Smith, SJ Burges, CV Alonso, and RW Darden. "Effect of bias adjustment and rain gauge data quality control on radar rainfall estimation." WRR (1999).

Evaluation of a reduced centrifugation time and higher centrifugal force on various general chemistry and immunochemistry analytes in plasma and serum.

PubMed

Møller, Mette F; Søndergaard, Tove R; Kristensen, Helle T; Münster, Anna-Marie B

2017-09-01

Background Centrifugation of blood samples is an essential preanalytical step in the clinical biochemistry laboratory. Centrifugation settings are often altered to optimize sample flow and turnaround time. Few studies have addressed the effect of altering centrifugation settings on analytical quality, and almost all studies have been done using collection tubes with gel separator. Methods In this study, we compared a centrifugation time of 5 min at 3000 ×  g to a standard protocol of 10 min at 2200 ×  g. Nine selected general chemistry and immunochemistry analytes and interference indices were studied in lithium heparin plasma tubes and serum tubes without gel separator. Results were evaluated using mean bias, difference plots and coefficient of variation, compared with maximum allowable bias and coefficient of variation used in laboratory routine quality control. Results For all analytes except lactate dehydrogenase, the results were within the predefined acceptance criteria, indicating that the analytical quality was not compromised. Lactate dehydrogenase showed higher values after centrifugation for 5 min at 3000 ×  g, mean bias was 6.3 ± 2.2% and the coefficient of variation was 5%. Conclusions We found that a centrifugation protocol of 5 min at 3000 ×  g can be used for the general chemistry and immunochemistry analytes studied, with the possible exception of lactate dehydrogenase, which requires further assessment.

Experimental evidence of intermittent chaos in a glow discharge plasma without external forcing and its numerical modelling

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

Ghosh, S., E-mail: sabuj.ghosh@saha.ac.in; Kumar Shaw, Pankaj; Sekar Iyengar, A. N.

Intermittent chaos was observed in a glow discharge plasma as the system evolved from regular type of relaxation oscillations (of larger amplitude) to an irregular type of oscillations (of smaller amplitude) as the discharge voltage was increased. Floating potential fluctuations were analyzed by different statistical and spectral methods. Features like a gradual change in the normal variance of the interpeak time intervals, a dip in the skewness, and a hump in the kurtosis with variation in the control parameter have been seen, which are strongly indicative of intermittent behavior in the system. Detailed analysis also suggests that the intrinsic noisemore » level in the experiment increases with the increasing discharge voltage. An attempt has been made to model the experimental observations by a second order nonlinear ordinary differential equation derived from the fluid equations for an unmagnetized plasma. Though the experiment had no external forcing, it was conjectured that the intrinsic noise in the experiment could be playing a vital role in the dynamics of the system. Hence, a constant bias and noise as forcing terms were included in the model. Results from the theoretical model are in close qualitative agreement with the experimental results.« less

The validity and reliability of an iPhone app for measuring vertical jump performance.

PubMed

Balsalobre-Fernández, Carlos; Glaister, Mark; Lockey, Richard Anthony

2015-01-01

The purpose of this investigation was to analyse the concurrent validity and reliability of an iPhone app (called: My Jump) for measuring vertical jump performance. Twenty recreationally active healthy men (age: 22.1 ± 3.6 years) completed five maximal countermovement jumps, which were evaluated using a force platform (time in the air method) and a specially designed iPhone app. My jump was developed to calculate the jump height from flight time using the high-speed video recording facility on the iPhone 5 s. Jump heights of the 100 jumps measured, for both devices, were compared using the intraclass correlation coefficient, Pearson product moment correlation coefficient (r), Cronbach's alpha (α), coefficient of variation and Bland-Altman plots. There was almost perfect agreement between the force platform and My Jump for the countermovement jump height (intraclass correlation coefficient = 0.997, P < 0.001; Bland-Altman bias = 1.1 ± 0.5 cm, P < 0.001). In comparison with the force platform, My Jump showed good validity for the CMJ height (r = 0.995, P < 0.001). The results of the present study showed that CMJ height can be easily, accurately and reliably evaluated using a specially developed iPhone 5 s app.

Reducing Modeling Error of Graphical Methods for Estimating Volume of Distribution Measurements in PIB-PET study

PubMed Central

Guo, Hongbin; Renaut, Rosemary A; Chen, Kewei; Reiman, Eric M

2010-01-01

Graphical analysis methods are widely used in positron emission tomography quantification because of their simplicity and model independence. But they may, particularly for reversible kinetics, lead to bias in the estimated parameters. The source of the bias is commonly attributed to noise in the data. Assuming a two-tissue compartmental model, we investigate the bias that originates from modeling error. This bias is an intrinsic property of the simplified linear models used for limited scan durations, and it is exaggerated by random noise and numerical quadrature error. Conditions are derived under which Logan's graphical method either over- or under-estimates the distribution volume in the noise-free case. The bias caused by modeling error is quantified analytically. The presented analysis shows that the bias of graphical methods is inversely proportional to the dissociation rate. Furthermore, visual examination of the linearity of the Logan plot is not sufficient for guaranteeing that equilibrium has been reached. A new model which retains the elegant properties of graphical analysis methods is presented, along with a numerical algorithm for its solution. We perform simulations with the fibrillar amyloid β radioligand [11C] benzothiazole-aniline using published data from the University of Pittsburgh and Rotterdam groups. The results show that the proposed method significantly reduces the bias due to modeling error. Moreover, the results for data acquired over a 70 minutes scan duration are at least as good as those obtained using existing methods for data acquired over a 90 minutes scan duration. PMID:20493196

Operational correction and validation of the VIIRS TEB longwave infrared band calibration bias during blackbody temperature changes

NASA Astrophysics Data System (ADS)

Wang, Wenhui; Cao, Changyong; Ignatov, Alex; Li, Zhenglong; Wang, Likun; Zhang, Bin; Blonski, Slawomir; Li, Jun

2017-09-01

The Suomi NPP VIIRS thermal emissive bands (TEB) have been performing very well since data became available on January 20, 2012. The longwave infrared bands at 11 and 12 um (M15 and M16) are primarily used for sea surface temperature (SST) retrievals. A long standing anomaly has been observed during the quarterly warm-up-cool-down (WUCD) events. During such event daytime SST product becomes anomalous with a warm bias shown as a spike in the SST time series on the order of 0.2 K. A previous study (CAO et al. 2017) suggested that the VIIRS TEB calibration anomaly during WUCD is due to a flawed theoretical assumption in the calibration equation and proposed an Ltrace method to address the issue. This paper complements that study and presents operational implementation and validation of the Ltrace method for M15 and M16. The Ltrace method applies bias correction during WUCD only. It requires a simple code change and one-time calibration parameter look-up-table update. The method was evaluated using colocated CrIS observations and the SST algorithm. Our results indicate that the method can effectively reduce WUCD calibration anomaly in M15, with residual bias of 0.02 K after the correction. It works less effectively for M16, with residual bias of 0.04 K. The Ltrace method may over-correct WUCD calibration biases, especially for M16. However, the residual WUCD biases are small in both bands. Evaluation results using the SST algorithm show that the method can effectively remove SST anomaly during WUCD events.

Adaptive momentum management for large space structures

NASA Technical Reports Server (NTRS)

Hahn, E.

1987-01-01

Momentum management is discussed for a Large Space Structure (LSS) with the structure selected configuration being the Initial Orbital Configuration (IOC) of the dual keel space station. The external forces considered were gravity gradient and aerodynamic torques. The goal of the momentum management scheme developed is to remove the bias components of the external torques and center the cyclic components of the stored angular momentum. The scheme investigated is adaptive to uncertainties of the inertia tensor and requires only approximate knowledge of principle moments of inertia. Computational requirements are minimal and should present no implementation problem in a flight type computer and the method proposed is shown to be effective in the presence of attitude control bandwidths as low as .01 radian/sec.

Shape measurement biases from underfitting and ellipticity gradients

DOE PAGES

Bernstein, Gary M.

2010-08-21

With this study, precision weak gravitational lensing experiments require measurements of galaxy shapes accurate to <1 part in 1000. We investigate measurement biases, noted by Voigt and Bridle (2009) and Melchior et al. (2009), that are common to shape measurement methodologies that rely upon fitting elliptical-isophote galaxy models to observed data. The first bias arises when the true galaxy shapes do not match the models being fit. We show that this "underfitting bias" is due, at root, to these methods' attempts to use information at high spatial frequencies that has been destroyed by the convolution with the point-spread function (PSF)more » and/or by sampling. We propose a new shape-measurement technique that is explicitly confined to observable regions of k-space. A second bias arises for galaxies whose ellipticity varies with radius. For most shape-measurement methods, such galaxies are subject to "ellipticity gradient bias". We show how to reduce such biases by factors of 20–100 within the new shape-measurement method. The resulting shear estimator has multiplicative errors < 1 part in 10 3 for high-S/N images, even for highly asymmetric galaxies. Without any training or recalibration, the new method obtains Q = 3000 in the GREAT08 Challenge of blind shear reconstruction on low-noise galaxies, several times better than any previous method.« less

A study on large-scale nudging effects in regional climate model simulation

NASA Astrophysics Data System (ADS)

Yhang, Yoo-Bin; Hong, Song-You

2011-05-01

The large-scale nudging effects on the East Asian summer monsoon (EASM) are examined using the National Centers for Environmental Prediction (NCEP) Regional Spectral Model (RSM). The NCEP/DOE reanalysis data is used to provide large-scale forcings for RSM simulations, configured with an approximately 50-km grid over East Asia, centered on the Korean peninsula. The RSM with a variant of spectral nudging, that is, the scale selective bias correction (SSBC), is forced by perfect boundary conditions during the summers (June-July-August) from 1979 to 2004. The two summers of 2000 and 2004 are investigated to demonstrate the impact of SSBC on precipitation in detail. It is found that the effect of SSBC on the simulated seasonal precipitation is in general neutral without a discernible advantage. Although errors in large-scale circulation for both 2000 and 2004 are reduced by using the SSBC method, the impact on simulated precipitation is found to be negative in 2000 and positive in 2004 summers. One possible reason for a different effect is that precipitation in the summer of 2004 is characterized by a strong baroclinicity, while precipitation in 2000 is caused by thermodynamic instability. The reduction of convective rainfall over the oceans by the application of the SSBC method seems to play an important role in modeled atmosphere.

Modulation-format-free and automatic bias control for optical IQ modulators based on dither-correlation detection.

PubMed

Li, Xiaolei; Deng, Lei; Chen, Xiaoman; Cheng, Mengfan; Fu, Songnian; Tang, Ming; Liu, Deming

2017-04-17

A novel automatic bias control (ABC) method for optical in-phase and quadrature (IQ) modulator is proposed and experimentally demonstrated. In the proposed method, two different low frequency sine wave dither signals are generated and added on to the I/Q bias signal respectively. Instead of power monitoring of the harmonics of the dither signal, dither-correlation detection is proposed and used to adjust the bias voltages of the optical IQ modulator. By this way, not only frequency spectral analysis isn't required but also the directional bias adjustment could be realized, resulting in the decrease of algorithm complexity and the growth of convergence rate of ABC algorithm. The results show that the sensitivity of the proposed ABC method outperforms that of the traditional dither frequency monitoring method. Moreover, the proposed ABC method is proved to be modulation-format-free, and the transmission penalty caused by this method for both 10 Gb/s optical QPSK and 17.9 Gb/s optical 16QAM-OFDM signal transmission are negligible in our experiment.

Preliminary Validation of a New Measure of Negative Response Bias: The Temporal Memory Sequence Test.

PubMed

Hegedish, Omer; Kivilis, Naama; Hoofien, Dan

2015-01-01

The Temporal Memory Sequence Test (TMST) is a new measure of negative response bias (NRB) that was developed to enrich the forced-choice paradigm. The TMST does not resemble the common structure of forced-choice tests and is presented as a temporal recall memory test. The validation sample consisted of 81 participants: 21 healthy control participants, 20 coached simulators, and 40 patients with acquired brain injury (ABI). The TMST had high reliability and significantly high positive correlations with the Test of Memory Malingering and Word Memory Test effort scales. Moreover, the TMST effort scales exhibited high negative correlations with the Glasgow Coma Scale, thus validating the previously reported association between probable malingering and mild traumatic brain injury. A suggested cutoff score yielded acceptable classification rates in the ABI group as well as in the simulator and control groups. The TMST appears to be a promising measure of NRB detection, with respectable rates of reliability and construct and criterion validity.

Host influence in the genomic composition of flaviviruses: A multivariate approach.

PubMed

Simón, Diego; Fajardo, Alvaro; Sóñora, Martín; Delfraro, Adriana; Musto, Héctor

2017-10-28

Flaviviruses present substantial differences in their host range and transmissibility. We studied the evolution of base composition, dinucleotide biases, codon usage and amino acid frequencies in the genus Flavivirus within a phylogenetic framework by principal components analysis. There is a mutual interplay between the evolutionary history of flaviviruses and their respective vectors and/or hosts. Hosts associated to distinct phylogenetic groups may be driving flaviviruses at different pace and through various sequence landscapes, as can be seen for viruses associated with Aedes or Culex spp., although phylogenetic inertia cannot be ruled out. In some cases, viruses face even opposite forces. For instance, in tick-borne flaviviruses, while vertebrate hosts exert pressure to deplete their CpG, tick vectors drive them to exhibit GC-rich codons. Within a vertebrate environment, natural selection appears to be acting on the viral genome to overcome the immune system. On the other side, within an arthropod environment, mutational biases seem to be the dominant forces. Copyright © 2017 Elsevier Inc. All rights reserved.

Dielectric barrier discharge plasma actuator for flow control

NASA Astrophysics Data System (ADS)

Opaits, Dmitry Florievich

Electrohydrodynamic (EHD) and magnetohydrodynamic phenomena are being widely studied for aerodynamic applications. The major effects of these phenomena are heating of the gas, body force generation, and enthalpy addition or extraction, [1, 2, 3]. In particular, asymmetric dielectric barrier discharge (DBD) plasma actuators are known to be effective EHD device in aerodynamic control, [4, 5]. Experiments have demonstrated their effectiveness in separation control, acoustic noise reduction, and other aeronautic applications. In contrast to conventional DBD actuators driven by sinusoidal voltages, we proposed and used a voltage profile consisting of nanosecond pulses superimposed on dc bias voltage. This produces what is essentially a non-self-sustained discharge: the plasma is generated by repetitive short pulses, and the pushing of the gas occurs primarily due to the bias voltage. The advantage of this non-self-sustained discharge is that the parameters of ionizing pulses and the driving bias voltage can be varied independently, which adds flexibility to control and optimization of the actuators performance. Experimental studies were conducted of a flow induced in a quiescent room air by a single DBD actuator. A new approach for non-intrusive diagnostics of plasma actuator induced flows in quiescent gas was proposed, consisting of three elements coupled together: the Schlieren technique, burst mode of plasma actuator operation, and 2-D numerical fluid modeling. During the experiments, it was found that DBD performance is severely limited by surface charge accumulation on the dielectric. Several ways to mitigate the surface charge were found: using a reversing DC bias potential, three-electrode configuration, slightly conductive dielectrics, and semi conductive coatings. Force balance measurements proved the effectiveness of the suggested configurations and advantages of the new voltage profile (pulses+bias) over the traditional sinusoidal one at relatively low voltages. In view of practical applications certain questions have been also addressed, such as electrodynamic effects which accompany scaling of the actuators to real size models, and environmental effects of ozone production by the plasma actuators.

Impact of shortwave radiation biases on ocean conditions in the Pacific Northwest waters: Results from the seasonal forecast system J-SCOPE.

NASA Astrophysics Data System (ADS)

Siedlecki, S. A.; Nguyen, T. T.; Hermann, A. J.; Bond, N. A.; Ackerman, T. P.; Hinkelman, L. M.

2016-02-01

JISAO Seasonal Coastal Ocean Prediction of the Ecosystem (J-SCOPE) is an experimental seasonal forecast system of ocean conditions that is designed to support ecosystem-based management of fisheries in the Northwest Pacific ocean. The forecast system consists of a high resolution ROMS model with biogeochemistry forced by atmospheric and oceanic fields from the Climate Forecast System (CFS). Recent research has focused on the systematic errors in this forcing. In 2013, the predicted CFS shortwave radiation fluxes for summer were higher than the observation fluxes by nearly 100 W/m2. This forecast bias varies interannually and regionally. Hindcast experiments were set up for 2013 to estimate the impact of the shortwave radiation bias on ocean conditions in the Pacific Northwest waters. Results demonstrate that a 20% increase (decrease) in radiation fluxes can cause a warm (cold) bias in sea surface temperature (SST) of up to 1 - 1.5°C on average, and an even higher bias (± 2°C) during the June - August upwelling season. In the response to an increased radiation flux, the increased stratification from the warmer SSTs can reduce mixing and deepen the maximum phytoplankton growth zone, which consequently modifies the oxygen concentration of the water column. The effect of the change in short wave radiation fluxes on the oxygen concentrations of shelf waters is more complicated than the effect on SST. A change of up to 1 to 1.5 ml/l in bottom oxygen concentration occurs in some areas in the region. Two potential mechanisms that govern the response of the shelf water oxygen concentration are explored in this study: reduced mixing and altered chlorophyll distributions. Through the use of an oxygen budget, we can examine the relative importance of each of these mechanisms to the change in radiation.

Obstacle traversal and route choice in flying honeybees: Evidence for individual handedness

PubMed Central

Ong, Marielle; Bulmer, Michael; Groening, Julia

2017-01-01

Flying insects constantly face the challenge of choosing efficient, safe and collision-free routes while navigating through dense foliage. We examined the route-choice behavior of foraging honeybees when they encountered a barrier which could be traversed by flying through one of two apertures, positioned side by side. When the bees’ choice behavior was averaged over the entire tested population, the two apertures were chosen with equal frequency when they were equally wide. When the apertures were of different width, the bees, on average, showed a preference for the wider aperture, which increased sharply with the difference between the aperture widths. Thus, bees are able to discriminate the widths of oncoming gaps and choose the passage which is presumably safer and quicker to transit. Examination of the behavior of individual bees revealed that, when the two apertures were equally wide, ca. 55% of the bees displayed no side bias in their choices. However, the remaining 45% showed varying degrees of bias, with one half of them preferring the left-hand aperture, and the other half the right-hand aperture. The existence of distinct individual biases was confirmed by measuring the times required by biased bees to transit various aperture configurations: The transit time was longer if a bee’s intrinsic bias forced it to engage with the narrower aperture. Our results show that, at the population level, bees do not exhibit ‘handedness’ in choosing routes; however, individual bees display an idiosyncratic bias that can range from a strong left bias, through zero bias, to a strong right bias. In honeybees, previous studies of olfactory and visual learning have demonstrated clear biases at the population level. To our knowledge, our study is the first to uncover the existence of individually distinct biases in honeybees. We also show how a distribution of biases among individual honeybees can be advantageous in facilitating rapid transit of a group of bees through a cluttered environment, without any centralized decision-making or control. PMID:29095830

Publication Bias ( The "File-Drawer Problem") in Scientific Inference

NASA Technical Reports Server (NTRS)

Scargle, Jeffrey D.; DeVincenzi, Donald (Technical Monitor)

1999-01-01

Publication bias arises whenever the probability that a study is published depends on the statistical significance of its results. This bias, often called the file-drawer effect since the unpublished results are imagined to be tucked away in researchers' file cabinets, is potentially a severe impediment to combining the statistical results of studies collected from the literature. With almost any reasonable quantitative model for publication bias, only a small number of studies lost in the file-drawer will produce a significant bias. This result contradicts the well known Fail Safe File Drawer (FSFD) method for setting limits on the potential harm of publication bias, widely used in social, medical and psychic research. This method incorrectly treats the file drawer as unbiased, and almost always miss-estimates the seriousness of publication bias. A large body of not only psychic research, but medical and social science studies, has mistakenly relied on this method to validate claimed discoveries. Statistical combination can be trusted only if it is known with certainty that all studies that have been carried out are included. Such certainty is virtually impossible to achieve in literature surveys.

Stochastic Parameterization: Toward a New View of Weather and Climate Models

DOE PAGES

Berner, Judith; Achatz, Ulrich; Batté, Lauriane; ...

2017-03-31

The last decade has seen the success of stochastic parameterizations in short-term, medium-range, and seasonal forecasts: operational weather centers now routinely use stochastic parameterization schemes to represent model inadequacy better and to improve the quantification of forecast uncertainty. Developed initially for numerical weather prediction, the inclusion of stochastic parameterizations not only provides better estimates of uncertainty, but it is also extremely promising for reducing long-standing climate biases and is relevant for determining the climate response to external forcing. This article highlights recent developments from different research groups that show that the stochastic representation of unresolved processes in the atmosphere, oceans,more » land surface, and cryosphere of comprehensive weather and climate models 1) gives rise to more reliable probabilistic forecasts of weather and climate and 2) reduces systematic model bias. We make a case that the use of mathematically stringent methods for the derivation of stochastic dynamic equations will lead to substantial improvements in our ability to accurately simulate weather and climate at all scales. Recent work in mathematics, statistical mechanics, and turbulence is reviewed; its relevance for the climate problem is demonstrated; and future research directions are outlined« less

Stochastic Parameterization: Toward a New View of Weather and Climate Models

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

Berner, Judith; Achatz, Ulrich; Batté, Lauriane

The last decade has seen the success of stochastic parameterizations in short-term, medium-range, and seasonal forecasts: operational weather centers now routinely use stochastic parameterization schemes to represent model inadequacy better and to improve the quantification of forecast uncertainty. Developed initially for numerical weather prediction, the inclusion of stochastic parameterizations not only provides better estimates of uncertainty, but it is also extremely promising for reducing long-standing climate biases and is relevant for determining the climate response to external forcing. This article highlights recent developments from different research groups that show that the stochastic representation of unresolved processes in the atmosphere, oceans,more » land surface, and cryosphere of comprehensive weather and climate models 1) gives rise to more reliable probabilistic forecasts of weather and climate and 2) reduces systematic model bias. We make a case that the use of mathematically stringent methods for the derivation of stochastic dynamic equations will lead to substantial improvements in our ability to accurately simulate weather and climate at all scales. Recent work in mathematics, statistical mechanics, and turbulence is reviewed; its relevance for the climate problem is demonstrated; and future research directions are outlined« less

Expansion of a quantum wave packet in a one-dimensional disordered potential in the presence of a uniform bias force

NASA Astrophysics Data System (ADS)

Crosnier de Bellaistre, C.; Trefzger, C.; Aspect, A.; Georges, A.; Sanchez-Palencia, L.

2018-01-01

We study numerically the expansion dynamics of an initially confined quantum wave packet in the presence of a disordered potential and a uniform bias force. For white-noise disorder, we find that the wave packet develops asymmetric algebraic tails for any ratio of the force to the disorder strength. The exponent of the algebraic tails decays smoothly with that ratio and no evidence of a critical behavior on the wave density profile is found. Algebraic localization features a series of critical values of the force-to-disorder strength where the m th position moment of the wave packet diverges. Below the critical value for the m th moment, we find fair agreement between the asymptotic long-time value of the m th moment and the predictions of diagrammatic calculations. Above it, we find that the m th moment grows algebraically in time. For correlated disorder, we find evidence of systematic delocalization, irrespective to the model of disorder. More precisely, we find a two-step dynamics, where both the center-of-mass position and the width of the wave packet show transient localization, similar to the white-noise case, at short time and delocalization at sufficiently long time. This correlation-induced delocalization is interpreted as due to the decrease of the effective de Broglie wavelength, which lowers the effective strength of the disorder in the presence of finite-range correlations.

A scanning tunneling microscope break junction method with continuous bias modulation.

PubMed

Beall, Edward; Yin, Xing; Waldeck, David H; Wierzbinski, Emil

2015-09-28

Single molecule conductance measurements on 1,8-octanedithiol were performed using the scanning tunneling microscope break junction method with an externally controlled modulation of the bias voltage. Application of an AC voltage is shown to improve the signal to noise ratio of low current (low conductance) measurements as compared to the DC bias method. The experimental results show that the current response of the molecule(s) trapped in the junction and the solvent media to the bias modulation can be qualitatively different. A model RC circuit which accommodates both the molecule and the solvent is proposed to analyze the data and extract a conductance for the molecule.

Breast density quantification using magnetic resonance imaging (MRI) with bias field correction: a postmortem study.

PubMed

Ding, Huanjun; Johnson, Travis; Lin, Muqing; Le, Huy Q; Ducote, Justin L; Su, Min-Ying; Molloi, Sabee

2013-12-01

Quantification of breast density based on three-dimensional breast MRI may provide useful information for the early detection of breast cancer. However, the field inhomogeneity can severely challenge the computerized image segmentation process. In this work, the effect of the bias field in breast density quantification has been investigated with a postmortem study. T1-weighted images of 20 pairs of postmortem breasts were acquired on a 1.5 T breast MRI scanner. Two computer-assisted algorithms were used to quantify the volumetric breast density. First, standard fuzzy c-means (FCM) clustering was used on raw images with the bias field present. Then, the coherent local intensity clustering (CLIC) method estimated and corrected the bias field during the iterative tissue segmentation process. Finally, FCM clustering was performed on the bias-field-corrected images produced by CLIC method. The left-right correlation for breasts in the same pair was studied for both segmentation algorithms to evaluate the precision of the tissue classification. Finally, the breast densities measured with the three methods were compared to the gold standard tissue compositions obtained from chemical analysis. The linear correlation coefficient, Pearson's r, was used to evaluate the two image segmentation algorithms and the effect of bias field. The CLIC method successfully corrected the intensity inhomogeneity induced by the bias field. In left-right comparisons, the CLIC method significantly improved the slope and the correlation coefficient of the linear fitting for the glandular volume estimation. The left-right breast density correlation was also increased from 0.93 to 0.98. When compared with the percent fibroglandular volume (%FGV) from chemical analysis, results after bias field correction from both the CLIC the FCM algorithms showed improved linear correlation. As a result, the Pearson's r increased from 0.86 to 0.92 with the bias field correction. The investigated CLIC method significantly increased the precision and accuracy of breast density quantification using breast MRI images by effectively correcting the bias field. It is expected that a fully automated computerized algorithm for breast density quantification may have great potential in clinical MRI applications.