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Sample records for local structural bias

  1. Sampling Realistic Protein Conformations Using Local Structural Bias

    PubMed Central

    Hamelryck, Thomas; Kent, John T; Krogh, Anders

    2006-01-01

    The prediction of protein structure from sequence remains a major unsolved problem in biology. The most successful protein structure prediction methods make use of a divide-and-conquer strategy to attack the problem: a conformational sampling method generates plausible candidate structures, which are subsequently accepted or rejected using an energy function. Conceptually, this often corresponds to separating local structural bias from the long-range interactions that stabilize the compact, native state. However, sampling protein conformations that are compatible with the local structural bias encoded in a given protein sequence is a long-standing open problem, especially in continuous space. We describe an elegant and mathematically rigorous method to do this, and show that it readily generates native-like protein conformations simply by enforcing compactness. Our results have far-reaching implications for protein structure prediction, determination, simulation, and design. PMID:17002495

  2. Bias structure to efficiently package a magnetic bubble domain device

    NASA Technical Reports Server (NTRS)

    Chen, Thomas T. (Inventor)

    1978-01-01

    A single, compact bias structure to efficiently package a plurality of magnetic bubble domain device chips having different bias requirements. The vertical magnetic field distribution within the bias structure air gap is selectively controlled by a magnetically soft field adjusting assembly suitably attached within the bias structure. The size and configuration of the field adjusting assembly tailors local field variations within the air gap to correspond with the bias requirements of the bubble domain chips disposed therein.

  3. Local bias-induced phase transitions

    SciTech Connect

    Seal, Katyayani; Baddorf, Arthur P.; Jesse, Stephen; Kalinin, Sergei V.; Nikiforov, Maxim; Proksch, Roger; Rodriguez, Brian J.; Maksymovych, Petro; Kholkin, Andrei L.

    2008-11-27

    Electrical bias-induced phase transitions underpin a wide range of applications from data storage to energy generation and conversion. The mechanisms behind these transitions are often quite complex and in many cases are extremely sensitive to local defects that act as centers for local transformations or pinning. Furthermore, using ferroelectrics as an example, we review methods for probing bias-induced phase transitions and discuss the current limitations and challenges for extending the methods to field-induced phase transitions and electrochemical reactions in energy storage, biological and molecular systems.

  4. Local bias-induced phase transitions

    DOE PAGES

    Seal, Katyayani; Baddorf, Arthur P.; Jesse, Stephen; ...

    2008-11-27

    Electrical bias-induced phase transitions underpin a wide range of applications from data storage to energy generation and conversion. The mechanisms behind these transitions are often quite complex and in many cases are extremely sensitive to local defects that act as centers for local transformations or pinning. Furthermore, using ferroelectrics as an example, we review methods for probing bias-induced phase transitions and discuss the current limitations and challenges for extending the methods to field-induced phase transitions and electrochemical reactions in energy storage, biological and molecular systems.

  5. Measuring non-local Lagrangian peak bias

    NASA Astrophysics Data System (ADS)

    Biagetti, Matteo; Chan, Kwan Chuen; Desjacques, Vincent; Paranjape, Aseem

    2014-06-01

    We investigate non-local Lagrangian bias contributions involving gradients of the linear density field, for which we have predictions from the excursion set peak formalism. We begin by writing down a bias expansion which includes all the bias terms, including the non-local ones. Having checked that the model furnishes a reasonable fit to the halo mass function, we develop a one-point cross-correlation technique to measure bias factors associated with χ2-distributed quantities. We validate the method with numerical realizations of peaks of Gaussian random fields before we apply it to N-body simulations. We focus on the lowest (quadratic) order non-local contributions -2χ _{10}(k_1\\cdot k_2) and χ _{01}[3(k_1\\cdot k_2)^2-k_1^2 k_2^2], where k_1, k_2 are wave modes. We can reproduce our measurement of χ10 if we allow for an offset between the Lagrangian halo centre-of-mass and the peak position. The sign and magnitude of χ10 is consistent with Lagrangian haloes sitting near linear density maxima. The resulting contribution to the halo bias can safely be ignored for M = 1013 M⊙ h-1, but could become relevant at larger halo masses. For the second non-local bias χ01 however, we measure a much larger magnitude than predicted by our model. We speculate that some of this discrepancy might originate from non-local Lagrangian contributions induced by non-spherical collapse.

  6. Local gravitational redshifts can bias cosmological measurements

    SciTech Connect

    Wojtak, Radosław; Davis, Tamara M.; Wiis, Jophiel E-mail: tamarad@physics.uq.edu.au

    2015-07-01

    Measurements of cosmological parameters via the distance-redshift relation usually rely on models that assume a homogenous universe. It is commonly presumed that the large-scale structure evident in our Universe has a negligible impact on the measurement if distances probed in observations are sufficiently large (compared to the scale of inhomogeneities) and are averaged over different directions on the sky. This presumption does not hold when considering the effect of the gravitational redshift caused by our local gravitational potential, which alters light coming from all distances and directions in the same way. Despite its small magnitude, this local gravitational redshift gives rise to noticeable effects in cosmological inference using SN Ia data. Assuming conservative prior knowledge of the local potential given by sampling a range of gravitational potentials at locations of Milky-Way-like galaxies identified in cosmological simulations, we show that ignoring the gravitational redshift effect in a standard data analysis leads to an additional systematic error of ∼1% in the determination of density parameters and the dark energy equation of state. We conclude that our local gravitational field affects our cosmological inference at a level that is important in future observations aiming to achieve percent-level accuracy.

  7. Local gravitational redshifts can bias cosmological measurements

    NASA Astrophysics Data System (ADS)

    Wojtak, Radosław; Davis, Tamara M.; Wiis, Jophiel

    2015-07-01

    Measurements of cosmological parameters via the distance-redshift relation usually rely on models that assume a homogenous universe. It is commonly presumed that the large-scale structure evident in our Universe has a negligible impact on the measurement if distances probed in observations are sufficiently large (compared to the scale of inhomogeneities) and are averaged over different directions on the sky. This presumption does not hold when considering the effect of the gravitational redshift caused by our local gravitational potential, which alters light coming from all distances and directions in the same way. Despite its small magnitude, this local gravitational redshift gives rise to noticeable effects in cosmological inference using SN Ia data. Assuming conservative prior knowledge of the local potential given by sampling a range of gravitational potentials at locations of Milky-Way-like galaxies identified in cosmological simulations, we show that ignoring the gravitational redshift effect in a standard data analysis leads to an additional systematic error of ~1% in the determination of density parameters and the dark energy equation of state. We conclude that our local gravitational field affects our cosmological inference at a level that is important in future observations aiming to achieve percent-level accuracy.

  8. Investigating bias in squared regression structure coefficients.

    PubMed

    Nimon, Kim F; Zientek, Linda R; Thompson, Bruce

    2015-01-01

    The importance of structure coefficients and analogs of regression weights for analysis within the general linear model (GLM) has been well-documented. The purpose of this study was to investigate bias in squared structure coefficients in the context of multiple regression and to determine if a formula that had been shown to correct for bias in squared Pearson correlation coefficients and coefficients of determination could be used to correct for bias in squared regression structure coefficients. Using data from a Monte Carlo simulation, this study found that squared regression structure coefficients corrected with Pratt's formula produced less biased estimates and might be more accurate and stable estimates of population squared regression structure coefficients than estimates with no such corrections. While our findings are in line with prior literature that identified multicollinearity as a predictor of bias in squared regression structure coefficients but not coefficients of determination, the findings from this study are unique in that the level of predictive power, number of predictors, and sample size were also observed to contribute bias in squared regression structure coefficients.

  9. Investigating bias in squared regression structure coefficients

    PubMed Central

    Nimon, Kim F.; Zientek, Linda R.; Thompson, Bruce

    2015-01-01

    The importance of structure coefficients and analogs of regression weights for analysis within the general linear model (GLM) has been well-documented. The purpose of this study was to investigate bias in squared structure coefficients in the context of multiple regression and to determine if a formula that had been shown to correct for bias in squared Pearson correlation coefficients and coefficients of determination could be used to correct for bias in squared regression structure coefficients. Using data from a Monte Carlo simulation, this study found that squared regression structure coefficients corrected with Pratt's formula produced less biased estimates and might be more accurate and stable estimates of population squared regression structure coefficients than estimates with no such corrections. While our findings are in line with prior literature that identified multicollinearity as a predictor of bias in squared regression structure coefficients but not coefficients of determination, the findings from this study are unique in that the level of predictive power, number of predictors, and sample size were also observed to contribute bias in squared regression structure coefficients. PMID:26217273

  10. Lateral length scales and local character of exchange bias.

    NASA Astrophysics Data System (ADS)

    Schuller, Ivan K.

    2005-03-01

    Exchange bias (EB) is a ferromagnet (F) -- antiferromagnet (AF) proximity effect. EB manifests itself as a horizontal shift of a single hysteresis loop. In our studies, an untwinned 38--100 nm-thick layer of (110) FeF2 is epitaxially grown on (110) MgF2, followed by a 4--70 nm-thick layer of Co, Ni or Fe. Easy axis magnetization curves (SQUID and spatially resolved MOKE) for different cooling fields and remanent magnetizations for zero-field cooled samples exhibit negatively or positively shifted single or tunable double hysteresis loops (DHL). In the untwinned epitaxial FeF2, the AF domains can be much larger than the grains, and, hence, as large as the F domains. When each F domain is in contact with only one AF domain, it does not average the direction and the magnitude of EB. In this regime, inhomogeneity of an AF-F sample, either structural or magnetic, can result in two subsystems formed upon cooling through the AF transition temperature. Each subsystem exhibits EB of the same magnitude but of the opposite sign, which gives rise to DHL. We conclude that when the domain size in the AF is larger than or comparable to that in the F, the local, non-averaging character of EB can be observed. Work supported by DOE and AFOSR.

  11. Morphology in autism spectrum disorders: local processing bias and language.

    PubMed

    Vulchanova, Mila; Talcott, Joel B; Vulchanov, Valentin; Stankova, Margarita; Eshuis, Hendrik

    2012-01-01

    We conducted a detailed study of a case of linguistic talent in the context of autism spectrum disorder, specifically Asperger syndrome. I.A. displays language strengths at the level of morphology and syntax. Yet, despite this grammar advantage, processing of figurative language and inferencing based on context presents a problem for him. The morphology advantage for I.A. is consistent with the weak central coherence (WCC) account of autism. From this account, the presence of a local processing bias is evident in the ways in which autistic individuals solve common problems, such as assessing similarities between objects and finding common patterns, and may therefore provide an advantage in some cognitive tasks compared to typical individuals. We extend the WCC account to language and provide evidence for a connection between the local processing bias and the acquisition of morphology and grammar.

  12. Precision measurement of the local bias of dark matter halos

    SciTech Connect

    Lazeyras, Titouan; Wagner, Christian; Schmidt, Fabian; Baldauf, Tobias E-mail: cwagner@mpa-garching.mpg.de E-mail: fabians@mpa-garching.mpg.de

    2016-02-01

    We present accurate measurements of the linear, quadratic, and cubic local bias of dark matter halos, using curved 'separate universe' N-body simulations which effectively incorporate an infinite-wavelength overdensity. This can be seen as an exact implementation of the peak-background split argument. We compare the results with the linear and quadratic bias measured from the halo-matter power spectrum and bispectrum, and find good agreement. On the other hand, the standard peak-background split applied to the Sheth and Tormen (1999) and Tinker et al. (2008) halo mass functions matches the measured linear bias parameter only at the level of 10%. The prediction from the excursion set-peaks approach performs much better, which can be attributed to the stochastic moving barrier employed in the excursion set-peaks prediction. We also provide convenient fitting formulas for the nonlinear bias parameters b{sub 2}(b{sub 1}) and b{sub 3}(b{sub 1}), which work well over a range of redshifts.

  13. A neurophysiological explanation for biases in visual localization.

    PubMed

    Moreland, James C; Boynton, Geoffrey M

    2017-02-01

    Observers show small but systematic deviations from equal weighting of all elements when asked to localize the center of an array of dots. Counter-intuitively, with small numbers of dots drawn from a Gaussian distribution, this bias results in subjects overweighting the influence of outlier dots - inconsistent with traditional statistical estimators of central tendency. Here we show that this apparent statistical anomaly can be explained by the observation that outlier dots also lie in regions of lower dot density. Using a standard model of V1 processing, which includes spatial integration followed by a compressive static nonlinearity, we can successfully predict the finding that dots in less dense regions of an array have a relatively greater influence on the perceived center.

  14. OPTIMIZATION BIAS IN ENERGY-BASED STRUCTURE PREDICTION.

    PubMed

    Petrella, Robert J

    2013-12-01

    Physics-based computational approaches to predicting the structure of macromolecules such as proteins are gaining increased use, but there are remaining challenges. In the current work, it is demonstrated that in energy-based prediction methods, the degree of optimization of the sampled structures can influence the prediction results. In particular, discrepancies in the degree of local sampling can bias the predictions in favor of the oversampled structures by shifting the local probability distributions of the minimum sampled energies. In simple systems, it is shown that the magnitude of the errors can be calculated from the energy surface, and for certain model systems, derived analytically. Further, it is shown that for energy wells whose forms differ only by a randomly assigned energy shift, the optimal accuracy of prediction is achieved when the sampling around each structure is equal. Energy correction terms can be used in cases of unequal sampling to reproduce the total probabilities that would occur under equal sampling, but optimal corrections only partially restore the prediction accuracy lost to unequal sampling. For multiwell systems, the determination of the correction terms is a multibody problem; it is shown that the involved cross-correlation multiple integrals can be reduced to simpler integrals. The possible implications of the current analysis for macromolecular structure prediction are discussed.

  15. OPTIMIZATION BIAS IN ENERGY-BASED STRUCTURE PREDICTION

    PubMed Central

    Petrella, Robert J.

    2014-01-01

    Physics-based computational approaches to predicting the structure of macromolecules such as proteins are gaining increased use, but there are remaining challenges. In the current work, it is demonstrated that in energy-based prediction methods, the degree of optimization of the sampled structures can influence the prediction results. In particular, discrepancies in the degree of local sampling can bias the predictions in favor of the oversampled structures by shifting the local probability distributions of the minimum sampled energies. In simple systems, it is shown that the magnitude of the errors can be calculated from the energy surface, and for certain model systems, derived analytically. Further, it is shown that for energy wells whose forms differ only by a randomly assigned energy shift, the optimal accuracy of prediction is achieved when the sampling around each structure is equal. Energy correction terms can be used in cases of unequal sampling to reproduce the total probabilities that would occur under equal sampling, but optimal corrections only partially restore the prediction accuracy lost to unequal sampling. For multiwell systems, the determination of the correction terms is a multibody problem; it is shown that the involved cross-correlation multiple integrals can be reduced to simpler integrals. The possible implications of the current analysis for macromolecular structure prediction are discussed. PMID:25552783

  16. Prism adaptation reverses the local processing bias in patients with right temporo-parietal junction lesions

    PubMed Central

    Rafal, Robert D.; List, Alexandra

    2009-01-01

    Lesions to the right temporo-parietal cortex commonly result in hemispatial neglect. Lesions to the same area are also associated with hyperattention to local details of a scene and difficulty perceiving the global structure. This local processing bias is an important factor contributing to neglect and may contribute to the higher prevalence of the disorder following right compared with left hemisphere strokes. In recent years, visuomotor adaptation to rightward-shifting prisms has been introduced as a promising treatment for hemispatial neglect. Explanations for these improvements have generally described a leftward realignment of attention, however, the present investigation provides evidence that prism adaptation reduces the local processing bias. Five patients with right temporal-parietal junction lesions were asked to identify the global or local levels of hierarchical figures before and after visuomotor adaptation to rightward-shifting prisms. Prior to prism adaptation the patients had difficulty ignoring the local elements when identifying the global component. Following prism adaptation, however, this pattern was reversed, with greater global interference during local level identification. The results suggest that prism adaptation may improve non-spatially lateralized deficits that contribute to the neglect syndrome. PMID:19416951

  17. Bias in the effective field theory of large scale structures

    SciTech Connect

    Senatore, Leonardo

    2015-11-01

    We study how to describe collapsed objects, such as galaxies, in the context of the Effective Field Theory of Large Scale Structures. The overdensity of galaxies at a given location and time is determined by the initial tidal tensor, velocity gradients and spatial derivatives of the regions of dark matter that, during the evolution of the universe, ended up at that given location. Similarly to what was recently done for dark matter, we show how this Lagrangian space description can be recovered by upgrading simpler Eulerian calculations. We describe the Eulerian theory. We show that it is perturbatively local in space, but non-local in time, and we explain the observational consequences of this fact. We give an argument for why to a certain degree of accuracy the theory can be considered as quasi time-local and explain what the operator structure is in this case. We describe renormalization of the bias coefficients so that, after this and after upgrading the Eulerian calculation to a Lagrangian one, the perturbative series for galaxies correlation functions results in a manifestly convergent expansion in powers of k/k{sub NL} and k/k{sub M}, where k is the wavenumber of interest, k{sub NL} is the wavenumber associated to the non-linear scale, and k{sub M} is the comoving wavenumber enclosing the mass of a galaxy.

  18. Bias in the effective field theory of large scale structures

    DOE PAGES

    Senatore, Leonardo

    2015-11-05

    We study how to describe collapsed objects, such as galaxies, in the context of the Effective Field Theory of Large Scale Structures. The overdensity of galaxies at a given location and time is determined by the initial tidal tensor, velocity gradients and spatial derivatives of the regions of dark matter that, during the evolution of the universe, ended up at that given location. Similarly to what was recently done for dark matter, we show how this Lagrangian space description can be recovered by upgrading simpler Eulerian calculations. We describe the Eulerian theory. We show that it is perturbatively local inmore » space, but non-local in time, and we explain the observational consequences of this fact. We give an argument for why to a certain degree of accuracy the theory can be considered as quasi time-local and explain what the operator structure is in this case. Furthermore, we describe renormalization of the bias coefficients so that, after this and after upgrading the Eulerian calculation to a Lagrangian one, the perturbative series for galaxies correlation functions results in a manifestly convergent expansion in powers of k/kNL and k/kM, where k is the wavenumber of interest, kNL is the wavenumber associated to the non-linear scale, and kM is the comoving wavenumber enclosing the mass of a galaxy.« less

  19. Bias in the effective field theory of large scale structures

    SciTech Connect

    Senatore, Leonardo

    2015-11-05

    We study how to describe collapsed objects, such as galaxies, in the context of the Effective Field Theory of Large Scale Structures. The overdensity of galaxies at a given location and time is determined by the initial tidal tensor, velocity gradients and spatial derivatives of the regions of dark matter that, during the evolution of the universe, ended up at that given location. Similarly to what was recently done for dark matter, we show how this Lagrangian space description can be recovered by upgrading simpler Eulerian calculations. We describe the Eulerian theory. We show that it is perturbatively local in space, but non-local in time, and we explain the observational consequences of this fact. We give an argument for why to a certain degree of accuracy the theory can be considered as quasi time-local and explain what the operator structure is in this case. Furthermore, we describe renormalization of the bias coefficients so that, after this and after upgrading the Eulerian calculation to a Lagrangian one, the perturbative series for galaxies correlation functions results in a manifestly convergent expansion in powers of k/kNL and k/kM, where k is the wavenumber of interest, kNL is the wavenumber associated to the non-linear scale, and kM is the comoving wavenumber enclosing the mass of a galaxy.

  20. Local-global processing bias is not a unitary individual difference in visual processing.

    PubMed

    Chamberlain, Rebecca; Van der Hallen, Ruth; Huygelier, Hanne; Van de Cruys, Sander; Wagemans, Johan

    2017-05-04

    A large body of research reports individual differences in local and global visual processing in relation to expertise, culture and psychopathology. However, recent research has suggested that various different measures of local-global processing are not strongly associated with one another, calling its construct validity into question. The current study sought to further explore the validity of local-global processing biases in perception by developing three tasks based on two existing paradigms: the Embedded Figures Test (EFT) and the Navon hierarchical letters task. The newly developed tasks aimed to control for stimulus and response factors that may have impacted upon the reliability of previous research. They were administered to a large sample of undergraduate students (N>100). The results of two new versions of the EFT indicated that disembedding performance is influenced by the structure of the embedding context. In addition, global precedence and interference in the Navon task remained present even when local attentional approaches to global hierarchical stimuli were restricted. Inter-task correlations within the EFT were high but low between the EFT and the Navon task, lending support to the notion that local-global processing is not a monolithic construct, but representative of a number of distinct perceptual abilities and biases. Future research may use these task distinctions to pinpoint more precisely which aspects of perceptual processing characterise specific (clinical) participant populations. Copyright © 2017 Elsevier Ltd. All rights reserved.

  1. Estimating the Bias of Local Polynomial Approximations Using the Peano Kernel

    SciTech Connect

    Blair, J., and Machorro, E.

    2012-03-22

    These presentation visuals define local polynomial approximations, give formulas for bias and random components of the error, and express bias error in terms of the Peano kernel. They further derive constants that give figures of merit, and show the figures of merit for 3 common weighting functions. The Peano kernel theorem yields estimates for the bias error for local-polynomial-approximation smoothing that are superior in several ways to the error estimates in the current literature.

  2. Non-local bias contribution to third-order galaxy correlations

    NASA Astrophysics Data System (ADS)

    Bel, J.; Hoffmann, K.; Gaztañaga, E.

    2015-10-01

    We study halo clustering bias with second- and third-order statistics of halo and matter density fields in the Marenostrum Institut de Ciències de l'Espai (MICE) Grand Challenge simulation. We verify that two-point correlations deliver reliable estimates of the linear bias parameters at large scales, while estimations from the variance can be significantly affected by non-linear and possibly non-local contributions to the bias function. Combining three-point auto- and cross-correlations we find, for the first time in configuration space, evidence for the presence of such non-local contributions. These contributions are consistent with predicted second-order non-local effects on the bias functions originating from the dark matter tidal field. Samples of massive haloes show indications of bias (local or non-local) beyond second order. Ignoring non-local bias causes 20-30 and 5-10 per cent overestimation of the linear bias from three-point auto- and cross-correlations, respectively. We study two third-order bias estimators that are not affected by second-order non-local contributions. One is a combination of three-point auto- and cross-correlations. The other is a combination of third-order one- and two-point cumulants. Both methods deliver accurate estimations of the linear bias. Ignoring non-local bias causes higher values of the second-order bias from three-point correlations. Our results demonstrate that third-order statistics can be employed for breaking the growth-bias degeneracy.

  3. Exposure to an Urban Environment Alters the Local Bias of a Remote Culture

    ERIC Educational Resources Information Center

    Caparos, Serge; Ahmed, Lubna; Bremner, Andrew J.; de Fockert, Jan W.; Linnell, Karina J.; Davidoff, Jules

    2012-01-01

    There is substantial evidence that populations in the Western world exhibit a local bias compared to East Asian populations that is widely ascribed to a difference between individualistic and collectivist societies. However, we report that traditional Himba--a remote interdependent society--exhibit a strong local bias compared to both Japanese and…

  4. Exposure to an urban environment alters the local bias of a remote culture.

    PubMed

    Caparos, Serge; Ahmed, Lubna; Bremner, Andrew J; de Fockert, Jan W; Linnell, Karina J; Davidoff, Jules

    2012-01-01

    There is substantial evidence that populations in the Western world exhibit a local bias compared to East Asian populations that is widely ascribed to a difference between individualistic and collectivist societies. However, we report that traditional Himba - a remote interdependent society - exhibit a strong local bias compared to both Japanese and British participants in the Ebbinghaus illusion and in a similarity-matching task with hierarchical figures. Critically, we measured the effect of exposure to an urban environment on local bias in the Himba. Even a brief exposure to an urban environment caused a shift in processing style: the local bias was reduced in traditional Himba who had visited a local town and even more reduced in urbanised Himba who had moved to that town on a permanent basis. We therefore propose that exposure to an urban environment contributes to the global bias found in Western and Japanese populations.

  5. Exchange bias training effect in coupled all ferromagnetic bilayer structures.

    PubMed

    Binek, Ch; Polisetty, S; He, Xi; Berger, A

    2006-02-17

    Exchange coupled bilayers of soft and hard ferromagnetic thin films show remarkable analogies to conventional antiferromagnetic/ferromagnetic exchange bias heterostructures. Not only do all these ferromagnetic bilayers exhibit a tunable exchange bias effect, they also show a distinct training behavior upon cycling the soft layer through consecutive hysteresis loops. In contrast with conventional exchange bias systems, such all ferromagnetic bilayer structures allow the observation of training induced changes in the bias-setting hardmagnetic layer by means of simple magnetometry. Our experiments show unambiguously that the exchange bias training effect is driven by deviations from equilibrium in the pinning layer. A comparison of our experimental data with predictions from a theory based upon triggered relaxation phenomena shows excellent agreement.

  6. Exchange Bias Training Effect in Coupled All Ferromagnetic Bilayer Structures

    NASA Astrophysics Data System (ADS)

    Binek, Ch.; Polisetty, S.; He, Xi; Berger, A.

    2006-02-01

    Exchange coupled bilayers of soft and hard ferromagnetic thin films show remarkable analogies to conventional antiferromagnetic/ferromagnetic exchange bias heterostructures. Not only do all these ferromagnetic bilayers exhibit a tunable exchange bias effect, they also show a distinct training behavior upon cycling the soft layer through consecutive hysteresis loops. In contrast with conventional exchange bias systems, such all ferromagnetic bilayer structures allow the observation of training induced changes in the bias-setting hardmagnetic layer by means of simple magnetometry. Our experiments show unambiguously that the exchange bias training effect is driven by deviations from equilibrium in the pinning layer. A comparison of our experimental data with predictions from a theory based upon triggered relaxation phenomena shows excellent agreement.

  7. Asymmetric bias in user guided segmentations of brain structures.

    PubMed

    Maltbie, Eric; Bhatt, Kshamta; Paniagua, Beatriz; Smith, Rachel G; Graves, Michael M; Mosconi, Matthew W; Peterson, Sarah; White, Scott; Blocher, Joseph; El-Sayed, Mohammed; Hazlett, Heather C; Styner, Martin A

    2012-01-16

    Brain morphometric studies often incorporate comparative hemispheric asymmetry analyses of segmented brain structures. In this work, we present evidence that common user guided structural segmentation techniques exhibit strong left-right asymmetric biases and thus fundamentally influence any left-right asymmetry analyses. In this study, MRI scans from ten pediatric subjects were employed for studying segmentations of amygdala, globus pallidus, putamen, caudate, and lateral ventricle. Additionally, two pediatric and three adult scans were used for studying hippocampus segmentation. Segmentations of the sub-cortical structures were performed by skilled raters using standard manual and semi-automated methods. The left-right mirrored versions of each image were included in the data and segmented in a random order to assess potential left-right asymmetric bias. Using shape analysis we further assessed whether the asymmetric bias is consistent across subjects and raters with the focus on the hippocampus. The user guided segmentation techniques on the sub-cortical structures exhibited left-right asymmetric volume bias with the hippocampus displaying the most significant asymmetry values (p<0.01). The hippocampal shape analysis revealed the bias to be strongest on the lateral side of the body and medial side of the head and tail. The origin of this asymmetric bias is considered to be based in laterality of visual perception; therefore segmentations with any degree of user interaction contain an asymmetric bias. The aim of our study is to raise awareness in the neuroimaging community regarding the presence of the asymmetric bias and its influence on any left-right hemispheric analyses. We also recommend reexamining previous research results in the light of this new finding.

  8. Biasing and the search for primordial non-Gaussianity beyond the local type

    NASA Astrophysics Data System (ADS)

    Gleyzes, Jérôme; de Putter, Roland; Green, Daniel; Doré, Olivier

    2017-04-01

    Primordial non-Gaussianity encodes valuable information about the physics of inflation, including the spectrum of particles and interactions. Significant improvements in our understanding of non-Gaussanity beyond Planck require information from large-scale structure. The most promising approach to utilize this information comes from the scale-dependent bias of halos. For local non-Gaussanity, the improvements available are well studied but the potential for non-Gaussianity beyond the local type, including equilateral and quasi-single field inflation, is much less well understood. In this paper, we forecast the capabilities of large-scale structure surveys to detect general non-Gaussianity through galaxy/halo power spectra. We study how non-Gaussanity can be distinguished from a general biasing model and where the information is encoded. For quasi-single field inflation, significant improvements over Planck are possible in some regions of parameter space. We also show that the multi-tracer technique can significantly improve the sensitivity for all non-Gaussianity types, providing up to an order of magnitude improvement for equilateral non-Gaussianity over the single-tracer measurement.

  9. A new configurational bias scheme for sampling supramolecular structures

    SciTech Connect

    De Gernier, Robin; Mognetti, Bortolo M.; Curk, Tine; Dubacheva, Galina V.; Richter, Ralf P.

    2014-12-28

    We present a new simulation scheme which allows an efficient sampling of reconfigurable supramolecular structures made of polymeric constructs functionalized by reactive binding sites. The algorithm is based on the configurational bias scheme of Siepmann and Frenkel and is powered by the possibility of changing the topology of the supramolecular network by a non-local Monte Carlo algorithm. Such a plan is accomplished by a multi-scale modelling that merges coarse-grained simulations, describing the typical polymer conformations, with experimental results accounting for free energy terms involved in the reactions of the active sites. We test the new algorithm for a system of DNA coated colloids for which we compute the hybridisation free energy cost associated to the binding of tethered single stranded DNAs terminated by short sequences of complementary nucleotides. In order to demonstrate the versatility of our method, we also consider polymers functionalized by receptors that bind a surface decorated by ligands. In particular, we compute the density of states of adsorbed polymers as a function of the number of ligand–receptor complexes formed. Such a quantity can be used to study the conformational properties of adsorbed polymers useful when engineering adsorption with tailored properties. We successfully compare the results with the predictions of a mean field theory. We believe that the proposed method will be a useful tool to investigate supramolecular structures resulting from direct interactions between functionalized polymers for which efficient numerical methodologies of investigation are still lacking.

  10. Local gravity versus local velocity: solutions for β and non-linear bias

    NASA Astrophysics Data System (ADS)

    Davis, Marc; Nusser, Adi; Masters, Karen L.; Springob, Christopher; Huchra, John P.; Lemson, Gerard

    2011-06-01

    We perform a reconstruction of the cosmological large-scale flows in the nearby Universe using two complementary observational sets. The first, the SFI++ sample of Tully-Fisher (TF) measurements of galaxies, provides a direct probe of the flows. The second, the whole sky distribution of galaxies in the 2MASS (Two Micron All Sky Survey) redshift survey (2MRS), yields a prediction of the flows given the cosmological density parameter, Ω, and a biasing relation between mass and galaxies. We aim at an unbiased comparison between the peculiar velocity fields extracted from the two data sets and its implication on the cosmological parameters and the biasing relation. We expand the fields in a set of orthonormal basis functions, each representing a plausible realization of a cosmological velocity field smoothed in such a way as to give a nearly constant error on the derived SFI++ velocities. The statistical analysis is done on the coefficients of the modal expansion of the fields by means of the basis functions. Our analysis completely avoids the strong error covariance in the smoothed TF velocities by the use of orthonormal basis functions and employs elaborate mock data sets to extensively calibrate the errors in 2MRS predicted velocities. We relate the 2MRS galaxy distribution to the mass density field by a linear bias factor, b, and include a luminosity-dependent, ∝Lα, galaxy weighting. We assess the agreement between the fields as a function of α and β=f(Ω)/b, where f is the growth factor of linear perturbations. The agreement is excellent with a reasonable χ2 per degree of freedom. For α= 0, we derive 0.28 < β < 0.37 and 0.24 < β < 0.43, respectively, at the 68.3 per cent and 95.4 per cent confidence levels (CLs). For β= 0.33, we get α < 0.25 and α < 0.5, respectively, at the 68.3 per cent and 95.4 per cent CLs. We set a constraint on the fluctuation normalization, finding σ8= 0.66 ± 0.10, which is only 1.5σ deviant from Wilkinson Microwave

  11. Asymmetric bias in user guided segmentations of brain structures

    NASA Astrophysics Data System (ADS)

    Styner, Martin; Smith, Rachel G.; Graves, Michael M.; Mosconi, Matthew W.; Peterson, Sarah; White, Scott; Blocher, Joe; El-Sayed, Mohammed; Hazlett, Heather C.

    2007-03-01

    Brain morphometric studies often incorporate comparative asymmetry analyses of left and right hemispheric brain structures. In this work we show evidence that common methods of user guided structural segmentation exhibit strong left-right asymmetric biases and thus fundamentally influence any left-right asymmetry analyses. We studied several structural segmentation methods with varying degree of user interaction from pure manual outlining to nearly fully automatic procedures. The methods were applied to MR images and their corresponding left-right mirrored images from an adult and a pediatric study. Several expert raters performed the segmentations of all structures. The asymmetric segmentation bias is assessed by comparing the left-right volumetric asymmetry in the original and mirrored datasets, as well as by testing each sides volumetric differences to a zero mean standard t-tests. The structural segmentations of caudate, putamen, globus pallidus, amygdala and hippocampus showed a highly significant asymmetric bias using methods with considerable manual outlining or landmark placement. Only the lateral ventricle segmentation revealed no asymmetric bias due to the high degree of automation and a high intensity contrast on its boundary. Our segmentation methods have been adapted in that they are applied to only one of the hemispheres in an image and its left-right mirrored image. Our work suggests that existing studies of hemispheric asymmetry without similar precautions should be interpreted in a new, skeptical light. Evidence of an asymmetric segmentation bias is novel and unknown to the imaging community. This result seems less surprising to the visual perception community and its likely cause is differences in perception of oppositely curved 3D structures.

  12. Asymptotic Biases in Exploratory Factor Analysis and Structural Equation Modeling

    ERIC Educational Resources Information Center

    Ogasawara, Haruhiko

    2004-01-01

    Formulas for the asymptotic biases of the parameter estimates in structural equation models are provided in the case of the Wishart maximum likelihood estimation for normally and nonnormally distributed variables. When multivariate normality is satisfied, considerable simplification is obtained for the models of unstandardized variables. Formulas…

  13. Recursive estimators of mean-areal and local bias in precipitation products that account for conditional bias

    NASA Astrophysics Data System (ADS)

    Zhang, Yu; Seo, Dong-Jun

    2017-03-01

    This paper presents novel formulations of Mean field bias (MFB) and local bias (LB) correction schemes that incorporate conditional bias (CB) penalty. These schemes are based on the operational MFB and LB algorithms in the National Weather Service (NWS) Multisensor Precipitation Estimator (MPE). By incorporating CB penalty in the cost function of exponential smoothers, we are able to derive augmented versions of recursive estimators of MFB and LB. Two extended versions of MFB algorithms are presented, one incorporating spatial variation of gauge locations only (MFB-L), and the second integrating both gauge locations and CB penalty (MFB-X). These two MFB schemes and the extended LB scheme (LB-X) are assessed relative to the original MFB and LB algorithms (referred to as MFB-O and LB-O, respectively) through a retrospective experiment over a radar domain in north-central Texas, and through a synthetic experiment over the Mid-Atlantic region. The outcome of the former experiment indicates that introducing the CB penalty to the MFB formulation leads to small, but consistent improvements in bias and CB, while its impacts on hourly correlation and Root Mean Square Error (RMSE) are mixed. Incorporating CB penalty in LB formulation tends to improve the RMSE at high rainfall thresholds, but its impacts on bias are also mixed. The synthetic experiment suggests that beneficial impacts are more conspicuous at low gauge density (9 per 58,000 km2), and tend to diminish at higher gauge density. The improvement at high rainfall intensity is partly an outcome of the conservativeness of the extended LB scheme. This conservativeness arises in part from the more frequent presence of negative eigenvalues in the extended covariance matrix which leads to no, or smaller incremental changes to the smoothed rainfall amounts.

  14. Localized structures in convective experiments

    NASA Astrophysics Data System (ADS)

    Burguete, J.; Mancini, H.

    2014-01-01

    In this work we review localized structures appearing in thermo-convective experiments performed in extended (large "aspect ratio") fluid layers. After a brief general review (not exhaustive), we focus on some results obtained in pure fluids in a Bénard-Marangoni system with non-homogeneous heating where some structures of this kind appear. The experimental results are compared in reference to the most classical observed in binary mixtures experiments or simulations. In the Bénard-Marangoni experiment we present the stability diagram where localized structures appear and the typical situations where these local mechanisms have been studied experimentally. Some new experimental results are also included. The authors want to honor Prof. H. Brand in his 60th. birthday and to thank him for helpful discussions.

  15. Estimating the Bias of Local Polynomial Approximation Methods Using the Peano Kernel

    SciTech Connect

    Blair, J.; Machorro, E.; Luttman, A.

    2013-03-01

    The determination of uncertainty of an estimate requires both the variance and the bias of the estimate. Calculating the variance of local polynomial approximation (LPA) estimates is straightforward. We present a method, using the Peano Kernel Theorem, to estimate the bias of LPA estimates and show how this can be used to optimize the LPA parameters in terms of the bias-variance tradeoff. Figures of merit are derived and values calculated for several common methods. The results in the literature are expanded by giving bias error bounds that are valid for all lengths of the smoothing interval, generalizing the currently available asymptotic results that are only valid in the limit as the length of this interval goes to zero.

  16. Exchange bias training effect in coupled all ferromagnetic bilayer structures

    NASA Astrophysics Data System (ADS)

    Polisetty, Srinivas; He, Xi; Binek, Christian; Berger, Andreas

    2006-03-01

    We study exchange coupled bilayers of soft and hard ferromagnetic (FM) thin films by means of Alternating Gradient Force Magnetometry. A CoCr thin film realizes the magnetically soft layer (SL) which is exchange coupled via a Ru-interlayer with a hard CoPtCrB pinning layer (HL). This new class of all FM bilayers shows remarkable analogies to conventional antiferromagnetic (AF)/FM exchange bias (EB) heterostructures. Not only do these all FM bilayers exhibit a tunable EB effect, they also show a distinct training behavior upon cycling the SL through consecutive hysteresis loops. Training resembles the cycle dependent evolution of the bias field and is to a large extend analogous to the gradual degradation of the EB field observed upon cycling the FM top layer of a AF/FM EB heterostructure through consecutive hysteresis loops. However, in contrast to these conventional EB systems, our all FM bilayer structures allow the observation of training induced changes in the bias-setting HL by means of simple magnetometry. Our experiments show unambiguously that the training effect is driven by deviations from equilibrium in the pinning layer. A comparison of the experimental data with predictions from a theory based upon triggered relaxation phenomena shows excellent agreement.

  17. Local magnetoresistance through Si and its bias voltage dependence in ferromagnet/MgO/silicon-on-insulator lateral spin valves

    SciTech Connect

    Saito, Y. Tanamoto, T.; Ishikawa, M.; Sugiyama, H.; Inokuchi, T.; Hamaya, K.; Tezuka, N.

    2014-05-07

    Local magnetoresistance (MR) through silicon (Si) and its bias voltage (V{sub bias}) (bias current (I{sub bias})) dependence in ferromagnet (FM)/MgO/silicon-on-insulator lateral spin valves are investigated. From the experimental measurements, we find that the local-MR through Si increases with increasing V{sub bias}. This anomalous increase of local-MR as a function of V{sub bias} can be understood by considering the standard drift-diffusion theory improved by taking into account the difference in the interface resistances and first order quantum effect between FM/MgO/Si (source) and Si/MgO/FM (drain) interfaces. The interface resistance dependence on experimentally obtained local-MR ratios also agrees with the improved standard spin diffusion theory. These results indicate that experimentally observed local-MR is certainly related to the spin signal through the Si bulk band.

  18. Verifying the consistency relation for the scale-dependent bias from local primordial non-Gaussianity

    NASA Astrophysics Data System (ADS)

    Biagetti, Matteo; Lazeyras, Titouan; Baldauf, Tobias; Desjacques, Vincent; Schmidt, Fabian

    2017-07-01

    We measure the large-scale bias of dark matter haloes in simulations with non-Gaussian initial conditions of the local type, and compare this bias to the response of the mass function to a change in the primordial amplitude of fluctuations. The two are found to be consistent, as expected from physical arguments, for the three halo-finder algorithms which use different spherical overdensity (SO) and friends-of-friends methods. On the other hand, we find that the commonly used prediction for universal mass functions, that the scale-dependent bias is proportional to the first-order Gaussian Lagrangian bias, does not yield a good agreement with the measurements. For all halo finders, high-mass haloes show a non-Gaussian bias suppressed by 10-15 per cent relative to the universal mass function prediction. For SO haloes, this deviation changes sign at low masses, where the non-Gaussian bias becomes larger than the universal prediction.

  19. Dy-V magnetic interaction and local structure bias on the complex spin and orbital ordering in Dy₁₋xTbxVO₃ (x=0 and 0.2)

    SciTech Connect

    Yan, J.-Q.; Cao, H. B.; McGuire, M. A.; Ren, Y.; Sales, B. C.; Mandrus, D. G.

    2013-06-10

    The spin and orbital ordering in Dy₁₋xTbxVO₃ (x=0 and 0.2) was studied by measuring x-ray powder diffraction, magnetization, specific heat, and neutron single-crystal diffraction. The results show that G-OO/C-AF and C-OO/G-AF phases coexist in Dy0.8Tb0.20VO3 in the temperature range 2–60 K, and the volume fraction of each phase is temperature and field dependent. The ordering of Dy moments at T* = 12 K induces a transition from G-OO/C-AF to a C-OO/G-AF phase. Magnetic fields suppress the long-range order of Dy moments and thus the C-OO/G-AF phase below T*. The polarized moments induced at the Dy sublattice by external magnetic fields couple to the V 3d moments, and this coupling favors the G-OO/C-AF state. Also discussed is the effect of the Dy-V magnetic interaction and local structure distortion on the spin and orbital ordering in Dy₁₋xTbxVO₃.

  20. Dy-V magnetic interaction and local structure bias on the complex spin and orbital ordering in Dy₁₋xTbxVO₃ (x=0 and 0.2)

    DOE PAGES

    Yan, J.-Q.; Cao, H. B.; McGuire, M. A.; ...

    2013-06-10

    The spin and orbital ordering in Dy₁₋xTbxVO₃ (x=0 and 0.2) was studied by measuring x-ray powder diffraction, magnetization, specific heat, and neutron single-crystal diffraction. The results show that G-OO/C-AF and C-OO/G-AF phases coexist in Dy0.8Tb0.20VO3 in the temperature range 2–60 K, and the volume fraction of each phase is temperature and field dependent. The ordering of Dy moments at T* = 12 K induces a transition from G-OO/C-AF to a C-OO/G-AF phase. Magnetic fields suppress the long-range order of Dy moments and thus the C-OO/G-AF phase below T*. The polarized moments induced at the Dy sublattice by external magnetic fieldsmore » couple to the V 3d moments, and this coupling favors the G-OO/C-AF state. Also discussed is the effect of the Dy-V magnetic interaction and local structure distortion on the spin and orbital ordering in Dy₁₋xTbxVO₃.« less

  1. Removal of local and biased global maxima in intensity-based registration.

    PubMed

    Salvado, Olivier; Wilson, David L

    2007-04-01

    Intensity based registration (e.g., mutual information) suffers from a scalloping artifact giving rise to local maxima and sometimes a biased global maximum in a similarity objective function. Here, we demonstrate that scalloping is principally due to the noise reduction filtering that occurs when image samples are interpolated. Typically at a much smaller scale (100 times less in our test cases), there are also fluctuations in the similarity objective function due to interpolation of the signal and to sampling of a continuous, band-limited image signal. Focusing on the larger problem from noise, we show that this phenomenon can even bias global maxima, giving inaccurate registrations. This phenomenon is readily seen when one registers an image onto itself with different noise realizations but is absent when the same noise realization is present in both images. For linear interpolation, local maxima and global bias are removed if one filters the interpolated image using a new constant variance filter for linear interpolation (cv-lin filter), which equalizes the variance across the interpolated image. We use 2D synthetic and MR images and characterize the effect of cv-lin on similarity objective functions. With a reduction of local and biased maxima, image registration becomes more robust and accurate. An efficient implementation adds insignificant computation time per iteration, and because optimization proceeds more smoothly, sometimes fewer iterations are needed.

  2. Non-local bias in the halo bispectrum with primordial non-Gaussianity

    SciTech Connect

    Tellarini, Matteo; Ross, Ashley J.; Wands, David; Tasinato, Gianmassimo E-mail: ross.1333@osu.edu E-mail: david.wands@port.ac.uk

    2015-07-01

    Primordial non-Gaussianity can lead to a scale-dependent bias in the density of collapsed halos relative to the underlying matter density. The galaxy power spectrum already provides constraints on local-type primordial non-Gaussianity complementary those from the cosmic microwave background (CMB), while the bispectrum contains additional shape information and has the potential to outperform CMB constraints in future. We develop the bias model for the halo density contrast in the presence of local-type primordial non-Gaussianity, deriving a bivariate expansion up to second order in terms of the local linear matter density contrast and the local gravitational potential in Lagrangian coordinates. Nonlinear evolution of the matter density introduces a non-local tidal term in the halo model. Furthermore, the presence of local-type non-Gaussianity in the Lagrangian frame leads to a novel non-local convective term in the Eulerian frame, that is proportional to the displacement field when going beyond the spherical collapse approximation. We use an extended Press-Schechter approach to evaluate the halo mass function and thus the halo bispectrum. We show that including these non-local terms in the halo bispectra can lead to corrections of up to 25% for some configurations, on large scales or at high redshift.

  3. Directional biases in phylogenetic structure quantification: a Mediterranean case study

    PubMed Central

    Molina-Venegas, Rafael; Roquet, Cristina

    2014-01-01

    Recent years have seen an increasing effort to incorporate phylogenetic hypotheses to the study of community assembly processes. The incorporation of such evolutionary information has been eased by the emergence of specialized software for the automatic estimation of partially resolved supertrees based on published phylogenies. Despite this growing interest in the use of phylogenies in ecological research, very few studies have attempted to quantify the potential biases related to the use of partially resolved phylogenies and to branch length accuracy, and no work has examined how tree shape may affect inference of community phylogenetic metrics. In this study, using a large plant community and elevational dataset, we tested the influence of phylogenetic resolution and branch length information on the quantification of phylogenetic structure; and also explored the impact of tree shape (stemminess) on the loss of accuracy in phylogenetic structure quantification due to phylogenetic resolution. For this purpose, we used 9 sets of phylogenetic hypotheses of varying resolution and branch lengths to calculate three indices of phylogenetic structure: the mean phylogenetic distance (NRI), the mean nearest taxon distance (NTI) and phylogenetic diversity (stdPD) metrics. The NRI metric was the less sensitive to phylogenetic resolution, stdPD showed an intermediate sensitivity, and NTI was the most sensitive one; NRI was also less sensitive to branch length accuracy than NTI and stdPD, the degree of sensitivity being strongly dependent on the dating method and the sample size. Directional biases were generally towards type II errors. Interestingly, we detected that tree shape influenced the accuracy loss derived from the lack of phylogenetic resolution, particularly for NRI and stdPD. We conclude that well-resolved molecular phylogenies with accurate branch length information are needed to identify the underlying phylogenetic structure of communities, and also that

  4. Local heating in noble metal nanocontacts under high biases at 77 K

    NASA Astrophysics Data System (ADS)

    Tsutsui, Makusu; Teramae, Yumi; Kurokawa, Shu; Sakai, Akira

    2006-10-01

    Effects of local heating of noble metal nanocontacts under high biases at 77 K are investigated by measuring the bias dependence of the two-level fluctuation (TLF) frequency of the contact conductance. The TLF frequency increases exponentially in a bias range from 0.2 to 0.6 V for Au and Cu nanocontacts. This result indicates that the effective contact temperature of these contacts remains unchanged up to 0.6 V, in accordance with the theoretical prediction by Todorov et al. [T.N. Todorov, J. Hoekstra, A.P. Sutton, Phys. Rev. Lett. 86 (2001) 3606]. In contrast, the TLF frequency of Ag nanocontacts starts to increase more rapidly above 0.45 V than that of Au and Cu nanocontacts. The steep rise in the TLF frequency is possibly attributed to a poor heat transfer to the bulk part of the contact and a resulting rapid increase in the effective temperature.

  5. Ion flow and sheath structure near positively biased electrodes

    NASA Astrophysics Data System (ADS)

    Hood, R.; Scheiner, B.; Baalrud, S. D.; Hopkins, M. M.; Barnat, E. V.; Yee, B. T.; Merlino, R. L.; Skiff, F.

    2016-11-01

    What effect does a dielectric material surrounding a small positively biased electrode have on the ion flow and sheath structure near the electrode? Measurements of the ion velocity distribution function and plasma potential near positively biased electrodes were made using laser-induced fluorescence and an emissive probe. The results were compared with 2D particle-in-cell simulations. Both measurements and simulations showed that when the positive electrode was surrounded by the dielectric material, ions were accelerated toward the electrode to approximately 0.5 times the ion sound speed before being deflected radially by the electron sheath potential barrier of the electrode. The axial potential profile in this case contained a virtual cathode. In comparison, when the dielectric material was removed from around the electrode, both the ion flow and virtual cathode depth near the electrode were dramatically reduced. These measurements suggest that the ion presheath from the dielectric material surrounding the electrode may enclose the electron sheath of the electrode, resulting in a virtual cathode that substantially influences the ion flow profile in the region.

  6. A Modified Brain MR Image Segmentation and Bias Field Estimation Model Based on Local and Global Information

    PubMed Central

    Cong, Wang; Luan, Kuan; Liang, Hong; Ma, Xingcheng

    2016-01-01

    Because of the poor radio frequency coil uniformity and gradient-driven eddy currents, there is much noise and intensity inhomogeneity (bias) in brain magnetic resonance (MR) image, and it severely affects the segmentation accuracy. Better segmentation results are difficult to achieve by traditional methods; therefore, in this paper, a modified brain MR image segmentation and bias field estimation model based on local and global information is proposed. We first construct local constraints including image neighborhood information in Gaussian kernel mapping space, and then the complete regularization is established by introducing nonlocal spatial information of MR image. The weighting between local and global information is automatically adjusted according to image local information. At the same time, bias field information is coupled with the model, and it makes the model reduce noise interference but also can effectively estimate the bias field information. Experimental results demonstrate that the proposed algorithm has strong robustness to noise and bias field is well corrected. PMID:27660649

  7. Ion flow and sheath structure near positively biased electrodes

    NASA Astrophysics Data System (ADS)

    Hood, Ryan; Scheiner, Brett; Baalrud, Scott; Hopkins, Matthew; Barnat, Ed; Yee, Benjamin; Merlino, Robert; Skiff, Fred

    2016-10-01

    Measurements of the ion velocity distribution function (IVDF) and plasma potential were made near small positively biased electrodes using laser-induced fluorescence (LIF) and an emissive probe. The effect of dielectric around the electrode was tested and compared with a 2D particle-in-cell (PIC) simulation. Both measurements and simulation reveal that if the electrode is embedded within a surrounding dielectric, ions are accelerated toward the electrode to approximately 0.5 times the ion sound speed before being deflected radially by the electron sheath potential barrier. The axial potential profile in this case contains a virtual cathode. In comparison, when the surrounding dielectric is removed, both the ion flow and virtual cathode depth are dramatically reduced. These measurements suggest that the ion presheath from the dielectric may enclose the electron sheath of the electrode resulting in a virtual cathode that substantially influences the local ion flow profile. This research was supported by the Office of Fusion Energy Sciences at the U.S. Department of Energy under contract DE-AC04-94SL85000.

  8. Color Representation Is Retinotopically Biased but Locally Intermingled in Mouse V1

    PubMed Central

    Aihara, Shuhei; Yoshida, Takashi; Hashimoto, Takayuki; Ohki, Kenichi

    2017-01-01

    Dichromatic vision is common in many mammals. However, color processing in the primary visual cortex (V1) of dichromatic mammals is relatively unknown compared to the trichromatic primates. In this study, we investigated the functional organization of color processing in mouse V1. The mouse retina has a graded expression pattern of two opsins along its dorsoventral axis. However, it is not clear whether and how this expression pattern is reflected in the cortical representation at local (several hundred microns) and areal (V1) level. Using in vivo two-photon calcium (Ca2+) imaging and wide-field Ca2+ imaging, we revealed that V1 neurons responded to S (UV)- and M (green)-opsin isolating stimuli with slightly biased color preference depending on retinotopic position in V1. This was consistent with the distribution of retinal opsins. At the cellular level, preferences for S- and M-opsin isolating stimuli were intermingled in a local region encompassing several hundred microns. These results suggest that functional organizations of color information are locally intermingled, but slightly biased depending on the retinotopic position in mouse V1. PMID:28405186

  9. Color Representation Is Retinotopically Biased but Locally Intermingled in Mouse V1.

    PubMed

    Aihara, Shuhei; Yoshida, Takashi; Hashimoto, Takayuki; Ohki, Kenichi

    2017-01-01

    Dichromatic vision is common in many mammals. However, color processing in the primary visual cortex (V1) of dichromatic mammals is relatively unknown compared to the trichromatic primates. In this study, we investigated the functional organization of color processing in mouse V1. The mouse retina has a graded expression pattern of two opsins along its dorsoventral axis. However, it is not clear whether and how this expression pattern is reflected in the cortical representation at local (several hundred microns) and areal (V1) level. Using in vivo two-photon calcium (Ca(2+)) imaging and wide-field Ca(2+) imaging, we revealed that V1 neurons responded to S (UV)- and M (green)-opsin isolating stimuli with slightly biased color preference depending on retinotopic position in V1. This was consistent with the distribution of retinal opsins. At the cellular level, preferences for S- and M-opsin isolating stimuli were intermingled in a local region encompassing several hundred microns. These results suggest that functional organizations of color information are locally intermingled, but slightly biased depending on the retinotopic position in mouse V1.

  10. Zooming into creativity: individual differences in attentional global-local biases are linked to creative thinking.

    PubMed

    Zmigrod, Sharon; Zmigrod, Leor; Hommel, Bernhard

    2015-01-01

    While recent studies have investigated how processes underlying human creativity are affected by particular visual-attentional states, we tested the impact of more stable attention-related preferences. These were assessed by means of Navon's global-local task, in which participants respond to the global or local features of large letters constructed from smaller letters. Three standard measures were derived from this task: the sizes of the global precedence effect, the global interference effect (i.e., the impact of incongruent letters at the global level on local processing), and the local interference effect (i.e., the impact of incongruent letters at the local level on global processing). These measures were correlated with performance in a convergent-thinking creativity task (the Remote Associates Task), a divergent-thinking creativity task (the Alternate Uses Task), and a measure of fluid intelligence (Raven's matrices). Flexibility in divergent thinking was predicted by the local interference effect while convergent thinking was predicted by intelligence only. We conclude that a stronger attentional bias to visual information about the "bigger picture" promotes cognitive flexibility in searching for multiple solutions.

  11. Zooming into creativity: individual differences in attentional global-local biases are linked to creative thinking

    PubMed Central

    Zmigrod, Sharon; Zmigrod, Leor; Hommel, Bernhard

    2015-01-01

    While recent studies have investigated how processes underlying human creativity are affected by particular visual-attentional states, we tested the impact of more stable attention-related preferences. These were assessed by means of Navon’s global-local task, in which participants respond to the global or local features of large letters constructed from smaller letters. Three standard measures were derived from this task: the sizes of the global precedence effect, the global interference effect (i.e., the impact of incongruent letters at the global level on local processing), and the local interference effect (i.e., the impact of incongruent letters at the local level on global processing). These measures were correlated with performance in a convergent-thinking creativity task (the Remote Associates Task), a divergent-thinking creativity task (the Alternate Uses Task), and a measure of fluid intelligence (Raven’s matrices). Flexibility in divergent thinking was predicted by the local interference effect while convergent thinking was predicted by intelligence only. We conclude that a stronger attentional bias to visual information about the “bigger picture” promotes cognitive flexibility in searching for multiple solutions. PMID:26579030

  12. Localized structure of Euglena bioconvection

    NASA Astrophysics Data System (ADS)

    Iima, Makoto; Shoji, Erika; Awazu, Akinori; Nishimori, Hiraku; Izumi, Shunsuke; Hiroshima University Collaboration

    2013-11-01

    Bioconvection of a suspension of Euglena gracilis, a photosensitive flagellate whose body length is approximately 50 micrometers, was experimentally studied. Under strong light intensity, Euglena has a negative phototaxis; they tend to go away from the light source. When the bright illumination is given from the bottom, a large scale spatio-temporal pattern is generated as a result of interaction between Euglena and surrounding flow. Recently, localized convection pattern had been reported, however, the generation process and interaction of the localized convection cells has not been analyzed. We performed experimental study to understand the localization mechanism, in particular, the onset of bioconvection and lateral localization behavior due to phototaxis. Experiments started from different initial condition suggests a bistability near the onset of the convection as binary fluid convection that also shows localized convection cells. Dynamics of localized convections cells, which is similar to the binary fluid convection case although the basic equations are not the same, is also reported.

  13. Local bias in autistic subjects as evidenced by graphic tasks: perceptual hierarchization or working memory deficit?

    PubMed

    Mottron, L; Belleville, S; Ménard, E

    1999-07-01

    In the present study, copying tasks were used to assess hierarchical aspects of visual perception in a group of 10 nonsavant autistic individuals with normal intelligence. In Experiment 1, the hierarchical order of graphic construction and the constancy of this order were measured for the copying of objects and nonobjects. In comparison to control participants, autistic individuals produced more local features at the start of the copying. However, they did not differ from controls with respect to graphic constancy. Experiment 2 measured the effect of geometrical impossibility on the copying of figures. Results revealed that autistic individuals were less affected by figure impossibility than were controls. Therefore, these experiments seem to support the notion of a local bias for visual information processing in individuals with autism. Two interpretations are proposed to account for this effect. According to the hierarchical deficit hypothesis, individuals with autism do not manifest the normal global bias in perceiving scenes and objects. Alternatively, the executive function hypothesis suggests that autism brings about limitations in the complexity of information that can be manipulated in short-term visual memory during graphic planning.

  14. Mapping the Similarities of Spectra: Global and Locally-biased Approaches to SDSS Galaxies

    NASA Astrophysics Data System (ADS)

    Lawlor, David; Budavári, Tamás; Mahoney, Michael W.

    2016-12-01

    We present a novel approach to studying the diversity of galaxies. It is based on a novel spectral graph technique, that of locally-biased semi-supervised eigenvectors. Our method introduces new coordinates that summarize an entire spectrum, similar to but going well beyond the widely used Principal Component Analysis (PCA). Unlike PCA, however, this technique does not assume that the Euclidean distance between galaxy spectra is a good global measure of similarity. Instead, we relax that condition to only the most similar spectra, and we show that doing so yields more reliable results for many astronomical questions of interest. The global variant of our approach can identify very finely numerous astronomical phenomena of interest. The locally-biased variants of our basic approach enable us to explore subtle trends around a set of chosen objects. The power of the method is demonstrated in the Sloan Digital Sky Survey Main Galaxy Sample, by illustrating that the derived spectral coordinates carry an unprecedented amount of information.

  15. On the spin bias of satellite galaxies in the local group-like environment

    SciTech Connect

    Lee, Jounghun; Lemson, Gerard E-mail: lemson@mpa-garching.mpg.de

    2013-05-01

    We utilize the Millennium-II simulation databases to study the spin bias of dark subhalos in the Local Group-like systems which have two prominent satellites with comparable masses. Selecting the group-size halos with total mass similar to that of the Local Group (LG) from the friends-of-friends halo catalog and locating their subhalos from the substructure catalog, we determine the most massive (main) and second to the most massive (submain) ones among the subhalos hosted by each selected halo. When the dimensionless spin parameter (λ) of each subhalo is derived from its specific angular momentum and circular velocity at virial radius, a signal of correlation is detected between the spin parameters of the subhalos and the main-to-submain mass ratios of their host halos at z = 0: the higher main-to-submain mass ratio a host halo has, the higher mean spin parameter its subhalos have. It is also found that the correlations exist even for the subhalo progenitors at z = 0.5 and 1. Our interpretation of this result is that the subhalo spin bias is not a transient effect but an intrinsic property of a LG-like system with higher main-to- submain mass ratio, caused by stronger anisotropic stress in the region. A cosmological implication of our result is also discussed.

  16. Biased diffusion in three-dimensional comb-like structures.

    PubMed

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

    2015-04-07

    In this paper, we study biased diffusion of point Brownian particles in a three-dimensional comb-like structure formed by a main cylindrical tube with identical periodic cylindrical dead ends. It is assumed that the dead ends are thin cylinders whose radius is much smaller than both the radius of the main tube and the distance between neighboring dead ends. It is also assumed that in the main tube, the particle, in addition to its regular diffusion, moves with a uniform constant drift velocity. For such a system, we develop a formalism that allows us to derive analytical expressions for the Laplace transforms of the first two moments of the particle displacement along the main tube axis. Inverting these Laplace transforms numerically, one can find the time dependences of the two moments for arbitrary values of both the drift velocity and the dead-end length, including the limiting case of infinitely long dead ends, where the unbiased diffusion becomes anomalous at sufficiently long times. The expressions for the Laplace transforms are used to find the effective drift velocity and diffusivity of the particle as functions of its drift velocity in the main tube and the tube geometric parameters. As might be expected from common-sense arguments, the effective drift velocity monotonically decreases from the initial drift velocity to zero as the dead-end length increases from zero to infinity. The effective diffusivity is a more complex, non-monotonic function of the dead-end length. As this length increases from zero to infinity, the effective diffusivity first decreases, reaches a minimum, and then increases approaching a plateau value which is proportional to the square of the particle drift velocity in the main tube.

  17. Insight into the split and asymmetry of charge distribution in biased M-structure superlattice

    NASA Astrophysics Data System (ADS)

    Liu, Lu; Bi, Han; Zhao, Yunhao; Zhao, Xuebing; Han, Xi; Wang, Guowei; Xu, Yingqiang; Li, Yuesheng; Che, Renchao

    2017-07-01

    The charge distribution in real space of an insertion variant based on an InAs/GaSb superlattice for an infrared detector is illustrated by in situ electron microscopy. The localization split of positive charge can be directly observed in the InAs/GaSb/AlSb/GaSb superlattice (M-structure) rather than in the InAs/GaSb superlattice. With the applied bias increasing from 0 to 4.5 V, the double peaks of positive charge density become asymmetrical gradually, with the peak integral ratio ranging from 1.13 to 2.54. Simultaneously, the negative charges move along the direction of the negative electric field. Without inserting the AlSb layer, the charge inversion occurs in both the hole wells and the electron wells of the InAs/GaSb superlattice under high bias. Such a discrepancy between the M-structure superlattice and the traditional superlattice suggests an effective reduction of tunneling probability of the M-structure design. Our result is of great help to understand the carrier immigration mechanism of the superlattice-based infrared detector.

  18. Removing the ISW-lensing bias from the local-form primordial non-Gaussianity estimation

    SciTech Connect

    Kim, Jaiseung; Komatsu, Eiichiro; Rotti, Aditya E-mail: aditya@iucaa.ernet.in

    2013-04-01

    The Integrated Sachs-Wolfe (ISW) effect produces a secondary temperature aniso\\-tropy of the cosmic microwave background (CMB), as CMB photons travel through time-varying potentials along the line-of-sight. The main contribution comes from redshifts z∼<2, where dark energy leads to a decay of potentials. As the same photons are gravitationally lensed by these decaying potentials, there exists a high degree of correlation between the ISW effect and CMB lensing, leading to a non-zero three-point correlation (bispectrum) of the observed temperature anisotropy. This ISW-lensing bispectrum, whose shape resembles that of the so-called ''local-form'' primordial bispectrum parametrized by f{sub NL}, is known to be the largest contamination of f{sub NL}. In order to avoid a spurious detection of primordial non-Gaussianity, we need to remove the ISW-lensing bias. In this work, we investigate three debiasing methods: (I) subtraction of an expected, ensemble average of the ISW-lensing bispectrum; (II) subtraction of a measured ISW-lensing bispectrum; and (III) direct subtraction of an estimated ISW signal from an observed temperature map. One may use an estimation of the ISW map from external non-CMB data or that from the CMB data themselves. As the methods II and III are based on fewer assumptions about the nature of dark energy, they are preferred over the method I. While the methods I and II yield unbiased estimates of f{sub NL} with comparable error bars, the method III yields a biased result when the underlying primordial f{sub NL} is non-zero and the ISW map is estimated from a lensing potential reconstructed from the observed temperature map. One of the sources of the bias is a lensing reconstruction noise bias which is independent of f{sub NL} and can be calculated precisely, but other f{sub NL}-dependent terms are difficult to compute reliably. We thus conclude that the method II is the best, model-independent way to remove the ISW-lensing bias of f{sub NL

  19. Bias-voltage-controlled ac and dc magnetotransport phenomena in hybrid structures

    NASA Astrophysics Data System (ADS)

    Volkov, N. V.; Tarasov, A. S.; Smolyakov, D. A.; Varnakov, S. N.; Ovchinnikov, S. G.

    2015-06-01

    We report some ac and dc magnetotransport phenomena in silicon-based hybrid structures. The giant impedance change under an applied magnetic field has been experimentally found in the metal/insulator/semiconductor (MIS) diode with the Schottky barrier based on the Fe/SiO2/p-Si and Fe/SiO2/n-Si structures. The maximum effect is found to observe at temperatures of 10-30 K in the frequency range 10 Hz-1 MHz. Below 1 kHz the magnetoresistance can be controlled in a wide range by applying a bias to the device. A photoinduced dc magnetoresistance of over 104% has been found in the Fe/SiO2/p-Si back-to-back Schottky diode. The observed magnetic-field-dependent effects are caused by the interface states localized in the insula-tor/semiconductor interface.

  20. Clustering of local group distances: Publication bias or correlated measurements? II. M31 and beyond

    SciTech Connect

    De Grijs, Richard; Bono, Giuseppe

    2014-07-01

    The accuracy of extragalactic distance measurements ultimately depends on robust, high-precision determinations of the distances to the galaxies in the local volume. Following our detailed study addressing possible publication bias in the published distance determinations to the Large Magellanic Cloud (LMC), here we extend our distance range of interest to include published distance moduli to M31 and M33, as well as to a number of their well-known dwarf galaxy companions. We aim at reaching consensus on the best, most homogeneous, and internally most consistent set of Local Group distance moduli to adopt for future, more general use based on the largest set of distance determinations to individual Local Group galaxies available to date. Based on a careful, statistically weighted combination of the main stellar population tracers (Cepheids, RR Lyrae variables, and the magnitude of the tip of the red-giant branch), we derive a recommended distance modulus to M31 of (m−M){sub 0}{sup M31}=24.46±0.10 mag—adopting as our calibration an LMC distance modulus of (m−M){sub 0}{sup LMC}=18.50 mag—and a fully internally consistent set of benchmark distances to key galaxies in the local volume, enabling us to establish a robust and unbiased, near-field extragalactic distance ladder.

  1. Removing Orientation-Induced Localization Biases in Single-Molecule Microscopy Using a Broadband Metasurface Mask

    PubMed Central

    Backlund, Mikael P.; Arbabi, Amir; Petrov, Petar N.; Arbabi, Ehsan; Saurabh, Saumya; Faraon, Andrei; Moerner, W. E.

    2016-01-01

    Nanoscale localization of single molecules is a crucial function in several advanced microscopy techniques, including single-molecule tracking and wide-field super-resolution imaging 1. To date, a central consideration of such techniques is how to optimize the precision of molecular localization. However, as these methods continue to push toward the nanometre size scale, an increasingly important concern is the localization accuracy. In particular, single fluorescent molecules emit with an anisotropic radiation pattern of an oscillating electric dipole, which can cause significant localization biases using common estimators 2-5. Here we present the theory and experimental demonstration of a solution to this problem based on azimuthal filtering in the Fourier plane of the microscope. We do so using a high efficiency dielectric metasurface polarization/phase device composed of nanoposts with sub-wavelength spacing 6. The method is demonstrated both on fluorophores embedded in a polymer matrix, and in dL5 protein complexes that bind Malachite green 7, 8. PMID:27574529

  2. Clustering of Local Group Distances: Publication Bias or Correlated Measurements? II. M31 and Beyond

    NASA Astrophysics Data System (ADS)

    de Grijs, Richard; Bono, Giuseppe

    2014-07-01

    The accuracy of extragalactic distance measurements ultimately depends on robust, high-precision determinations of the distances to the galaxies in the local volume. Following our detailed study addressing possible publication bias in the published distance determinations to the Large Magellanic Cloud (LMC), here we extend our distance range of interest to include published distance moduli to M31 and M33, as well as to a number of their well-known dwarf galaxy companions. We aim at reaching consensus on the best, most homogeneous, and internally most consistent set of Local Group distance moduli to adopt for future, more general use based on the largest set of distance determinations to individual Local Group galaxies available to date. Based on a careful, statistically weighted combination of the main stellar population tracers (Cepheids, RR Lyrae variables, and the magnitude of the tip of the red-giant branch), we derive a recommended distance modulus to M31 of (m-M)_0^M31 = 24.46 +/- 0.10 mag—adopting as our calibration an LMC distance modulus of (m-M)_0^LMC = 18.50 mag—and a fully internally consistent set of benchmark distances to key galaxies in the local volume, enabling us to establish a robust and unbiased, near-field extragalactic distance ladder.

  3. Exchange bias in ferrite hollow nanoparticles originated by complex internal magnetic structure

    NASA Astrophysics Data System (ADS)

    De Biasi, Emilio; Lima, Enio, Jr.; Vargas, Jose M.; Zysler, Roberto D.; Arbiol, Jordi; Ibarra, Alfonso; Goya, Gerardo F.; Ibarra, M. Ricardo

    2015-10-01

    Iron-oxide hollow nanospheres (HNS) may present unusual magnetic behavior as a consequence of their unique morphology. Here, we report the unusual magnetic behavior of HNS that are 9 nm in diameter. The magnetic properties of HNS originate in their complex magnetic structure, as evidenced by Mössbauer spectroscopy and magnetization measurements. We observe a bias in the hysteresis when measured at very low temperature in the field cooling protocol (10 kOe). In addition, dc (static) and ac (dynamic) magnetization measurements against temperature and applied field reveal a frustrated order of the system below 10 K. High-resolution transmission electron microscopy (HRTEM) studies reveal that the HNS are composed of small crystalline clusters of about 2 nm in diameter, which behave as individual magnetic entities. Micromagnetic simulations (using conjugate gradient in order to minimize the total energy of the system) reproduce the experimentally observed magnetic behavior. The model considers the hollow particles as constituted by small ordered clusters embedded in an antiferromagnetic environment (spins localized outside the clusters). In addition, the surface spins (in both inner and outer surfaces of the HNS) are affected by a local surface anisotropy. The strong effective magnetic anisotropy field of the clusters induces the bias observed when the system is cooled in the presence of a magnetic external field. This effect propagates through the exchange interaction into the entire particle.

  4. Network Structure and Biased Variance Estimation in Respondent Driven Sampling

    PubMed Central

    Verdery, Ashton M.; Mouw, Ted; Bauldry, Shawn; Mucha, Peter J.

    2015-01-01

    This paper explores bias in the estimation of sampling variance in Respondent Driven Sampling (RDS). Prior methodological work on RDS has focused on its problematic assumptions and the biases and inefficiencies of its estimators of the population mean. Nonetheless, researchers have given only slight attention to the topic of estimating sampling variance in RDS, despite the importance of variance estimation for the construction of confidence intervals and hypothesis tests. In this paper, we show that the estimators of RDS sampling variance rely on a critical assumption that the network is First Order Markov (FOM) with respect to the dependent variable of interest. We demonstrate, through intuitive examples, mathematical generalizations, and computational experiments that current RDS variance estimators will always underestimate the population sampling variance of RDS in empirical networks that do not conform to the FOM assumption. Analysis of 215 observed university and school networks from Facebook and Add Health indicates that the FOM assumption is violated in every empirical network we analyze, and that these violations lead to substantially biased RDS estimators of sampling variance. We propose and test two alternative variance estimators that show some promise for reducing biases, but which also illustrate the limits of estimating sampling variance with only partial information on the underlying population social network. PMID:26679927

  5. Network Structure and Biased Variance Estimation in Respondent Driven Sampling.

    PubMed

    Verdery, Ashton M; Mouw, Ted; Bauldry, Shawn; Mucha, Peter J

    2015-01-01

    This paper explores bias in the estimation of sampling variance in Respondent Driven Sampling (RDS). Prior methodological work on RDS has focused on its problematic assumptions and the biases and inefficiencies of its estimators of the population mean. Nonetheless, researchers have given only slight attention to the topic of estimating sampling variance in RDS, despite the importance of variance estimation for the construction of confidence intervals and hypothesis tests. In this paper, we show that the estimators of RDS sampling variance rely on a critical assumption that the network is First Order Markov (FOM) with respect to the dependent variable of interest. We demonstrate, through intuitive examples, mathematical generalizations, and computational experiments that current RDS variance estimators will always underestimate the population sampling variance of RDS in empirical networks that do not conform to the FOM assumption. Analysis of 215 observed university and school networks from Facebook and Add Health indicates that the FOM assumption is violated in every empirical network we analyze, and that these violations lead to substantially biased RDS estimators of sampling variance. We propose and test two alternative variance estimators that show some promise for reducing biases, but which also illustrate the limits of estimating sampling variance with only partial information on the underlying population social network.

  6. Bias assisted scanning probe microscopy direct write lithography enables local oxygen enrichment of lanthanum cuprates thin films

    SciTech Connect

    Lavini, Francesco; Yang, Nan; Vasudevan, Rama K.; Strelcov, Evgheni; Jesse, Stephen; Okatan, Mahmut Baris; Kravchenko, Ivan I.; Di Castro, Daniele; Kalinin, Sergei V.; Balestrino, Giuseppe; Foglietti, Vittorio; Aruta, Carmela

    2015-01-01

    Here, scanning probe bias techniques have been used as a method to locally dope thin epitaxial films of La2CuO4 (LCO) fabricated by pulsed laser deposition. The local electrochemical oxidation of LCO very efficiently introduces interstitial oxygen defects in the thin film. Details on the influence of the tip voltage bias and environmental conditions on the surface morphology have been investigated. The results show that a local uptake of oxygen occurs in the oxidized films.

  7. Drawing Firmer Conclusions: Autistic Children Show No Evidence of a Local Processing Bias in a Controlled Copying Task

    ERIC Educational Resources Information Center

    Smith, Alastair D.; Kenny, Lorcan; Rudnicka, Anna; Briscoe, Josie; Pellicano, Elizabeth

    2016-01-01

    Drawing tasks are frequently used to test competing theories of visuospatial skills in autism. Yet, methodological differences between studies have led to inconsistent findings. To distinguish between accounts based on local bias or global deficit, we present a simple task that has previously revealed dissociable local/global impairments in…

  8. Drawing Firmer Conclusions: Autistic Children Show No Evidence of a Local Processing Bias in a Controlled Copying Task

    ERIC Educational Resources Information Center

    Smith, Alastair D.; Kenny, Lorcan; Rudnicka, Anna; Briscoe, Josie; Pellicano, Elizabeth

    2016-01-01

    Drawing tasks are frequently used to test competing theories of visuospatial skills in autism. Yet, methodological differences between studies have led to inconsistent findings. To distinguish between accounts based on local bias or global deficit, we present a simple task that has previously revealed dissociable local/global impairments in…

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

    SciTech Connect

    Li, Qian; Jesse, Stephen; Tselev, Alexander; Collins, Liam; Yu, Pu; Kravchenko, Ivan; Kalinin, Sergei V.; Balke, Nina

    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 and 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.

  10. 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

  11. MRI tissue classification and bias field estimation based on coherent local intensity clustering: a unified energy minimization framework.

    PubMed

    Li, Chunming; Xu, Chenyang; Anderson, Adam W; Gore, John C

    2009-01-01

    This paper presents a new energy minimization method for simultaneous tissue classification and bias field estimation of magnetic resonance (MR) images. We first derive an important characteristic of local image intensities--the intensities of different tissues within a neighborhood form separable clusters, and the center of each cluster can be well approximated by the product of the bias within the neighborhood and a tissue-dependent constant. We then introduce a coherent local intensity clustering (CLIC) criterion function as a metric to evaluate tissue classification and bias field estimation. An integration of this metric defines an energy on a bias field, membership functions of the tissues, and the parameters that approximate the true signal from the corresponding tissues. Thus, tissue classification and bias field estimation are simultaneously achieved by minimizing this energy. The smoothness of the derived optimal bias field is ensured by the spatially coherent nature of the CLIC criterion function. As a result, no extra effort is needed to smooth the bias field in our method. Moreover, the proposed algorithm is robust to the choice of initial conditions, thereby allowing fully automatic applications. Our algorithm has been applied to high field and ultra high field MR images with promising results.

  12. Densest Local Structures of Uniaxial Ellipsoids

    NASA Astrophysics Data System (ADS)

    Schaller, Fabian M.; Weigel, Robert F. B.; Kapfer, Sebastian C.

    2016-10-01

    Connecting the collective behavior of disordered systems with local structure on the particle scale is an important challenge, for example, in granular and glassy systems. Compounding complexity, in many scientific and industrial applications, particles are polydisperse, aspherical, or even of varying shape. Here, we investigate a generalization of the classical kissing problem in order to understand the local building blocks of packings of aspherical grains. We numerically determine the densest local structures of uniaxial ellipsoids by minimizing the Set Voronoi cell volume around a given particle. Depending on the particle aspect ratio, different local structures are observed and classified by symmetry and Voronoi coordination number. In extended disordered packings of frictionless particles, knowledge of the densest structures allows us to rescale the Voronoi volume distributions onto the single-parameter family of k -Gamma distributions. Moreover, we find that approximate icosahedral clusters are found in random packings, while the optimal local structures for more aspherical particles are not formed.

  13. Bias-Corrected Estimation of Noncentrality Parameters of Covariance Structure Models

    ERIC Educational Resources Information Center

    Raykov, Tenko

    2005-01-01

    A bias-corrected estimator of noncentrality parameters of covariance structure models is discussed. The approach represents an application of the bootstrap methodology for purposes of bias correction, and utilizes the relation between average of resample conventional noncentrality parameter estimates and their sample counterpart. The…

  14. Bias-Corrected Estimation of Noncentrality Parameters of Covariance Structure Models

    ERIC Educational Resources Information Center

    Raykov, Tenko

    2005-01-01

    A bias-corrected estimator of noncentrality parameters of covariance structure models is discussed. The approach represents an application of the bootstrap methodology for purposes of bias correction, and utilizes the relation between average of resample conventional noncentrality parameter estimates and their sample counterpart. The…

  15. Combinatorics of locally optimal RNA secondary structures.

    PubMed

    Fusy, Eric; Clote, Peter

    2014-01-01

    It is a classical result of Stein and Waterman that the asymptotic number of RNA secondary structures is 1.104366∙n-3/2∙2.618034n. Motivated by the kinetics of RNA secondary structure formation, we are interested in determining the asymptotic number of secondary structures that are locally optimal, with respect to a particular energy model. In the Nussinov energy model, where each base pair contributes -1 towards the energy of the structure, locally optimal structures are exactly the saturated structures, for which we have previously shown that asymptotically, there are 1.07427∙n-3/2∙2.35467n many saturated structures for a sequence of length n. In this paper, we consider the base stacking energy model, a mild variant of the Nussinov model, where each stacked base pair contributes -1 toward the energy of the structure. Locally optimal structures with respect to the base stacking energy model are exactly those secondary structures, whose stems cannot be extended. Such structures were first considered by Evers and Giegerich, who described a dynamic programming algorithm to enumerate all locally optimal structures. In this paper, we apply methods from enumerative combinatorics to compute the asymptotic number of such structures. Additionally, we consider analogous combinatorial problems for secondary structures with annotated single-stranded, stacking nucleotides (dangles).

  16. Follow-the-leader cell migration requires biased cell-cell contact and local microenvironmental signals

    NASA Astrophysics Data System (ADS)

    Wynn, Michelle L.; Rupp, Paul; Trainor, Paul A.; Schnell, Santiago; Kulesa, Paul M.

    2013-06-01

    Directed cell migration often involves at least two types of cell motility that include multicellular streaming and chain migration. However, what is unclear is how cell contact dynamics and the distinct microenvironments through which cells travel influence the selection of one migratory mode or the other. The embryonic and highly invasive neural crest (NC) are an excellent model system to study this question since NC cells have been observed in vivo to display both of these types of cell motility. Here, we present data from tissue transplantation experiments in chick and in silico modeling that test our hypothesis that cell contact dynamics with each other and the microenvironment promote and sustain either multicellular stream or chain migration. We show that when premigratory cranial NC cells (at the pre-otic level) are transplanted into a more caudal region in the head (at the post-otic level), cells alter their characteristic stream behavior and migrate in chains. Similarly, post-otic NC cells migrate in streams after transplantation into the pre-otic hindbrain, suggesting that local microenvironmental signals dictate the mode of NC cell migration. Simulations of an agent-based model (ABM) that integrates the NC cell behavioral data predict that chain migration critically depends on the interplay of biased cell-cell contact and local microenvironment signals. Together, this integrated modeling and experimental approach suggests new experiments and offers a powerful tool to examine mechanisms that underlie complex cell migration patterns.

  17. Latent structure in random sequences drives neural learning toward a rational bias

    PubMed Central

    Sun, Yanlong; O’Reilly, Randall C.; Bhattacharyya, Rajan; Smith, Jack W.; Liu, Xun; Wang, Hongbin

    2015-01-01

    People generally fail to produce random sequences by overusing alternating patterns and avoiding repeating ones—the gambler’s fallacy bias. We can explain the neural basis of this bias in terms of a biologically motivated neural model that learns from errors in predicting what will happen next. Through mere exposure to random sequences over time, the model naturally develops a representation that is biased toward alternation, because of its sensitivity to some surprisingly rich statistical structure that emerges in these random sequences. Furthermore, the model directly produces the best-fitting bias-gain parameter for an existing Bayesian model, by which we obtain an accurate fit to the human data in random sequence production. These results show that our seemingly irrational, biased view of randomness can be understood instead as the perfectly reasonable response of an effective learning mechanism to subtle statistical structure embedded in random sequences. PMID:25775565

  18. Local statistical interpretation for water structure

    NASA Astrophysics Data System (ADS)

    Sun, Qiang

    2013-05-01

    In this Letter, Raman spectroscopy is employed to study supercooled water down to a temperature of 248 K at ambient pressure. Based on our interpretation of the Raman OH stretching band, decreasing temperature mainly leads to a structural transition from the single donor-single acceptor (DA) to the double donor-double acceptor (DDAA) hydrogen bonding motif. Additionally, a local statistical interpretation of the water structure is proposed, which reveals that a water molecule interacts with molecules in the first shell through various local hydrogen-bonded networks. From this, a local structure order parameter is proposed to explain the short-range order and long-range disorder.

  19. Investigation on particle swarm optimisation for feature selection on high-dimensional data: local search and selection bias

    NASA Astrophysics Data System (ADS)

    Tran, Binh; Xue, Bing; Zhang, Mengjie; Nguyen, Su

    2016-07-01

    Feature selection is an essential step in classification tasks with a large number of features, such as in gene expression data. Recent research has shown that particle swarm optimisation (PSO) is a promising approach to feature selection. However, it also has potential limitation to get stuck into local optima, especially for gene selection problems with a huge search space. Therefore, we developed a PSO algorithm (PSO-LSRG) with a fast "local search" combined with a gbest resetting mechanism as a way to improve the performance of PSO for feature selection. Furthermore, since many existing PSO-based feature selection approaches on the gene expression data have feature selection bias, i.e. no unseen test data is used, 2 sets of experiments on 10 gene expression datasets were designed: with and without feature selection bias. As compared to standard PSO, PSO with gbest resetting only, and PSO with local search only, PSO-LSRG obtained a substantial dimensionality reduction and a significant improvement on the classification performance in both sets of experiments. PSO-LSRG outperforms the other three algorithms when feature selection bias exists. When there is no feature selection bias, PSO-LSRG selects the smallest number of features in all cases, but the classification performance is slightly worse in a few cases, which may be caused by the overfitting problem. This shows that feature selection bias should be avoided when designing a feature selection algorithm to ensure its generalisation ability on unseen data.

  20. Deterministic weak localization in periodic structures.

    PubMed

    Tian, C; Larkin, A

    2005-12-09

    In some perfect periodic structures classical motion exhibits deterministic diffusion. For such systems we present the weak localization theory. As a manifestation for the velocity autocorrelation function a universal power law decay is predicted to appear at four Ehrenfest times. This deterministic weak localization is robust against weak quenched disorders, which may be confirmed by coherent backscattering measurements of periodic photonic crystals.

  1. Not a Copernican observer: biased peculiar velocity statistics in the local Universe

    NASA Astrophysics Data System (ADS)

    Hellwing, Wojciech A.; Nusser, Adi; Feix, Martin; Bilicki, Maciej

    2017-01-01

    We assess the effect of the local large scale structure on the estimation of two-point statistics of the observed radial peculiar velocities of galaxies. A large N-body simulation is used to examine these statistics from the perspective of random observers as well as "Local Group (LG)-like" observers conditioned to reside in an environment resembling the observed universe within 20 Mpc. The local environment systematically distorts the shape and amplitude of velocity statistics with respect to ensemble-averaged measurements made by a Copernican (random) observer. The Virgo cluster has the most significant impact, introducing large systematic deviations in all the statistics. For a simple "top-hat" selection function, an idealized survey extending to ˜160h-1 Mpc or deeper is needed to completely mitigate the effects of the local environment. Using shallower catalogues leads to systematic deviations of the order of 50 to 200% depending on the scale considered. For a flat redshift distribution similar to the one of the CosmicFlows-3 survey, the deviations are even more prominent in both the shape and amplitude at all separations considered (≲100h^{-1} Mpc). Conclusions based on statistics calculated without taking into account the impact of the local environment should be revisited.

  2. Not a Copernican observer: biased peculiar velocity statistics in the local Universe

    NASA Astrophysics Data System (ADS)

    Hellwing, Wojciech A.; Nusser, Adi; Feix, Martin; Bilicki, Maciej

    2017-05-01

    We assess the effect of the local large-scale structure on the estimation of two-point statistics of the observed radial peculiar velocities of galaxies. A large N-body simulation is used to examine these statistics from the perspective of random observers as well as 'Local Group-like' observers conditioned to reside in an environment resembling the observed Universe within 20 Mpc. The local environment systematically distorts the shape and amplitude of velocity statistics with respect to ensemble-averaged measurements made by a Copernican (random) observer. The Virgo cluster has the most significant impact, introducing large systematic deviations in all the statistics. For a simple 'top-hat' selection function, an idealized survey extending to ˜160 h-1 Mpc or deeper is needed to completely mitigate the effects of the local environment. Using shallower catalogues leads to systematic deviations of the order of 50-200 per cent depending on the scale considered. For a flat redshift distribution similar to the one of the CosmicFlows-3 survey, the deviations are even more prominent in both the shape and amplitude at all separations considered (≲100 h-1 Mpc). Conclusions based on statistics calculated without taking into account the impact of the local environment should be revisited.

  3. Bias to CMB lensing measurements from the bispectrum of large-scale structure

    NASA Astrophysics Data System (ADS)

    Böhm, Vanessa; Schmittfull, Marcel; Sherwin, Blake D.

    2016-08-01

    The rapidly improving precision of measurements of gravitational lensing of the cosmic microwave background (CMB) also requires a corresponding increase in the precision of theoretical modeling. A commonly made approximation is to model the CMB deflection angle or lensing potential as a Gaussian random field. In this paper, however, we analytically quantify the influence of the non-Gaussianity of large-scale structure (LSS) lenses, arising from nonlinear structure formation, on CMB lensing measurements. In particular, evaluating the impact of the nonzero bispectrum of large-scale structure on the relevant CMB four-point correlation functions, we find that there is a bias to estimates of the CMB lensing power spectrum. For temperature-based lensing reconstruction with CMB stage III and stage IV experiments, we find that this lensing power spectrum bias is negative and is of order 1% of the signal. This corresponds to a shift of multiple standard deviations for these upcoming experiments. We caution, however, that our numerical calculation only evaluates two of the largest bias terms and, thus, only provides an approximate estimate of the full bias. We conclude that further investigation into lensing biases from nonlinear structure formation is required and that these biases should be accounted for in future lensing analyses.

  4. Introduction: Dissipative localized structures in extended systems

    NASA Astrophysics Data System (ADS)

    Tlidi, Mustapha; Taki, Majid; Kolokolnikov, Theodore

    2007-09-01

    Localized structures belong to the class of dissipative structures found far from equilibrium. Contributions from the most representative groups working on a various fields of natural science such as biology, chemistry, plant ecology, mathematics, optics, and laser physics are presented. The aim of this issue is to gather specialists from these fields towards a cross-fertilization among these active areas of research and thereby to present an overview of the state of art in the formation and the characterization of dissipative localized structures. Nonlinear optics and laser physics have an important part in this issue because of potential applications in information technology. In particular, localized structures could be used as "bits" for parallel information storage and processing.

  5. Visual capture of a stereo sound: Interactions between cue reliability, sound localization variability, and cross-modal bias.

    PubMed

    Montagne, Christopher; Zhou, Yi

    2016-07-01

    Multisensory interactions involve coordination and sometimes competition between multiple senses. Vision usually dominates audition in spatial judgments when light and sound stimuli are presented from two different physical locations. This study investigated the influence of vision on the perceived location of a phantom sound source placed in a stereo sound field using a pair of loudspeakers emitting identical signals that were delayed or attenuated relative to each other. Results show that although a similar horizontal range (+/-45°) was reported for timing-modulated and level-modulated signals, listeners' localization performance showed greater variability for the timing signals. When visual stimuli were presented simultaneously with the auditory stimuli, listeners showed stronger visual bias for timing-modulated signals than level-modulated and single-speaker control signals. Trial-to-trial errors remained relatively stable over time, suggesting that sound localization uncertainty has an immediate and long-lasting effect on the across-modal bias. Binaural signal analyses further reveal that interaural differences of time and intensity-the two primary cues for sound localization in the azimuthal plane-are inherently more ambiguous for signals placed using timing. These results suggest that binaural ambiguity is intrinsically linked with localization variability and the strength of cross-modal bias in sound localization.

  6. Priming global and local processing of composite faces: revisiting the processing-bias effect on face perception.

    PubMed

    Gao, Zaifeng; Flevaris, Anastasia V; Robertson, Lynn C; Bentin, Shlomo

    2011-07-01

    We used the composite-face illusion and Navon stimuli to determine the consequences of priming local or global processing on subsequent face recognition. The composite-face illusion reflects the difficulty of ignoring the task-irrelevant half-face while attending the task-relevant half if the half-faces in the composite are aligned. On each trial, participants first matched two Navon stimuli, attending to either the global or the local level, and then matched the upper halves of two composite faces presented sequentially. Global processing of Navon stimuli increased the sensitivity to incongruence between the upper and the lower halves of the composite face, relative to a baseline in which the composite faces were not primed. Local processing of Navon stimuli did not influence the sensitivity to incongruence. Although incongruence induced a bias toward different responses, this bias was not modulated by priming. We conclude that global processing of Navon stimuli augments holistic processing of the face.

  7. Clustering of local group distances: publication bias or correlated measurements? I. The large Magellanic cloud

    SciTech Connect

    De Grijs, Richard; Wicker, James E.; Bono, Giuseppe

    2014-05-01

    The distance to the Large Magellanic Cloud (LMC) represents a key local rung of the extragalactic distance ladder yet the galaxy's distance modulus has long been an issue of contention, in particular in view of claims that most newly determined distance moduli cluster tightly—and with a small spread—around the 'canonical' distance modulus, (m – M){sub 0} = 18.50 mag. We compiled 233 separate LMC distance determinations published between 1990 and 2013. Our analysis of the individual distance moduli, as well as of their two-year means and standard deviations resulting from this largest data set of LMC distance moduli available to date, focuses specifically on Cepheid and RR Lyrae variable-star tracer populations, as well as on distance estimates based on features in the observational Hertzsprung-Russell diagram. We conclude that strong publication bias is unlikely to have been the main driver of the majority of published LMC distance moduli. However, for a given distance tracer, the body of publications leading to the tightly clustered distances is based on highly non-independent tracer samples and analysis methods, hence leading to significant correlations among the LMC distances reported in subsequent articles. Based on a careful, weighted combination, in a statistical sense, of the main stellar population tracers, we recommend that a slightly adjusted canonical distance modulus of (m – M){sub 0} = 18.49 ± 0.09 mag be used for all practical purposes that require a general distance scale without the need for accuracies of better than a few percent.

  8. Are the paleoclimatic reconstructions based on mammals biased by the local landscape?

    NASA Astrophysics Data System (ADS)

    Garcia-Alix, Antonio

    2017-04-01

    The paleoclimatic reconstructions deduced from mammal associations might have been biased by the complex local effect of the landscape. This effect is especially important in tectonically active regions where important landscape changes occurred in short-time periods. In this abstract, I present a coupled paleoenvironmental approach 1) using the ecological requirement of the faunal associations, and 2) using isotopic analyses in both sediments and small mammal teeth in order to discern between climate and landscape effects. Southern Iberian Peninsula was a tectonically active area during the late Miocene and Pliocene, and the environmental and humidity data deduced from the faunal associations agree with the sedimentary evolution of the basin. However, these humidity trends are usually opposite to the humidity reconstruction deduced from the carbon isotopic data in rodent teeth and from the isotopic composition of the sediments (C and O), which are scarcely influenced by the landscape. So, changes in the landscape, probably boosted by tectonics, gave rise to the development of endorheic and/or exorheic systems in the areas and conditioned the extension of these systems, affecting taxa with high dependence on humidity. Similar outcomes have been observed in early-middle Miocene records from north Spain. In those cases, the response of small mammal associations to abrupt climate changes might have been also buffered by the landscape. On the other hand, records where there was no important landscape changes, such as those from an early- middle Miocene coastal area of eastern Spain, do not show that disagreement in the humidity and environmental reconstructions following both methods.

  9. Clustering of Local Group Distances: Publication Bias or Correlated Measurements? I. The Large Magellanic Cloud

    NASA Astrophysics Data System (ADS)

    de Grijs, Richard; Wicker, James E.; Bono, Giuseppe

    2014-05-01

    The distance to the Large Magellanic Cloud (LMC) represents a key local rung of the extragalactic distance ladder yet the galaxy's distance modulus has long been an issue of contention, in particular in view of claims that most newly determined distance moduli cluster tightly—and with a small spread—around the "canonical" distance modulus, (m - M)0 = 18.50 mag. We compiled 233 separate LMC distance determinations published between 1990 and 2013. Our analysis of the individual distance moduli, as well as of their two-year means and standard deviations resulting from this largest data set of LMC distance moduli available to date, focuses specifically on Cepheid and RR Lyrae variable-star tracer populations, as well as on distance estimates based on features in the observational Hertzsprung-Russell diagram. We conclude that strong publication bias is unlikely to have been the main driver of the majority of published LMC distance moduli. However, for a given distance tracer, the body of publications leading to the tightly clustered distances is based on highly non-independent tracer samples and analysis methods, hence leading to significant correlations among the LMC distances reported in subsequent articles. Based on a careful, weighted combination, in a statistical sense, of the main stellar population tracers, we recommend that a slightly adjusted canonical distance modulus of (m - M)0 = 18.49 ± 0.09 mag be used for all practical purposes that require a general distance scale without the need for accuracies of better than a few percent.

  10. Lost in the Forest, Stuck in the Trees: Dispositional Global/Local Bias Is Resistant to Exposure to High and Low Spatial Frequencies

    PubMed Central

    Dale, Gillian; Arnell, Karen M.

    2014-01-01

    Visual stimuli can be perceived at a broad, “global” level, or at a more focused, “local” level. While research has shown that many individuals demonstrate a preference for global information, there are large individual differences in the degree of global/local bias, such that some individuals show a large global bias, some show a large local bias, and others show no bias. The main purpose of the current study was to examine whether these dispositional differences in global/local bias could be altered through various manipulations of high/low spatial frequency. Through 5 experiments, we examined various measures of dispositional global/local bias and whether performance on these measures could be altered by manipulating previous exposure to high or low spatial frequency information (with high/low spatial frequency faces, gratings, and Navon letters). Ultimately, there was little evidence of change from pre-to-post manipulation on the dispositional measures, and dispositional global/local bias was highly reliable pre- to post-manipulation. The results provide evidence that individual differences in global/local bias or preference are relatively resistant to exposure to spatial frequency information, and suggest that the processing mechanisms underlying high/low spatial frequency use and global/local bias may be more independent than previously thought. PMID:24992321

  11. Deeper than Shallow: Evidence for Structure-Based Parsing Biases in Second-Language Sentence Processing

    ERIC Educational Resources Information Center

    Witzel, Jeffrey; Witzel, Naoko; Nicol, Janet

    2012-01-01

    This study examines the reading patterns of native speakers (NSs) and high-level (Chinese) nonnative speakers (NNSs) on three English sentence types involving temporarily ambiguous structural configurations. The reading patterns on each sentence type indicate that both NSs and NNSs were biased toward specific structural interpretations. These…

  12. Polarization properties of localized structures in VCSELs

    NASA Astrophysics Data System (ADS)

    Averlant, Etienne; Tlidi, Mustapha; Ackemann, Thorsten; Thienpont, Hugo; Panajotov, Krassimir

    2016-04-01

    Broad area Vertical-Cavity Surface-Emitting Lasers (VCSELs) have peculiar polarization properties which are a field of study by itself.1-3 These properties have already been used for localized structure generation, in a simple configuration, where only one polarization component was used.4 Here, we present new experimental and theoretical results on the complex polarization behavior of localized structures generated in an optically-injected broad area VCSEL. A linear stability analysis of the spin-flip VCSEL model is performed for the case of broad area devices, in a restrained and experimentally relevant parameter set. Numerical simulations are performed, in one and two dimensions. They reveal existence of vector localized structures. These structures have a complex polarization state, which is not simply a linear polarization following the one of the optical injection. Experimental results confirm theoretical predictions. Applications of this work can lead to the encoding of small color images in the polarization state of an ensemble of localized structures at the surface of a broad area VCSEL.

  13. Alcohol-attentional bias and motivational structure as independent predictors of social drinkers' alcohol consumption.

    PubMed

    Fadardi, Javad Salehi; Cox, W Miles

    2008-10-01

    Prior studies aimed at explaining cognitive-motivational reasons for drinking have focused on either cognitive or motivational factors, but not on both. This study examined the ability of both alcohol-attentional bias and motivational structure to predict alcohol consumption. Participants were university students (N=87) who completed a battery of tests, including the Personal Concerns Inventory (a measure of adaptive and maladaptive motivation), an alcohol Stroop test (a measure of alcohol-attentional bias), and an alcohol-use inventory. Regression, moderation, and mediation analyses showed that (a) maladaptive motivation and alcohol-attentional bias were positive predictors of alcohol consumption after participants' age, gender, and executive cognitive functioning had been controlled, and (b) maladaptive motivation and alcohol-attentional bias independently predicted alcohol consumption. The implications of the results for both theory and practice are discussed.

  14. Realistic Drawing Talent in Typical Adults Is Associated with the Same Kind of Local Processing Bias Found in Individuals with ASD

    ERIC Educational Resources Information Center

    Drake, Jennifer E.; Winner, Ellen

    2011-01-01

    A local processing bias has been found in individuals with autism as well as in typical children with a gift for drawing realistically. This study investigated whether a local processing bias in typical adults is more strongly associated with drawing realism or autistic-like traits. Forty-two adults made an observational drawing (scored for…

  15. Realistic Drawing Talent in Typical Adults Is Associated with the Same Kind of Local Processing Bias Found in Individuals with ASD

    ERIC Educational Resources Information Center

    Drake, Jennifer E.; Winner, Ellen

    2011-01-01

    A local processing bias has been found in individuals with autism as well as in typical children with a gift for drawing realistically. This study investigated whether a local processing bias in typical adults is more strongly associated with drawing realism or autistic-like traits. Forty-two adults made an observational drawing (scored for…

  16. Charge transfer-induced magnetic exchange bias and electron localization in (111)- and (001)-oriented LaNiO3/LaMnO3 superlattices

    NASA Astrophysics Data System (ADS)

    Wei, Haoming; Barzola-Quiquia, Jose Luis; Yang, Chang; Patzig, Christian; Höche, Thomas; Esquinazi, Pablo; Grundmann, Marius; Lorenz, Michael

    2017-03-01

    High-quality lattice-matched LaNiO3/LaMnO3 superlattices with monolayer terrace structure have been grown on both (111)- and (001)-oriented SrTiO3 substrates by pulsed laser deposition. In contrast to the previously reported experiments, a magnetic exchange bias is observed that reproducibly occurs in both (111)- and (001)-oriented superlattices with the thin single layers of 5 and 7 unit cells, respectively. The exchange bias is theoretically explained by charge transfer-induced magnetic moments at Ni atoms. Furthermore, magnetization data at low temperature suggest two magnetic phases in the superlattices, with Néel temperature around 10 K. Electrical transport measurements reveal a metal-insulator transition with strong localization of electrons in the superlattices with the thin LaNiO3 layers of 4 unit cells, in which the electrical transport is dominated by two-dimensional variable range hopping.

  17. Population structure with localized haplotype clusters.

    PubMed

    Browning, Sharon R; Weir, Bruce S

    2010-08-01

    We propose a multilocus version of F(ST) and a measure of haplotype diversity using localized haplotype clusters. Specifically, we use haplotype clusters identified with BEAGLE, which is a program implementing a hidden Markov model for localized haplotype clustering and performing several functions including inference of haplotype phase. We apply this methodology to HapMap phase 3 data. With this haplotype-cluster approach, African populations have highest diversity and lowest divergence from the ancestral population, East Asian populations have lowest diversity and highest divergence, and other populations (European, Indian, and Mexican) have intermediate levels of diversity and divergence. These relationships accord with expectation based on other studies and accepted models of human history. In contrast, the population-specific F(ST) estimates obtained directly from single-nucleotide polymorphisms (SNPs) do not reflect such expected relationships. We show that ascertainment bias of SNPs has less impact on the proposed haplotype-cluster-based F(ST) than on the SNP-based version, which provides a potential explanation for these results. Thus, these new measures of F(ST) and haplotype-cluster diversity provide an important new tool for population genetic analysis of high-density SNP data.

  18. Detecting structure of haplotypes and local ancestry

    USDA-ARS?s Scientific Manuscript database

    We present a two-layer hidden Markov model to detect the structure of haplotypes for unrelated individuals. This allows us to model two scales of linkage disequilibrium (one within a group of haplotypes and one between groups), thereby taking advantage of rich haplotype information to infer local an...

  19. Interface electronic structure in a metal/ferroelectric heterostructure under applied bias

    NASA Astrophysics Data System (ADS)

    Rault, J. E.; Agnus, G.; Maroutian, T.; Pillard, V.; Lecoeur, Ph.; Niu, G.; Vilquin, B.; Silly, M. G.; Bendounan, A.; Sirotti, F.; Barrett, N.

    2013-04-01

    The effective barrier height between an electrode and a ferroelectric (FE) depends on both macroscopic electrical properties and microscopic chemical and electronic structure. The behavior of a prototypical electrode/FE/electrode structure, Pt/BaTiO3/Nb-doped SrTiO3, under in-situ bias voltage is investigated using x-ray photoelectron spectroscopy. The full band alignment is measured and is supported by transport measurements. Barrier heights depend on interface chemistry and on the FE polarization. A differential response of the core levels to applied bias as a function of the polarization state is observed, consistent with Callen charge variations near the interface.

  20. Landau levels in biased graphene structures with monolayer-bilayer interfaces

    NASA Astrophysics Data System (ADS)

    Mirzakhani, M.; Zarenia, M.; Vasilopoulos, P.; Ketabi, S. A.; Peeters, F. M.

    2017-09-01

    The electron energy spectrum in monolayer-bilayer-monolayer and in bilayer-monolayer-bilayer graphene structures is investigated and the effects of a perpendicular magnetic field and electric bias are studied. Different types of monolayer-bilayer interfaces are considered as zigzag (ZZ) or armchair (AC) junctions which modify considerably the bulk Landau levels (LLs) when the spectra are plotted as a function of the center coordinate of the cyclotron orbit. Far away from the two interfaces, one obtains the well-known LLs for extended monolayer or bilayer graphene. The LL structure changes significantly at the two interfaces or junctions where the valley degeneracy is lifted for both types of junctions, especially when the distance between them is approximately equal to the magnetic length. Varying the nonuniform bias and the width of this junction-to-junction region in either structure strongly influence the resulting spectra. Significant differences exist between ZZ and AC junctions in both structures. The densities of states (DOSs) for unbiased structures are symmetric in energy whereas those for biased structures are asymmetric. An external bias creates interface LLs in the gaps between the LLs of the unbiased system in which the DOS can be quite small. Such a pattern of LLs can be probed by scanning tunneling microscopy.

  1. Observation selection bias in contact prediction and its implications for structural bioinformatics

    PubMed Central

    Orlando, G.; Raimondi, D.; Vranken, W. F.

    2016-01-01

    Next Generation Sequencing is dramatically increasing the number of known protein sequences, with related experimentally determined protein structures lagging behind. Structural bioinformatics is attempting to close this gap by developing approaches that predict structure-level characteristics for uncharacterized protein sequences, with most of the developed methods relying heavily on evolutionary information collected from homologous sequences. Here we show that there is a substantial observational selection bias in this approach: the predictions are validated on proteins with known structures from the PDB, but exactly for those proteins significantly more homologs are available compared to less studied sequences randomly extracted from Uniprot. Structural bioinformatics methods that were developed this way are thus likely to have over-estimated performances; we demonstrate this for two contact prediction methods, where performances drop up to 60% when taking into account a more realistic amount of evolutionary information. We provide a bias-free dataset for the validation for contact prediction methods called NOUMENON. PMID:27857150

  2. Tuning structure and roughness in exchange biased NiO/permalloy bilayers

    NASA Astrophysics Data System (ADS)

    Thomas, Luc; Negulescu, Béatrice; Dumont, Yves; Tessier, Michel; Keller, Niels; Wack, André; Guyot, Marcel

    2003-05-01

    Polycrystalline NiO thin films have been grown by pulsed laser deposition on quartz substrates. These films exhibit a strong texture, which can be tuned by changing deposition parameters such as substrate temperature or oxygen partial pressure. By varying the deposition temperature from room temperature up to 900 °C, (220), (111), and (200) textured films are prepared. In the temperature zones separating these orientations, competition between different growth directions leads to smaller crystallites, characterized by broader diffraction lines. Surface roughness measured by atomic force microscopy is strongly correlated with these structural features. Roughness is minimum for highly textured samples (about 7Å for 500 Å thick films), and it exhibits two peaks in the intermediate zones, with maximum values of about 40 Å. In order to correlate exchange bias with these structural features, 100 Å thick FeNi layers were deposited by rf sputtering on top of the 500 Å thick NiO films. Hysteresis loops were measured at 10 K by superconducting quantum interference device magnetometry after the samples were cooled in a 100 Oe magnetic field. Exchange bias is maximum for (111) oriented samples. No clear correlation between exchange bias and surface roughness is observed at low temperature. Exchange bias temperature dependence strongly depends upon NiO films deposition temperature. The blocking temperature, for which the exchange bias vanishes, varies between 150 K for (220) oriented samples and 250 K for (111) textured samples, and it exceeds room temperature for (200) films.

  3. Parietal structure and function explain human variation in working memory biases of visual attention.

    PubMed

    Soto, David; Rotshtein, Pia; Kanai, Ryota

    2014-04-01

    Recent research indicates that human attention appears inadvertently biased by items that match the contents of working memory (WM). WM-biases can lead to attentional costs when the memory content matches goal-irrelevant items and to attentional benefits when it matches the sought target. Here we used functional and structural MRI data to determine the neural basis of human variation in WM biases. We asked whether human variation in WM-benefits and WM-costs merely reflects the process of attentional capture by the contents of WM or whether variation in WM biases may be associated with distinct forms of cognitive control over internal WM signals based on selection goals. Human ability to use WM contents to facilitate selection was positively correlated with gray matter volume in the left superior posterior parietal cortex (PPC), while the ability to overcome interference by WM-matching distracters was associated with the left inferior PPC in the anterior IPS. Functional activity in the left PPC, measured by functional MRI, also predicted the magnitude of WM-costs on selection. Both structure and function of left PPC mediate the expression of WM biases in human visual attention.

  4. Modulation of Global and Local Processing Biases in Adults with Autistic-Like Traits

    ERIC Educational Resources Information Center

    English, Michael C. W.; Maybery, Murray T.; Visser, Troy A. W.

    2017-01-01

    Previous work shows that doing a continuous performance task (CPT) shifts attentional biases in neurotypical individuals towards global aspects of hierarchical Navon figures by selectively activating right hemisphere regions associated with global processing. The present study examines whether CPT can induce similar modulations of attention in…

  5. Local fields in conductor surface electromigration: A first-principles study in the low-bias ballistic limit

    SciTech Connect

    Bevan, Kirk H; Zhu, Wenguang; Stocks, George Malcolm; Guo, Hong; Zhang, Zhenyu

    2012-01-01

    Utilizing first-principles quantum transport calculations, we investigate the role of local fields in conductor surface electromigration. A nanometer-thick Ag(100) thin film is adopted as our prototypical conductor, where we demonstrate the existence of intense local electric fields at atomic surface defects under an external bias. It is shown that such local fields can play an important role in driving surface electromigration and electrical breakdown. The intense fields originate from the relatively short (atomic-scale) screening lengths common to most elemental metals. This general short-range screening trend is established self-consistently within an intuitive picture of linear response electrostatics. The findings shed new light on the underlying physical origins of surface electromigration and point to the possibility of harnessing local fields to engineer electromigration at the nanoscale.

  6. MR image segmentation and bias field estimation based on coherent local intensity clustering with total variation regularization.

    PubMed

    Tu, Xiaoguang; Gao, Jingjing; Zhu, Chongjing; Cheng, Jie-Zhi; Ma, Zheng; Dai, Xin; Xie, Mei

    2016-12-01

    Though numerous segmentation algorithms have been proposed to segment brain tissue from magnetic resonance (MR) images, few of them consider combining the tissue segmentation and bias field correction into a unified framework while simultaneously removing the noise. In this paper, we present a new unified MR image segmentation algorithm whereby tissue segmentation, bias correction and noise reduction are integrated within the same energy model. Our method is presented by a total variation term introduced to the coherent local intensity clustering criterion function. To solve the nonconvex problem with respect to membership functions, we add auxiliary variables in the energy function such as Chambolle's fast dual projection method can be used and the optimal segmentation and bias field estimation can be achieved simultaneously throughout the reciprocal iteration. Experimental results show that the proposed method has a salient advantage over the other three baseline methods on either tissue segmentation or bias correction, and the noise is significantly reduced via its applications on highly noise-corrupted images. Moreover, benefiting from the fast convergence of the proposed solution, our method is less time-consuming and robust to parameter setting.

  7. Drifting localized structures in doubly diffusive convection

    NASA Astrophysics Data System (ADS)

    Knobloch, Edgar; Lo Jacono, David; Bergeon, Alain

    2016-11-01

    We use numerical continuation to compute a multiplicity of spatially localized states in doubly diffusive convection in a vertical slot driven by imposed horizontal temperature and concentration differences. The calculations focus on the so-called opposing case, in which the resulting gradients are in balance. No-slip boundary conditions are used at the sides and periodic boundary conditions with large spatial period are used in the vertical direction. This system exhibits homoclinic snaking of stationary spatially localized structures with point symmetry. In this talk we demonstrate the existence, near threshold, of drifting pulses of spatially localized convection that appear when mixed concentration boundary conditions are used, and use homotopic continuation to identify similar states in the case of fixed concentration boundary conditions. We show that these states persist to large values of the Grasshof number and provide a detailed study of their properties.

  8. How response bias affects the factorial structure of personality self-reports.

    PubMed

    Navarro-González, David; Lorenzo-Seva, Urbano; Vigil-Colet, Andreu

    2016-11-01

    Various studies have shown that acquiescence can distort the factor structure of personality questionnaires based on the five-factor model.  In the present study, we analysed how acquiescence and social desirability affect the factor structure of a measure based on this personality model and a measure of aggression. We analysed the factor structures of both tests before and after removing both biases in a sample of 532 adolescents aged between 11 and 18 (M= 14.75, SD= 2.1). The factor structure of both tests presented a worse fit to the expected model when response bias was not controlled, and the congruence indexes for the personality and aggression measures showed a moderate (from C= .948 to C= .872) or great (from C= .931 to C= .475) decrease, respectively. Furthermore, acquiescence was largely responsible for these effects, and social desirability effects were only shown on the aggression measure.   Response bias, and especially acquiescence, should be controlled during the development of personality measures to avoid distorting them, especially with samples of people with a high level of acquiescence (for example, those with little education, the young or the elderly). Furthermore, the use of response bias loadings as a criterion for choosing the items minimizes those distortions.

  9. Local gravity and large-scale structure

    NASA Technical Reports Server (NTRS)

    Juszkiewicz, Roman; Vittorio, Nicola; Wyse, Rosemary F. G.

    1990-01-01

    The magnitude and direction of the observed dipole anisotropy of the galaxy distribution can in principle constrain the amount of large-scale power present in the spectrum of primordial density fluctuations. This paper confronts the data, provided by a recent redshift survey of galaxies detected by the IRAS satellite, with the predictions of two cosmological models with very different levels of large-scale power: the biased Cold Dark Matter dominated model (CDM) and a baryon-dominated model (BDM) with isocurvature initial conditions. Model predictions are investigated for the Local Group peculiar velocity, v(R), induced by mass inhomogeneities distributed out to a given radius, R, for R less than about 10,000 km/s. Several convergence measures for v(R) are developed, which can become powerful cosmological tests when deep enough samples become available. For the present data sets, the CDM and BDM predictions are indistinguishable at the 2 sigma level and both are consistent with observations. A promising discriminant between cosmological models is the misalignment angle between v(R) and the apex of the dipole anisotropy of the microwave background.

  10. Local gravity and large-scale structure

    NASA Technical Reports Server (NTRS)

    Juszkiewicz, Roman; Vittorio, Nicola; Wyse, Rosemary F. G.

    1990-01-01

    The magnitude and direction of the observed dipole anisotropy of the galaxy distribution can in principle constrain the amount of large-scale power present in the spectrum of primordial density fluctuations. This paper confronts the data, provided by a recent redshift survey of galaxies detected by the IRAS satellite, with the predictions of two cosmological models with very different levels of large-scale power: the biased Cold Dark Matter dominated model (CDM) and a baryon-dominated model (BDM) with isocurvature initial conditions. Model predictions are investigated for the Local Group peculiar velocity, v(R), induced by mass inhomogeneities distributed out to a given radius, R, for R less than about 10,000 km/s. Several convergence measures for v(R) are developed, which can become powerful cosmological tests when deep enough samples become available. For the present data sets, the CDM and BDM predictions are indistinguishable at the 2 sigma level and both are consistent with observations. A promising discriminant between cosmological models is the misalignment angle between v(R) and the apex of the dipole anisotropy of the microwave background.

  11. Automatic Tool for Local Assembly Structures

    SciTech Connect

    2016-10-11

    Whole community shotgun sequencing of total DNA (i.e. metagenomics) and total RNA (i.e. metatranscriptomics) has provided a wealth of information in the microbial community structure, predicted functions, metabolic networks, and is even able to reconstruct complete genomes directly. Here we present ATLAS (Automatic Tool for Local Assembly Structures) a comprehensive pipeline for assembly, annotation, genomic binning of metagenomic and metatranscriptomic data with an integrated framework for Multi-Omics. This will provide an open source tool for the Multi-Omic community at large.

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

    DTIC Science & Technology

    2016-03-16

    Architectural Bias • Comparison of Petroleum -Based and Bio-Based Chemical Architectures • Continuing Research on Structure-Property Relationships using...inexpensive supply of phenol from petroleum refining. Consequently, certain architectures are over-represented in a “random” sample of network-forming...A much wider array of structures can be accessed from these sources than is available from refining petroleum 11Distribution A: Approved for public

  13. Correlation between substrate bias, growth process and structural properties of phosphorus incorporated tetrahedral amorphous carbon films

    NASA Astrophysics Data System (ADS)

    Liu, Aiping; Zhu, Jiaqi; Han, Jiecai; Wu, Huaping; Jia, Zechun

    2007-09-01

    We investigate the growth process and structural properties of phosphorus incorporated tetrahedral amorphous carbon (ta-C:P) films which are deposited at different substrate biases by filtered cathodic vacuum arc technique with PH 3 as the dopant source. The films are characterized by X-ray photoelectron spectroscopy (XPS), atomic force microscopy, Raman spectroscopy, residual stress measurement, UV/VIS/NIR absorption spectroscopy and temperature-dependent conductivity measurement. The atomic fraction of phosphorus in the films as a function of substrate bias is obtained by XPS analysis. The optimum bias for phosphorus incorporation is about -80 V. Raman spectra show that the amorphous structures of all samples with atomic-scaled smooth surface are not remarkably changed when PH 3 is implanted, but some small graphitic crystallites are formed. Moreover, phosphorus impurities and higher-energetic impinging ions are favorable for the clustering of sp 2 sites dispersed in sp 3 skeleton and increase the level of structural ordering for ta-C:P films, which further releases the compressive stress and enhances the conductivity of the films. Our analysis establishes an interrelationship between microstructure, stress state, electrical properties, and substrate bias, which helps to understand the deposition mechanism of ta-C:P films.

  14. Sister cohesion and structural axis components mediate homolog bias of meiotic recombination

    PubMed Central

    Kim, Keun P.; Weiner, Beth M.; Zhang, Liangran; Jordan, Amy; Dekker, Job; Kleckner, Nancy

    2010-01-01

    SUMMARY Meiotic recombination occurs between one chromatid of each maternal and paternal homolog (homolog bias) versus between sister chromatids (sister bias). Physical DNA analysis reveals that meiotic cohesin/axis component Rec8 promotes sister bias, likely via its cohesion activity. Two meiosis-specific axis components, Red1/Mek1kinase, counteract this effect. With this precondition satisfied, other molecules directly specify homolog bias per se. Rec8 also acts positively to maintain homolog bias during crossover recombination. These observations point to sequential release of double-strand break ends from association with their sister. Red1 and Rec8 are found to play distinct roles for sister cohesion, DSB formation and recombination progression kinetics. Also, the two components are enriched in spatially distinct domains of axial structure that develop prior to DSB formation. We propose that Red1 and Rec8 domains provide functionally complementary environments whereby inputs evolved from DSB repair and late-stage chromosome morphogenesis are integrated to give the complete meiotic chromosomal program. PMID:21145459

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

    NASA Astrophysics Data System (ADS)

    Yagi, Mamiko; Ito, Mitsuki; Shirakashi, Jun-ichi

    2015-07-01

    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 SiO2/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 thus 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.

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

    SciTech Connect

    Yagi, Mamiko; Ito, Mitsuki; Shirakashi, Jun-ichi

    2015-07-07

    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 thus 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.

  17. Frequency based localization of structural discrepancies

    NASA Technical Reports Server (NTRS)

    Shepard, G. D.; Milani, J.

    1988-01-01

    The intent of modal analysis is to develop a reliable model of a structure by working with the analytical and experimental modal properties of frequency, damping and mode shape. In addition to identifying these modal properties, it would be desirable to determine spatially which parts of the structure are modelled poorly or well. It is shown how the pattern of discrepancies in the analytical and experimental test values for the pole and the driving point zero frequencies of a structure can be linked to discrepancies in the mass or stiffness of the structural elements. The success of the procedure depends on the numerical conditioning of a modal reference matrix. Strategies to insure adequate numerical conditioning require a formulation which avoids geometric and energy storage symmetries of the structure, and ignores structural elements which contribute negligibly small potential or kinetic energy to the excited modes. Physical insight into the numerical conditioning problem is provided by a numerical example and by localization of a mass discrepancy in a real structure based on lab tests.

  18. The Structure of the Local Hot Bubble

    NASA Technical Reports Server (NTRS)

    Liu, W.; Chiao, M.; Collier, M. R.; Cravens, T.; Galeazzi, M.; Koutroumpa, D.; Kuntz, K. D.; Lallement, R.; Lepri, S. T.; McCammon, Dan; hide

    2016-01-01

    Diffuse X-rays from the Local Galaxy (DXL) is a sounding rocket mission designed to quantify and characterize the contribution of Solar Wind Charge eXchange (SWCX) to the Diffuse X-ray Background and study the properties of the Local Hot Bubble (LHB). Based on the results from the DXL mission, we quantified and removed the contribution of SWCX to the diffuse X-ray background measured by the ROSAT All Sky Survey. The cleaned maps were used to investigate the physical properties of the LHB. Assuming thermal ionization equilibrium, we measured a highly uniform temperature distributed around kT = 0.097 keV +/- 0.013 keV (FWHM) +/- 0.006 keV(systematic). We also generated a thermal emission measure map and used it to characterize the three-dimensional (3D) structure of the LHB, which we found to be in good agreement with the structure of the local cavity measured from dust and gas.

  19. The Structure of the Local Hot Bubble

    NASA Astrophysics Data System (ADS)

    Liu, W.; Chiao, M.; Collier, M. R.; Cravens, T.; Galeazzi, M.; Koutroumpa, D.; Kuntz, K. D.; Lallement, R.; Lepri, S. T.; McCammon, D.; Morgan, K.; Porter, F. S.; Snowden, S. L.; Thomas, N. E.; Uprety, Y.; Ursino, E.; Walsh, B. M.

    2017-01-01

    Diffuse X-rays from the Local Galaxy (DXL) is a sounding rocket mission designed to quantify and characterize the contribution of Solar Wind Charge eXchange (SWCX) to the Diffuse X-ray Background and study the properties of the Local Hot Bubble (LHB). Based on the results from the DXL mission, we quantified and removed the contribution of SWCX to the diffuse X-ray background measured by the ROSAT All Sky Survey. The “cleaned” maps were used to investigate the physical properties of the LHB. Assuming thermal ionization equilibrium, we measured a highly uniform temperature distributed around kT = 0.097 keV ± 0.013 keV (FWHM) ± 0.006 keV (systematic). We also generated a thermal emission measure map and used it to characterize the three-dimensional (3D) structure of the LHB, which we found to be in good agreement with the structure of the local cavity measured from dust and gas.

  20. Indoor footstep localization from structural dynamics instrumentation

    NASA Astrophysics Data System (ADS)

    Poston, Jeffrey D.; Buehrer, R. Michael; Tarazaga, Pablo A.

    2017-05-01

    Measurements from accelerometers originally deployed to measure a building's structural dynamics can serve a new role: locating individuals moving within a building. Specifically, this paper proposes measurements of footstep-generated vibrations as a novel source of information for localization. The complexity of wave propagation in a building (e.g., dispersion and reflection) limits the utility of existing algorithms designed to locate, for example, the source of sound in a room or radio waves in free space. This paper develops enhancements for arrival time determination and time difference of arrival localization in order to address the complexities posed by wave propagation within a building's structure. Experiments with actual measurements from an instrumented public building demonstrate the potential of locating footsteps to sub-meter accuracy. Furthermore, this paper explains how to forecast performance in other buildings with different sensor configurations. This localization capability holds the potential to assist public safety agencies in building evacuation and incidence response, to facilitate occupancy-based optimization of heating or cooling and to inform facility security.

  1. Localizing Target Structures in Ultrasound Video

    PubMed Central

    Kwitt, R.; Vasconcelos, N.; Razzaque, S.; Aylward, S.

    2013-01-01

    The problem of localizing specific anatomic structures using ultrasound (US) video is considered. This involves automatically determining when an US probe is acquiring images of a previously defined object of interest, during the course of an US examination. Localization using US is motivated by the increased availability of portable, low-cost US probes, which inspire applications where inexperienced personnel and even first-time users acquire US data that is then sent to experts for further assessment. This process is of particular interest for routine examinations in underserved populations as well as for patient triage after natural disasters and large-scale accidents, where experts may be in short supply. The proposed localization approach is motivated by research in the area of dynamic texture analysis and leverages several recent advances in the field of activity recognition. For evaluation, we introduce an annotated and publicly available database of US video, acquired on three phantoms. Several experiments reveal the challenges of applying video analysis approaches to US images and demonstrate that good localization performance is possible with the proposed solution. PMID:23746488

  2. A discriminative Ramachandran potential of mean force aimed at minimizing secondary structure bias.

    PubMed

    Koppole, Sampath; Schaefer, Michael

    2012-03-15

    We introduce PMF*, a novel potential of mean force (PMF) for the Ramachandran ϕ/Ψ dihedral plot of the 20 standard amino acids and assess its relevance to the conformation of polypeptides by scoring structures in the protein data bank and decoy datasets. The new energy function is a linear combination of the conventional, unreferenced PMF and the ΔPMF relative to the free energy of all amino acids in the parameterization set of structures, effectively removing their respective biases toward α-helix and β-strand. It is shown that low-resolution crystal structures, NMR structures, and theoretical models have on average significantly higher energies than high-resolution crystal structures; also PMF* is more discriminative for structure quality than the individual PMF and ΔPMF energy functions. PMF* may be well suited for use as a restraint energy term in the refinement of experimental structures and theoretical models.

  3. Influence of bias voltage on structural and optical properties of TiNx thin films

    NASA Astrophysics Data System (ADS)

    Singh, Omveer; Dahiya, Raj P.; Malik, Hitendra K.; Kumar, Parmod

    2015-08-01

    In the present work, Ti thin films were deposited on Si substrate using DC sputtering technique. Indigenous hot cathode arc discharge plasma system was used for nitriding over these samples, where the plasma parameters and work piece can be controlled independently. A mixture of H2 and N2 gases (in the ratio of 80:20) was supplied into the plasma chamber. The effect of bias voltage on the crystal structure, morphology and optical properties was investigated by employing various physical techniques such as X-ray Diffraction, Atomic Force Microscopy and UV-Vis spectrometry. It was found that bias voltage affects largely the crystal structure and band gap which in turn is responsible for the modifications in optical properties of the deposited films.

  4. Vortical structures generated by a localized forcing

    NASA Astrophysics Data System (ADS)

    Korabel, Vasily N.

    Vortex structures (monopoles, dipoles, quadrupoles) as well as more complex structures (vortex streets) are fundamental elements of geophysical turbulence. Because they can effectively transport momentum, heat, salt and biochemical products, they play an essential role in ocean dynamics. Organized vortex structures are a well known feature of quasi-two-dimensional flows where motion in one direction is suppressed due to one of the following physical mechanisms: background rotation of the system, density stratification or geometrical restrictions such as for the flows in thin layers or soap films. Vortex dipoles are formed in a viscous fluid when a force is applied locally to some volume of fluid. If the force acts impulsively, a translating vortex dipole is generated. If the force starts at t = 0 and then acts continuously a starting jet with a dipole at its front is generated. Solutions for unsteady viscous flows generated by the action of continuous or impulsive localized forces are obtained in Oseen approximation. The solutions are compared with direct numerical simulations of vortex dipoles as well as with laboratory experiments. The comparison shows good quantitative agreement in both cases. A physical problem where the localized force acting continuously on fluid is placed in a uniform stream is equivalent to a problem of a fixed body in a uniform stream, while the couple of forces acting in opposite direction are equivalent to the problem of self-propelled body moving at constant velocity through a fluid. The solutions for the two-dimensional far-field wake are obtained in both cases. At a certain Reynolds number, wakes become unstable and form vortex streets. New series of high-resolution 2D numerical simulations is performed to study the characteristics of the wakes including the shedding frequency for a wide range of control parameters such as translational velocity, magnitude and spatial extent of a localized force. The results of numerical experiments

  5. Segmentation of knee MRI using structure enhanced local phase filtering

    NASA Astrophysics Data System (ADS)

    Lim, Mikhiel; Hacihaliloglu, Ilker

    2016-03-01

    The segmentation of bone surfaces from magnetic resonance imaging (MRI) data has applications in the quanti- tative measurement of knee osteoarthritis, surgery planning for patient specific total knee arthroplasty and its subsequent fabrication of artificial implants. However, due to the problems associated with MRI imaging such as low contrast between bone and surrounding tissues, noise, bias fields, and the partial volume effect, segmentation of bone surfaces continues to be a challenging operation. In this paper, a new framework is presented for the enhancement of knee MRI scans prior to segmentation in order to obtain high contrast bone images. During the first stage, a new contrast enhanced relative total variation (RTV) regularization method is used in order to remove textural noise from the bone structures and surrounding soft tissue interface. This salient bone edge information is further enhanced using a sparse gradient counting method based on L0 gradient minimization, which globally controls how many non-zero gradients are resulted in order to approximate prominent bone structures in a structure-sparsity-management manner. The last stage of the framework involves incorporation of local phase bone boundary information in order to provide an intensity invariant enhancement of contrast between the bone and surrounding soft tissue. The enhanced images are segmented using a fast random walker algorithm. Validation against expert segmentation was performed on 10 clinical knee MRI images, and achieved a mean dice similarity coefficient (DSC) of 0.975.

  6. Performance enhancement of ITO/oxide/semiconductor MOS-structure silicon solar cells with voltage biasing.

    PubMed

    Ho, Wen-Jeng; Huang, Min-Chun; Lee, Yi-Yu; Hou, Zhong-Fu; Liao, Changn-Jyun

    2014-01-01

    In this study, we demonstrate the photovoltaic performance enhancement of a p-n junction silicon solar cell using a transparent-antireflective ITO/oxide film deposited on the spacing of the front-side finger electrodes and with a DC voltage applied on the ITO-electrode. The depletion width of the p-n junction under the ITO-electrode was induced and extended while the absorbed volume and built-in electric field were also increased when the biasing voltage was increased. The photocurrent and conversion efficiency were increased because more photo-carriers are generated in a larger absorbed volume and because the carriers transported and collected more effectively due to higher biasing voltage effects. Compared to a reference solar cell (which was biased at 0 V), a conversion efficiency enhancement of 26.57% (from 12.42% to 15.72%) and short-circuit current density enhancement of 42.43% (from 29.51 to 42.03 mA/cm(2)) were obtained as the proposed MOS-structure solar cell biased at 2.5 V. In addition, the capacitance-volt (C-V) measurement was also used to examine the mechanism of photovoltaic performance enhancement due to the depletion width being enlarged by applying a DC voltage on an ITO-electrode.

  7. Performance enhancement of ITO/oxide/semiconductor MOS-structure silicon solar cells with voltage biasing

    PubMed Central

    2014-01-01

    In this study, we demonstrate the photovoltaic performance enhancement of a p-n junction silicon solar cell using a transparent-antireflective ITO/oxide film deposited on the spacing of the front-side finger electrodes and with a DC voltage applied on the ITO-electrode. The depletion width of the p-n junction under the ITO-electrode was induced and extended while the absorbed volume and built-in electric field were also increased when the biasing voltage was increased. The photocurrent and conversion efficiency were increased because more photo-carriers are generated in a larger absorbed volume and because the carriers transported and collected more effectively due to higher biasing voltage effects. Compared to a reference solar cell (which was biased at 0 V), a conversion efficiency enhancement of 26.57% (from 12.42% to 15.72%) and short-circuit current density enhancement of 42.43% (from 29.51 to 42.03 mA/cm2) were obtained as the proposed MOS-structure solar cell biased at 2.5 V. In addition, the capacitance-volt (C-V) measurement was also used to examine the mechanism of photovoltaic performance enhancement due to the depletion width being enlarged by applying a DC voltage on an ITO-electrode. PMID:25593550

  8. Clustering of Local Group Distances: Publication Bias or Correlated Measurements? IV. The Galactic Center

    NASA Astrophysics Data System (ADS)

    de Grijs, Richard; Bono, Giuseppe

    2016-11-01

    Aiming at deriving a statistically well-justified Galactic Center distance, R 0, and reducing any occurrence of publication bias, we compiled the most comprehensive and most complete database of Galactic Center distances available to date, containing 273 new or revised R 0 estimates published since records began in 1918 October until 2016 June. We separate our R 0 compilation into direct and indirect distance measurements. The latter include a large body of estimates that rely on centroid determinations for a range of tracer populations, as well as measurements based on kinematic observations of objects at the solar circle, combined with a mass and/or rotational model of the Milky Way. Careful assessment of the Galactic Center distances resulting from orbital modeling and statistical parallax measurements in the Galactic nucleus yields our final Galactic Center distance recommendation of {R}0=8.3+/- 0.2 {{(statistical)}}+/- 0.4 {{(systematic)}} {kpc}. The centroid-based distances are in good agreement with this recommendation. Neither the direct measurements nor the post-1990 centroid-based distance determinations suggest that publication bias may be important. The kinematics-based distance estimates are affected by significantly larger uncertainties, but they can be used to constrain the Galaxy’s rotation velocity at the solar galactocentric distance, {{{\\Theta }}}0. Our results imply that the International-Astronomical-Union-recommended Galactic Center distance ({R}0{IAU}=8.5 {kpc}) needs a downward adjustment, while its {{{\\Theta }}}0 recommendation ({{{\\Theta }}}0=220 km s-1) requires a substantial upward revision.

  9. Origin of bias-independent conductance plateaus and zero-bias conductance peaks in Bi2Se3/NbSe2 hybrid structures

    NASA Astrophysics Data System (ADS)

    Li, Hui; Zhou, Tong; He, Jun; Wang, Huan-Wen; Zhang, Huachen; Liu, Hong-Chao; Yi, Ya; Wu, Changming; Law, Kam Tuen; He, Hongtao; Wang, Jiannong

    2017-08-01

    Superconducting proximity effect in topological insulator and superconductor hybrid structure has attracted intense attention in recent years in an effort to search for Majorana fermions in condensed matter systems. Here we report on the superconducting proximity effect in a Bi2Se3 /NbSe2 junction fabricated with an all-dry transfer method. Experimentally measured differential conductance spectra exhibit a bias-independent conductance plateau (BICP) in the vicinity of zero bias below 7 K and a zero-bias conductance peak (ZBCP) appears below 2 K. We show that the BICP is due to the strong superconducting proximity effect between the superconductor and the topological surface states while the ZBCP is due to the bulk states of Bi2Se3 . Our study gives direct evidence that the topological surface states can be strongly coupled to a superconductor and clarifies the different roles of surface states and bulk states in superconducting proximity effect.

  10. Identifying and removing structural biases in climate models with history matching

    NASA Astrophysics Data System (ADS)

    Williamson, Daniel; Blaker, Adam T.; Hampton, Charlotte; Salter, James

    2015-09-01

    We describe the method of history matching, a method currently used to help quantify parametric uncertainty in climate models, and argue for its use in identifying and removing structural biases in climate models at the model development stage. We illustrate the method using an investigation of the potential to improve upon known ocean circulation biases in a coupled non-flux-adjusted climate model (the third Hadley Centre Climate Model; HadCM3). In particular, we use history matching to investigate whether or not the behaviour of the Antarctic Circumpolar Current (ACC), which is known to be too strong in HadCM3, represents a structural bias that could be corrected using the model parameters. We find that it is possible to improve the ACC strength using the parameters and observe that doing this leads to more realistic representations of the sub-polar and sub-tropical gyres, sea surface salinities (both globally and in the North Atlantic), sea surface temperatures in the sinking regions in the North Atlantic and in the Southern Ocean, North Atlantic Deep Water flows, global precipitation, wind fields and sea level pressure. We then use history matching to locate a region of parameter space predicted not to contain structural biases for ACC and SSTs that is around 1 % of the original parameter space. We explore qualitative features of this space and show that certain key ocean and atmosphere parameters must be tuned carefully together in order to locate climates that satisfy our chosen metrics. Our study shows that attempts to tune climate model parameters that vary only a handful of parameters relevant to a given process at a time will not be as successful or as efficient as history matching.

  11. The antiferromagnetic structures of IrMn3 and their influence on exchange-bias

    PubMed Central

    Kohn, A.; Kovács, A.; Fan, R.; McIntyre, G. J.; Ward, R. C. C.; Goff, J. P.

    2013-01-01

    We have determined the magnetic structures of single-crystal thin-films of IrMn3 for the crystallographic phases of chemically-ordered L12, and for chemically-disordered face-centred-cubic, which is the phase typically chosen for information-storage devices. For the chemically-ordered L12 thin-film, we find the same triangular magnetic structure as reported for the bulk material. We determine the magnetic structure of the chemically-disordered face-centred-cubic alloy for the first time, which differs from theoretical predictions, with magnetic moments tilted away from the crystal diagonals towards the face-planes. We study the influence of these two antiferromagnetic structures on the exchange-bias properties of an epitaxial body-centred-cubic Fe layer showing that magnetization reversal mechanism and bias-field in the ferromagnetic layer is altered significantly. We report a change of reversal mechanism from in-plane nucleation of 90° domain-walls when coupled to the newly reported cubic structure towards a rotational process, including an out-of-plane magnetization component when coupled to the L12 triangular structure. PMID:23934541

  12. Influence of codon usage bias on FGLamide-allatostatin mRNA secondary structure.

    PubMed

    Martínez-Pérez, Francisco; Bendena, William G; Chang, Belinda S W; Tobe, Stephen S

    2011-03-01

    The FGLamide allatostatins (ASTs) are invertebrate neuropeptides which inhibit juvenile hormone biosynthesis in Dictyoptera and related orders. They also show myomodulatory activity. FGLamide AST nucleotide frequencies and codon bias were investigated with respect to possible effects on mRNA secondary structure. 367 putative FGLamide ASTs and their potential endoproteolytic cleavage sites were identified from 40 species of crustaceans, chelicerates and insects. Among these, 55% comprised only 11 amino acids. An FGLamide AST consensus was identified to be (X)(1→16)Y(S/A/N/G)FGLGKR, with a strong bias for the codons UUU encoding for Phe and AAA for Lys, which can form strong Watson-Crick pairing in all peptides analyzed. The physical distance between these codons favor a loop structure from Ser/Ala-Phe to Lys-Arg. Other loop and hairpin loops were also inferred from the codon frequencies in the N-terminal motif, and the first amino acids from the C-terminal motif, or the dibasic potential endoproteolytic cleavage site. Our results indicate that nucleotide frequencies and codon usage bias in FGLamide ASTs tend to favor mRNA folds in the codon sequence in the C-terminal active peptide core and at the dibasic potential endoproteolytic cleavage site. Copyright © 2010 Elsevier Inc. All rights reserved.

  13. Local Order in the Unfolded State: Conformational Biases and Nearest Neighbor Interactions

    PubMed Central

    Toal, Siobhan; Schweitzer-Stenner, Reinhard

    2014-01-01

    The discovery of Intrinsically Disordered Proteins, which contain significant levels of disorder yet perform complex biologically functions, as well as unwanted aggregation, has motivated numerous experimental and theoretical studies aimed at describing residue-level conformational ensembles. Multiple lines of evidence gathered over the last 15 years strongly suggest that amino acids residues display unique and restricted conformational preferences in the unfolded state of peptides and proteins, contrary to one of the basic assumptions of the canonical random coil model. To fully understand residue level order/disorder, however, one has to gain a quantitative, experimentally based picture of conformational distributions and to determine the physical basis underlying residue-level conformational biases. Here, we review the experimental, computational and bioinformatic evidence for conformational preferences of amino acid residues in (mostly short) peptides that can be utilized as suitable model systems for unfolded states of peptides and proteins. In this context particular attention is paid to the alleged high polyproline II preference of alanine. We discuss how these conformational propensities may be modulated by peptide solvent interactions and so called nearest-neighbor interactions. The relevance of conformational propensities for the protein folding problem and the understanding of IDPs is briefly discussed. PMID:25062017

  14. Structure-functional selectivity relationship studies of β-arrestin-biased dopamine D₂ receptor agonists.

    PubMed

    Chen, Xin; Sassano, Maria F; Zheng, Lianyou; Setola, Vincent; Chen, Meng; Bai, Xu; Frye, Stephen V; Wetsel, William C; Roth, Bryan L; Jin, Jian

    2012-08-23

    Functionally selective G protein-coupled receptor (GPCR) ligands, which differentially modulate canonical and noncanonical signaling, are extremely useful for elucidating key signal transduction pathways essential for both the therapeutic actions and side effects of drugs. However, few such ligands have been created, and very little purposeful attention has been devoted to studying what we term: "structure-functional selectivity relationships" (SFSR). We recently disclosed the first β-arrestin-biased dopamine D(2) receptor (D(2)R) agonists UNC9975 (44) and UNC9994 (36), which have robust in vivo antipsychotic drug-like activities. Here we report the first comprehensive SFSR studies focused on exploring four regions of the aripiprazole scaffold, which resulted in the discovery of these β-arrestin-biased D(2)R agonists. These studies provide a successful proof-of-concept for how functionally selective ligands can be discovered.

  15. Giant exchange bias in Mn2FeGa with hexagonal structure

    NASA Astrophysics Data System (ADS)

    Liu, Z. H.; Zhang, Y. J.; Zhang, H. G.; Zhang, X. J.; Ma, X. Q.

    2016-07-01

    In this study, we present the experimental observation that polycrystalline Mn2+xFe1-xGa (x = -0.2, 0, 0.2, 0.4) compounds can be synthesized to be D019-type (Ni3Sn-type) hexagonal structure with space group P63/mmc. A giant exchange bias field up to 1.32 kOe was achieved in hexagonal Mn2FeGa alloy at 5 K. A cluster glass state is confirmed by ac susceptibility measurement under different driving frequencies. Interestingly, robust horizontal and vertical shifts in magnetic hysteresis loop were simultaneously observed at 5 K under high cooling field up to 90 kOe. The large exchange bias is originated from the large exchange anisotropy between cluster glass phase and ferrimagnetic matrix. The vertical shift is thought to be attributed to the incomplete reversal of frozen cluster spins.

  16. On the effect of bias on the behavior of MOS structures subjected to ionizing radiation

    SciTech Connect

    Aleksandrov, O. V.

    2015-06-15

    Using a quantitative model [6], the analysis of published data on the effect of the gate bias on the behavior of MOS structure subjected to ionizing radiation is performed. It is shown that, along with hydrogen-containing traps, there are hydrogen-free hole traps in samples with a low content of hydrogen; traps of both types are distributed inhomogeneously over the thickness of the gate insulator. In addition to ionized hydrogen, neutral hydrogen is involved in the formation of surface states and provides the main contribution to this process at negative gate bias. A decrease in the shift of the threshold voltage in the case of high fields is caused by an increase in the drift component of the hole drain to the electrodes.

  17. A "looming bias" in spatial hearing? Effects of acoustic intensity and spectrum on categorical sound source localization.

    PubMed

    McCarthy, Lisa; Olsen, Kirk N

    2017-01-01

    Continuous increases of acoustic intensity (up-ramps) can indicate a looming (approaching) sound source in the environment, whereas continuous decreases of intensity (down-ramps) can indicate a receding sound source. From psychoacoustic experiments, an "adaptive perceptual bias" for up-ramp looming tonal stimuli has been proposed (Neuhoff, 1998). This theory postulates that (1) up-ramps are perceptually salient because of their association with looming and potentially threatening stimuli in the environment; (2) tonal stimuli are perceptually salient because of an association with single and potentially threatening biological sound sources in the environment, relative to white noise, which is more likely to arise from dispersed signals and nonthreatening/nonbiological sources (wind/ocean). In the present study, we extrapolated the "adaptive perceptual bias" theory and investigated its assumptions by measuring sound source localization in response to acoustic stimuli presented in azimuth to imply looming, stationary, and receding motion in depth. Participants (N = 26) heard three directions of intensity change (up-ramps, down-ramps, and steady state, associated with looming, receding, and stationary motion, respectively) and three levels of acoustic spectrum (a 1-kHz pure tone, the tonal vowel /ә/, and white noise) in a within-subjects design. We first hypothesized that if up-ramps are "perceptually salient" and capable of eliciting adaptive responses, then they would be localized faster and more accurately than down-ramps. This hypothesis was supported. However, the results did not support the second hypothesis. Rather, the white-noise and vowel conditions were localized faster and more accurately than the pure-tone conditions. These results are discussed in the context of auditory and visual theories of motion perception, auditory attentional capture, and the spectral causes of spatial ambiguity.

  18. Does amplitude scaling of ground motion records result in biased nonlinear structural drift responses?

    USGS Publications Warehouse

    Luco, N.; Bazzurro, P.

    2007-01-01

    Limitations of the existing earthquake ground motion database lead to scaling of records to obtain seismograms consistent with a ground motion target for structural design and evaluation. In the engineering seismology community, acceptable limits for 'legitimate' scaling vary from one (no scaling allowed) to 10 or more. The concerns expressed by detractors of scaling are mostly based on the knowledge of, for example, differences in ground motion characteristics for different earthquake magnitude-distance (Mw-Rclose) scenarios, and much less on their effects on structures. At the other end of the spectrum, proponents have demonstrated that scaling is not only legitimate but also useful for assessing structural response statistics for Mw-Rclose scenarios. Their studies, however, have not investigated more recent purposes of scaling and have not always drawn conclusions for a wide spectrum of structural vibration periods and strengths. This article investigates whether scaling of records randomly selected from an Mw-Rclose bin (or range) to a target fundamental-mode spectral acceleration (Sa) level introduces bias in the expected nonlinear structural drift response of both single-degree-of-freedom oscillators and one multi-degree-of-freedom building. The bias is quantified relative to unscaled records from the target Mw-Rclose bin that are 'naturally' at the target Sa level. We consider scaling of records from the target Mw-Rclose bin and from other Mw-Rclose bins. The results demonstrate that scaling can indeed introduce a bias that, for the most part, ca be explained by differences between the elastic response spectra of the scaled versus unscaled records. Copyright ?? 2007 John Wiley & Sons, Ltd.

  19. Geometrical optimization for strictly localized structures

    NASA Astrophysics Data System (ADS)

    Mo, Yirong

    2003-07-01

    Recently we proposed the block localized wavefunction (BLW) approach which takes the advantages of valence bond theory and molecular orbital theory and defines the wavefunctions for resonance structures based on the assumption that all electrons and orbitals are partitioned into a few subgroups. In this work, we implement the geometrical optimization of the BLW method based on the algorithm proposed by Gianinetti and coworkers. Thus, we can study the conjugation effect on not only the molecular stability, but also the molecular geometry. With this capability, the π conjugation effect in trans-polyenes C2nH2n+2 (n=2-5) as well as in formamide and its analogs are studied by optimizing their delocalized and strictly localized forms with the 6-31G(d) and 6-311+G(d,p) basis sets. Although it has been well presumed that the π resonance shortens the single bonds and lengthens the double bonds with the delocalization of π electrons across the whole line in polyenes, our optimization of the strictly localized structures quantitatively shows that when the conjugation effect is "turned off," the double bond lengths will be identical to the CC bond length in ethylene and the single Csp2-Csp2 bond length will be about 1.513-1.517 Å. In agreement with the classical Hückel theory, the resonance energies in polyenes are approximately in proportion to the number of double bonds. Similarly, resonance is responsible not only for the planarity of formamide, thioformamide, and selenoformamide, but also for the lengthening of the CX (X=O,S,Se) double bond and the shortening of the CN bonds. Although it is assumed that the CX bond polarization decreases in the order of O>S>Se, the π electronic delocalization increases in the opposite order, i.e., formamide

  20. Amazonian landscapes and the bias in field studies of forest structure and biomass

    PubMed Central

    Marvin, David C.; Asner, Gregory P.; Knapp, David E.; Anderson, Christopher B.; Martin, Roberta E.; Sinca, Felipe; Tupayachi, Raul

    2014-01-01

    Tropical forests convert more atmospheric carbon into biomass each year than any terrestrial ecosystem on Earth, underscoring the importance of accurate tropical forest structure and biomass maps for the understanding and management of the global carbon cycle. Ecologists have long used field inventory plots as the main tool for understanding forest structure and biomass at landscape-to-regional scales, under the implicit assumption that these plots accurately represent their surrounding landscape. However, no study has used continuous, high-spatial-resolution data to test whether field plots meet this assumption in tropical forests. Using airborne LiDAR (light detection and ranging) acquired over three regions in Peru, we assessed how representative a typical set of field plots are relative to their surrounding host landscapes. We uncovered substantial mean biases (9–98%) in forest canopy structure (height, gaps, and layers) and aboveground biomass in both lowland Amazonian and montane Andean landscapes. Moreover, simulations reveal that an impractical number of 1-ha field plots (from 10 to more than 100 per landscape) are needed to develop accurate estimates of aboveground biomass at landscape scales. These biases should temper the use of plots for extrapolations of forest dynamics to larger scales, and they demonstrate the need for a fundamental shift to high-resolution active remote sensing techniques as a primary sampling tool in tropical forest biomass studies. The potential decrease in the bias and uncertainty of remotely sensed estimates of forest structure and biomass is a vital step toward successful tropical forest conservation and climate-change mitigation policy. PMID:25422434

  1. Amazonian landscapes and the bias in field studies of forest structure and biomass.

    PubMed

    Marvin, David C; Asner, Gregory P; Knapp, David E; Anderson, Christopher B; Martin, Roberta E; Sinca, Felipe; Tupayachi, Raul

    2014-12-02

    Tropical forests convert more atmospheric carbon into biomass each year than any terrestrial ecosystem on Earth, underscoring the importance of accurate tropical forest structure and biomass maps for the understanding and management of the global carbon cycle. Ecologists have long used field inventory plots as the main tool for understanding forest structure and biomass at landscape-to-regional scales, under the implicit assumption that these plots accurately represent their surrounding landscape. However, no study has used continuous, high-spatial-resolution data to test whether field plots meet this assumption in tropical forests. Using airborne LiDAR (light detection and ranging) acquired over three regions in Peru, we assessed how representative a typical set of field plots are relative to their surrounding host landscapes. We uncovered substantial mean biases (9-98%) in forest canopy structure (height, gaps, and layers) and aboveground biomass in both lowland Amazonian and montane Andean landscapes. Moreover, simulations reveal that an impractical number of 1-ha field plots (from 10 to more than 100 per landscape) are needed to develop accurate estimates of aboveground biomass at landscape scales. These biases should temper the use of plots for extrapolations of forest dynamics to larger scales, and they demonstrate the need for a fundamental shift to high-resolution active remote sensing techniques as a primary sampling tool in tropical forest biomass studies. The potential decrease in the bias and uncertainty of remotely sensed estimates of forest structure and biomass is a vital step toward successful tropical forest conservation and climate-change mitigation policy.

  2. Hα-FUV Flux Ratios of Local Volume Galaxies: Effects of Systematic Biases on Upper IMF Constraints

    NASA Astrophysics Data System (ADS)

    Johnson, Lent C.; Weisz, D. R.; Johnson, B. D.; Skillman, E. D.; LVL Team

    2011-01-01

    Recent observational evidence has shown that dwarf galaxies exhibit lower Hα-FUV flux ratios than typical star-forming galaxies. While this fact has been interpreted as evidence for a variable upper IMF, these results are subject to systematics due to imperfect internal dust attenuation corrections and other biases. Using observations of 127 Local Volume star-forming galaxies derived from the LVL and SDSS datasets, we explore how different internal dust corrections and sample completeness can affect the resulting physical interpretation. We also examine the susceptibility of our Hα-FUV ratio distribution and correlation analyses to biases that result from our choice of independent parameter (e.g., stellar mass, R-band surface brightness). We then apply our understanding of these factors to test the possibility that the observed ratio distribution could be the result of age effects. Using model star formation histories, we can explain the distribution of Hα-FUV ratios without invoking variations in the upper IMF.

  3. Characterization of structurally novel G protein biased CB1 agonists: Implications for drug development.

    PubMed

    Ford, Benjamin M; Franks, Lirit N; Tai, Sherrica; Fantegrossi, William E; Stahl, Edward L; Berquist, Michael D; Cabanlong, Christian V; Wilson, Catheryn D; Penthala, Narsimha R; Crooks, Peter A; Prather, Paul L

    2017-08-23

    similar treatment with CP-55,940. PNR-4-20 (i.p.) is active in the cannabinoid tetrad in mice and chronic treatment results in development of less persistent tolerance and no significant withdrawal signs when compared to animals repeatedly exposed to the non-biased full agoinst JWH-018 or Δ(9)-THC. Finally, studies of a structurally similar analog PNR- 4-02 show that it is also a G protein biased hCB1R agonist. It is predicted that cannabinoid agonists that bias hCB1R activation toward G protein, relative to β-arrestin 2 signaling, will produce fewer and less severe adverse effects both acutely and chronically. Copyright © 2017 Elsevier Ltd. All rights reserved.

  4. Female-biased sex difference in vasotocin-immunoreactive neural structures in the developing quail brain.

    PubMed

    Aste, Nicoletta; Yoshioka, Naoki; Sakamoto, Emiko; Saito, Noboru

    2016-11-01

    The bed nucleus of the stria terminalis pars medialis (BSTM), medial preoptic nucleus (POM), and lateral septal region (LS) exhibit more vasotocin-immunoreactive (VT-ir) neural structures in male than in female adult quail. VT-ir cells and fibers in these regions are sensitive to gonadal steroids only in males. The insensitivity of adult female VT-ir neural structures to sex steroids is attributed to estradiol exposure during a critical period in embryonic life. Although the VT-ir system has been intensively examined in adult quail, information is limited in embryos and juveniles. Therefore, we herein investigated the development of VT-immunoreactive neural structures from embryonic day (E) 9 to adulthood with a particular focus on the BSTM, POM and LS of both sexes. VT-ir neural structures were more evident in female than in male embryos from E9 (BSTM and POM) and E11 (LS). This sex difference disappeared between E15 and post-hatch day 1 in the BSTM and POM, and during the first week of life in the LS. Male-biased sex differences in VT-ir structures appeared at puberty. Female-biased sexual dimorphism in the density of the VT-ir structures of BSTM was reflected by the stronger expression of VT mRNA in females than in males. However, the density of VT mRNA somata was comparable in the two sexes. The exposure of male embryos to estradiol resulted in the feminization of VT-ir neural structures in the BSTM, but not in the POM or LS at E11. Collectively, these results suggest that sex differences in VT-ir neural structures changes drastically throughout quail life. In embryos, endogenous estradiol may stimulate the expression of VT in females, resulting in a robust sex difference in VT-ir cells and fibers in favor of this sex.

  5. A single bout of meditation biases cognitive control but not attentional focusing: Evidence from the global-local task.

    PubMed

    Colzato, Lorenza S; van der Wel, Pauline; Sellaro, Roberta; Hommel, Bernhard

    2016-01-01

    Recent studies show that a single bout of meditation can impact information processing. We were interested to see whether this impact extends to attentional focusing and the top-down control over irrelevant information. Healthy adults underwent brief single bouts of either focused attention meditation (FAM), which is assumed to increase top-down control, or open monitoring meditation (OMM), which is assumed to weaken top-down control, before performing a global-local task. While the size of the global-precedence effect (reflecting attentional focusing) was unaffected by type of meditation, the congruency effect (indicating the failure to suppress task-irrelevant information) was considerably larger after OMM than after FAM. Our findings suggest that engaging in particular kinds of meditation creates particular cognitive-control states that bias the individual processing style toward either goal-persistence or cognitive flexibility.

  6. Empirical analysis of locality, heritability and heuristic bias in evolutionary algorithms: a case study for the multidimensional knapsack problem.

    PubMed

    Raidl, Günther R; Gottlieb, Jens

    2005-01-01

    Our main aim is to provide guidelines and practical help for the design of appropriate representations and operators for evolutionary algorithms (EAs). For this purpose, we propose techniques to obtain a better understanding of various effects in the interplay of the representation and the operators. We study six different representations and associated variation operators in the context of a steady-state evolutionary algorithm for the multidimensional knapsack problem. Four of them are indirect decoder-based techniques, and two are direct encodings combined with different initialization, repair, and local improvement strategies. The complex decoders and the local improvement and repair strategies make it practically impossible to completely analyze such EAs in a fully theoretical way. After comparing the general performance of the chosen EA variants for the multidimensional knapsack problem on two benchmark suites, we present a hands-on approach for empirically analyzing important aspects of initialization, mutation, and crossover in an isolated fashion. Static, inexpensive measurements based on randomly created solutions are performed in order to quantify and visualize specific properties with respect to heuristic bias, locality, and heritability. These tests shed light onto the complex behavior of such EAs and point out reasons for good or bad performance. In addition, the proposed measures are also examined during actual EA runs, which gives further insight into dynamic aspects of evolutionary search and verifies the validity of the isolated static measurements. All measurements are described in a general way, allowing for an easy adaption to other representations and problems.

  7. Novel measures of linkage disequilibrium that correct the bias due to population structure and relatedness.

    PubMed

    Mangin, B; Siberchicot, A; Nicolas, S; Doligez, A; This, P; Cierco-Ayrolles, C

    2012-03-01

    Among the several linkage disequilibrium measures known to capture different features of the non-independence between alleles at different loci, the most commonly used for diallelic loci is the r(2) measure. In the present study, we tackled the problem of the bias of r(2) estimate, which results from the sample structure and/or the relatedness between genotyped individuals. We derived two novel linkage disequilibrium measures for diallelic loci that are both extensions of the usual r(2) measure. The first one, r(S)(2), uses the population structure matrix, which consists of information about the origins of each individual and the admixture proportions of each individual genome. The second one, r(V)(2), includes the kinship matrix into the calculation. These two corrections can be applied together in order to correct for both biases and are defined either on phased or unphased genotypes.We proved that these novel measures are linked to the power of association tests under the mixed linear model including structure and kinship corrections. We validated them on simulated data and applied them to real data sets collected on Vitis vinifera plants. Our results clearly showed the usefulness of the two corrected r(2) measures, which actually captured 'true' linkage disequilibrium unlike the usual r(2) measure.

  8. Novel measures of linkage disequilibrium that correct the bias due to population structure and relatedness

    PubMed Central

    Mangin, B; Siberchicot, A; Nicolas, S; Doligez, A; This, P; Cierco-Ayrolles, C

    2012-01-01

    Among the several linkage disequilibrium measures known to capture different features of the non-independence between alleles at different loci, the most commonly used for diallelic loci is the r2 measure. In the present study, we tackled the problem of the bias of r2 estimate, which results from the sample structure and/or the relatedness between genotyped individuals. We derived two novel linkage disequilibrium measures for diallelic loci that are both extensions of the usual r2 measure. The first one, rS2, uses the population structure matrix, which consists of information about the origins of each individual and the admixture proportions of each individual genome. The second one, rV2, includes the kinship matrix into the calculation. These two corrections can be applied together in order to correct for both biases and are defined either on phased or unphased genotypes. We proved that these novel measures are linked to the power of association tests under the mixed linear model including structure and kinship corrections. We validated them on simulated data and applied them to real data sets collected on Vitis vinifera plants. Our results clearly showed the usefulness of the two corrected r2 measures, which actually captured ‘true' linkage disequilibrium unlike the usual r2 measure. PMID:21878986

  9. On the statistics of biased tracers in the Effective Field Theory of Large Scale Structures

    DOE PAGES

    Angulo, Raul; Fasiello, Matteo; Senatore, Leonardo; ...

    2015-09-09

    With the completion of the Planck mission, in order to continue to gather cosmological information it has become crucial to understand the Large Scale Structures (LSS) of the universe to percent accuracy. The Effective Field Theory of LSS (EFTofLSS) is a novel theoretical framework that aims to develop an analytic understanding of LSS at long distances, where inhomogeneities are small. We further develop the description of biased tracers in the EFTofLSS to account for the effect of baryonic physics and primordial non-Gaussianities, finding that new bias coefficients are required. Then, restricting to dark matter with Gaussian initial conditions, we describemore » the prediction of the EFTofLSS for the one-loop halo-halo and halo-matter two-point functions, and for the tree-level halo-halo-halo, matter-halo-halo and matter-matter-halo three-point functions. Several new bias coefficients are needed in the EFTofLSS, even though their contribution at a given order can be degenerate and the same parameters contribute to multiple observables. We develop a method to reduce the number of biases to an irreducible basis, and find that, at the order at which we work, seven bias parameters are enough to describe this extremely rich set of statistics. We then compare with the output of an N-body simulation where the normalization parameter of the linear power spectrum is set to σ8 = 0.9. For the lowest mass bin, we find percent level agreement up to k ≃ 0.3 h Mpc–1 for the one-loop two-point functions, and up to k ≃ 0.15 h Mpc–1 for the tree-level three-point functions, with the k-reach decreasing with higher mass bins. In conclusion, this is consistent with the theoretical estimates, and suggests that the cosmological information in LSS amenable to analytical control is much more than previously believed.« less

  10. On the statistics of biased tracers in the Effective Field Theory of Large Scale Structures

    SciTech Connect

    Angulo, Raul; Fasiello, Matteo; Senatore, Leonardo; Vlah, Zvonimir

    2015-09-09

    With the completion of the Planck mission, in order to continue to gather cosmological information it has become crucial to understand the Large Scale Structures (LSS) of the universe to percent accuracy. The Effective Field Theory of LSS (EFTofLSS) is a novel theoretical framework that aims to develop an analytic understanding of LSS at long distances, where inhomogeneities are small. We further develop the description of biased tracers in the EFTofLSS to account for the effect of baryonic physics and primordial non-Gaussianities, finding that new bias coefficients are required. Then, restricting to dark matter with Gaussian initial conditions, we describe the prediction of the EFTofLSS for the one-loop halo-halo and halo-matter two-point functions, and for the tree-level halo-halo-halo, matter-halo-halo and matter-matter-halo three-point functions. Several new bias coefficients are needed in the EFTofLSS, even though their contribution at a given order can be degenerate and the same parameters contribute to multiple observables. We develop a method to reduce the number of biases to an irreducible basis, and find that, at the order at which we work, seven bias parameters are enough to describe this extremely rich set of statistics. We then compare with the output of an N-body simulation where the normalization parameter of the linear power spectrum is set to σ8 = 0.9. For the lowest mass bin, we find percent level agreement up to k ≃ 0.3 h Mpc–1 for the one-loop two-point functions, and up to k ≃ 0.15 h Mpc–1 for the tree-level three-point functions, with the k-reach decreasing with higher mass bins. In conclusion, this is consistent with the theoretical estimates, and suggests that the cosmological information in LSS amenable to analytical control is much more than previously believed.

  11. On the statistics of biased tracers in the Effective Field Theory of Large Scale Structures

    SciTech Connect

    Angulo, Raul; Fasiello, Matteo; Senatore, Leonardo; Vlah, Zvonimir E-mail: matteorf@stanford.edu E-mail: zvlah@stanford.edu

    2015-09-01

    With the completion of the Planck mission, in order to continue to gather cosmological information it has become crucial to understand the Large Scale Structures (LSS) of the universe to percent accuracy. The Effective Field Theory of LSS (EFTofLSS) is a novel theoretical framework that aims to develop an analytic understanding of LSS at long distances, where inhomogeneities are small. We further develop the description of biased tracers in the EFTofLSS to account for the effect of baryonic physics and primordial non-Gaussianities, finding that new bias coefficients are required. Then, restricting to dark matter with Gaussian initial conditions, we describe the prediction of the EFTofLSS for the one-loop halo-halo and halo-matter two-point functions, and for the tree-level halo-halo-halo, matter-halo-halo and matter-matter-halo three-point functions. Several new bias coefficients are needed in the EFTofLSS, even though their contribution at a given order can be degenerate and the same parameters contribute to multiple observables. We develop a method to reduce the number of biases to an irreducible basis, and find that, at the order at which we work, seven bias parameters are enough to describe this extremely rich set of statistics. We then compare with the output of an N-body simulation where the normalization parameter of the linear power spectrum is set to σ{sub 8} = 0.9. For the lowest mass bin, we find percent level agreement up to k≅ 0.3 h Mpc{sup −1} for the one-loop two-point functions, and up to k≅ 0.15 h Mpc{sup −1} for the tree-level three-point functions, with the k-reach decreasing with higher mass bins. This is consistent with the theoretical estimates, and suggests that the cosmological information in LSS amenable to analytical control is much more than previously believed.

  12. Structure-Based Discovery of New Antagonist and Biased Agonist Chemotypes for the Kappa Opioid Receptor.

    PubMed

    Zheng, Zhong; Huang, Xi-Ping; Mangano, Thomas J; Zou, Rodger; Chen, Xin; Zaidi, Saheem A; Roth, Bryan L; Stevens, Raymond C; Katritch, Vsevolod

    2017-04-13

    The ongoing epidemics of opioid overdose raises an urgent need for effective antiaddiction therapies and addiction-free painkillers. The κ-opioid receptor (KOR) has emerged as a promising target for both indications, raising demand for new chemotypes of KOR antagonists as well as G-protein-biased agonists. We employed the crystal structure of the KOR-JDTic complex and ligand-optimized structural templates to perform virtual screening of available compound libraries for new KOR ligands. The prospective virtual screening campaign yielded a high 32% hit rate, identifying novel fragment-like and lead-like chemotypes of KOR ligands. A round of optimization resulted in 11 new submicromolar KOR binders (best Ki = 90 nM). Functional assessment confirmed at least two compounds as potent KOR antagonists, while compound 81 was identified as a potent Gi biased agonist for KOR with minimal β-arrestin recruitment. These results support virtual screening as an effective tool for discovery of new lead chemotypes with therapeutically relevant functional profiles.

  13. How Category Structure Influences the Perception of Object Similarity: The Atypicality Bias

    PubMed Central

    Tanaka, James William; Kantner, Justin; Bartlett, Marni

    2011-01-01

    Why do some faces appear more similar than others? Beyond structural factors, we speculate that similarity is governed by the organization of faces located in a multi-dimensional face space. To test this hypothesis, we morphed a typical face with an atypical face. If similarity judgments are guided purely by their physical properties, the morph should be perceived to be equally similar to its typical parent as its atypical parent. However, contrary to the structural prediction, our results showed that the morph face was perceived to be more similar to the atypical face than the typical face. Our empirical studies show that the atypicality bias is not limited to faces, but extends to other object categories (birds) whose members share common shape properties. We also demonstrate atypicality bias is malleable and can change subject to category learning and experience. Collectively, the empirical evidence indicates that perceptions of face and object similarity are affected by the distribution of stimuli in a face or object space. In this framework, atypical stimuli are located in a sparser region of the space where there is less competition for recognition and therefore, these representations capture a broader range of inputs. In contrast, typical stimuli are located in a denser region of category space where there is increased competition for recognition and hence, these representation draw a more restricted range of face inputs. These results suggest that the perceived likeness of an object is influenced by the organization of surrounding exemplars in the category space. PMID:22685441

  14. Striatal structure and function predict individual biases in learning to avoid pain.

    PubMed

    Eldar, Eran; Hauser, Tobias U; Dayan, Peter; Dolan, Raymond J

    2016-04-26

    Pain is an elemental inducer of avoidance. Here, we demonstrate that people differ in how they learn to avoid pain, with some individuals refraining from actions that resulted in painful outcomes, whereas others favor actions that helped prevent pain. These individual biases were best explained by differences in learning from outcome prediction errors and were associated with distinct forms of striatal responses to painful outcomes. Specifically, striatal responses to pain were modulated in a manner consistent with an aversive prediction error in individuals who learned predominantly from pain, whereas in individuals who learned predominantly from success in preventing pain, modulation was consistent with an appetitive prediction error. In contrast, striatal responses to success in preventing pain were consistent with an appetitive prediction error in both groups. Furthermore, variation in striatal structure, encompassing the region where pain prediction errors were expressed, predicted participants' predominant mode of learning, suggesting the observed learning biases may reflect stable individual traits. These results reveal functional and structural neural components underlying individual differences in avoidance learning, which may be important contributors to psychiatric disorders involving pathological harm avoidance behavior.

  15. Striatal structure and function predict individual biases in learning to avoid pain

    PubMed Central

    Eldar, Eran; Hauser, Tobias U.; Dayan, Peter; Dolan, Raymond J.

    2016-01-01

    Pain is an elemental inducer of avoidance. Here, we demonstrate that people differ in how they learn to avoid pain, with some individuals refraining from actions that resulted in painful outcomes, whereas others favor actions that helped prevent pain. These individual biases were best explained by differences in learning from outcome prediction errors and were associated with distinct forms of striatal responses to painful outcomes. Specifically, striatal responses to pain were modulated in a manner consistent with an aversive prediction error in individuals who learned predominantly from pain, whereas in individuals who learned predominantly from success in preventing pain, modulation was consistent with an appetitive prediction error. In contrast, striatal responses to success in preventing pain were consistent with an appetitive prediction error in both groups. Furthermore, variation in striatal structure, encompassing the region where pain prediction errors were expressed, predicted participants’ predominant mode of learning, suggesting the observed learning biases may reflect stable individual traits. These results reveal functional and structural neural components underlying individual differences in avoidance learning, which may be important contributors to psychiatric disorders involving pathological harm avoidance behavior. PMID:27071092

  16. Local conservation laws and the structure of the many-body localized states.

    PubMed

    Serbyn, Maksym; Papić, Z; Abanin, Dmitry A

    2013-09-20

    We construct a complete set of local integrals of motion that characterize the many-body localized (MBL) phase. Our approach relies on the assumption that local perturbations act locally on the eigenstates in the MBL phase, which is supported by numerical simulations of the random-field XXZ spin chain. We describe the structure of the eigenstates in the MBL phase and discuss the implications of local conservation laws for its nonequilibrium quantum dynamics. We argue that the many-body localization can be used to protect coherence in the system by suppressing relaxation between eigenstates with different local integrals of motion.

  17. Reduction of model structure bias in the prediction of critical source areas

    NASA Astrophysics Data System (ADS)

    Frey, M.; Stamm, C.; Schneider, M. K.; Reichert, P.

    2009-04-01

    Effective mitigation strategies to reduce the contamination of surface waters by agrochemicals rely on an accurate identification of critical source areas (CSA). We used a spatially distributed hydrological model to identify CSA in a small agricultural catchment in Switzerland. Since the knowledge about model parameters is coarse, prior predictions of CSA involve large uncertainties. We investigated to which degree river discharge data can constrain parameter values and improve the prediction. Thereby, we combined the prior knowledge used for the prior prediction with additional river discharge data within a Bayesian inference approach. In order to consider the effect of uncertainty in input data and in the model structure we formulated the likelihood function with an autoregressive error model additive to the river discharge calculated by the deterministic hydrological model. The additional information gained from river discharge data slightly reduced the width of some of the marginal parameter distributions and the prediction uncertainty for high or low-risk areas. However, the analysis of the statistical assumptions of the inference process revealed deficits in the model structure. Thus the base flow during dry periods tended to be overestimated. By making the percolation process water table dependent the base flow prediction could be improved. These improvements in model structure significantly reduced the model structure bias and thus improved the statistical basis of the probabilistic CSA prediction. Furthermore, the improved model structure led to a large constraint of the CSA prediction uncertainty.

  18. NiO/Fe(001): Magnetic anisotropy, exchange bias, and interface structure

    NASA Astrophysics Data System (ADS)

    Młyńczak, E.; Luches, P.; Valeri, S.; Korecki, J.

    2013-06-01

    The magnetic and structural properties of NiO/Fe epitaxial bilayers grown on MgO(001) were studied using magnetooptic Kerr effect (MOKE) and conversion electron Mössbauer spectroscopy (CEMS). The bilayers were prepared under ultra high vacuum conditions using molecular beam epitaxy with oblique deposition. Two systems were compared: one showing the exchange bias (100ML-NiO/24ML-Fe), ML stands for a monolayer, and another where the exchange bias was not observed (50ML-NiO/50ML-Fe). For both, the magnetic anisotropy was found to be complex, yet dominated by the growth-induced uniaxial anisotropy. The training effect was observed for the 100ML-NiO/24ML-Fe system and quantitatively described using the spin glass model. The composition and magnetic state of the interfacial Fe layers were studied using 57Fe-CEMS. An iron oxide phase (Fe3+4Fe2+1O7), as thick as 31 Å, was identified at the NiO/Fe interface in the as-deposited samples. The ferrimagnetic nature of the interfacial iron oxide film explains the complex magnetic anisotropy observed in the samples.

  19. NiO/Fe(001): Magnetic anisotropy, exchange bias, and interface structure

    SciTech Connect

    Mlynczak, E.; Luches, P.

    2013-06-21

    The magnetic and structural properties of NiO/Fe epitaxial bilayers grown on MgO(001) were studied using magnetooptic Kerr effect (MOKE) and conversion electron Moessbauer spectroscopy (CEMS). The bilayers were prepared under ultra high vacuum conditions using molecular beam epitaxy with oblique deposition. Two systems were compared: one showing the exchange bias (100ML-NiO/24ML-Fe), ML stands for a monolayer, and another where the exchange bias was not observed (50ML-NiO/50ML-Fe). For both, the magnetic anisotropy was found to be complex, yet dominated by the growth-induced uniaxial anisotropy. The training effect was observed for the 100ML-NiO/24ML-Fe system and quantitatively described using the spin glass model. The composition and magnetic state of the interfacial Fe layers were studied using {sup 57}Fe-CEMS. An iron oxide phase (Fe{sup 3+}{sub 4}Fe{sup 2+}{sub 1}O{sub 7}), as thick as 31 A, was identified at the NiO/Fe interface in the as-deposited samples. The ferrimagnetic nature of the interfacial iron oxide film explains the complex magnetic anisotropy observed in the samples.

  20. Does survey method bias the description of northern goshawk nest-site structure?

    USGS Publications Warehouse

    Daw, S.K.; DeStefano, S.; Steidl, R.J.

    1998-01-01

    Past studies on the nesting habitat of northern goshawks (Accipiter gentilis) often relied on nests found opportunistically, either during timber-sale operations, by searching apparently 'good' goshawk habitat, or by other search methods where areas were preselected based on known forest conditions. Therefore, a bias in the characterization of habitat surrounding northern goshawk nest sites may exist toward late-forest structure (large trees, high canopy closure). This potential problem has confounded interpretation of data on nesting habitat of northern goshawks and added to uncertainty in the review process to consider the species for federal listing as threatened or endangered. Systematic survey methods, which strive for complete coverage of an area and often use broadcasts of conspecific calls, have been developed to overcome these potential biases, but no study has compared habitat characteristics around nests found opportunistically with those found systematically. We compared habitat characteristics in a 0.4-ha area around nests found systematically (n = 27) versus those found opportunistically (n = 22) on 3 national forests in eastern Oregon. We found that both density of large trees (systematic: x?? = 16.4 ?? 3.1 trees/ha; x?? ?? SE; opportunistic: x?? = 21.3 ?? 3.2; P = 0.56) and canopy closure (systematic: x?? = 72 ?? 2%; opportunistic: x?? = 70 ?? 2%; P = 0.61) were similar around nests found with either search method. Our results diminish concern that past survey methods mischaracterized northern goshawk nest-site structure. However, because northern goshawks nest in a variety of forest cover types with a wide range of structural characteristics, these results do not decrease the value of systematic survey methods in determining the most representative habitat descriptions for northern goshawks. Rigorous survey protocols allow repeatability and comparability of monitoring efforts and results over time.

  1. Selection bias in species distribution models: An econometric approach on forest trees based on structural modeling

    NASA Astrophysics Data System (ADS)

    Martin-StPaul, N. K.; Ay, J. S.; Guillemot, J.; Doyen, L.; Leadley, P.

    2014-12-01

    Species distribution models (SDMs) are widely used to study and predict the outcome of global changes on species. In human dominated ecosystems the presence of a given species is the result of both its ecological suitability and human footprint on nature such as land use choices. Land use choices may thus be responsible for a selection bias in the presence/absence data used in SDM calibration. We present a structural modelling approach (i.e. based on structural equation modelling) that accounts for this selection bias. The new structural species distribution model (SSDM) estimates simultaneously land use choices and species responses to bioclimatic variables. A land use equation based on an econometric model of landowner choices was joined to an equation of species response to bioclimatic variables. SSDM allows the residuals of both equations to be dependent, taking into account the possibility of shared omitted variables and measurement errors. We provide a general description of the statistical theory and a set of applications on forest trees over France using databases of climate and forest inventory at different spatial resolution (from 2km to 8km). We also compared the outputs of the SSDM with outputs of a classical SDM (i.e. Biomod ensemble modelling) in terms of bioclimatic response curves and potential distributions under current climate and climate change scenarios. The shapes of the bioclimatic response curves and the modelled species distribution maps differed markedly between SSDM and classical SDMs, with contrasted patterns according to species and spatial resolutions. The magnitude and directions of these differences were dependent on the correlations between the errors from both equations and were highest for higher spatial resolutions. A first conclusion is that the use of classical SDMs can potentially lead to strong miss-estimation of the actual and future probability of presence modelled. Beyond this selection bias, the SSDM we propose represents

  2. Local hydrophobicity stabilizes secondary structures in proteins

    SciTech Connect

    Kanehisa, M.I.; Tsong, T.Y.

    1980-01-01

    The probability of occurrence of helix and ..beta..-sheet residues in 47 globular proteins was determined as a function of local hydrophobicity, which was defined by the sum of the Nozaki-Tanford transfer free energies at two nearest-neighbors on both sides of the amino acid sequence. In general, hydrophilic amino acids favor neither helix nor ..beta..-sheet formations when neighbor residues are also hydrophilic but favor helix formation at higher local hydrophobicity. On the other hand, some hydrophobic amino acids such as Met, Leu, and Ile favor helix formation when neighbor residues are hydrophilic. None of the hydrophobic amino acids favor ..beta..-sheet formation with hydrophilic neighbors, but most of them strongly favor ..beta..-sheet formation at high local hydrophobicity. When the average of 20 amino acids is taken, both helix and ..beta..-sheet residue probabilities are higher at higher local hydrophobicity, although the increase is steeper for ..beta..-sheets. Therefore, ..beta..-sheet formation is more influenced by local hydrophobicity than helix formation. Generally, helices are nearer the surface and tend to have hydrophilic and hydrophobic faces at opposite sides. The tendency of alternating regions of hydrophilic and hydrophobic residues in a helical sequence was revealed by calculating the correlation of the Nozaki-Tanford values. Such amphipathic helices may be important in protein-protein-lipid interactions and in forming hydrophilic channels in the membrane. The choice of 30 nonhomologous proteins as the data set did not alter the above results.

  3. How semantic biases in simple adjacencies affect learning a complex structure with non-adjacencies in AGL: a statistical account

    PubMed Central

    Poletiek, Fenna H.; Lai, Jun

    2012-01-01

    A major theoretical debate in language acquisition research regards the learnability of hierarchical structures. The artificial grammar learning methodology is increasingly influential in approaching this question. Studies using an artificial centre-embedded AnBn grammar without semantics draw conflicting conclusions. This study investigates the facilitating effect of distributional biases in simple AB adjacencies in the input sample—caused in natural languages, among others, by semantic biases—on learning a centre-embedded structure. A mathematical simulation of the linguistic input and the learning, comparing various distributional biases in AB pairs, suggests that strong distributional biases might help us to grasp the complex AnBn hierarchical structure in a later stage. This theoretical investigation might contribute to our understanding of how distributional features of the input—including those caused by semantic variation—help learning complex structures in natural languages. PMID:22688639

  4. The relationship between level of autistic traits and local bias in the context of the McGurk effect

    PubMed Central

    Ujiie, Yuta; Asai, Tomohisa; Wakabayashi, Akio

    2015-01-01

    The McGurk effect is a well-known illustration that demonstrates the influence of visual information on hearing in the context of speech perception. Some studies have reported that individuals with autism spectrum disorder (ASD) display abnormal processing of audio-visual speech integration, while other studies showed contradictory results. Based on the dimensional model of ASD, we administered two analog studies to examine the link between level of autistic traits, as assessed by the Autism Spectrum Quotient (AQ), and the McGurk effect among a sample of university students. In the first experiment, we found that autistic traits correlated negatively with fused (McGurk) responses. Then, we manipulated presentation types of visual stimuli to examine whether the local bias toward visual speech cues modulated individual differences in the McGurk effect. The presentation included four types of visual images, comprising no image, mouth only, mouth and eyes, and full face. The results revealed that global facial information facilitates the influence of visual speech cues on McGurk stimuli. Moreover, individual differences between groups with low and high levels of autistic traits appeared when the full-face visual speech cue with an incongruent voice condition was presented. These results suggest that individual differences in the McGurk effect might be due to a weak ability to process global facial information in individuals with high levels of autistic traits. PMID:26175705

  5. Structures of Local Rearrangements in Soft Colloidal Glasses

    NASA Astrophysics Data System (ADS)

    Yang, Xiunan; Liu, Rui; Yang, Mingcheng; Wang, Wei-Hua; Chen, Ke

    2016-06-01

    We image local structural rearrangements in soft colloidal glasses under small periodic perturbations induced by thermal cycling. Local structural entropy S2 positively correlates with observed rearrangements in colloidal glasses. The high S2 values of the rearranging clusters in glasses indicate that fragile regions in glasses are structurally less correlated, similar to structural defects in crystalline solids. Slow-evolving high S2 spots are capable of predicting local rearrangements long before the relaxations occur, while fluctuation-created high S2 spots best correlate with local deformations right before the rearrangement events. Local free volumes are also found to correlate with particle rearrangements at extreme values, although the ability to identify relaxation sites is substantially lower than S2. Our experiments provide an efficient structural identifier for the fragile regions in glasses and highlight the important role of structural correlations in the physics of glasses.

  6. Male-biased dispersal causes intersexual differences in the subpopulation structure of the gray-sided vole.

    PubMed

    Ishibashi, Yasuyuki; Zenitani, Junpei; Saitoh, Takashi

    2013-01-01

    The genetic structure of gray-sided voles was investigated at a spatial scale of 2 km using mtDNA sequences. The control region (674bp) of 162 voles was sequenced and 18 haplotypes were identified. Within 0.5-ha trapping plots (n = 8), the number of haplotypes and gene diversity was significantly greater in males than in females. The fixation index among plots for females (F GP = 0.241) was 3 times as large as that for males (0.075), implying male-biased dispersal. A simulation analysis showed that the observed genetic structure in males could be generated by modifying the observed haplotype distribution of females by adding the effects of local male dispersal. Half of the pairwise F GP (15/28) showed significant differentiation in females, whereas almost none (1/28) were significant in males. Isolation by distance was observed in females, whereas no clear spatial pattern was observed in males. Most pairwise F GP for females were not significant in the short- and intermediate-distance classes (≤1.0 km) as with those for males, whereas all showed significant differentiation in the long-distance class (>1.0 km) for females, but not for males. These findings indicate that the extent of subpopulations within which individuals interact differs between sexes.

  7. AFM-induced amine deprotection: triggering localized bond cleavage by application of tip/substrate voltage bias for the surface self-assembly of nanosized dendritic objects.

    PubMed

    Fresco, Zachary M; Suez, Itai; Backer, Scott A; Fréchet, Jean M J

    2004-07-14

    An alpha,alpha-dimethyl-3,5-dimethoxybenzyloxycarbonyl (DDZ)-protected amine monolayer can be selectively deprotected by the application of a voltage bias from a conducting AFM tip to afford localized nanoscale patterns that can be visualized by self-assembly of dendritic molecular objects with terminal carboxylic acid groups and different aspect ratios.

  8. Rodlike localized structure in isotropic pattern-forming systems.

    PubMed

    Bordeu, Ignacio; Clerc, Marcel G

    2015-10-01

    Stationary two-dimensional localized structures have been observed in a wide variety of dissipative systems. The existence, stability properties, dynamical evolution, and bifurcation diagram of an azimuthal symmetry breaking, rodlike localized structure in the isotropic prototype model of pattern formation, the Swift-Hohenberg model, is studied. These rodlike structures persist under the presence of nongradient perturbations. Interaction properties of the rodlike structures are studied. This allows us to envisage the possibility of different crystal-like configurations.

  9. Local Surface Structure From Disparity Measurements

    NASA Astrophysics Data System (ADS)

    Jenkin, Michael R. M.; Jepson, Allan D.; Tsotsos, John K.

    1988-02-01

    Current theories of stereopsis involve three distinct stages: First, the two images of a stereo pair are processed separately to extract monocular features. One common choice of feature is the presence of a zero-crossing in a bandpassed versions of the image. Second, the monocular features in one image are matched with corresponding features found in the other image. In practice this second stage cannot be expected to produce only the correct matches, and a third stage must be considered in order to remove the incorrect matches ("false targets"). There are therefore three main issues the design of such a traditional algorithm for stereopsis, namely i) the choice of image features; the choice of matching criteria; and iii) the way false targets are avoided or eliminated. In this paper we introduce a different approach. We propose that symbolic features should not be extracted from the monocular images in the first stage of processing. Rather we examine a technique for measuring the local phase difference between the two images. We show how local phase difference in a bandpassed version of the image can be interpreted as disparity. This essentially combines the first two stages of the traditional approach. These disparity measurements may contain "false targets" which must be eliminated. Building upon the results of these disparty detectors, we show that a simple surface model based on object cohesiveness and local surface planarity across a range of spatial-frequency tuned channels can be used to reduce false matches. The resulting local planar surface support can be used to segment the image into planar regions in depth. Due to the independent nature of both the disparity detection and local planar support mechanism, this method is capable of dealing with both opaque and transparent stimuli.

  10. Local Large-Scale Structure and the Assumption of Homogeneity

    NASA Astrophysics Data System (ADS)

    Keenan, Ryan C.; Barger, Amy J.; Cowie, Lennox L.

    2016-10-01

    Our recent estimates of galaxy counts and the luminosity density in the near-infrared (Keenan et al. 2010, 2012) indicated that the local universe may be under-dense on radial scales of several hundred megaparsecs. Such a large-scale local under-density could introduce significant biases in the measurement and interpretation of cosmological observables, such as the inferred effects of dark energy on the rate of expansion. In Keenan et al. (2013), we measured the K-band luminosity density as a function of distance from us to test for such a local under-density. We made this measurement over the redshift range 0.01 < z < 0.2 (radial distances D ~ 50 - 800 h 70 -1 Mpc). We found that the shape of the K-band luminosity function is relatively constant as a function of distance and environment. We derive a local (z < 0.07, D < 300 h 70 -1 Mpc) K-band luminosity density that agrees well with previously published studies. At z > 0.07, we measure an increasing luminosity density that by z ~ 0.1 rises to a value of ~ 1.5 times higher than that measured locally. This implies that the stellar mass density follows a similar trend. Assuming that the underlying dark matter distribution is traced by this luminous matter, this suggests that the local mass density may be lower than the global mass density of the universe at an amplitude and on a scale that is sufficient to introduce significant biases into the measurement of basic cosmological observables. At least one study has shown that an under-density of roughly this amplitude and scale could resolve the apparent tension between direct local measurements of the Hubble constant and those inferred by Planck team. Other theoretical studies have concluded that such an under-density could account for what looks like an accelerating expansion, even when no dark energy is present.

  11. Multipeak self-biased magnetoelectric coupling characteristics in four-phase Metglas/Terfenol-D/Be-bronze/PMN-PT structure

    NASA Astrophysics Data System (ADS)

    Huang, Dongyan; Lu, Caijiang; Bing, Han

    2015-04-01

    This letter develops a self-biased magnetoelectric (ME) structure Metglas/Terfenol-D/Be-bronze/PMN-PT (MTBP) consisting of a magnetization-graded Metglas/Terfenol-D layer, a elastic Be-bronze plate, and a piezoelectric 0.67Pb(Mg1/3Nb2/3)O3-0.33PbTiO3 (PMN-PT) plate. By using the magnetization-graded Metglas/Terfenol-D layer and the elastic Be-bronze plate, multi-peak self-biased ME responses are obtained in MTBP structure. The experimental results show that the MTBP structure with two layers of Metglas foil has maximum zero-biased ME voltage coefficient (MEVC). As frequency increases from 0.5 to 90 kHz, eleven large peaks of MEVC with magnitudes of 0.75-33 V/(cm Oe) are observed at zero-biased magnetic field. The results demonstrate that the proposed multi-peak self-biased ME structure may be useful for multifunctional devices such as multi-frequency energy harvesters or low-frequency ac magnetic field sensors.

  12. Spatial structure arising from neighbour-dependent bias in collective cell movement.

    PubMed

    Binny, Rachelle N; Haridas, Parvathi; James, Alex; Law, Richard; Simpson, Matthew J; Plank, Michael J

    2016-01-01

    Mathematical models of collective cell movement often neglect the effects of spatial structure, such as clustering, on the population dynamics. Typically, they assume that individuals interact with one another in proportion to their average density (the mean-field assumption) which means that cell-cell interactions occurring over short spatial ranges are not accounted for. However, in vitro cell culture studies have shown that spatial correlations can play an important role in determining collective behaviour. Here, we take a combined experimental and modelling approach to explore how individual-level interactions give rise to spatial structure in a moving cell population. Using imaging data from in vitro experiments, we quantify the extent of spatial structure in a population of 3T3 fibroblast cells. To understand how this spatial structure arises, we develop a lattice-free individual-based model (IBM) and simulate cell movement in two spatial dimensions. Our model allows an individual's direction of movement to be affected by interactions with other cells in its neighbourhood, providing insights into how directional bias generates spatial structure. We consider how this behaviour scales up to the population level by using the IBM to derive a continuum description in terms of the dynamics of spatial moments. In particular, we account for spatial correlations between cells by considering dynamics of the second spatial moment (the average density of pairs of cells). Our numerical results suggest that the moment dynamics description can provide a good approximation to averaged simulation results from the underlying IBM. Using our in vitro data, we estimate parameters for the model and show that it can generate similar spatial structure to that observed in a 3T3 fibroblast cell population.

  13. Spatial structure arising from neighbour-dependent bias in collective cell movement

    PubMed Central

    Haridas, Parvathi; James, Alex; Law, Richard; Simpson, Matthew J.; Plank, Michael J.

    2016-01-01

    Mathematical models of collective cell movement often neglect the effects of spatial structure, such as clustering, on the population dynamics. Typically, they assume that individuals interact with one another in proportion to their average density (the mean-field assumption) which means that cell–cell interactions occurring over short spatial ranges are not accounted for. However, in vitro cell culture studies have shown that spatial correlations can play an important role in determining collective behaviour. Here, we take a combined experimental and modelling approach to explore how individual-level interactions give rise to spatial structure in a moving cell population. Using imaging data from in vitro experiments, we quantify the extent of spatial structure in a population of 3T3 fibroblast cells. To understand how this spatial structure arises, we develop a lattice-free individual-based model (IBM) and simulate cell movement in two spatial dimensions. Our model allows an individual’s direction of movement to be affected by interactions with other cells in its neighbourhood, providing insights into how directional bias generates spatial structure. We consider how this behaviour scales up to the population level by using the IBM to derive a continuum description in terms of the dynamics of spatial moments. In particular, we account for spatial correlations between cells by considering dynamics of the second spatial moment (the average density of pairs of cells). Our numerical results suggest that the moment dynamics description can provide a good approximation to averaged simulation results from the underlying IBM. Using our in vitro data, we estimate parameters for the model and show that it can generate similar spatial structure to that observed in a 3T3 fibroblast cell population. PMID:26893970

  14. Localization bias and spatial resolution of adaptive and non-adaptive spatial filters for MEG source reconstruction

    PubMed Central

    Sekihara, Kensuke; Sahani, Maneesh; Nagarajan, Srikantan S.

    2014-01-01

    This paper discusses the location bias and the spatial resolution in the reconstruction of a single dipole source by various spatial filtering techniques used for neuromagnetic imaging. We first analyze the location bias for several representative adaptive and non-adaptive spatial filters using their resolution kernels. This analysis theoretically validates previously reported empirical findings that standardized low-resolution electromagnetic tomography (sLORETA) has no location bias. We also find that the minimum-variance spatial filter does exhibit bias in the reconstructed location of a single source, but that this bias is eliminated by using the normalized lead field. We then focus on the comparison of sLORETA and the lead-field normalized minimum-variance spatial filter, and analyze the effect of noise on source location bias. We find that the signal-to-noise ratio (SNR) in the measurements determines whether the sLORETA reconstruction has source location bias, while the lead-field normalized minimum-variance spatial filter has no location bias even in the presence of noise. Finally, we compare the spatial resolution for sLORETA and the minimum-variance filter, and show that the minimum-variance filter attains much higher resolution than sLORETA does. The results of these analyses are validated by numerical experiments as well as by reconstructions based on two sets of evoked magnetic responses. PMID:15850724

  15. Localization bias and spatial resolution of adaptive and non-adaptive spatial filters for MEG source reconstruction.

    PubMed

    Sekihara, Kensuke; Sahani, Maneesh; Nagarajan, Srikantan S

    2005-05-01

    This paper discusses the location bias and the spatial resolution in the reconstruction of a single dipole source by various spatial filtering techniques used for neuromagnetic imaging. We first analyze the location bias for several representative adaptive and non-adaptive spatial filters using their resolution kernels. This analysis theoretically validates previously reported empirical findings that standardized low-resolution electromagnetic tomography (sLORETA) has no location bias. We also find that the minimum-variance spatial filter does exhibit bias in the reconstructed location of a single source, but that this bias is eliminated by using the normalized lead field. We then focus on the comparison of sLORETA and the lead-field normalized minimum-variance spatial filter, and analyze the effect of noise on source location bias. We find that the signal-to-noise ratio (SNR) in the measurements determines whether the sLORETA reconstruction has source location bias, while the lead-field normalized minimum-variance spatial filter has no location bias even in the presence of noise. Finally, we compare the spatial resolution for sLORETA and the minimum-variance filter, and show that the minimum-variance filter attains much higher resolution than sLORETA does. The results of these analyses are validated by numerical experiments as well as by reconstructions based on two sets of evoked magnetic responses.

  16. Uniparental Markers in Italy Reveal a Sex-Biased Genetic Structure and Different Historical Strata

    PubMed Central

    Sarno, Stefania; Harmant, Christine; Useli, Antonella; Sanz, Paula; Yang-Yao, Daniele; Manry, Jeremy; Ciani, Graziella; Luiselli, Donata; Quintana-Murci, Lluis; Comas, David; Pettener, Davide

    2013-01-01

    Located in the center of the Mediterranean landscape and with an extensive coastal line, the territory of what is today Italy has played an important role in the history of human settlements and movements of Southern Europe and the Mediterranean Basin. Populated since Paleolithic times, the complexity of human movements during the Neolithic, the Metal Ages and the most recent history of the two last millennia (involving the overlapping of different cultural and demic strata) has shaped the pattern of the modern Italian genetic structure. With the aim of disentangling this pattern and understanding which processes more importantly shaped the distribution of diversity, we have analyzed the uniparentally-inherited markers in ∼900 individuals from an extensive sampling across the Italian peninsula, Sardinia and Sicily. Spatial PCAs and DAPCs revealed a sex-biased pattern indicating different demographic histories for males and females. Besides the genetic outlier position of Sardinians, a North West–South East Y-chromosome structure is found in continental Italy. Such structure is in agreement with recent archeological syntheses indicating two independent and parallel processes of Neolithisation. In addition, date estimates pinpoint the importance of the cultural and demographic events during the late Neolithic and Metal Ages. On the other hand, mitochondrial diversity is distributed more homogeneously in agreement with older population events that might be related to the presence of an Italian Refugium during the last glacial period in Europe. PMID:23734255

  17. Uniparental markers in Italy reveal a sex-biased genetic structure and different historical strata.

    PubMed

    Boattini, Alessio; Martinez-Cruz, Begoña; Sarno, Stefania; Harmant, Christine; Useli, Antonella; Sanz, Paula; Yang-Yao, Daniele; Manry, Jeremy; Ciani, Graziella; Luiselli, Donata; Quintana-Murci, Lluis; Comas, David; Pettener, Davide

    2013-01-01

    Located in the center of the Mediterranean landscape and with an extensive coastal line, the territory of what is today Italy has played an important role in the history of human settlements and movements of Southern Europe and the Mediterranean Basin. Populated since Paleolithic times, the complexity of human movements during the Neolithic, the Metal Ages and the most recent history of the two last millennia (involving the overlapping of different cultural and demic strata) has shaped the pattern of the modern Italian genetic structure. With the aim of disentangling this pattern and understanding which processes more importantly shaped the distribution of diversity, we have analyzed the uniparentally-inherited markers in ∼900 individuals from an extensive sampling across the Italian peninsula, Sardinia and Sicily. Spatial PCAs and DAPCs revealed a sex-biased pattern indicating different demographic histories for males and females. Besides the genetic outlier position of Sardinians, a North West-South East Y-chromosome structure is found in continental Italy. Such structure is in agreement with recent archeological syntheses indicating two independent and parallel processes of Neolithisation. In addition, date estimates pinpoint the importance of the cultural and demographic events during the late Neolithic and Metal Ages. On the other hand, mitochondrial diversity is distributed more homogeneously in agreement with older population events that might be related to the presence of an Italian Refugium during the last glacial period in Europe.

  18. Geometry motivated alternative view on local protein backbone structures.

    PubMed

    Zacharias, Jan; Knapp, Ernst Walter

    2013-11-01

    We present an alternative to the classical Ramachandran plot (R-plot) to display local protein backbone structure. Instead of the (φ, ψ)-backbone angles relating to the chemical architecture of polypeptides generic helical parameters are used. These are the rotation or twist angle ϑ and the helical rise parameter d. Plots with these parameters provide a different view on the nature of local protein backbone structures. It allows to display the local structures in polar (d, ϑ)-coordinates, which is not possible for an R-plot, where structural regimes connected by periodicity appear disconnected. But there are other advantages, like a clear discrimination of the handedness of a local structure, a larger spread of the different local structure domains--the latter can yield a better separation of different local secondary structure motives--and many more. Compared to the R-plot we are not aware of any major disadvantage to classify local polypeptide structures with the (d, ϑ)-plot, except that it requires some elementary computations. To facilitate usage of the new (d, ϑ)-plot for protein structures we provide a web application (http://agknapp.chemie.fu-berlin.de/secsass), which shows the (d, ϑ)-plot side-by-side with the R-plot.

  19. Localization of defects using checkerboard test structures

    NASA Astrophysics Data System (ADS)

    Schellenberg, Sven-Olaf

    2001-04-01

    Defects in semiconductor industry become more important by shrinking structures and increasing complexity of process. Therefore the size of a killer defect becomes smaller and it is not easy to find them with optical inspection tools. In addition Inspection tools are not able to say something about electrical effects from defects which are found. With Checkerboard Test Structures it is possible to locate electrical defects. In fact these special test structures will be tested at the end of the process, like an usual function test. A special developed algorithm allows low quantity of pads. This gives a high spatial resolution and on the other hand we have good ratio between active and passive area. A reduction of a statistical failure could be reached, because it is not necessary to calculate the defect density from a small region. In particular special defect distribution like cluster can be considered. With this structures different layers can be examined for disconnections and short-circuits. Therefore it is possible to locate defects in one layer or between two layers. So the defect density for the sensitive dielectrica between two layers, like any kind of oxide can be calculated. The karree test structures can be used very good as an inline-defectmonitoring, because there is no difference from the original technology of proces. There are also no differences in time for processing and for testing, so Karreeteststructures is an optimal representation for your process.

  20. Enhancing community detection by using local structural information

    NASA Astrophysics Data System (ADS)

    Xiang, Ju; Hu, Ke; Zhang, Yan; Bao, Mei-Hua; Tang, Liang; Tang, Yan-Ni; Gao, Yuan-Yuan; Li, Jian-Ming; Chen, Benyan; Hu, Jing-Bo

    2016-03-01

    Many real-world networks, such as gene networks, protein-protein interaction networks and metabolic networks, exhibit community structures, meaning the existence of groups of densely connected vertices in the networks. Many local similarity measures in the networks are closely related to the concept of the community structures, and may have a positive effect on community detection in the networks. Here, various local similarity measures are used to extract local structural information, which is then applied to community detection in the networks by using the edge-reweighting strategy. The effect of the local similarity measures on community detection is carefully investigated and compared in various networks. The experimental results show that the local similarity measures are crucial for the improvement of community detection methods, while the positive effect of the local similarity measures is closely related to the networks under study and applied community detection methods.

  1. Is local selection so widespread in river organisms? Fractal geometry of river networks leads to high bias in outlier detection.

    PubMed

    Fourcade, Yoan; Chaput-Bardy, Audrey; Secondi, Jean; Fleurant, Cyril; Lemaire, Christophe

    2013-04-01

    Identifying local adaptation is crucial in conservation biology to define ecotypes and establish management guidelines. Local adaptation is often inferred from the detection of loci showing a high differentiation between populations, the so-called FST outliers. Methods of detection of loci under selection are reputed to be robust in most spatial population models. However, using simulations we showed that FST outlier tests provided a high rate of false-positives (up to 60%) in fractal environments such as river networks. Surprisingly, the number of sampled demes was correlated with parameters of population genetic structure, such as the variance of FST s, and hence strongly influenced the rate of outliers. This unappreciated property of river networks therefore needs to be accounted for in genetic studies on adaptation and conservation of river organisms.

  2. Sex-biased dispersal in sperm whales: contrasting mitochondrial and nuclear genetic structure of global populations.

    PubMed Central

    Lyrholm, T; Leimar, O; Johanneson, B; Gyllensten, U

    1999-01-01

    The social organization of most mammals is characterized by female philopatry and male dispersal. Such sex-biased dispersal can cause the genetic structure of populations to differ between the maternally inherited mitochondrial DNA (mtDNA) and the bi-parental nuclear genome. Here we report on the global genetic structure of oceanic populations of the sperm whale, one of the most widely distributed mammalian species. Groups of females and juveniles are mainly found at low latitudes, while males reach polar waters, returning to tropical and subtropical waters to breed. In comparisons between oceans, we did not find significant heterogeneity in allele frequencies of microsatellite loci (exact test; p = 0.23). Estimates of GST = 0.001 and RST = 0.005 also indicated negligible if any nuclear DNA differentiation. We have previously reported significant differentiation between oceans in mtDNA sequences. These contrasting patterns suggest that interoceanic movements have been more prevalent among males than among females, consistent with observations of females being the philopatric sex and having a more limited latitudinal distribution than males. Consequently, the typical mammalian dispersal pattern may have operated on a global scale in sperm whales. PMID:10097396

  3. Non-Local currents and the structure of eigenstates in planar discrete systems with local symmetries

    NASA Astrophysics Data System (ADS)

    Röntgen, M.; Morfonios, C. V.; Diakonos, F. K.; Schmelcher, P.

    2017-05-01

    Local symmetries are spatial symmetries present in a subdomain of a complex system. By using and extending a framework of so-called non-local currents that has been established recently, we show that one can gain knowledge about the structure of eigenstates in locally symmetric setups through a Kirchhoff-type law for the non-local currents. The framework is applicable to all discrete planar Schrödinger setups, including those with non-uniform connectivity. Conditions for spatially constant non-local currents are derived and we explore two types of locally symmetric subsystems in detail, closed-loops and one-dimensional open ended chains. We find these systems to support locally similar or even locally symmetric eigenstates.

  4. The nearby structure of the Local Arm

    NASA Astrophysics Data System (ADS)

    Cersosimo, J. C.; Muller, R. J.; Santiago Figueroa, N.; Figueroa Vélez, S.; Báez, P.; Testori, J. C.

    The continuum emission of the galactic region located at G85-0.5 is well defined by the weak 11 cm wavelength emission. The region catalogued as W80 is extended 3° in diameter and the optical images show the North America and the Pelican Nebulae (NPN) complex. In this paper we derive new distances wich were obtained from the radiorecombination line observations made at a frequency near 1.4 GHz. The results suggest that the ionized hydrogen is spread along the line of sight instead of being clumped at one specific distance. We identified three structures located at distances of about 0.7 kpc, 1.7 kpc, and 2.7 kpc, respectively. Using a simple model where we assume homogeneity and a constant electron temperature the electron densities of each structure are obtained. We conclude that W80 is composed of different regions located along the line of sight.

  5. Resonance ultrasonic actuation and local structural rejuvenation in metallic glasses

    NASA Astrophysics Data System (ADS)

    Wang, D. P.; Yang, Y.; Niu, X. R.; Lu, J.; Yang, G. N.; Wang, W. H.; Liu, C. T.

    2017-06-01

    Using the method of contact resonance ultrasonic actuation (CRUA), we observed evidence of local structural rejuvenation at the surface of metallic glasses (MGs), arising from the increase of the vibration amplitude of the atoms after the resonance actuation. By adjusting the CRUA parameters, the size, pattern, and extent of the rejuvenated zones could be tailored. Nanoindentation tests revealed suppressed nucleation of shear bands after CRUA, originating from the homogenization of the local structure induced by the ultrasonic vibration. Compared with the structural homogenization from annealing, this method will not sacrifice the concentration of the free volume for the local structural constraint. These results are useful to understand the evolution of the microstructure and local structural rejuvenation of MGs, as well as the design of MGs with improved plasticity from the nanoscale to the microscale.

  6. Local structural study of doped-ceria by EXAFS spectroscopy

    SciTech Connect

    Shirbhate, S. C.; Acharya, S. A.; Yadav, A. K.; Sagdeo, A. P.; Jha, S. N.

    2016-05-23

    In the present work, Structural and Local structural study of Sm, Gd doped and Sm-Gd co-doped ceria system has been studied by Extended X-ray Absorption Fine Structure Spectroscopy (EXAFS). These ceria based systems are synthesized by hydrothermal synthesis route. Fluorite structure is confirmed by X-ray diffraction (XRD) and data is well fitted using Rietveld refinement by Full-Prof suite. Local structural changes in terms of coordination with surrounding, inter atomic distances and Debye Waller factor of nearest neighbor and next nearest neighbor has been discussed.

  7. Local structural study of doped-ceria by EXAFS spectroscopy

    NASA Astrophysics Data System (ADS)

    Shirbhate, S. C.; Yadav, A. K.; Acharya, S. A.; Sagdeo, A. P.; Jha, S. N.

    2016-05-01

    In the present work, Structural and Local structural study of Sm, Gd doped and Sm-Gd co-doped ceria system has been studied by Extended X-ray Absorption Fine Structure Spectroscopy (EXAFS). These ceria based systems are synthesized by hydrothermal synthesis route. Fluorite structure is confirmed by X-ray diffraction (XRD) and data is well fitted using Rietveld refinement by Full-Prof suite. Local structural changes in terms of coordination with surrounding, inter atomic distances and Debye Waller factor of nearest neighbor and next nearest neighbor has been discussed.

  8. Band structures and localization properties of aperiodic layered phononic crystals

    NASA Astrophysics Data System (ADS)

    Yan, Zhi-Zhong; Zhang, Chuanzeng

    2012-03-01

    The band structures and localization properties of in-plane elastic waves with coupling of longitudinal and transverse modes oblique propagating in aperiodic phononic crystals based on Thue-Morse and Rudin-Shapiro sequences are studied. Using transfer matrix method, the concept of the localization factor is introduced and the correctness is testified through the Rytov dispersion relation. For comparison, the perfect periodic structure and the quasi-periodic Fibonacci system are also considered. In addition, the influences of the random disorder, local resonance, translational and/or mirror symmetries on the band structures of the aperiodic phononic crystals are analyzed in this paper.

  9. Effect of negative bias on the composition and structure of the tungsten oxide thin films deposited by magnetron sputtering

    NASA Astrophysics Data System (ADS)

    Wang, Meihan; Lei, Hao; Wen, Jiaxing; Long, Haibo; Sawada, Yutaka; Hoshi, Yoichi; Uchida, Takayuki; Hou, Zhaoxia

    2015-12-01

    Tungsten oxide thin films were deposited at room temperature under different negative bias voltages (Vb, 0 to -500 V) by DC reactive magnetron sputtering, and then the as-deposited films were annealed at 500 °C in air atmosphere. The crystal structure, surface morphology, chemical composition and transmittance of the tungsten oxide thin films were characterized by X-ray diffraction (XRD), field emission scanning electron microscopy (FE-SEM), X-ray photoelectron spectroscopy (XPS) and UV-vis spectrophotometer. The XRD analysis reveals that the tungsten oxide films deposited at different negative bias voltages present a partly crystallized amorphous structure. All the films transfer from amorphous to crystalline (monoclinic + hexagonal) after annealing 3 h at 500 °C. Furthermore, the crystallized tungsten oxide films show different preferred orientation. The morphology of the tungsten oxide films deposited at different negative bias voltages is consisted of fine nanoscale grains. The grains grow up and conjunct with each other after annealing. The tungsten oxide films deposited at higher negative bias voltages after annealing show non-uniform special morphology. Substoichiometric tungsten oxide films were formed as evidenced by XPS spectra of W4f and O1s. As a result, semi-transparent films were obtained in the visible range for all films deposited at different negative bias voltages.

  10. Detection of Chromosomal Structural Alterations in Single Cells by SNP Arrays: A Systematic Survey of Amplification Bias and Optimized Workflow

    PubMed Central

    Iwamoto, Kazuya; Bundo, Miki; Ueda, Junko; Nakano, Yoko; Ukai, Wataru; Hashimoto, Eri; Saito, Toshikazu; Kato, Tadafumi

    2007-01-01

    Background In single-cell human genome analysis using whole-genome amplified product, a strong amplification bias involving allele dropout and preferential amplification hampers the quality of results. Using an oligonucleotide single nucleotide polymorphism (SNP) array, we systematically examined the nature of this amplification bias, including frequency, degree, and preference for genomic location, and we assessed the effects of this amplification bias on subsequent genotype and chromosomal copy number analyses. Methodology/Principal Findings We found a large variability in amplification bias among the amplified products obtained by multiple displacement amplification (MDA), and this bias had a severe effect on the genotype and chromosomal copy number analyses. We established optimal experimental conditions for pre-screening for high-quality amplified products, processing array data, and analyzing chromosomal structural alterations. Using this optimized protocol, we successfully detected previously unidentified chromosomal structural alterations in single cells from a lymphoblastoid cell line. These alterations were subsequently confirmed by karyotype analysis. In addition, we successfully obtained reproducible chromosomal copy number profiles of single cells from the cell line with a complex karyotype, indicating the applicability and potential of our optimized workflow. Conclusions/Significance Our results suggest that the quality of amplification products should be critically assessed before using them for genomic analyses. The method of MDA-based whole-genome amplification followed by SNP array analysis described here will be useful for exploring chromosomal alterations in single cells. PMID:18074030

  11. Berkson's bias, selection bias, and missing data.

    PubMed

    Westreich, Daniel

    2012-01-01

    Although Berkson's bias is widely recognized in the epidemiologic literature, it remains underappreciated as a model of both selection bias and bias due to missing data. Simple causal diagrams and 2 × 2 tables illustrate how Berkson's bias connects to collider bias and selection bias more generally, and show the strong analogies between Berksonian selection bias and bias due to missing data. In some situations, considerations of whether data are missing at random or missing not at random are less important than the causal structure of the missing data process. Although dealing with missing data always relies on strong assumptions about unobserved variables, the intuitions built with simple examples can provide a better understanding of approaches to missing data in real-world situations.

  12. The effect of sex-biased dispersal on opposite-sexed spatial genetic structure and inbreeding risk.

    PubMed

    Blyton, Michaela D J; Banks, Sam C; Peakall, Rod

    2015-04-01

    Natal sex-biased dispersal has long been thought to reduce the risk of inbreeding by spatially separating opposite-sexed kin. Yet, comprehensive and quantitative evaluations of this hypothesis are lacking. In this study, we quantified the effectiveness of sex-biased dispersal as an inbreeding avoidance strategy by combining spatially explicit simulations and empirical data. We quantified the extent of kin clustering by measuring the degree of spatial autocorrelation among opposite-sexed individuals (FM structure). This allowed us to systematically explore how the extent of sex-biased dispersal, generational overlap, and mate searching distance, influenced both kin clustering, and the resulting inbreeding in the absence of complementary inbreeding avoidance strategies. Simulations revealed that when sex-biased dispersal was limited, positive FM genetic structure developed quickly and increased as the mate searching distance decreased or as generational overlap increased. Interestingly, complete long-range sex-biased dispersal did not prevent the development of FM genetic structure when generations overlapped. We found a very strong correlation between FM genetic structure and both FIS under random mating, and pedigree-based measures of inbreeding. Thus, we show that the detection of FM genetic structure can be a strong indicator of inbreeding risk. Empirical data for two species with different life history strategies yielded patterns congruent with our simulations. Our study illustrates a new application of spatial genetic autocorrelation analysis that offers a framework for quantifying the risk of inbreeding that is easily extendable to other species. Furthermore, our findings provide other researchers with a context for interpreting observed patterns of opposite-sexed spatial genetic structure.

  13. Identifying local structural states in atomic imaging by computer vision

    DOE PAGES

    Laanait, Nouamane; Ziatdinov, Maxim; He, Qian; ...

    2016-11-02

    The availability of atomically resolved imaging modalities enables an unprecedented view into the local structural states of materials, which manifest themselves by deviations from the fundamental assumptions of periodicity and symmetry. Consequently, approaches that aim to extract these local structural states from atomic imaging data with minimal assumptions regarding the average crystallographic configuration of a material are indispensable to advances in structural and chemical investigations of materials. Here, we present an approach to identify and classify local structural states that is rooted in computer vision. This approach introduces a definition of a structural state that is composed of both localmore » and non-local information extracted from atomically resolved images, and is wholly untethered from the familiar concepts of symmetry and periodicity. Instead, this approach relies on computer vision techniques such as feature detection, and concepts such as scale-invariance. We present the fundamental aspects of local structural state extraction and classification by application to simulated scanning transmission electron microscopy images, and analyze the robustness of this approach in the presence of common instrumental factors such as noise, limited spatial resolution, and weak contrast. Finally, we apply this computer vision-based approach for the unsupervised detection and classification of local structural states in an experimental electron micrograph of a complex oxides interface, and a scanning tunneling micrograph of a defect engineered multilayer graphene surface.« less

  14. Matching structural densities from different biophysical origins with gain and bias.

    PubMed

    Wriggers, Willy; Alamo, Lorenzo; Padrón, Raúl

    2011-03-01

    The registration of volumetric structures in real space involves geometric and density transformations that align a target map and a probe map in the best way possible. Many computational docking strategies exist for finding the geometric transformations that superimpose maps, but the problem of finding an optimal density transformation, for the purposes of difference calculations or segmentation, has received little attention in the literature. We report results based on simulated and experimental electron microscopy maps, showing that a single scale factor (gain) may be insufficient when it comes to minimizing the density discrepancy between an aligned target and probe. We propose an affine transformation, with gain and bias, that is parameterized by known surface isovalues and by an interactive centering of the "cancellation peak" in the surface thresholded difference map histogram. The proposed approach minimizes discrepancies across a wide range of interior densities. Owing to having only two parameters, it avoids overfitting and requires only minimal knowledge of the probe and target maps. The linear transformation also preserves phases and relative amplitudes in Fourier space. The histogram matching strategy was implemented in the newly revised volhist tool of the Situs package, version 2.6.

  15. Sample Size Requirements for Structural Equation Models: An Evaluation of Power, Bias, and Solution Propriety.

    PubMed

    Wolf, Erika J; Harrington, Kelly M; Clark, Shaunna L; Miller, Mark W

    2013-12-01

    Determining sample size requirements for structural equation modeling (SEM) is a challenge often faced by investigators, peer reviewers, and grant writers. Recent years have seen a large increase in SEMs in the behavioral science literature, but consideration of sample size requirements for applied SEMs often relies on outdated rules-of-thumb. This study used Monte Carlo data simulation techniques to evaluate sample size requirements for common applied SEMs. Across a series of simulations, we systematically varied key model properties, including number of indicators and factors, magnitude of factor loadings and path coefficients, and amount of missing data. We investigated how changes in these parameters affected sample size requirements with respect to statistical power, bias in the parameter estimates, and overall solution propriety. Results revealed a range of sample size requirements (i.e., from 30 to 460 cases), meaningful patterns of association between parameters and sample size, and highlight the limitations of commonly cited rules-of-thumb. The broad "lessons learned" for determining SEM sample size requirements are discussed.

  16. Climate, physiological tolerance and sex-biased dispersal shape genetic structure of Neotropical orchid bees.

    PubMed

    López-Uribe, Margarita M; Zamudio, Kelly R; Cardoso, Carolina F; Danforth, Bryan N

    2014-04-01

    Understanding the impact of past climatic events on the demographic history of extant species is critical for predicting species' responses to future climate change. Palaeoclimatic instability is a major mechanism of lineage diversification in taxa with low dispersal and small geographical ranges in tropical ecosystems. However, the impact of these climatic events remains questionable for the diversification of species with high levels of gene flow and large geographical distributions. In this study, we investigate the impact of Pleistocene climate change on three Neotropical orchid bee species (Eulaema bombiformis, E. meriana and E. cingulata) with transcontinental distributions and different physiological tolerances. We first generated ecological niche models to identify species-specific climatically stable areas during Pleistocene climatic oscillations. Using a combination of mitochondrial and nuclear markers, we inferred calibrated phylogenies and estimated historical demographic parameters to reconstruct the phylogeographical history of each species. Our results indicate species with narrower physiological tolerance experienced less suitable habitat during glaciations and currently exhibit strong population structure in the mitochondrial genome. However, nuclear markers with low and high mutation rates show lack of association with geography. These results combined with lower migration rate estimates from the mitochondrial than the nuclear genome suggest male-biased dispersal. We conclude that despite large effective population sizes and capacity for long-distance dispersal, climatic instability is an important mechanism of maternal lineage diversification in orchid bees. Thus, these Neotropical pollinators are susceptible to disruption of genetic connectivity in the event of large-scale climatic changes.

  17. Using previous models to bias structural learning in the hierarchical BOA.

    PubMed

    Hauschild, M W; Pelikan, M; Sastry, K; Goldberg, D E

    2012-01-01

    Estimation of distribution algorithms (EDAs) are stochastic optimization techniques that explore the space of potential solutions by building and sampling explicit probabilistic models of promising candidate solutions. While the primary goal of applying EDAs is to discover the global optimum or at least its accurate approximation, besides this, any EDA provides us with a sequence of probabilistic models, which in most cases hold a great deal of information about the problem. Although using problem-specific knowledge has been shown to significantly improve performance of EDAs and other evolutionary algorithms, this readily available source of problem-specific information has been practically ignored by the EDA community. This paper takes the first step toward the use of probabilistic models obtained by EDAs to speed up the solution of similar problems in the future. More specifically, we propose two approaches to biasing model building in the hierarchical Bayesian optimization algorithm (hBOA) based on knowledge automatically learned from previous hBOA runs on similar problems. We show that the proposed methods lead to substantial speedups and argue that the methods should work well in other applications that require solving a large number of problems with similar structure.

  18. Local structural modeling for implementation of optimal active damping

    NASA Astrophysics Data System (ADS)

    Blaurock, Carl A.; Miller, David W.

    1993-09-01

    Local controllers are good candidates for active control of flexible structures. Local control generally consists of low order, frequency benign compensators using collocated hardware. Positive real compensators and plant transfer functions ensure that stability margins and performance robustness are high. The typical design consists of an experimentally chosen gain on a fixed form controller such as rate feedback. The resulting compensator performs some combination of damping (dissipating energy) and structural modification (changing the energy flow paths). Recent research into structural impedance matching has shown how to optimize dissipation based on the local behavior of the structure. This paper investigates the possibility of improving performance by influencing global energy flow, using local controllers designed using a global performance metric.

  19. Structure-Activity Analysis of Biased Agonism at the Human Adenosine A3 Receptor

    PubMed Central

    Baltos, Jo-Anne; Paoletta, Silvia; Nguyen, Anh T. N.; Gregory, Karen J.; Tosh, Dilip K.; Christopoulos, Arthur; Jacobson, Kenneth A.

    2016-01-01

    Biased agonism at G protein–coupled receptors (GPCRs) has significant implications for current drug discovery, but molecular determinants that govern ligand bias remain largely unknown. The adenosine A3 GPCR (A3AR) is a potential therapeutic target for various conditions, including cancer, inflammation, and ischemia, but for which biased agonism remains largely unexplored. We now report the generation of bias “fingerprints” for prototypical ribose containing A3AR agonists and rigidified (N)-methanocarba 5′-N-methyluronamide nucleoside derivatives with regard to their ability to mediate different signaling pathways. Relative to the reference prototypical agonist IB-MECA, (N)-methanocarba 5′-N-methyluronamide nucleoside derivatives with significant N6 or C2 modifications, including elongated aryl-ethynyl groups, exhibited biased agonism. Significant positive correlation was observed between the C2 substituent length (in Å) and bias toward cell survival. Molecular modeling suggests that extended C2 substituents on (N)-methanocarba 5′-N-methyluronamide nucleosides promote a progressive outward shift of the A3AR transmembrane domain 2, which may contribute to the subset of A3AR conformations stabilized on biased agonist binding. PMID:27136943

  20. Biased allosteric modulation at the CaS receptor engendered by structurally diverse calcimimetics

    PubMed Central

    Cook, A E; Mistry, S N; Gregory, K J; Furness, S G B; Sexton, P M; Scammells, P J; Conigrave, A D; Christopoulos, A; Leach, K

    2015-01-01

    BACKGROUND AND PURPOSE Clinical use of cinacalcet in hyperparathyroidism is complicated by its tendency to induce hypocalcaemia, arising partly from activation of calcium-sensing receptors (CaS receptors) in the thyroid and stimulation of calcitonin release. CaS receptor allosteric modulators that selectively bias signalling towards pathways that mediate desired effects [e.g. parathyroid hormone (PTH) suppression] rather than those mediating undesirable effects (e.g. elevated serum calcitonin), may offer better therapies. EXPERIMENTAL APPROACH We characterized the ligand-biased profile of novel calcimimetics in HEK293 cells stably expressing human CaS receptors, by monitoring intracellular calcium (Ca2+i) mobilization, inositol phosphate (IP)1 accumulation, ERK1/2 phosphorylation (pERK1/2) and receptor expression. KEY RESULTS Phenylalkylamine calcimimetics were biased towards allosteric modulation of Ca2+i mobilization and IP1 accumulation. S,R-calcimimetic B was biased only towards IP1 accumulation. R,R-calcimimetic B and AC-265347 were biased towards IP1 accumulation and pERK1/2. Nor-calcimimetic B was unbiased. In contrast to phenylalkylamines and calcimimetic B analogues, AC-265347 did not promote trafficking of a loss-of-expression, naturally occurring, CaS receptor mutation (G670E). CONCLUSIONS AND IMPLICATIONS The ability of R,R-calcimimetic B and AC-265347 to bias signalling towards pERK1/2 and IP1 accumulation may explain their suppression of PTH levels in vivo at concentrations that have no effect on serum calcitonin levels. The demonstration that AC-265347 promotes CaS receptor receptor signalling, but not trafficking reveals a novel profile of ligand-biased modulation at CaS receptors The identification of allosteric modulators that bias CaS receptor signalling towards distinct intracellular pathways provides an opportunity to develop desirable biased signalling profiles in vivo for mediating selective physiological responses. PMID:25220431

  1. Automated Localization of Multiple Pelvic Bone Structures on MRI.

    PubMed

    Onal, Sinan; Lai-Yuen, Susana; Bao, Paul; Weitzenfeld, Alfredo; Hart, Stuart

    2016-01-01

    In this paper, we present a fully automated localization method for multiple pelvic bone structures on magnetic resonance images (MRI). Pelvic bone structures are at present identified manually on MRI to locate reference points for measurement and evaluation of pelvic organ prolapse (POP). Given that this is a time-consuming and subjective procedure, there is a need to localize pelvic bone structures automatically. However, bone structures are not easily differentiable from soft tissue on MRI as their pixel intensities tend to be very similar. In this paper, we present a model that combines support vector machines and nonlinear regression capturing global and local information to automatically identify the bounding boxes of bone structures on MRI. The model identifies the location of the pelvic bone structures by establishing the association between their relative locations and using local information such as texture features. Results show that the proposed method is able to locate the bone structures of interest accurately (dice similarity index >0.75) in 87-91% of the images. This research aims to enable accurate, consistent, and fully automated localization of bone structures on MRI to facilitate and improve the diagnosis of health conditions such as female POP.

  2. Proteins comparison through probabilistic optimal structure local alignment.

    PubMed

    Micale, Giovanni; Pulvirenti, Alfredo; Giugno, Rosalba; Ferro, Alfredo

    2014-01-01

    Multiple local structure comparison helps to identify common structural motifs or conserved binding sites in 3D structures in distantly related proteins. Since there is no best way to compare structures and evaluate the alignment, a wide variety of techniques and different similarity scoring schemes have been proposed. Existing algorithms usually compute the best superposition of two structures or attempt to solve it as an optimization problem in a simpler setting (e.g., considering contact maps or distance matrices). Here, we present PROPOSAL (PROteins comparison through Probabilistic Optimal Structure local ALignment), a stochastic algorithm based on iterative sampling for multiple local alignment of protein structures. Our method can efficiently find conserved motifs across a set of protein structures. Only the distances between all pairs of residues in the structures are computed. To show the accuracy and the effectiveness of PROPOSAL we tested it on a few families of protein structures. We also compared PROPOSAL with two state-of-the-art tools for pairwise local alignment on a dataset of manually annotated motifs. PROPOSAL is available as a Java 2D standalone application or a command line program at http://ferrolab.dmi.unict.it/proposal/proposal.html.

  3. Comparative Proteomics Reveals a Significant Bias Toward Alternative Protein Isoforms with Conserved Structure and Function

    PubMed Central

    Ezkurdia, Iakes; del Pozo, Angela; Frankish, Adam; Rodriguez, Jose Manuel; Harrow, Jennifer; Ashman, Keith; Valencia, Alfonso; Tress, Michael L.

    2012-01-01

    Advances in high-throughput mass spectrometry are making proteomics an increasingly important tool in genome annotation projects. Peptides detected in mass spectrometry experiments can be used to validate gene models and verify the translation of putative coding sequences (CDSs). Here, we have identified peptides that cover 35% of the genes annotated by the GENCODE consortium for the human genome as part of a comprehensive analysis of experimental spectra from two large publicly available mass spectrometry databases. We detected the translation to protein of “novel” and “putative” protein-coding transcripts as well as transcripts annotated as pseudogenes and nonsense-mediated decay targets. We provide a detailed overview of the population of alternatively spliced protein isoforms that are detectable by peptide identification methods. We found that 150 genes expressed multiple alternative protein isoforms. This constitutes the largest set of reliably confirmed alternatively spliced proteins yet discovered. Three groups of genes were highly overrepresented. We detected alternative isoforms for 10 of the 25 possible heterogeneous nuclear ribonucleoproteins, proteins with a key role in the splicing process. Alternative isoforms generated from interchangeable homologous exons and from short indels were also significantly enriched, both in human experiments and in parallel analyses of mouse and Drosophila proteomics experiments. Our results show that a surprisingly high proportion (almost 25%) of the detected alternative isoforms are only subtly different from their constitutive counterparts. Many of the alternative splicing events that give rise to these alternative isoforms are conserved in mouse. It was striking that very few of these conserved splicing events broke Pfam functional domains or would damage globular protein structures. This evidence of a strong bias toward subtle differences in CDS and likely conserved cellular function and structure is

  4. Comparative proteomics reveals a significant bias toward alternative protein isoforms with conserved structure and function.

    PubMed

    Ezkurdia, Iakes; del Pozo, Angela; Frankish, Adam; Rodriguez, Jose Manuel; Harrow, Jennifer; Ashman, Keith; Valencia, Alfonso; Tress, Michael L

    2012-09-01

    Advances in high-throughput mass spectrometry are making proteomics an increasingly important tool in genome annotation projects. Peptides detected in mass spectrometry experiments can be used to validate gene models and verify the translation of putative coding sequences (CDSs). Here, we have identified peptides that cover 35% of the genes annotated by the GENCODE consortium for the human genome as part of a comprehensive analysis of experimental spectra from two large publicly available mass spectrometry databases. We detected the translation to protein of "novel" and "putative" protein-coding transcripts as well as transcripts annotated as pseudogenes and nonsense-mediated decay targets. We provide a detailed overview of the population of alternatively spliced protein isoforms that are detectable by peptide identification methods. We found that 150 genes expressed multiple alternative protein isoforms. This constitutes the largest set of reliably confirmed alternatively spliced proteins yet discovered. Three groups of genes were highly overrepresented. We detected alternative isoforms for 10 of the 25 possible heterogeneous nuclear ribonucleoproteins, proteins with a key role in the splicing process. Alternative isoforms generated from interchangeable homologous exons and from short indels were also significantly enriched, both in human experiments and in parallel analyses of mouse and Drosophila proteomics experiments. Our results show that a surprisingly high proportion (almost 25%) of the detected alternative isoforms are only subtly different from their constitutive counterparts. Many of the alternative splicing events that give rise to these alternative isoforms are conserved in mouse. It was striking that very few of these conserved splicing events broke Pfam functional domains or would damage globular protein structures. This evidence of a strong bias toward subtle differences in CDS and likely conserved cellular function and structure is remarkable and

  5. Implications of room temperature oxidation on crystal structure and exchange bias effect in Co/CoO nanoparticles

    SciTech Connect

    Feygenson, Mikhail; Formo, Eric V.; Freeman, Katherine; Schieber, Natalie P.; Gai, Zheng; Rondinone, Adam J.

    2015-11-02

    In this study, we describe how the exchange bias effect in Co/CoO nanoparticles depends on the size focusing and temperature treatment of precursor Co nanoparticles before oxidation at ambient conditions. By appealing to magnetization, microscopy, neutron and synchrotron x-ray measurements we found that as-synthesized Co nanoparticles readily oxidize in air only after 20 days. The highest exchange bias field of 814 Oe is observed at T = 2K. When the same nanoparticles are centrifuged and annealed at 70 °C in vacuum prior to oxidation, the exchange bias field is increased to 2570 Oe. Annealing of Co nanoparticles in vacuum improves their crystallinity and prevents complete oxidation, so that Co-core/CoO-shell structure is preserved even after 120 days. The crystal structure of CoO shell in both samples is different from its bulk counterpart. Implications of such distorted CoO shells on exchange bias are discussed. Coating of Co nanoparticles with amorphous silica shell makes them resistant to oxidation, but ultimately modifies the crystal structure of both Co core and SiO2 shell.

  6. Implications of room temperature oxidation on crystal structure and exchange bias effect in Co/CoO nanoparticles

    DOE PAGES

    Feygenson, Mikhail; Formo, Eric V.; Freeman, Katherine; ...

    2015-11-02

    In this study, we describe how the exchange bias effect in Co/CoO nanoparticles depends on the size focusing and temperature treatment of precursor Co nanoparticles before oxidation at ambient conditions. By appealing to magnetization, microscopy, neutron and synchrotron x-ray measurements we found that as-synthesized Co nanoparticles readily oxidize in air only after 20 days. The highest exchange bias field of 814 Oe is observed at T = 2K. When the same nanoparticles are centrifuged and annealed at 70 °C in vacuum prior to oxidation, the exchange bias field is increased to 2570 Oe. Annealing of Co nanoparticles in vacuum improvesmore » their crystallinity and prevents complete oxidation, so that Co-core/CoO-shell structure is preserved even after 120 days. The crystal structure of CoO shell in both samples is different from its bulk counterpart. Implications of such distorted CoO shells on exchange bias are discussed. Coating of Co nanoparticles with amorphous silica shell makes them resistant to oxidation, but ultimately modifies the crystal structure of both Co core and SiO2 shell.« less

  7. Local structure preserving sparse coding for infrared target recognition

    PubMed Central

    Han, Jing; Yue, Jiang; Zhang, Yi; Bai, Lianfa

    2017-01-01

    Sparse coding performs well in image classification. However, robust target recognition requires a lot of comprehensive template images and the sparse learning process is complex. We incorporate sparsity into a template matching concept to construct a local sparse structure matching (LSSM) model for general infrared target recognition. A local structure preserving sparse coding (LSPSc) formulation is proposed to simultaneously preserve the local sparse and structural information of objects. By adding a spatial local structure constraint into the classical sparse coding algorithm, LSPSc can improve the stability of sparse representation for targets and inhibit background interference in infrared images. Furthermore, a kernel LSPSc (K-LSPSc) formulation is proposed, which extends LSPSc to the kernel space to weaken the influence of the linear structure constraint in nonlinear natural data. Because of the anti-interference and fault-tolerant capabilities, both LSPSc- and K-LSPSc-based LSSM can implement target identification based on a simple template set, which just needs several images containing enough local sparse structures to learn a sufficient sparse structure dictionary of a target class. Specifically, this LSSM approach has stable performance in the target detection with scene, shape and occlusions variations. High performance is demonstrated on several datasets, indicating robust infrared target recognition in diverse environments and imaging conditions. PMID:28323824

  8. Local Sparse Structure Denoising for Low-Light-Level Image.

    PubMed

    Han, Jing; Yue, Jiang; Zhang, Yi; Bai, Lianfa

    2015-12-01

    Sparse and redundant representations perform well in image denoising. However, sparsity-based methods fail to denoise low-light-level (LLL) images because of heavy and complex noise. They consider sparsity on image patches independently and tend to lose the texture structures. To suppress noises and maintain textures simultaneously, it is necessary to embed noise invariant features into the sparse decomposition process. We, therefore, used a local structure preserving sparse coding (LSPSc) formulation to explore the local sparse structures (both the sparsity and local structure) in image. It was found that, with the introduction of spatial local structure constraint into the general sparse coding algorithm, LSPSc could improve the robustness of sparse representation for patches in serious noise. We further used a kernel LSPSc (K-LSPSc) formulation, which extends LSPSc into the kernel space to weaken the influence of linear structure constraint in nonlinear data. Based on the robust LSPSc and K-LSPSc algorithms, we constructed a local sparse structure denoising (LSSD) model for LLL images, which was demonstrated to give high performance in the natural LLL images denoising, indicating that both the LSPSc- and K-LSPSc-based LSSD models have the stable property of noise inhibition and texture details preservation.

  9. Local structure preserving sparse coding for infrared target recognition.

    PubMed

    Han, Jing; Yue, Jiang; Zhang, Yi; Bai, Lianfa

    2017-01-01

    Sparse coding performs well in image classification. However, robust target recognition requires a lot of comprehensive template images and the sparse learning process is complex. We incorporate sparsity into a template matching concept to construct a local sparse structure matching (LSSM) model for general infrared target recognition. A local structure preserving sparse coding (LSPSc) formulation is proposed to simultaneously preserve the local sparse and structural information of objects. By adding a spatial local structure constraint into the classical sparse coding algorithm, LSPSc can improve the stability of sparse representation for targets and inhibit background interference in infrared images. Furthermore, a kernel LSPSc (K-LSPSc) formulation is proposed, which extends LSPSc to the kernel space to weaken the influence of the linear structure constraint in nonlinear natural data. Because of the anti-interference and fault-tolerant capabilities, both LSPSc- and K-LSPSc-based LSSM can implement target identification based on a simple template set, which just needs several images containing enough local sparse structures to learn a sufficient sparse structure dictionary of a target class. Specifically, this LSSM approach has stable performance in the target detection with scene, shape and occlusions variations. High performance is demonstrated on several datasets, indicating robust infrared target recognition in diverse environments and imaging conditions.

  10. Aluminum alloy material structure impact localization by using FBG sensors

    NASA Astrophysics Data System (ADS)

    Zhu, Xiubin

    2014-12-01

    The aluminum alloy structure impact localization system by using fiber Bragg grating (FBG) sensors and impact localization algorithm was investigated. A four-FBG sensing network was established. And the power intensity demodulation method was initialized employing the narrow-band tunable laser. The wavelet transform was used to weaken the impact signal noise. And the impact signal time difference was extracted to build the time difference localization algorithm. At last, a fiber Bragg grating impact localization system was established and experimentally verified. The experimental results showed that in the aluminum alloy plate with the 500 mm*500 mm*2 mm test area, the maximum and average impact abscissa localization errors were 11 mm and 6.25 mm, and the maximum and average impact ordinate localization errors were 9 mm and 4.25 mm, respectively. The fiber Bragg grating sensors and demodulation system are feasible to realize the aviation aluminum alloy material structure impact localization. The research results provide a reliable method for the aluminum alloy material structure impact localization.

  11. Local structures around the substituted elements in mixed layered oxides

    PubMed Central

    Akama, Shota; Kobayashi, Wataru; Amaha, Kaoru; Niwa, Hideharu; Nitani, Hiroaki; Moritomo, Yutaka

    2017-01-01

    The chemical substitution of a transition metal (M) is an effective method to improve the functionality of a material, such as its electrochemical, magnetic, and dielectric properties. The substitution, however, causes local lattice distortion because the difference in the ionic radius (r) modifies the local interatomic distances. Here, we systematically investigated the local structures in the pure (x = 0.0) and mixed (x = 0.05 or 0.1) layered oxides, Na(M1−xM′x)O2 (M and M′ are the majority and minority transition metals, respectively), by means of extended X-ray absorption fine structure (EXAFS) analysis. We found that the local interatomic distance (dM-O) around the minority element approaches that around the majority element to reduces the local lattice distortion. We further found that the valence of the minority Mn changes so that its ionic radius approaches that of the majority M. PMID:28252008

  12. Local structures around the substituted elements in mixed layered oxides

    NASA Astrophysics Data System (ADS)

    Akama, Shota; Kobayashi, Wataru; Amaha, Kaoru; Niwa, Hideharu; Nitani, Hiroaki; Moritomo, Yutaka

    2017-03-01

    The chemical substitution of a transition metal (M) is an effective method to improve the functionality of a material, such as its electrochemical, magnetic, and dielectric properties. The substitution, however, causes local lattice distortion because the difference in the ionic radius (r) modifies the local interatomic distances. Here, we systematically investigated the local structures in the pure (x = 0.0) and mixed (x = 0.05 or 0.1) layered oxides, Na(M1-xM‧x)O2 (M and M‧ are the majority and minority transition metals, respectively), by means of extended X-ray absorption fine structure (EXAFS) analysis. We found that the local interatomic distance (dM-O) around the minority element approaches that around the majority element to reduces the local lattice distortion. We further found that the valence of the minority Mn changes so that its ionic radius approaches that of the majority M.

  13. Two-dimensional localized structures in harmonically forced oscillatory systems

    NASA Astrophysics Data System (ADS)

    Ma, Y.-P.; Knobloch, E.

    2016-12-01

    Two-dimensional spatially localized structures in the complex Ginzburg-Landau equation with 1:1 resonance are studied near the simultaneous presence of a steady front between two spatially homogeneous equilibria and a supercritical Turing bifurcation on one of them. The bifurcation structures of steady circular fronts and localized target patterns are computed in the Turing-stable and Turing-unstable regimes. In particular, localized target patterns grow along the solution branch via ring insertion at the core in a process reminiscent of defect-mediated snaking in one spatial dimension. Stability of axisymmetric solutions on these branches with respect to axisymmetric and nonaxisymmetric perturbations is determined, and parameter regimes with stable axisymmetric oscillons are identified. Direct numerical simulations reveal novel depinning dynamics of localized target patterns in the radial direction, and of circular and planar localized hexagonal patterns in the fully two-dimensional system.

  14. Local Factors Determine Plant Community Structure on Closely Neighbored Islands

    PubMed Central

    Lu, Jianbo; Jiang, Lin; Yu, Lin; Sun, Que

    2011-01-01

    Despite the recent popularity of the metacommunity concept, ecologists have not evaluated the applicability of different metacommunity frameworks to insular organisms. We surveyed 50 closely spaced islands in the Thousand-Island Lake of China to examine the role of local (environmental) and regional (dispersal) factors in structuring woody plant assemblages (tree and shrub species) on these islands. By partitioning the variation in plant community structure into local and regional causes, we showed that local environmental conditions, specifically island morphometric characteristics, accounted for the majority of the variation in plant community structure among the studied islands. Spatial variables, representing the potential importance of species dispersal, explained little variation. We conclude that one metacommunity framework–species sorting–best characterizes these plant communities. This result reinforces the idea that the traditional approach of emphasizing the local perspective when studying ecological communities continues to hold its value. PMID:21572960

  15. Genetic Population Structure of the Ground Beetle, Pterostichus oblongopunctatus, Inhabiting a Fragmented and Polluted Landscape: Evidence for Sex-Biased Dispersal

    PubMed Central

    Lagisz, Malgorzata; Wolff, Kirsten; Sanderson, Roy A; Laskowski, Ryszard

    2010-01-01

    Ground beetles are an integral and functionally important part of many terrestrial ecosystems. Habitat change often influences population genetic structure of carabid beetles. In this study, genetic variation, population differentiation, and sex-specific dispersal patterns were studied in the forest ground beetle, Pterostichus oblongopunctatus F. (Coleoptera: Carabidae), in a fragmented and metal-polluted landscape to assess the consequences of human-induced changes on the population genetic structure. Genotypic variation at five microsatellite loci was screened in 309 beetles from 21 sample locations around zinc-and-lead smelter in southern Poland. Low levels of genetic differentiation among sampling sites were observed, suggesting high gene flow among populations. A negative correlation was found between levels of genetic differentiation and habitat patch size. No significant effects of metal pollution, in terms of genetic bottlenecks and genetic differentiation, were observed. Analyses revealed weak genetic clustering that is loosely tied to the geographic position of the sampled populations. Several tests of sex-biased dispersal were conducted. Most of them indicated male-biased dispersal. Differing levels of dispersal between females and males resulted in sex-specific spatial genetic patterns. Genetic differentiation was significantly correlated with geographical distance for males, but not for females, who were more diverged locally. Also, the effect of habitat patch size was sex-dependent, supporting the finding of different dispersal patterns between the sexes. This study demonstrated the application of microsatellite markers to answer questions regarding complex interactions between population structure and physical properties of the landscape. In the study system, migration appears to be sufficient to override potential effects of environmental pollution as well as habitat fragmentation. This investigation of population genetic structure indicated, for

  16. Fully automated localization of multiple pelvic bone structures on MRI.

    PubMed

    Onal, Sinan; Lai-Yuen, Susana; Bao, Paul; Weitzenfeld, Alfredo; Hart, Stuart

    2014-01-01

    In this paper, we present a fully automated localization method for multiple pelvic bone structures on magnetic resonance images (MRI). Pelvic bone structures are currently identified manually on MRI to identify reference points for measurement and evaluation of pelvic organ prolapse (POP). Given that this is a time-consuming and subjective procedure, there is a need to localize pelvic bone structures without any user interaction. However, bone structures are not easily differentiable from soft tissue on MRI as their pixel intensities tend to be very similar. In this research, we present a model that automatically identifies the bounding boxes of the bone structures on MRI using support vector machines (SVM) based classification and non-linear regression model that captures global and local information. Based on the relative locations of pelvic bones and organs, and local information such as texture features, the model identifies the location of the pelvic bone structures by establishing the association between their locations. Results show that the proposed method is able to locate the bone structures of interest accurately. The pubic bone, sacral promontory, and coccyx were correctly detected (DSI > 0.75) in 92%, 90%, and 88% of the testing images. This research aims to enable accurate, consistent and fully automated identification of pelvic bone structures on MRI to facilitate and improve the diagnosis of female pelvic organ prolapse.

  17. Non Linear Optimization Applied to Angle-Of Satellite Based Geo-Localization for Biased and Time-Drifting Sensors

    NASA Astrophysics Data System (ADS)

    Levy, Daniel; Roos, Jason; Robinson, Jace; Carpenter, William; Martin, Richard; Taylor, Clark; Sugrue, Joseph; Terzuoli, Andrew

    2016-06-01

    Multiple sensors are used in a variety of geolocation systems. Many use Time Difference of Arrival (TDOA) or Received Signal Strength (RSS) measurements to estimate the most likely location of a signal. When an object does not emit an RF signal, Angle of Arrival (AOA) measurements using optical or infrared frequencies become more feasible than TDOA or RSS measurements. AOA measurements can be created from any sensor platform with any sort of optical sensor, location and attitude knowledge to track passive objects. Previous work has created a non-linear optimization (NLO) method for calculating the most likely estimate from AOA measurements. Two new modifications to the NLO algorithm are created and shown to correct AOA measurement errors by estimating the inherent bias and time-drift in the Inertial Measurement Unit (IMU) of the AOA sensing platform. One method corrects the sensor bias in post processing while treating the NLO method as a module. The other method directly corrects the sensor bias within the NLO algorithm by incorporating the bias parameters as a state vector in the estimation process. These two methods are analyzed using various Monte-Carlo simulations to check the general performance of the two modifications in comparison to the original NLO algorithm.

  18. Vortex emission accompanies the advection of optical localized structures.

    PubMed

    Haudin, F; Rojas, R G; Bortolozzo, U; Clerc, M G; Residori, S

    2011-02-11

    We show that the advection of optical localized structures is accompanied by the emission of vortices, with phase singularities appearing in the wake of the drifting structure. Localized structures are obtained in a light-valve experiment and made to drift by a mirror tilt in the feedback loop. Pairs of oppositely charged vortices are detected for small drifts, whereas for large drifts a vortex array develops. Observations are supported by numerical simulations and linear stability analysis of the system equations and are expected to be generic for a large class of translated optical patterns.

  19. Deriving quantum theory from its local structure and reversibility.

    PubMed

    de la Torre, Gonzalo; Masanes, Lluís; Short, Anthony J; Müller, Markus P

    2012-08-31

    We investigate the class of physical theories with the same local structure as quantum theory but potentially different global structure. It has previously been shown that any bipartite correlations generated by such a theory can be simulated in quantum theory but that this does not hold for tripartite correlations. Here we explore whether imposing an additional constraint on this space of theories-that of dynamical reversibility-will allow us to recover the global quantum structure. In the particular case in which the local systems are identical qubits, we show that any theory admitting at least one continuous reversible interaction must be identical to quantum theory.

  20. Structure of local interactions in complex financial dynamics

    PubMed Central

    Jiang, X. F.; Chen, T. T.; Zheng, B.

    2014-01-01

    With the network methods and random matrix theory, we investigate the interaction structure of communities in financial markets. In particular, based on the random matrix decomposition, we clarify that the local interactions between the business sectors (subsectors) are mainly contained in the sector mode. In the sector mode, the average correlation inside the sectors is positive, while that between the sectors is negative. Further, we explore the time evolution of the interaction structure of the business sectors, and observe that the local interaction structure changes dramatically during a financial bubble or crisis. PMID:24936906

  1. Impact of biased scores on ranking in bipartite competition networks and inference of modular structure via generalized modularity

    NASA Astrophysics Data System (ADS)

    Jeon, Gyuhyeon; Park, Juyong

    2017-02-01

    In the common jury-contestant competition format, a jury consisting of multiple judges grade contestants on their performances to determine their ranking. Unlike in another common competition format where two contestants play a head-to-head match to produce the winner such as in football or basketball, the objectivity of judges are often called into question, potentially undermining the public's trust in the fairness of the competition. In this work we show, by modeling the jury-contestant competition format as a weighted bipartite network, how one can identify biased scores and how they impact the competition and its structure. Analyzing the prestigious International Chopin Piano Competition of 2015 as an example with a well-publicized scoring controversy, we show that the presence of even a very small fraction of biased edges can gravely distort our inference of the network structure —in the example a single biased edge is shown to lead to an incorrect “solution” that also wrongly appears to be robust exclusively, dominating other reasonable solutions— highlighting the importance of bias detection and elimination in network inference. In the process our work also presents a modified modularity measure for the one-mode projection of weighted complete bipartite networks.

  2. Geometrical Structure and Interface Dependence of Bias Stress Induced Threshold Voltage Shift in C60-Based OFETs

    PubMed Central

    2014-01-01

    The influence of the nature of interface between organic semiconductor and gate dielectric on bias stress electrical stability of n-type C60-based organic field effect transistors (OFETs) was studied. The bias stress induced threshold voltage (Vth) shift was found to depend critically on the OFET device structure: the direction of Vth shift in top-gate OFETs was opposite to that in bottom-gate OFETs, while the use of the dual-gate OFET structure resulted in just very small variations in Vth. The opposite direction of Vth shift is attributed to the different nature of interfaces between C60 semiconductor and Parylene dielectric in these devices. The Vth shift to more positive voltages upon bias stress in bottom-gate C60-OFET was similar to that observed for other n-type semiconductors and rationalized by electron trapping in the dielectric or at the gate dielectric/C60 interface. The opposite direction of Vth shift in top-gate C60-OFETs is attributed to free radical species created in the course of Parylene deposition on the surface of C60 during device fabrication, which produce plenty of hole traps. It was also realized that the dual-gate OFETs gives stable characteristics, which are immune to bias stress effects. PMID:25142130

  3. Alignment-free local structural search by writhe decomposition.

    PubMed

    Zhi, Degui; Shatsky, Maxim; Brenner, Steven E

    2010-05-01

    Rapid methods for protein structure search enable biological discoveries based on flexibly defined structural similarity, unleashing the power of the ever greater number of solved protein structures. Projection methods show promise for the development of fast structural database search solutions. Projection methods map a structure to a point in a high-dimensional space and compare two structures by measuring distance between their projected points. These methods offer a tremendous increase in speed over residue-level structural alignment methods. However, current projection methods are not practical, partly because they are unable to identify local similarities. We propose a new projection-based approach that can rapidly detect global as well as local structural similarities. Local structural search is enabled by a topology-inspired writhe decomposition protocol that produces a small number of fragments while ensuring that similar structures are cut in a similar manner. In benchmark tests, we show that our method, writher, improves accuracy over existing projection methods in terms of recognizing scop domains out of multi-domain proteins, while maintaining accuracy comparable with existing projection methods in a standard single-domain benchmark test. The source code is available at the following website: http://compbio.berkeley.edu/proj/writher/.

  4. Reconstruction of biofilm images: combining local and global structural parameters

    SciTech Connect

    Resat, Haluk; Renslow, Ryan S.; Beyenal, Haluk

    2014-10-20

    Digitized images can be used for quantitative comparison of biofilms grown under different conditions. Using biofilm image reconstruction, it was previously found that biofilms with a completely different look can have nearly identical structural parameters and that the most commonly utilized global structural parameters were not sufficient to uniquely define these biofilms. Here, additional local and global parameters are introduced to show that these parameters considerably increase the reliability of the image reconstruction process. Assessment using human evaluators indicated that the correct identification rate of the reconstructed images increased from 50% to 72% with the introduction of the new parameters into the reconstruction procedure. An expanded set of parameters especially improved the identification of biofilm structures with internal orientational features and of structures in which colony sizes and spatial locations varied. Hence, the newly introduced structural parameter sets helped to better classify the biofilms by incorporating finer local structural details into the reconstruction process.

  5. Local thermal energy as a structural indicator in glasses

    NASA Astrophysics Data System (ADS)

    Zylberg, Jacques; Lerner, Edan; Bar-Sinai, Yohai; Bouchbinder, Eran

    2017-07-01

    Identifying heterogeneous structures in glasses—such as localized soft spots—and understanding structure-dynamics relations in these systems remain major scientific challenges. Here, we derive an exact expression for the local thermal energy of interacting particles (the mean local potential energy change caused by thermal fluctuations) in glassy systems by a systematic low-temperature expansion. We show that the local thermal energy can attain anomalously large values, inversely related to the degree of softness of localized structures in a glass, determined by a coupling between internal stresses—an intrinsic signature of glassy frustration—anharmonicity and low-frequency vibrational modes. These anomalously large values follow a fat-tailed distribution, with a universal exponent related to the recently observed universal ω4ω4 density of states of quasilocalized low-frequency vibrational modes. When the spatial thermal energy field—a “softness field”—is considered, this power law tail manifests itself by highly localized spots, which are significantly softer than their surroundings. These soft spots are shown to be susceptible to plastic rearrangements under external driving forces, having predictive powers that surpass those of the normal modes-based approach. These results offer a general, system/model-independent, physical/observable-based approach to identify structural properties of quiescent glasses and relate them to glassy dynamics.

  6. Local thermal energy as a structural indicator in glasses.

    PubMed

    Zylberg, Jacques; Lerner, Edan; Bar-Sinai, Yohai; Bouchbinder, Eran

    2017-07-11

    Identifying heterogeneous structures in glasses-such as localized soft spots-and understanding structure-dynamics relations in these systems remain major scientific challenges. Here, we derive an exact expression for the local thermal energy of interacting particles (the mean local potential energy change caused by thermal fluctuations) in glassy systems by a systematic low-temperature expansion. We show that the local thermal energy can attain anomalously large values, inversely related to the degree of softness of localized structures in a glass, determined by a coupling between internal stresses-an intrinsic signature of glassy frustration-anharmonicity and low-frequency vibrational modes. These anomalously large values follow a fat-tailed distribution, with a universal exponent related to the recently observed universal [Formula: see text] density of states of quasilocalized low-frequency vibrational modes. When the spatial thermal energy field-a "softness field"-is considered, this power law tail manifests itself by highly localized spots, which are significantly softer than their surroundings. These soft spots are shown to be susceptible to plastic rearrangements under external driving forces, having predictive powers that surpass those of the normal modes-based approach. These results offer a general, system/model-independent, physical/observable-based approach to identify structural properties of quiescent glasses and relate them to glassy dynamics.

  7. Dynamic quasi-energy-band modulation and exciton effects in biased superlattices driven by a two-color far-infrared field: Disappearance of dynamic localization

    NASA Astrophysics Data System (ADS)

    Yashima, Kenta; Hino, Ken-Ichi; Toshima, Nobuyuki

    2003-12-01

    A theoretical study of the optical and electronic properties of semiconductor superlattices in ac-dc fields, termed the dynamic Wannier-Stark ladder (DWSL), is done. The biased superlattices are driven by two far-infrared fields with different frequencies and relative phase of δ. Here, the frequency of the first laser is equal to the Bloch frequency ωB of the system under study, while that of the second laser is equal to 2ωB. Quasienergies of the DWSL are calculated based on the Floquet theorem, and the associated linear photoabsorption spectra are evaluated. For δ=0, a gourd-shaped quasi-energy structure characteristic of both dynamic localization (DL) and delocalization (DDL), similar to the usual DWSL driven by a single laser, appears. By changing the ratio of the two laser strengths, however, the width of the quasi-energy band and the locations of both DL and DDL vary noticeably. As for δ≠0, on the other hand, band collapse and the associated DL do not necessarily follow. In fact, DL vanishes and the quasi-energy degeneracy is lifted in a certain range of δ. Just DDL remains over the entire range of the laser strength, eventually resulting in a plateaulike band structure in the linear absorption spectra. The basic physics underlying this phenomenon, which can be readily interpreted in terms of a closed analytical expression, is that all quasi-energies for given crystal momenta are out of phase with each other as a function of laser strength without converging to a single point of energy. This is a feature of this DWSL which sharply distinguishes it from a conventional DWSL generated using a single laser to drive it. Furthermore, an exciton effect is incorporated with the above noninteracting problem, so that exciton dressed states are formed. It is found that this effect gives rise to more involved quasi-energy structures and a more pronounced release of the energy degeneracy of DL, leading again to the formation of a band structure in the absorption

  8. Protein domain assignment from the recurrence of locally similar structures

    PubMed Central

    Tai, Chin-Hsien; Sam, Vichetra; Gibrat, Jean-Francois; Garnier, Jean; Munson, Peter J.

    2010-01-01

    Domains are basic units of protein structure and essential for exploring protein fold space and structure evolution. With the structural genomics initiative, the number of protein structures in the Protein Databank (PDB) is increasing dramatically and domain assignments need to be done automatically. Most existing structural domain assignment programs define domains using the compactness of the domains and/or the number and strength of intra-domain versus inter-domain contacts. Here we present a different approach based on the recurrence of locally similar structural pieces (LSSPs) found by one-against-all structure comparisons with a dataset of 6,373 protein chains from the PDB. Residues of the query protein are clustered using LSSPs via three different procedures to define domains. This approach gives results that are comparable to several existing programs that use geometrical and other structural information explicitly. Remarkably, most of the proteins that contribute the LSSPs defining a domain do not themselves contain the domain of interest. This study shows that domains can be defined by a collection of relatively small locally similar structural pieces containing, on average, four secondary structure elements. In addition, it indicates that domains are indeed made of recurrent small structural pieces that are used to build protein structures of many different folds as suggested by recent studies. PMID:21287617

  9. A local difference in Hedgehog signal transduction increases mechanical cell bond tension and biases cell intercalations along the Drosophila anteroposterior compartment boundary.

    PubMed

    Rudolf, Katrin; Umetsu, Daiki; Aliee, Maryam; Sui, Liyuan; Jülicher, Frank; Dahmann, Christian

    2015-11-15

    Tissue organization requires the interplay between biochemical signaling and cellular force generation. The formation of straight boundaries separating cells with different fates into compartments is important for growth and patterning during tissue development. In the developing Drosophila wing disc, maintenance of the straight anteroposterior (AP) compartment boundary involves a local increase in mechanical tension at cell bonds along the boundary. The biochemical signals that regulate mechanical tension along the AP boundary, however, remain unknown. Here, we show that a local difference in Hedgehog signal transduction activity between anterior and posterior cells is necessary and sufficient to increase mechanical tension along the AP boundary. This difference in Hedgehog signal transduction is also required to bias cell rearrangements during cell intercalations to keep the characteristic straight shape of the AP boundary. Moreover, severing cell bonds along the AP boundary does not reduce tension at neighboring bonds, implying that active mechanical tension is upregulated, cell bond by cell bond. Finally, differences in the expression of the homeodomain-containing protein Engrailed also contribute to the straight shape of the AP boundary, independently of Hedgehog signal transduction and without modulating cell bond tension. Our data reveal a novel link between local differences in Hedgehog signal transduction and a local increase in active mechanical tension of cell bonds that biases junctional rearrangements. The large-scale shape of the AP boundary thus emerges from biochemical signals inducing patterns of active tension on cell bonds. © 2015. Published by The Company of Biologists Ltd.

  10. Quantitative imaging of local defects in very thin silicon dioxide films at low bias voltage by true oxide electron-beam-induced current

    NASA Astrophysics Data System (ADS)

    Lau, W. S.; Chan, D. S. H.; Phang, J. C. H.; Chow, K. W.; Pey, K. S.; Lim, Y. P.; Sane, V.; Cronquist, B.

    1995-01-01

    A new low-voltage contrast mechanism due to electron-hole pairs generated in the oxide by an electron beam was observed at electric fields lower than 3.5 MV/cm. This is in addition to the tunneling current microscopy (TCM) contrast mechanism observed at electric fiels higher than 3.5 MV/cm. The new contrast mechanism is opposite in sign to the TCM contrast mechanism such that the image of a local thinning defect in the oxide is dark at low bias voltage and bright at higher bias voltage. Good contrast can be obtained at electric field as low as 2.4 MV/cm. Applications include large area imaging of oxide defects and quantitative mapping of small oxide thickness variations.

  11. Effect of substrate bias on the structural and electrical properties of sputtered Mo thin films on flexible substrates.

    PubMed

    Xu, Jiaxiong

    2016-07-04

    The metal molybdenum (Mo) thin films deposited on flexible substrates can act as the contact electrode of flexible Cu(In,Ga)Se2 or Cu2ZnSn(S,Se)4 solar cells. In this work, in order to enhance the structural and electrical characteristics of flexible Mo thin films, a negative substrate bias was applied during the direct current sputtering of Mo thin films. The flexible substrates used for growing the Mo films were stainless steel foils and polyimides. The characteristics of Mo thin films were studied by x-ray diffraction and sheet resistance measurements. The measured results reveal that an optimal value of negative substrate bias can be found for improving the electrical and structural characteristics of Mo thin films on flexible substrates. The minimum sheet resistances of Mo thin films are 2.50 Ω/sq and 2.73 Ω/sq for the stainless steel foil and polyimide substrates, respectively.

  12. Influence of bias voltage on structural and optical properties of TiN{sub x} thin films

    SciTech Connect

    Singh, Omveer; Dahiya, Raj P.; Malik, Hitendra K.; Kumar, Parmod

    2015-08-28

    In the present work, Ti thin films were deposited on Si substrate using DC sputtering technique. Indigenous hot cathode arc discharge plasma system was used for nitriding over these samples, where the plasma parameters and work piece can be controlled independently. A mixture of H{sub 2} and N{sub 2} gases (in the ratio of 80:20) was supplied into the plasma chamber. The effect of bias voltage on the crystal structure, morphology and optical properties was investigated by employing various physical techniques such as X-ray Diffraction, Atomic Force Microscopy and UV-Vis spectrometry. It was found that bias voltage affects largely the crystal structure and band gap which in turn is responsible for the modifications in optical properties of the deposited films.

  13. Observation of pure inverse spin Hall effect in ferromagnetic metals via ferromagnetic/antiferromagnetic exchange-bias structures

    NASA Astrophysics Data System (ADS)

    Wu, H.; Wan, C. H.; Yuan, Z. H.; Zhang, X.; Jiang, J.; Zhang, Q. T.; Wen, Z. C.; Han, X. F.

    2015-08-01

    We report that the spin current generated by the spin Seebeck effect (SSE) in yttrium iron garnet (YIG) can be detected by a ferromagnetic metal (NiFe). By using the ferromagnetic/antiferromagnetic (FM/AFM) exchange bias structure (NiFe/IrMn), the inverse spin Hall effect (ISHE) and planar Nernst effect (PNE) of NiFe can be unambiguously separated, allowing us to observe a pure ISHE signal. After eliminating the in-plane temperature gradient in NiFe, we can even observe a pure ISHE signal without PNE from NiFe itself. It is worth noting that a large spin Hall angle (0.098) of NiFe is obtained, which is comparable with Pt. This work provides a kind of FM/AFM exchange bias structure to detect the spin current by charge signals, and highlights that ISHE in ferromagnetic metals can be used in spintronic research and applications.

  14. Local structure and polarization in Pb containing ferroelectric oxides

    NASA Astrophysics Data System (ADS)

    Egami, T.; Dmowski, W.; Akbas, M.; Davies, P. K.

    1998-06-01

    While the Pb containing ferroelectric and antiferroelectric oxides show a large variety in crystal structure, the pulsed neutron atomic pair-distribution function (PDF) studies indicate that their local atomic structures are surprisingly similar to each other. In particular the environment of Pb is nearly independent of composition, with Pb being strongly off-centered in the PbO12 cluster, resulting in a large local polarization. A new model is proposed to describe the interplay between the Pb polarization and the random local structural fluctuation. This model explains the relaxor ferroelectricity from a general point of view, while other models such as nano-domain space charge model and the random field model were introduced specifically for hetero-valent systems such as Pb(Mg1/3Nb2/3)O3 (PMN).

  15. Strain localization and percolation of stable structure in amorphous solids.

    PubMed

    Shi, Yunfeng; Falk, Michael L

    2005-08-26

    Spontaneous strain localization occurs during mechanical tests of a model amorphous solid simulated using molecular dynamics. The degree of localization depends upon the extent of structural relaxation prior to mechanical testing. In the most rapidly quenched samples higher strain rates lead to increased localization, while the more gradually quenched samples exhibit the opposite strain rate dependence. This transition coincides with the k-core percolation of atoms with quasi-crystal-like short range order. The authors infer the existence of a related microstructural length scale.

  16. Local and sex-specific biases in crossover vs. noncrossover outcomes at meiotic recombination hot spots in mice

    PubMed Central

    de Boer, Esther; Jasin, Maria; Keeney, Scott

    2015-01-01

    Meiotic recombination initiated by programmed double-strand breaks (DSBs) yields two types of interhomolog recombination products, crossovers and noncrossovers, but what determines whether a DSB will yield a crossover or noncrossover is not understood. In this study, we analyzed the influence of sex and chromosomal location on mammalian recombination outcomes by constructing fine-scale recombination maps in both males and females at two mouse hot spots located in different regions of the same chromosome. These include the most comprehensive maps of recombination hot spots in oocytes to date. One hot spot, located centrally on chromosome 1, behaved similarly in male and female meiosis: Crossovers and noncrossovers formed at comparable levels and ratios in both sexes. In contrast, at a distal hot spot, crossovers were recovered only in males even though noncrossovers were obtained at similar frequencies in both sexes. These findings reveal an example of extreme sex-specific bias in recombination outcome. We further found that estimates of relative DSB levels are surprisingly poor predictors of relative crossover frequencies between hot spots in males. Our results demonstrate that the outcome of mammalian meiotic recombination can be biased, that this bias can vary depending on location and cellular context, and that DSB frequency is not the only determinant of crossover frequency. PMID:26251527

  17. Local and sex-specific biases in crossover vs. noncrossover outcomes at meiotic recombination hot spots in mice.

    PubMed

    de Boer, Esther; Jasin, Maria; Keeney, Scott

    2015-08-15

    Meiotic recombination initiated by programmed double-strand breaks (DSBs) yields two types of interhomolog recombination products, crossovers and noncrossovers, but what determines whether a DSB will yield a crossover or noncrossover is not understood. In this study, we analyzed the influence of sex and chromosomal location on mammalian recombination outcomes by constructing fine-scale recombination maps in both males and females at two mouse hot spots located in different regions of the same chromosome. These include the most comprehensive maps of recombination hot spots in oocytes to date. One hot spot, located centrally on chromosome 1, behaved similarly in male and female meiosis: Crossovers and noncrossovers formed at comparable levels and ratios in both sexes. In contrast, at a distal hot spot, crossovers were recovered only in males even though noncrossovers were obtained at similar frequencies in both sexes. These findings reveal an example of extreme sex-specific bias in recombination outcome. We further found that estimates of relative DSB levels are surprisingly poor predictors of relative crossover frequencies between hot spots in males. Our results demonstrate that the outcome of mammalian meiotic recombination can be biased, that this bias can vary depending on location and cellular context, and that DSB frequency is not the only determinant of crossover frequency.

  18. How structural adaptability exists alongside HLA-A2 bias in the human αβ TCR repertoire

    PubMed Central

    Blevins, Sydney J.; Pierce, Brian G.; Singh, Nishant K.; Riley, Timothy P.; Wang, Yuan; Spear, Timothy T.; Nishimura, Michael I.; Weng, Zhiping; Baker, Brian M.

    2016-01-01

    How T-cell receptors (TCRs) can be intrinsically biased toward MHC proteins while simultaneously display the structural adaptability required to engage diverse ligands remains a controversial puzzle. We addressed this by examining αβ TCR sequences and structures for evidence of physicochemical compatibility with MHC proteins. We found that human TCRs are enriched in the capacity to engage a polymorphic, positively charged “hot-spot” region that is almost exclusive to the α1-helix of the common human class I MHC protein, HLA-A*0201 (HLA-A2). TCR binding necessitates hot-spot burial, yielding high energetic penalties that must be offset via complementary electrostatic interactions. Enrichment of negative charges in TCR binding loops, particularly the germ-line loops encoded by the TCR Vα and Vβ genes, provides this capacity and is correlated with restricted positioning of TCRs over HLA-A2. Notably, this enrichment is absent from antibody genes. The data suggest a built-in TCR compatibility with HLA-A2 that biases receptors toward, but does not compel, particular binding modes. Our findings provide an instructional example for how structurally pliant MHC biases can be encoded within TCRs. PMID:26884163

  19. Using Category Structures to Test Iterated Learning as a Method for Identifying Inductive Biases

    ERIC Educational Resources Information Center

    Griffiths, Thomas L.; Christian, Brian R.; Kalish, Michael L.

    2008-01-01

    Many of the problems studied in cognitive science are inductive problems, requiring people to evaluate hypotheses in the light of data. The key to solving these problems successfully is having the right inductive biases--assumptions about the world that make it possible to choose between hypotheses that are equally consistent with the observed…

  20. Analysis of Latino populations from GALA and MEC studies reveals genomic loci with biased local ancestry estimation

    PubMed Central

    Pasaniuc, Bogdan; Sankararaman, Sriram; Torgerson, Dara G.; Gignoux, Christopher; Zaitlen, Noah; Eng, Celeste; Rodriguez-Cintron, William; Chapela, Rocio; Ford, Jean G.; Avila, Pedro C.; Rodriguez-Santana, Jose; Chen, Gary K.; Le Marchand, Loic; Henderson, Brian; Reich, David; Haiman, Christopher A.; Gonzàlez Burchard, Esteban; Halperin, Eran

    2013-01-01

    Motivation: Local ancestry analysis of genotype data from recently admixed populations (e.g. Latinos, African Americans) provides key insights into population history and disease genetics. Although methods for local ancestry inference have been extensively validated in simulations (under many unrealistic assumptions), no empirical study of local ancestry accuracy in Latinos exists to date. Hence, interpreting findings that rely on local ancestry in Latinos is challenging. Results: Here, we use 489 nuclear families from the mainland USA, Puerto Rico and Mexico in conjunction with 3204 unrelated Latinos from the Multiethnic Cohort study to provide the first empirical characterization of local ancestry inference accuracy in Latinos. Our approach for identifying errors does not rely on simulations but on the observation that local ancestry in families follows Mendelian inheritance. We measure the rate of local ancestry assignments that lead to Mendelian inconsistencies in local ancestry in trios (MILANC), which provides a lower bound on errors in the local ancestry estimates. We show that MILANC rates observed in simulations underestimate the rate observed in real data, and that MILANC varies substantially across the genome. Second, across a wide range of methods, we observe that loci with large deviations in local ancestry also show enrichment in MILANC rates. Therefore, local ancestry estimates at such loci should be interpreted with caution. Finally, we reconstruct ancestral haplotype panels to be used as reference panels in local ancestry inference and show that ancestry inference is significantly improved by incoroprating these reference panels. Availability and implementation: We provide the reconstructed reference panels together with the maps of MILANC rates as a public resource for researchers analyzing local ancestry in Latinos at http://bogdanlab.pathology.ucla.edu. Contact: bpasaniuc@mednet.ucla.edu Supplementary information: Supplementary data are

  1. Local function conservation in sequence and structure space.

    PubMed

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

    2008-07-04

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

  2. Charge movement in a GaN-based hetero-structure field effect transistor structure with carbon doped buffer under applied substrate bias

    SciTech Connect

    Pooth, Alexander; Uren, Michael J.; Cäsar, Markus; Kuball, Martin; Martin, Trevor

    2015-12-07

    Charge trapping and transport in the carbon doped GaN buffer of a GaN-based hetero-structure field effect transistor (HFET) has been investigated under both positive and negative substrate bias. Clear evidence of redistribution of charges in the carbon doped region by thermally generated holes is seen, with electron injection and capture observed during positive bias. Excellent agreement is found with simulations. It is shown that these effects are intrinsic to the carbon doped GaN and need to be controlled to provide reliable and efficient GaN-based power HFETs.

  3. Stabilizing hierarchical compensation for locally controlled large flexible structures

    NASA Technical Reports Server (NTRS)

    Das, B.; Balas, M.

    1989-01-01

    A two-level hierarchical control strategy is proposed for large flexible space structures. The lower level consists of a set of local controllers. The higher level is a stabilizing compensator to account for any instabilities caused by controller-structure interaction with unmodeled dynamics. The advantage of this hierarchical strategy is that the lower level can be designed to meet the performance requirements, and the higher level can be designed independently to produce overall stability.

  4. Local structure analysis in ab initio liquid water

    NASA Astrophysics Data System (ADS)

    Santra, Biswajit; DiStasio, Robert A., Jr.; Martelli, Fausto; Car, Roberto

    2015-09-01

    Within the framework of density functional theory, the inclusion of exact exchange and non-local van der Waals/dispersion (vdW) interactions is crucial for predicting a microscopic structure of ambient liquid water that quantitatively agrees with experiment. In this work, we have used the local structure index (LSI) order parameter to analyse the local structure in such highly accurate ab initio liquid water. At ambient conditions, the LSI probability distribution, P(I ), was unimodal with most water molecules characterised by more disordered high-density-like local environments. With thermal excitations removed, the resultant bimodal P(I ) in the inherent potential energy surface (IPES) exhibited a 3:1 ratio between high-density- and low-density-like molecules, with the latter forming small connected clusters amid the predominant population. By considering the spatial correlations and hydrogen bond network topologies among water molecules with the same LSI identities, we demonstrate that the signatures of the experimentally observed low- and high-density amorphous phases of ice are present in the IPES of ambient liquid water. Analysis of the LSI autocorrelation function uncovered a persistence time of ∼ 4 ps - a finding consistent with the fact that natural thermal fluctuations are responsible for transitions between these distinct yet transient local aqueous environments in ambient liquid water.

  5. How lasing localized structures evolve out of passive mode locking.

    PubMed

    Marconi, M; Javaloyes, J; Balle, S; Giudici, M

    2014-06-06

    We investigate the relationship between passive mode locking and the formation of time-localized structures in the output intensity of a laser. We show how the mode-locked pulses transform into lasing localized structures, allowing for individual addressing and arbitrary low repetition rates. Our analysis reveals that this occurs when (i) the cavity round-trip is much larger than the slowest medium time scale, namely the gain recovery time, and (ii) the mode-locked solution coexists with the zero intensity (off) solution. These conditions enable the coexistence of a large quantity of stable solutions, each of them being characterized by a different number of pulses per round-trip and with different arrangements. Then, each mode-locked pulse becomes localized, i.e., individually addressable.

  6. One Single Static Measurement Predicts Wave Localization in Complex Structures.

    PubMed

    Lefebvre, Gautier; Gondel, Alexane; Dubois, Marc; Atlan, Michael; Feppon, Florian; Labbé, Aimé; Gillot, Camille; Garelli, Alix; Ernoult, Maxence; Mayboroda, Svitlana; Filoche, Marcel; Sebbah, Patrick

    2016-08-12

    A recent theoretical breakthrough has brought a new tool, called the localization landscape, for predicting the localization regions of vibration modes in complex or disordered systems. Here, we report on the first experiment which measures the localization landscape and demonstrates its predictive power. Holographic measurement of the static deformation under uniform load of a thin plate with complex geometry provides direct access to the landscape function. When put in vibration, this system shows modes precisely confined within the subregions delineated by the landscape function. Also the maxima of this function match the measured eigenfrequencies, while the minima of the valley network gives the frequencies at which modes become extended. This approach fully characterizes the low frequency spectrum of a complex structure from a single static measurement. It paves the way for controlling and engineering eigenmodes in any vibratory system, especially where a structural or microscopic description is not accessible.

  7. Renormalized halo bias

    SciTech Connect

    Assassi, Valentin; Baumann, Daniel; Green, Daniel; Zaldarriaga, Matias E-mail: dbaumann@damtp.cam.ac.uk E-mail: matiasz@ias.edu

    2014-08-01

    This paper provides a systematic study of renormalization in models of halo biasing. Building on work of McDonald, we show that Eulerian biasing is only consistent with renormalization if non-local terms and higher-derivative contributions are included in the biasing model. We explicitly determine the complete list of required bias parameters for Gaussian initial conditions, up to quartic order in the dark matter density contrast and at leading order in derivatives. At quadratic order, this means including the gravitational tidal tensor, while at cubic order the velocity potential appears as an independent degree of freedom. Our study naturally leads to an effective theory of biasing in which the halo density is written as a double expansion in fluctuations and spatial derivatives. We show that the bias expansion can be organized in terms of Galileon operators which aren't renormalized at leading order in derivatives. Finally, we discuss how the renormalized bias parameters impact the statistics of halos.

  8. Local Structure of CuIn3Se5

    SciTech Connect

    Chang, C. H.; Wei, S. H.; Leyarovska, N.; Johnson, J. W.; Zhang, S. B.; Stanbery, B. J.; Anderson, T. J.

    2000-01-01

    The results of a detailed EXAFS study of the Cu-K, In-K, and Se-K edges CuIn3Se5 are reported. The Cu and In first nearest neighbor local structures were found to be almost identical to those in CuInSe2.

  9. The Changing Market Structure of Local Television News.

    ERIC Educational Resources Information Center

    Powers, Angela

    The growth in competition for revenues, along with the advent of cable, independent television and video cassette recorders (VCR), may signify a change in the market structure of local television news. To explain if and how this change may be occurring, an explanation of economic theory as well as evidence from "Broadcast and Cable…

  10. Constrained spectral clustering under a local proximity structure assumption

    NASA Technical Reports Server (NTRS)

    Wagstaff, Kiri; Xu, Qianjun; des Jardins, Marie

    2005-01-01

    This work focuses on incorporating pairwise constraints into a spectral clustering algorithm. A new constrained spectral clustering method is proposed, as well as an active constraint acquisition technique and a heuristic for parameter selection. We demonstrate that our constrained spectral clustering method, CSC, works well when the data exhibits what we term local proximity structure.

  11. Local structure of numerically generated worm hole spacetime.

    NASA Astrophysics Data System (ADS)

    Siino, M.

    The author investigates the evolution of the apparent horizons in a numerically gererated worm hole spacetime. The behavior of the apparent horizons is affected by the dynamics of the matter field. By using the local mass of the system, he interprets the evolution of the worm hole structure.

  12. Structures of Participation in the "University of Local Knowledge"

    ERIC Educational Resources Information Center

    Evans, Penny; Irish, Sharon

    2013-01-01

    "Structures of Participation" concerns a recent media arts project, the University of Local Knowledge (ULK). ULK is simultaneously a critique of established academic institutions and disciplines and a system for self-organized learning among the residents of Knowle West, an area of south Bristol (UK). Beginning in 2009, the Knowle West…

  13. Structure and interfacial analysis of nanoscale TiNi thin film prepared by biased target ion beam deposition

    SciTech Connect

    Hou, Huilong; Hamilton, Reginald F. Horn, Mark W.

    2015-07-15

    Ultrathin, 65 nm thick, TiNi alloy films were fabricated by cosputtering Ti and Ni targets using the recently developed biased target ion beam deposition technique. Preheating the substrate by exposure to a low energy ion source resulted in as-deposited films with a pure B2 atomic crystal structure containing no secondary crystal structures or precipitates. Continuous films were produced with a smooth surface and minimal substrate/film interfacial diffusion. The diffusion layer was a small ratio of film thickness, which is a prerequisite for the B2 phase to undergo the martensitic transformation in ultrathin films.

  14. A novel integrated structure with a radial displacement sensor and a permanent magnet biased radial magnetic bearing.

    PubMed

    Sun, Jinji; Zhang, Yin

    2014-01-24

    In this paper, a novel integrated structure is proposed in order to reduce the axial length of the high speed of a magnetically suspended motor (HSMSM) to ensure the maximum speed, which combines radial displacement sensor probes and the permanent magnet biased radial magnetic bearing in HSMSM. The sensor probes are integrated in the magnetic bearing, and the sensor preamplifiers are placed in the control system of the HSMSM, separate from the sensor probes. The proposed integrated structure can save space in HSMSMs, improve the working frequency, reduce the influence of temperature on the sensor circuit, and improve the stability of HSMSMs.

  15. A Novel Integrated Structure with a Radial Displacement Sensor and a Permanent Magnet Biased Radial Magnetic Bearing

    PubMed Central

    Sun, Jinji; Zhang, Yin

    2014-01-01

    In this paper, a novel integrated structure is proposed in order to reduce the axial length of the high speed of a magnetically suspended motor (HSMSM) to ensure the maximum speed, which combines radial displacement sensor probes and the permanent magnet biased radial magnetic bearing in HSMSM. The sensor probes are integrated in the magnetic bearing, and the sensor preamplifiers are placed in the control system of the HSMSM, separate from the sensor probes. The proposed integrated structure can save space in HSMSMs, improve the working frequency, reduce the influence of temperature on the sensor circuit, and improve the stability of HSMSMs. PMID:24469351

  16. Giant Perpendicular Exchange Bias in a Subnanometer Inverted (Co /Pt )n/Co /IrMn Structure

    NASA Astrophysics Data System (ADS)

    Feng, Jiafeng; Liu, H. F.; Wei, H. X.; Zhang, X.-G.; Ren, Yong; Li, Xinxi; Wang, Yan; Wang, J. P.; Han, X. F.

    2017-05-01

    We report a giant perpendicular exchange bias Hexper exhibited in the R -H curves of an inverted (Co /Pt )n/Co /IrMn multilayer and an inverted (Co /Pt )n/Co /Cu /(Co /Pt )4/Co /IrMn spin-valve structure, in which the Pt layers are only 1 /4 nm in thickness and thinner than the Co layers. Hexper shows an unusual linear scaling with the repetition n +1 of the (Co /Pt )n/Co free layer, reaching 792 Oe for n +1 =9 . In contrast, the in-plane exchange bias Hexin is almost constant. This effect originates from Co /IrMn interfacial magnetic coupling in the inverted (Co /Pt )4/Co /IrMn reference layer and is magnified by a near-perpendicular exchange coupling between the interface Co layer and the multilayer (Co /Pt )n (n =4 for the spin-valve structures) in the reference layer. The latter also leads to a linear scaling of the exchange bias with the number of repetitions of Co /Pt in the reference layer.

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

    SciTech Connect

    Bieler, Noah S.; Hünenberger, Philippe H.

    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” 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.

  18. 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.

  19. Local production of pharmaceuticals in Africa and access to essential medicines: 'urban bias' in access to imported medicines in Tanzania and its policy implications.

    PubMed

    Mujinja, Phares G M; Mackintosh, Maureen; Justin-Temu, Mary; Wuyts, Marc

    2014-03-10

    International policy towards access to essential medicines in Africa has focused until recently on international procurement of large volumes of medicines, mainly from Indian manufacturers, and their import and distribution. This emphasis is now being challenged by renewed policy interest in the potential benefits of local pharmaceutical production and supply. However, there is a shortage of evidence on the role of locally produced medicines in African markets, and on potential benefits of local production for access to medicines. This article contributes to filling that gap. This article uses WHO/HAI data from Tanzania for 2006 and 2009 on prices and sources of a set of tracer essential medicines. It employs innovative graphical methods of analysis alongside conventional statistical testing. Medicines produced in Tanzania were equally likely to be found in rural and in urban areas. Imported medicines, especially those imported from countries other than Kenya (mainly from India) displayed 'urban bias': that is, they were significantly more likely to be available in urban than in rural areas. This finding holds across the range of sample medicines studied, and cannot be explained by price differences alone. While different private distribution networks for essential medicines may provide part of the explanation, this cannot explain why the urban bias in availability of imported medicines is also found in the public sector. The findings suggest that enhanced local production may improve rural access to medicines. The potential benefits of local production and scope for their improvement are an important field for further research, and indicate a key policy area in which economic development and health care objectives may reinforce each other.

  20. Substrate-bias effect on the breakdown characteristic in a new silicon high-voltage device structure

    NASA Astrophysics Data System (ADS)

    Qi, Li; Weidong, Wang; Qiuming, Zhao; Xueming, Wei

    2012-05-01

    A novel silicon double-RESURF LDMOS structure with an improved breakdown characteristic by substrate bias technology (SB) is reported. The P-type epitaxial layer is embedded between an N-type drift region and an N-type substrate to block the conduction path in the off-state and change the distributions of the bulk electric field. The substrate bias strengthens the charge share effect of the drift region near the source, and the vertical electric field peak under the drain is decreased, which is especially helpful in improving the vertical breakdown voltage in a lateral power device with a thin drift region. The numerical results by MEDICI indicate that the breakdown voltage of the proposed device is increased by 97% compared with a conventional LDMOS, while maintaining a lowon-resistance.

  1. Suppression of photo-bias induced instability for amorphous indium tungsten oxide thin film transistors with bi-layer structure

    SciTech Connect

    Liu, Po-Tsun Chang, Chih-Hsiang; Chang, Chih-Jui

    2016-06-27

    This study investigates the instability induced by bias temperature illumination stress (NBTIS) for an amorphous indium-tungsten-oxide thin film transistor (a-IWO TFT) with SiO{sub 2} backchannel passivation layer (BPL). It is found that this electrical degradation phenomenon can be attributed to the generation of defect states during the BPL process, which deteriorates the photo-bias stability of a-IWO TFTs. A method proposed by adding an oxygen-rich a-IWO thin film upon the a-IWO active channel layer could effectively suppress the plasma damage to channel layer during BPL deposition process. The bi-layer a-IWO TFT structure with an oxygen-rich back channel exhibits superior electrical reliability of device under NBTIS.

  2. Enhanced optical second-harmonic generation from the current-biased graphene/SiO2/Si(001) structure.

    PubMed

    An, Yong Q; Nelson, Florence; Lee, Ji Ung; Diebold, Alain C

    2013-05-08

    We find that optical second-harmonic generation (SHG) in reflection from a chemical-vapor-deposition graphene monolayer transferred onto a SiO2/Si(001) substrate is enhanced about 3 times by the flow of direct current electric current in graphene. Measurements of rotational-anisotropy SHG revealed that the current-induced SHG from the current-biased graphene/SiO2/Si(001) structure undergoes a phase inversion as the measurement location on graphene is shifted laterally along the current flow direction. The enhancement is due to current-associated charge trapping at the graphene/SiO2 interface, which introduces a vertical electric field across the SiO2/Si interface that produces electric field-induced SHG. The phase inversion is due to the positive-to-negative polarity switch in the current direction of the trapped charges at the current-biased graphene/SiO2 interface.

  3. Effect of pulsed laser irradiation on the structural and the magnetic properties of NiMn/Co exchange bias system

    SciTech Connect

    Mohanan, Senthilnathan; Diebolder, Rolf; Hibst, Raimund; Herr, Ulrich

    2008-04-01

    We report about the influence of pulsed laser irradiation on the structural and magnetic properties of NiMn/Co thin films. Rocking curve measurements showed a significant improvement of the (111) texture of NiMn after laser irradiation which was accompanied by grain growth. We have studied the ordering transition in as-prepared and irradiated (laser fluence of 0.15 J/cm{sup 2}) samples during subsequent annealing. The onset of the fcc to fct phase transformation occurs at 325 deg. C irrespective of laser irradiation. Exchange bias fields for the laser irradiated samples are higher than those of the as-prepared samples. The observed increase in the exchange bias field for laser irradiated samples has been attributed to the increased grain size and the improved (111) texture of the NiMn layer after laser irradiation.

  4. How does the cosmic large-scale structure bias the Hubble diagram?

    NASA Astrophysics Data System (ADS)

    Fleury, Pierre; Clarkson, Chris; Maartens, Roy

    2017-03-01

    The Hubble diagram is one of the cornerstones of observational cosmology. It is usually analysed assuming that, on average, the underlying relation between magnitude and redshift matches the prediction of a Friedmann-Lemaître-Robertson-Walker model. However, the inhomogeneity of the Universe generically biases these observables, mainly due to peculiar velocities and gravitational lensing, in a way that depends on the notion of average used in theoretical calculations. In this article, we carefully derive the notion of average which corresponds to the observation of the Hubble diagram. We then calculate its bias at second-order in cosmological perturbations, and estimate the consequences on the inference of cosmological parameters, for various current and future surveys. We find that this bias deeply affects direct estimations of the evolution of the dark-energy equation of state. However, errors in the standard inference of cosmological parameters remain smaller than observational uncertainties, even though they reach percent level on some parameters; they reduce to sub-percent level if an optimal distance indicator is used.

  5. Structures of apolipoprotein A-I in high density lipoprotein generated by electron microscopy and biased simulations.

    PubMed

    Zhu, Lin; Petrlova, Jitka; Gysbers, Peter; Hebert, Hans; Wallin, Stefan; Jegerschöld, Caroline; Lagerstedt, Jens O

    2017-07-25

    Apolipoprotein A-I (apoA-I) in high-density lipoprotein (HDL) is a key protein for the transport of cholesterol from the vascular wall to the liver. The formation and structure of nascent HDL, composed of apoA-I and phospholipids, is critical to this process. The HDL was assembled in vitro from apoA-I, cholesterol and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) at a 1:4:50 molar ratio. The structure of HDL was investigated in vitreous samples, frozen at cryogenic temperatures, as well as in negatively stained samples by transmission electron microscopy. Low resolution electron density maps were next used as restraints in biased Monte Carlo simulations of apolipoprotein A-I dimers, with an initial structure derived from atomic resolution X-ray structures. Two final apoA-I structure models for the full-length structure of apoA-I dimer in the lipid bound conformation were generated, showing a nearly circular, flat particle with an uneven particle thickness. The generated structures provide evidence for the discoidal, antiparallel arrangement of apoA-I in nascent HDL, and propose two preferred conformations of the flexible N-termini. The novel full-length structures of apoA-I dimers deepens the understanding to the structure-function relationship of nascent HDL with significance for the prevention of lipoprotein-related disease. The biased simulation method used in this study provides a powerful and convenient modelling tool with applicability for structural studies and modelling of other proteins and protein complexes. Copyright © 2017 Elsevier B.V. All rights reserved.

  6. Localization of acoustic modes in periodic porous silicon structures

    PubMed Central

    2014-01-01

    The propagation of longitudinal acoustic waves in multilayer structures based on porous silicon and the experimental measurement of acoustic transmission for the structures in the gigahertz range are reported and studied theoretically. The considered structures exhibit band gaps in the transmission spectrum and these are localized modes inside the band gap, coming from defect layers introduced in periodic systems. The frequency at which the acoustic resonances appear can be tuned by changing the porosity and/or thickness of the defect layer. PMID:25206317

  7. OPEN PROBLEM: Spatially localized structures in dissipative systems: open problems

    NASA Astrophysics Data System (ADS)

    Knobloch, E.

    2008-04-01

    Stationary spatially localized structures, sometimes called dissipative solitons, arise in many interesting and important applications, including buckling of slender structures under compression, nonlinear optics, fluid flow, surface catalysis, neurobiology and many more. The recent resurgence in interest in these structures has led to significant advances in our understanding of the origin and properties of these states, and these in turn suggest new questions, both general and system-specific. This paper surveys these results focusing on open problems, both mathematical and computational, as well as on new applications.

  8. Local magnetic structure determination using polarized neutron holography

    NASA Astrophysics Data System (ADS)

    Szakál, Alex; Markó, Márton; Cser, László

    2015-05-01

    A unique and important property of the neutron is that it possesses magnetic moment. This property is widely used for determination of magnetic structure of crystalline samples observing the magnetic components of the diffraction peaks. Investigations of diffraction patterns give information only about the averaged structure of a crystal but for discovering of local spin arrangement around a specific (e.g., impurity) nucleus remains still a challenging problem. Neutron holography is a useful tool to investigate the local structure around a specific nucleus embedded in a crystal lattice. The method has been successfully applied experimentally in several cases using non-magnetic short range interaction of the neutron and the nucleus. A mathematical model of the hologram using interaction between magnetic moment of the atom and the neutron spin for polarized neutron holography is provided. Validity of a polarized neutron holographic experiment is demonstrated by applying the proposed method on model systems.

  9. Local magnetic structure determination using polarized neutron holography

    SciTech Connect

    Szakál, Alex Markó, Márton Cser, László

    2015-05-07

    A unique and important property of the neutron is that it possesses magnetic moment. This property is widely used for determination of magnetic structure of crystalline samples observing the magnetic components of the diffraction peaks. Investigations of diffraction patterns give information only about the averaged structure of a crystal but for discovering of local spin arrangement around a specific (e.g., impurity) nucleus remains still a challenging problem. Neutron holography is a useful tool to investigate the local structure around a specific nucleus embedded in a crystal lattice. The method has been successfully applied experimentally in several cases using non-magnetic short range interaction of the neutron and the nucleus. A mathematical model of the hologram using interaction between magnetic moment of the atom and the neutron spin for polarized neutron holography is provided. Validity of a polarized neutron holographic experiment is demonstrated by applying the proposed method on model systems.

  10. Underreporting in traffic accident data, bias in parameters and the structure of injury severity models.

    PubMed

    Yamamoto, Toshiyuki; Hashiji, Junpei; Shankar, Venkataraman N

    2008-07-01

    Injury severities in traffic accidents are usually recorded on ordinal scales, and statistical models have been applied to investigate the effects of driver factors, vehicle characteristics, road geometrics and environmental conditions on injury severity. The unknown parameters in the models are in general estimated assuming random sampling from the population. Traffic accident data however suffer from underreporting effects, especially for lower injury severities. As a result, traffic accident data can be regarded as outcome-based samples with unknown population shares of the injury severities. An outcome-based sample is overrepresented by accidents of higher severities. As a result, outcome-based samples result in biased parameters which skew our inferences on the effect of key safety variables such as safety belt usage. The pseudo-likelihood function for the case with unknown population shares, which is the same as the conditional maximum likelihood for the case with known population shares, is applied in this study to examine the effects of severity underreporting on the parameter estimates. Sequential binary probit models and ordered-response probit models of injury severity are developed and compared in this study. Sequential binary probit models assume that the factors determining the severity change according to the level of the severity itself, while ordered-response probit models assume that the same factors correlate across all levels of severity. Estimation results suggest that the sequential binary probit models outperform the ordered-response probit models, and that the coefficient estimates for lap and shoulder belt use are biased if underreporting is not considered. Mean parameter bias due to underreporting can be significant. The findings show that underreporting on the outcome dimension may induce bias in inferences on a variety of factors. In particular, if underreporting is not accounted for, the marginal impacts of a variety of factors appear

  11. Topological framework for local structure analysis in condensed matter

    PubMed Central

    Lazar, Emanuel A.; Han, Jian; Srolovitz, David J.

    2015-01-01

    Physical systems are frequently modeled as sets of points in space, each representing the position of an atom, molecule, or mesoscale particle. As many properties of such systems depend on the underlying ordering of their constituent particles, understanding that structure is a primary objective of condensed matter research. Although perfect crystals are fully described by a set of translation and basis vectors, real-world materials are never perfect, as thermal vibrations and defects introduce significant deviation from ideal order. Meanwhile, liquids and glasses present yet more complexity. A complete understanding of structure thus remains a central, open problem. Here we propose a unified mathematical framework, based on the topology of the Voronoi cell of a particle, for classifying local structure in ordered and disordered systems that is powerful and practical. We explain the underlying reason why this topological description of local structure is better suited for structural analysis than continuous descriptions. We demonstrate the connection of this approach to the behavior of physical systems and explore how crystalline structure is compromised at elevated temperatures. We also illustrate potential applications to identifying defects in plastically deformed polycrystals at high temperatures, automating analysis of complex structures, and characterizing general disordered systems. PMID:26460045

  12. Mapping local deformation behavior in single cell metal lattice structures

    DOE PAGES

    Carlton, Holly D.; Lind, Jonathan; Messner, Mark C.; ...

    2017-02-08

    The deformation behavior of metal lattice structures is extremely complex and challenging to predict, especially since strain is not uniformly distributed throughout the structure. Understanding and predicting the failure behavior for these types of light-weighting structures is of great interest due to the excellent scaling of stiffness- and strength-to weight ratios they display. Therefore, there is a need to perform simplified experiments that probe unit cell mechanisms. This study reports on high resolution mapping of the heterogeneous structural response of single unit cells to the macro-scale loading condition. Two types of structures, known to show different stress-strain responses, were evaluatedmore » using synchrotron radiation micro-tomography while performing in-situ uniaxial compression tests to capture the local micro-strain deformation. These structures included the octet-truss, a stretch-dominated lattice, and the rhombic-dodecahedron, a bend-dominated lattice. The tomographic analysis showed that the stretch- and bend-dominated lattices exhibit different failure mechanisms and that the defects built into the structure cause a heterogeneous localized deformation response. Also shown here is a change in failure mode for stretch-dominated lattices, where there appears to be a transition from buckling to plastic yielding for samples with a relative density between 10 and 20%. In conclusion, the experimental results were also used to inform computational studies designed to predict the mesoscale deformation behavior of lattice structures. Here an equivalent continuum model and a finite element model were used to predict both local strain fields and mechanical behavior of lattices with different topologies.« less

  13. Effective electron-density map improvement and structure validation on a Linux multi-CPU web cluster: The TB Structural Genomics Consortium Bias Removal Web Service.

    PubMed

    Reddy, Vinod; Swanson, Stanley M; Segelke, Brent; Kantardjieff, Katherine A; Sacchettini, James C; Rupp, Bernhard

    2003-12-01

    Anticipating a continuing increase in the number of structures solved by molecular replacement in high-throughput crystallography and drug-discovery programs, a user-friendly web service for automated molecular replacement, map improvement, bias removal and real-space correlation structure validation has been implemented. The service is based on an efficient bias-removal protocol, Shake&wARP, and implemented using EPMR and the CCP4 suite of programs, combined with various shell scripts and Fortran90 routines. The service returns improved maps, converted data files and real-space correlation and B-factor plots. User data are uploaded through a web interface and the CPU-intensive iteration cycles are executed on a low-cost Linux multi-CPU cluster using the Condor job-queuing package. Examples of map improvement at various resolutions are provided and include model completion and reconstruction of absent parts, sequence correction, and ligand validation in drug-target structures.

  14. Tracking Coherent Structures and Source Localization in Geophysical Flows

    NASA Astrophysics Data System (ADS)

    Forgoston, Eric; Hsieh, Ani; Schwartz, Ira; Yecko, Philip

    There has been a steady increase in the deployment of autonomous underwater and surface vehicles for applications such as ocean monitoring, tracking of marine processes, and forecasting contaminant transport. The underwater environment poses unique challenges since robots must operate in a communication and localization-limited environment where their dynamics are tightly coupled with the environmental dynamics. This work presents current efforts in understanding the impact of geophysical fluid dynamics on underwater vehicle control and autonomy. The focus of the talk is on the use of collaborative vehicles to track Lagrangian coherent structures and to localize contaminant spills. Research supported by the National Science Foundation and the Office of Naval Research.

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

    PubMed

    Xiang, Qian

    2013-01-01

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

  16. Polar-biased localization of the cold stress-induced RNA helicase, CrhC, in the Cyanobacterium Anabaena sp. strain PCC 7120.

    PubMed

    El-Fahmawi, Bassam; Owttrim, George W

    2003-11-01

    Shift of the filamentous cyanobacterium, Anabaena sp. strain PCC 7120, from 30 degrees C to 20 degrees C induces expression of a cold shock response gene encoding the RNA helicase CrhC. Subcellular localization using cellular fractionation and membrane purification indicated that CrhC is localized to the plasma membrane with no evidence of a soluble-cytoplasmic form. Treatment of spheroplasts with trypsin and membrane fractions with various denaturing agents identified CrhC as an integral membrane protein associated with the cytoplasmic face of the plasma membrane. Immunoelectron microscopy confirmed the plasma membrane association of CrhC. Interestingly, a higher specific labelling was observed at the cell poles on the septa between adjacent cells within cell filaments. On a per cell area basis, CrhC localization to the cell pole was 3.5- and >1000-fold higher than to the lateral portion of the plasma membrane or cytoplasm respectively. In addition, CrhC also localizes to new cell poles forming within a dividing cell. Polar-biased localization of the CrhC RNA helicase implies a role in RNA metabolism that is plasma membrane associated and preferentially occurs at the cell poles during cyanobacterial response to cold stress.

  17. Effects of substrate bias on structure and mechanical properties of (AlCrNbSiTiV)N coatings

    NASA Astrophysics Data System (ADS)

    Huang, Ping-Kang; Yeh, Jien-Wei

    2009-06-01

    AlCrNbSiTiV nitride films were deposited by reactive radio-frequency magnetron sputtering and the effects of substrate bias on the chemical composition, structure and mechanical properties of the deposited films were investigated. AlCrNbSiTiV nitride films exhibit a single FCC NaCl-type structure and have the stoichiometric nitride ratio of (Al, Cr, Nb, Si, Ti, V)50N50. The deposition rate decreases with increasing substrate bias due to resputtering effects and densification of films, which also leads to less obvious columnar structure, reduced grain size, smaller surface roughness and transition of preferred orientation from the (1 1 1) plane to the (2 0 0) plane. The nitride film deposited at -100 V exhibits the maximum compressive stress around 4.5 GPa and attains a peak hardness and an elastic modulus of 42 GPa and 350 GPa, respectively, which fall in the superhard grade. Moreover, the film keeps its hardness at the superhard grade even after its residual compressive stress was partially released by annealing at 1073 K for 5 h. The structural evolution mechanism and strengthening mechanism are both discussed.

  18. Nucleic acid structure analysis: Local, mathematically rigorous, comparable

    SciTech Connect

    Babcock, M.S.

    1993-01-01

    A more sophisticated mathematical treatments for analyzing nucleic acid coordinate data is presented. The methodology is both rigorous and comparable for parameterizing nucleic acids in terms of the local structural morphology of complementary and neighboring base pairs. Chapter 1 clearly defines the problems of nucleic acid structure parameterization by examining the consequences of the EMBO workshop guidelines published in 1989. Chapter 2 defines mathematics to rigorously and comparably calculate all of the parameters for nucleic acid structure from a local viewpoint. The mathematics satisfies all EMBO guidelines for local structural parameters. One of the main features making this program flexible is that any base pair relationship can be rigorously analyzed. This is because the meaning of zero for the complementary base parameters is clearly definable for any base pairing relationship. Chapter 3 analyses and explains why certain pairwise parameter correlations were observed between rotational and translational parameters. It was observed that the method of calculating the rotational parameters greatly affected the calculated translational parameters. As a result of our analysis, we determined the optimum location about which rotations should be performed in order to reduce and/or eliminate the correlations which are artifacts of the mathematics employed and do not reflect true structural properties of nucleic acids. Chapter 4 presents an analysis of the available nucleic acid X-ray crystallographic structural data, showing that the experimental base pairs do not generally have the ideal Watson-Crick structure. By utilizing a hybrid between helical and Cartesian parameterization methods, the relative distribution of the complementary base parameters was examined as a function of the nearest neighboring base pairs. The final chapter includes a review article explaining each of the available methods in plain English as well as giving the mathematics.

  19. Fluctuations and local ice structure in model supercooled water.

    PubMed

    Overduin, S D; Patey, G N

    2015-09-07

    Large-scale simulations (up to 32,000 molecules) are used to analyze local structures and fluctuations for the TIP4P/2005 and TIP5P water models, under deeply supercooled conditions, near previously proposed liquid-liquid critical points. Bulk freezing does not occur in our simulations, but correlations between molecules with local ice-like structure (ice-like molecules) are strong and long ranged (∼4 nm), exceeding the shortest dimension of smaller simulation cells at the lowest temperatures considered. Correlations between ice-like molecules decay slowly at low temperature, on the order of a hundred nanoseconds. Local ice-like structure is strongly correlated with highly tetrahedral liquid structure at all times, both structures contribute to density fluctuations, and to the associated anomalous scattering. For the TIP4P/2005 and TIP5P models, we show that the apparent spontaneous liquid-liquid phase separations, recently reported [T. Yagasaki, M. Matsumoto, and H. Tanaka, Phys. Rev. E 89, 020301 (2014)] for small rectangular simulation cells below the proposed critical points, exhibit strong system size dependence and do not occur at all in the largest systems we consider. Furthermore, in the smaller rectangular systems where layers of different densities do occur, we find that the appearance of a region of low density is always accompanied simultaneously by an excess of local ice density, with no separation in time. Our results suggest that the density differences observed in direct simulations for the two models considered here are likely due to long-range correlations between ice-like molecules and do not provide strong evidence of liquid-liquid phase separation.

  20. Recognition of Local DNA Structures by p53 Protein

    PubMed Central

    Brázda, Václav; Coufal, Jan

    2017-01-01

    p53 plays critical roles in regulating cell cycle, apoptosis, senescence and metabolism and is commonly mutated in human cancer. These roles are achieved by interaction with other proteins, but particularly by interaction with DNA. As a transcription factor, p53 is well known to bind consensus target sequences in linear B-DNA. Recent findings indicate that p53 binds with higher affinity to target sequences that form cruciform DNA structure. Moreover, p53 binds very tightly to non-B DNA structures and local DNA structures are increasingly recognized to influence the activity of wild-type and mutant p53. Apart from cruciform structures, p53 binds to quadruplex DNA, triplex DNA, DNA loops, bulged DNA and hemicatenane DNA. In this review, we describe local DNA structures and summarize information about interactions of p53 with these structural DNA motifs. These recent data provide important insights into the complexity of the p53 pathway and the functional consequences of wild-type and mutant p53 activation in normal and tumor cells. PMID:28208646

  1. Recognition of Local DNA Structures by p53 Protein.

    PubMed

    Brázda, Václav; Coufal, Jan

    2017-02-10

    p53 plays critical roles in regulating cell cycle, apoptosis, senescence and metabolism and is commonly mutated in human cancer. These roles are achieved by interaction with other proteins, but particularly by interaction with DNA. As a transcription factor, p53 is well known to bind consensus target sequences in linear B-DNA. Recent findings indicate that p53 binds with higher affinity to target sequences that form cruciform DNA structure. Moreover, p53 binds very tightly to non-B DNA structures and local DNA structures are increasingly recognized to influence the activity of wild-type and mutant p53. Apart from cruciform structures, p53 binds to quadruplex DNA, triplex DNA, DNA loops, bulged DNA and hemicatenane DNA. In this review, we describe local DNA structures and summarize information about interactions of p53 with these structural DNA motifs. These recent data provide important insights into the complexity of the p53 pathway and the functional consequences of wild-type and mutant p53 activation in normal and tumor cells.

  2. Toward structurally integrated locally resonant metamaterials for vibration attenuation

    NASA Astrophysics Data System (ADS)

    Schmied, Jascha U.; Sugino, Christopher; Bergamini, Andrea; Ermanni, Paolo; Ruzzene, Massimo; Erturk, Alper

    2017-04-01

    In this contribution, we explore the use of locally resonant metamaterials for multi-functional structural load- bearing concepts using analytical, numerical, and experimental techniques. Locally resonant metamaterials exhibit bandgaps at wavelengths much larger than the lattice dimension. This is a promising feature for low- frequency vibration attenuation. The presented work aims to investigate highly integrated structural concepts and experimentally validated prototypes for vibration reduction in load-bearing applications. The goal is to explore and extend the design space of lightweight structural systems, by designing multi-functional periodic structural elements, preserving structural stiffness while concurrently enabling sufficiently wideband damping performance over a target frequency range of interest. Following a generalized theoretical modeling framework for bandgap design and analysis in finite structures, the focus is placed on the design, fabrication, and analysis of a load-carrying frame development with internally resonant components. Finite-element modeling is employed to design and analyze the frequency response of the frame and simplified analytical solution is compared with this numerical solution. Experimental validations are presented for a 3D-printed prototype. The effects of various parameters are reported both based on numerical and experimental findings.

  3. Models of models: filtering and bias rings in depiction of knowledge structures and their implications for design.

    PubMed

    Revell, Kirsten M A; Stanton, Neville A

    2012-01-01

    Mental models are poorly specified in three ways: in their defining criteria, their source and the bias to which they have been subjected. Literature from psychology, HCI and human factors sources was reviewed to determine the utility of 'mental models' as a design tool. The definitions and theories offered by key contributors to the notion of mental models were compared. Schematics, representing both the knowledge structures proposed in cognitive processing, as well as the layers of bias evident when forming or accessing mental models, were constructed. Fundamental similarities and differences in the use of this notion, as well as ambiguities in definition, were highlighted graphically. The need for specificity in the use of mental models was emphasised as essential for pragmatic application in design. The use of graphical comparison was proposed as a means of identifying the risk of bias and a means to categorise approaches to mental model research. Practitioner Summary: Mental models are considered significant in user centred design. To apply this notion pragmatically, its definition and methods of construction and access need to be sufficiently specified. This article offers a graphical method to compare existing research in mental models, highlighting similarities, differences and ambiguities.

  4. Primordial non-Gaussianity: Large-scale structure signature in the perturbative bias model

    NASA Astrophysics Data System (ADS)

    McDonald, Patrick

    2008-12-01

    I compute the effect on the power spectrum of tracers of the large-scale mass-density field (e.g., galaxies) of primordial non-Gaussianity of the form Φ=ϕ+fNL(ϕ2-⟨ϕ2⟩)+gNLϕ3+…, where Φ is proportional to the initial potential fluctuations and ϕ is a Gaussian field, using beyond-linear-order perturbation theory. I find that the need to eliminate large higher-order corrections necessitates the addition of a new term to the bias model, proportional to ϕ, i.e., δg=bδδ+bϕfNLϕ+…, with all the consequences this implies for clustering statistics, e.g., Pgg(k)=bδ2Pδδ(k)+2bδbϕfNLPϕδ(k)+bϕ2fNL2Pϕϕ(k)+…. This result is consistent with calculations based on a model for dark matter halo clustering, showing that the form is quite general, not requiring assumptions about peaks, or the formation or existence of halos. The halo model plays the same role it does in the usual bias picture, giving a prediction for bϕ for galaxies known to sit in a certain type of halo. Previous projections for future constraints based on this effect have been very conservative—there is enough volume at z≲2 to measure fNL to ˜±1, with much more volume at higher z. As a prelude to the bias calculation, I point out that the beyond-linear (in ϕ) corrections to the power spectrum of mass-density perturbations are naively infinite, so it is dangerous to assume they are negligible; however, the infinite part can be removed by a renormalization of the fluctuation amplitude, with the residual k-dependent corrections negligible for models allowed by current constraints.

  5. Non-collinear magnetism and exchange bias at the FM NiFe/AFM NiMn interface: local spin density FLAPW study

    NASA Astrophysics Data System (ADS)

    Nakamura, K.; Freeman, A. J.; Wang, D.-S.; Zhong, L.; Fernandez-de-Castro, J.

    2001-03-01

    Magnetism at interfaces, such as the exchange bias between ferromagnetic (FM) and antiferromagnetic (AFM) materials, has attracted great attention because of technological applications. In order to investigate magnetic structures at the FM/AFM interface, we have implemented the FLAPW (E. Wimmer, H. Krakauer, M. Weinert and A.J. Freeman, PRB 24, 864(1981)) methodologies including non-collinear magnetism, in which the magnetic moment direction as well as the magnitude can vary continuously all over space. We first demonstrate this approach to determine the structure of a magnetic structure at an interface between FM NiFe and AFM NiMn. Although both bulk systems each show collinear FM and AFM structures, we found that a perpendicular magnetic orientation at their interface is energetically favorable, where the magnetic moments of the FM NiFe tend to lie perpendicular to those of AFM NiMn.

  6. Monaural sound localization based on structure-induced acoustic resonance.

    PubMed

    Kim, Keonwook; Kim, Youngwoong

    2015-02-06

    A physical structure such as a cylindrical pipe controls the propagated sound spectrum in a predictable way that can be used to localize the sound source. This paper designs a monaural sound localization system based on multiple pyramidal horns around a single microphone. The acoustic resonance within the horn provides a periodicity in the spectral domain known as the fundamental frequency which is inversely proportional to the radial horn length. Once the system accurately estimates the fundamental frequency, the horn length and corresponding angle can be derived by the relationship. The modified Cepstrum algorithm is employed to evaluate the fundamental frequency. In an anechoic chamber, localization experiments over azimuthal configuration show that up to 61% of the proper signal is recognized correctly with 30% misfire. With a speculated detection threshold, the system estimates direction 52% in positive-to-positive and 34% in negative-to-positive decision rate, on average.

  7. A local average distance descriptor for flexible protein structure comparison

    PubMed Central

    2014-01-01

    Background Protein structures are flexible and often show conformational changes upon binding to other molecules to exert biological functions. As protein structures correlate with characteristic functions, structure comparison allows classification and prediction of proteins of undefined functions. However, most comparison methods treat proteins as rigid bodies and cannot retrieve similarities of proteins with large conformational changes effectively. Results In this paper, we propose a novel descriptor, local average distance (LAD), based on either the geodesic distances (GDs) or Euclidean distances (EDs) for pairwise flexible protein structure comparison. The proposed method was compared with 7 structural alignment methods and 7 shape descriptors on two datasets comprising hinge bending motions from the MolMovDB, and the results have shown that our method outperformed all other methods regarding retrieving similar structures in terms of precision-recall curve, retrieval success rate, R-precision, mean average precision and F1-measure. Conclusions Both ED- and GD-based LAD descriptors are effective to search deformed structures and overcome the problems of self-connection caused by a large bending motion. We have also demonstrated that the ED-based LAD is more robust than the GD-based descriptor. The proposed algorithm provides an alternative approach for blasting structure database, discovering previously unknown conformational relationships, and reorganizing protein structure classification. PMID:24694083

  8. Effect of the back bias on the analog performance of standard FD and UTBB transistors-based self-cascode structures

    NASA Astrophysics Data System (ADS)

    Doria, Rodrigo T.; Flandre, Denis; Trevisoli, Renan; de Souza, Michelly; Pavanello, Marcelo A.

    2017-09-01

    This work demonstrates that active back biasing can improve significantly the analog performance of two-transistors self-cascode structures. The study was performed by applying both standard and UTBB fully depleted (FD) SOI MOSFETs to the structures and has shown that a voltage gain improvement of about 7 dB is obtained when a forward back bias is applied to the drain-sided transistor of standard FD devices-based structure. In the case of UTBB transistors, an improvement larger than 5 dB of the output voltage gain is shown depending on the back bias applied to both n- or p-type devices. Finally, it is shown that the mirroring precision of current mirrors composed by SC structures can be more than 20% better than the one composed by single devices and the improvement is better when adequate back bias is applied.

  9. Earth Structure, Ice Mass Changes, and the Local Dynamic Geoid

    NASA Astrophysics Data System (ADS)

    Harig, C.; Simons, F. J.

    2014-12-01

    Spherical Slepian localization functions are a useful method for studying regional mass changes observed by satellite gravimetry. By projecting data onto a sparse basis set, the local field can be estimated more easily than with the full spherical harmonic basis. We have used this method previously to estimate the ice mass change in Greenland from GRACE data, and it can also be applied to other planetary problems such as global magnetic fields. Earth's static geoid, in contrast to the time-variable field, is in large part related to the internal density and rheological structure of the Earth. Past studies have used dynamic geoid kernels to relate this density structure and the internal deformation it induces to the surface geopotential at large scales. These now classical studies of the eighties and nineties were able to estimate the mantle's radial rheological profile, placing constraints on the ratio between upper and lower mantle viscosity. By combining these two methods, spherical Slepian localization and dynamic geoid kernels, we have created local dynamic geoid kernels which are sensitive only to density variations within an area of interest. With these kernels we can estimate the approximate local radial rheological structure that best explains the locally observed geoid on a regional basis. First-order differences of the regional mantle viscosity structure are accessible to this technique. In this contribution we present our latest, as yet unpublished results on the geographical and temporal pattern of ice mass changes in Antarctica over the past decade, and we introduce a new approach to extract regional information about the internal structure of the Earth from the static global gravity field. Both sets of results are linked in terms of the relevant physics, but also in being developed from the marriage of Slepian functions and geoid kernels. We make predictions on the utility of our approach to derive fully three-dimensional rheological Earth models, to

  10. Local density corrected three-body distribution functions for probing local structure reorganization in liquids.

    PubMed

    Bhattacharjee, Anirban; Hofer, Thomas S; Rode, Bernd M

    2008-11-28

    Three-body distribution functions are calculated for metal ions in an aqueous medium in order to investigate and characterise solvent structure reorganization. Based on the existing formulation of three body correlation function, a local density correction is introduced to enable a comparison of different sub-regions within a solvate as well as different systems, thus taking into account the varying density arising from the influence of the solute.

  11. Dynamics of Localized Structures in Systems with Broken Parity Symmetry

    NASA Astrophysics Data System (ADS)

    Javaloyes, J.; Camelin, P.; Marconi, M.; Giudici, M.

    2016-04-01

    A great variety of nonlinear dissipative systems are known to host structures having a correlation range much shorter than the size of the system. The dynamics of these localized structures (LSs) has been investigated so far in situations featuring parity symmetry. In this Letter we extend this analysis to systems lacking this property. We show that the LS drifting speed in a parameter varying landscape is not simply proportional to the parameter gradient, as found in parity preserving situations. The symmetry breaking implies a new contribution to the velocity field which is a function of the parameter value, thus leading to a new paradigm for LSs manipulation. We illustrate this general concept by studying the trajectories of the LSs found in a passively mode-locked laser operated in the localization regime. Moreover, the lack of parity affects significantly LSs interactions which are governed by asymmetrical repulsive forces.

  12. Alfvénic localized structures in partially ionized plasmas

    NASA Astrophysics Data System (ADS)

    Borhanian, Jafar; Rezaei, Arash

    2017-02-01

    The existence and dynamics of Alfvénic localized structures are investigated in partially ionized plasmas. We have employed the Hall magnetohydrodynamics model for partially ionized plasmas and shown that the evolution of a weakly nonlinear and weakly dispersive Alfvén wave is governed by a derivative nonlinear Schrödinger (DNLS) type equation. In the Hall effect domination limit, this equation reduces to a standard DNLS equation that possesses localized solutions in the form of solitons and rogue waves. The dependence of the profile of these structures on the Hall parameter is addressed. When the ohmic and ambipolar effects are small but finite in comparison to the Hall effect, the evolution equation takes the form of a perturbed DNLS equation. In this limit, the dynamics of envelope soliton solution is examined by means of the soliton perturbation method, the moment method, to be precise.

  13. Neuronal selectivity and local map structure in visual cortex

    PubMed Central

    Nauhaus, I.; Benucci, A.; Carandini, M.; Ringach, D. L.

    2008-01-01

    Summary The organization of primary visual cortex into functional maps makes individual cells operate in a variety of contexts. For instance, some neurons lie in regions of fairly homogeneous orientation preference (iso-orientation domains), while others lie in regions with a variety of preferences (e.g., pinwheel centers). We asked whether this diversity in local map structure correlates with the degree of selectivity of spike responses. We used a novel combination of imaging and electrophysiology to reveal that neurons in regions of homogeneous orientation preference have much sharper tuning. Moreover, in both monkeys and cats, a common principle links the structure of the orientation map, on the spatial scale of dendritic integration, to the degree of selectivity of individual cells. We conclude that neural computation is not invariant across the cortical surface: its relationship to local context must be considered by theories of receptive field wiring and map development. PMID:18341988

  14. Local structure co-occurrence pattern for image retrieval

    NASA Astrophysics Data System (ADS)

    Zhang, Ke; Zhang, Fan; Lu, Jia; Lu, Yinghua; Kong, Jun; Zhang, Ming

    2016-03-01

    Image description and annotation is an active research topic in content-based image retrieval. How to utilize human visual perception is a key approach to intelligent image feature extraction and representation. This paper has proposed an image feature descriptor called the local structure co-occurrence pattern (LSCP). LSCP extracts the whole visual perception for an image by building a local binary structure, and it is represented by a color-shape co-occurrence matrix which explores the relationship of multivisual feature spaces according to visual attention mechanism. As a result, LSCP not only describes low-level visual features integrated with texture feature, color feature, and shape feature but also bridges high-level semantic comprehension. Extensive experimental results on an image retrieval task on the benchmark datasets, corel-10,000, MIT VisTex, and INRIA Holidays, have demonstrated the usefulness, effectiveness, and robustness of the proposed LSCP.

  15. Electronic structure and localized states in a model amorphous silicon

    NASA Astrophysics Data System (ADS)

    Allan, G.; Delerue, C.; Lannoo, M.

    1998-03-01

    The electronic structure of a model amorphous silicon (a-Si) represented by a supercell of 4096 silicon atoms [B.R. Djordjevic, M.F. Thorpe, and F. Wooten, Phys. Rev. B 52, 5685 (1995)] and of a model hydrogenated amorphous silicon (a-Si:H) that we have built from the a-Si model are calculated in the tight-binding approximation. The band edges near the gap are characterized by exponential tails of localized states induced mainly by the variations in bond angles. The spatial localization of the states is compared between a-Si and a-Si:H. Comparison with experiments suggests that the structural models give good descriptions of the amorphous materials.

  16. The local spiral structure of the Milky Way

    PubMed Central

    Xu, Ye; Reid, Mark; Dame, Thomas; Menten, Karl; Sakai, Nobuyuki; Li, Jingjing; Brunthaler, Andreas; Moscadelli, Luca; Zhang, Bo; Zheng, Xingwu

    2016-01-01

    The nature of the spiral structure of the Milky Way has long been debated. Only in the last decade have astronomers been able to accurately measure distances to a substantial number of high-mass star-forming regions, the classic tracers of spiral structure in galaxies. We report distance measurements at radio wavelengths using the Very Long Baseline Array for eight regions of massive star formation near the Local spiral arm of the Milky Way. Combined with previous measurements, these observations reveal that the Local Arm is larger than previously thought, and both its pitch angle and star formation rate are comparable to those of the Galaxy’s major spiral arms, such as Sagittarius and Perseus. Toward the constellation Cygnus, sources in the Local Arm extend for a great distance along our line of sight and roughly along the solar orbit. Because of this orientation, these sources cluster both on the sky and in velocity to form the complex and long enigmatic Cygnus X region. We also identify a spur that branches between the Local and Sagittarius spiral arms. PMID:27704048

  17. The local spiral structure of the Milky Way.

    PubMed

    Xu, Ye; Reid, Mark; Dame, Thomas; Menten, Karl; Sakai, Nobuyuki; Li, Jingjing; Brunthaler, Andreas; Moscadelli, Luca; Zhang, Bo; Zheng, Xingwu

    2016-09-01

    The nature of the spiral structure of the Milky Way has long been debated. Only in the last decade have astronomers been able to accurately measure distances to a substantial number of high-mass star-forming regions, the classic tracers of spiral structure in galaxies. We report distance measurements at radio wavelengths using the Very Long Baseline Array for eight regions of massive star formation near the Local spiral arm of the Milky Way. Combined with previous measurements, these observations reveal that the Local Arm is larger than previously thought, and both its pitch angle and star formation rate are comparable to those of the Galaxy's major spiral arms, such as Sagittarius and Perseus. Toward the constellation Cygnus, sources in the Local Arm extend for a great distance along our line of sight and roughly along the solar orbit. Because of this orientation, these sources cluster both on the sky and in velocity to form the complex and long enigmatic Cygnus X region. We also identify a spur that branches between the Local and Sagittarius spiral arms.

  18. Tunable Surface Structuration of Silicon by Metal Assisted Chemical Etching with Pt Nanoparticles under Electrochemical Bias.

    PubMed

    Torralba, Encarnación; Le Gall, Sylvain; Lachaume, Raphaël; Magnin, Vincent; Harari, Joseph; Halbwax, Mathieu; Vilcot, Jean-Pierre; Cachet-Vivier, Christine; Bastide, Stéphane

    2016-11-16

    An in-depth study of metal assisted chemical etching (MACE) of p-type c-Si in HF/H2O2 aqueous solutions using Pt nanoparticles as catalysts is presented. Combination of cyclic voltammetry, open circuit measurements, chronoamperometry, impedance spectroscopy, and 2D band bending modeling of the metal/semiconductor/electrolyte interfaces at the nanoscale and under different etching conditions allows gaining physical insights into this system. Additionally, in an attempt to mimic the etching conditions, the modeling has been performed with a positively biased nanoparticle buried in the Si substrate. Following these findings, the application of an external polarization during etching is introduced as a novel efficient approach for achieving straightforward control of the pore morphology by acting upon the band bending at the Si/electrolyte junction. In this way, nanostructures ranging from straight mesopores to cone-shaped macropores are obtained as the Si sample is biased from negative to positive potentials. Remarkably, macroscopic cone-shaped pores in the 1-5 μm size range with a high aspect ratio (L/W ∼ 1.6) are obtained by this method. This morphology leads to a reduction of the surface reflectance below 5% over the entire VIS-NIR domain, which outperforms macrostructures made by state of the art texturization techniques for Si solar cells.

  19. Viscosity of aqueous solutions and local microscopic structure.

    PubMed

    Corridoni, T; Mancinelli, R; Ricci, M A; Bruni, F

    2011-12-08

    The effect of solutes on the structure of water has been debated intensively over the past years. Typical scenarios label different ions as water structure "makers" or "breakers": this is a quite elusive definition, which has been first introduced in the description of the effect of solutes on the viscosity of water and, although criticized, is still used in the current literature. Here, using a combination of neutron diffraction and computer modeling, we present a possible relation between the viscosity B coefficient and a local structural property of the solution. In particular, B appears in the Jones-Dole relation and its sign is traditionally used to characterize a solute as "structure maker" or "breaker". We find that B is linearly correlated to the difference between the average solute-water distance and the water-water distance in the pure liquid, in the case of monovalent electrolyte solutions.

  20. Localized structural frustration for evaluating the impact of sequence variants

    PubMed Central

    Kumar, Sushant; Clarke, Declan; Gerstein, Mark

    2016-01-01

    Population-scale sequencing is increasingly uncovering large numbers of rare single-nucleotide variants (SNVs) in coding regions of the genome. The rarity of these variants makes it challenging to evaluate their deleteriousness with conventional phenotype–genotype associations. Protein structures provide a way of addressing this challenge. Previous efforts have focused on globally quantifying the impact of SNVs on protein stability. However, local perturbations may severely impact protein functionality without strongly disrupting global stability (e.g. in relation to catalysis or allostery). Here, we describe a workflow in which localized frustration, quantifying unfavorable local interactions, is employed as a metric to investigate such effects. Using this workflow on the Protein Databank, we find that frustration produces many immediately intuitive results: for instance, disease-related SNVs create stronger changes in localized frustration than non-disease related variants, and rare SNVs tend to disrupt local interactions to a larger extent than common variants. Less obviously, we observe that somatic SNVs associated with oncogenes and tumor suppressor genes (TSGs) induce very different changes in frustration. In particular, those associated with TSGs change the frustration more in the core than the surface (by introducing loss-of-function events), whereas those associated with oncogenes manifest the opposite pattern, creating gain-of-function events. PMID:27915290

  1. Influence of pulsed substrate bias on the structure and properties of Ti-Al-N films deposited by cathodic vacuum arc

    NASA Astrophysics Data System (ADS)

    Zhang, G. P.; Gao, G. J.; Wang, X. Q.; Lv, G. H.; Zhou, L.; Chen, H.; Pang, H.; Yang, S. Z.

    2012-07-01

    Ti-Al-N films were deposited by cathodic vacuum arc (CVA) technique in N2 atmosphere with different pulsed substrate bias. The influence of pulsed substrate bias (0 to -800 V) on the deposition rate, surface morphology, crystal structure, and mechanical properties of the Ti-Al-N films were systematically investigated. Increasing pulsed bias voltage resulted in the decrease of deposition rate but the increase of surface roughness. It was found that there was a strong correlation between the pulsed bias and film structure. All the films studied in this paper were composed of TiN, AlN, and Ti-Al-N ternary phases. The grains changed from equiaxial to columnar and exhibited preferred orientation when the pulsed bias increased. With the increase of pulsed bias voltage, the atomic ratio of Ti to Al element increased gradually, while the N to (Ti + Al) ratio decreased. The composite films present an enhanced nanohardness compared with binary TiN and ZrN films. The film deposited with pulsed bias of -200 V possessed the maximum scratch critical load and nanohardness. The minimum friction coefficient with pulsed bias of -300 V was obtained.

  2. Distal chromatin structure influences local nucleosome positions and gene expression.

    PubMed

    Jansen, An; van der Zande, Elisa; Meert, Wim; Fink, Gerald R; Verstrepen, Kevin J

    2012-05-01

    The positions of nucleosomes across the genome influence several cellular processes, including gene transcription. However, our understanding of the factors dictating where nucleosomes are located and how this affects gene regulation is still limited. Here, we perform an extensive in vivo study to investigate the influence of the neighboring chromatin structure on local nucleosome positioning and gene expression. Using truncated versions of the Saccharomyces cerevisiae URA3 gene, we show that nucleosome positions in the URA3 promoter are at least partly determined by the local DNA sequence, with so-called 'anti-nucleosomal elements' like poly(dA:dT) tracts being key determinants of nucleosome positions. In addition, we show that changes in the nucleosome positions in the URA3 promoter strongly affect the promoter activity. Most interestingly, in addition to demonstrating the effect of the local DNA sequence, our study provides novel in vivo evidence that nucleosome positions are also affected by the position of neighboring nucleosomes. Nucleosome structure may therefore be an important selective force for conservation of gene order on a chromosome, because relocating a gene to another genomic position (where the positions of neighboring nucleosomes are different from the original locus) can have dramatic consequences for the gene's nucleosome structure and thus its expression.

  3. Visualization of structures and cosmic flows in the local Universe

    NASA Astrophysics Data System (ADS)

    Pomarède, Daniel; Courtois, Hélène; Tully, R. Brent

    2013-02-01

    A visualization of 3D structures and cosmic flows is presented using information from the Extragalactic Distance Database V8k redshift catalog and peculiar velocities from the Cosmicflows-1 survey. Structures within a volume bounded at 8000 km s-1 on the cardinal Supergalactic axes are explored in terms of both displaying the positions of the 30,124 galaxies of the catalog and its reconstructed luminosity density field, corrected to account for growing incompleteness with increasing distance. Cosmography of the local Universe is discussed with the intent to identify the most prominent structures, including voids, galaxy clusters, filaments, and walls. The mapping also benefits from precise distance measures provided through the Cosmicflows-1 observational program. Three-dimensional visualizations of the coherent flows of galaxies in the nearby Universe are presented, using recent results based on reconstruction of cosmic flows with the Wiener filter approach. The three major components of the Milky Way's motion, namely expulsion from the Local Void, infall toward the Virgo Cluster, and the bulk flow of the historic Local Supercluster toward the Great Attractor are illustrated using different visualization techniques and analyzed in light of the cosmography derived from the V8k redshift and Cosmicflows-1 distance catalogs.

  4. Cosmic structure and dynamics of the local Universe

    NASA Astrophysics Data System (ADS)

    Kitaura, Francisco-Shu; Erdoǧdu, Pirin; Nuza, Sebastián. E.; Khalatyan, Arman; Angulo, Raul E.; Hoffman, Yehuda; Gottlöber, Stefan

    2012-11-01

    We present a cosmography analysis of the local Universe based on the recently released Two-Micron All-Sky Redshift Survey catalogue. Our method is based on a Bayesian Networks Machine Learning algorithm (the KIGEN-code) which self-consistently samples the initial density fluctuations compatible with the observed galaxy distribution and a structure formation model given by second-order Lagrangian perturbation theory (2LPT). From the initial conditions we obtain an ensemble of reconstructed density and peculiar velocity fields which characterize the local cosmic structure with high accuracy unveiling non-linear structures like filaments and voids in detail. Coherent redshift-space distortions are consistently corrected within 2LPT. From the ensemble of cross-correlations between the reconstructions and the galaxy field and the variance of the recovered density fields, we find that our method is extremely accurate up to k˜ 1 h Mpc-1 and still yields reliable results down to scales of about 3-4 h-1 Mpc. The motion of the Local Group we obtain within ˜80 h-1 Mpc (vLG = 522 ± 86 km s-1, lLG = 291° ± 16°, bLG = 34° ± 8°) is in good agreement with measurements derived from the cosmic microwave background and from direct observations of peculiar motions and is consistent with the predictions of ΛCDM.

  5. Training effects and the microscopic magnetic structure of exchange biased Co/CoO bilayers.

    SciTech Connect

    Berger, A.; Dahlberg, E. D.; Felcher, G. P.; Hill, B. K.; te Velthius, S. G. E.

    1999-09-01

    Exchange bias of a partially oxidized thin film of ferromagnetic Co was studied by magnetization measurements and polarized neutron reflectivity (PNR). The magnetization curve shows strong effects of training with cycling of the magnetic field. Reflectivity measurements with the field parallel to the cooling field showed the onset of spin-dependent diffuse scattering--off the specular reflection--after a training cycle. Such scattering, of the Yoneda type, is due to misaligned Co domains possibly close to the Co/CoO interface. Subjecting the field cooled Co/CoO pair to a field perpendicular to the cooling field causes a rotation of the magnetization. PNR measurements confirmed earlier susceptibility studies by indicating that the rotation of the magnetization is reversible in fields up to 400 Oe. The rotation of the magnetization of Co is uniform across the film thickness.

  6. Clipping the cosmos: the bias and bispectrum of large scale structure.

    PubMed

    Simpson, Fergus; James, J Berian; Heavens, Alan F; Heymans, Catherine

    2011-12-30

    A large fraction of the information collected by cosmological surveys is simply discarded to avoid length scales which are difficult to model theoretically. We introduce a new technique which enables the extraction of useful information from the bispectrum of galaxies well beyond the conventional limits of perturbation theory. Our results strongly suggest that this method increases the range of scales where the relation between the bispectrum and power spectrum in tree-level perturbation theory may be applied, from k(max) ∼ 0.1 to ∼0.7 hMpc(-1). This leads to correspondingly large improvements in the determination of galaxy bias. Since the clipped matter power spectrum closely follows the linear power spectrum, there is the potential to use this technique to probe the growth rate of linear perturbations and confront theories of modified gravity with observation.

  7. Electronic Structure, Localization and 5f Occupancy in Pu Materials

    SciTech Connect

    Joyce, John J.; Beaux, Miles F.; Durakiewicz, Tomasz; Graham, Kevin S.; Bauer, Eric D.; Mitchell, Jeremy N.; Tobash, Paul H.; Richmond, Scott

    2012-05-03

    The electronic structure of delta plutonium ({delta}-Pu) and plutonium compounds is investigated using photoelectron spectroscopy (PES). Results for {delta}-Pu show a small component of the valence electronic structure which might reasonably be associated with a 5f{sup 6} configuration. PES results for PuTe are used as an indication for the 5f{sup 6} configuration due to the presence of atomic multiplet structure. Temperature dependent PES data on {delta}-Pu indicate a narrow peak centered 20 meV below the Fermi energy and 100 meV wide. The first PES data for PuCoIn5 indicate a 5f electronic structure more localized than the 5fs in the closely related PuCoGa{sub 5}. There is support from the PES data for a description of Pu materials with an electronic configuration of 5f{sup 5} with some admixture of 5f{sup 6} as well as a localized/delocalized 5f{sup 5} description.

  8. Structural damage localization using wavelet-based silhouette statistics

    NASA Astrophysics Data System (ADS)

    Jung, Uk; Koh, Bong-Hwan

    2009-04-01

    This paper introduces a new methodology for classifying and localizing structural damage in a truss structure. The application of wavelet analysis along with signal classification techniques in engineering problems allows us to discover novel characteristics that can be used for the diagnosis and classification of structural defects. This study exploits the data discriminating capability of silhouette statistics, which is eventually combined with the wavelet-based vertical energy threshold technique for the purpose of extracting damage-sensitive features and clustering signals of the same class. This threshold technique allows us to first obtain a suitable subset of the extracted or modified features of our data, i.e. good predictor sets should contain features that are strongly correlated to the characteristics of the data without considering the classification method used, although each of these features should be as uncorrelated with each other as possible. The silhouette statistics have been used to assess the quality of clustering by measuring how well an object is assigned to its corresponding cluster. We use this concept for the discriminant power function used in this paper. The simulation results of damage detection in a truss structure show that the approach proposed in this study can be successfully applied for locating both open- and breathing-type damage even in the presence of a considerable amount of process and measurement noise. Finally, a typical data mining tool such as classification and regression tree (CART) quantitatively evaluates the performance of the damage localization results in terms of the misclassification error.

  9. Probing local structure in glass by the application of shear

    NASA Astrophysics Data System (ADS)

    Weingartner, Nicholas B.; Nussinov, Zohar

    2016-09-01

    The glass transition remains one of the great unsolved mysteries of contemporary condensed matter physics. When crystallization is bypassed by rapid cooling, a supercooled liquid, retaining amorphous particle arrangement, results. The physical phenomenology of supercooled liquids is as vast as it is interesting. Most significant, the viscosity of the supercooled liquid displays an incredible increase over a narrow temperature range. Eventually, the supercooled liquid ceases to flow, becomes a glass, and gains rigidity and solid-like behaviors. Understanding what underpins the monumental growth of viscosity, and how rigidity results without long range order is a long-sought goal. Furthermore, discerning what role local structure plays in the kinetics of supercooled liquids remains an open question. Many theories of the glassy slowdown require the growth of static lengthscale related to structure with lowering of the temperature and provide a link between slowdown and propagation of ‘amorphous order’. In light of this, we examine the recently proposed shear penetration depth in the context of other length scales and its relation to local structure. We provide numerical data, based on the simulations of NiZr2, illustrating that this length scale exhibits dramatic growth upon approach to the glass transition and further discuss this in relation to percolating structural connectivity in similar glassforming systems.

  10. Local Structure of Cerium in Aluminophosphate and Silicophosphate Glasses

    SciTech Connect

    J Rygel; Y Chen; C Pantano; T Shibata; J Du; L Kokou; R Woodman; J Belcher

    2011-12-31

    The local structure of cerium in two systematic compositional series of glasses, nominally CeP{sub 3}O{sub 9}-AlP{sub 3}O{sub 9} and CeP{sub 3}O{sub 9}-SiP{sub 2}O{sub 7}, was interrogated using X-ray photoelectron spectroscopy (XPS) and X-ray absorption fine structure (XAFS) spectroscopy. XPS revealed that, for glasses melted in air, {>=}95% of cerium ions are Ce{sup 3+}. This was independently confirmed using X-ray absorption near edge spectroscopy (XANES). Ce K-edge extended X-ray absorption fine structure (EXAFS) has been used to determine the local structure of Ce{sup 3+}. Near the metaphosphate composition, cerium was found to have an average cerium coordination number of {approx}7.0 and an average cerium-oxygen bond length of 2.41 {angstrom}. The average cerium coordination number and average cerium-oxygen bond distance were found to increase with decreasing cerium concentration in both compositional series. Rare-earth clustering is suggested based on numerical calculations for glasses containing {>=}14 and {>=}15 mol% Ce{sub 2}O{sub 3} for the aluminophosphate and silicophosphate series, respectively.

  11. Local Structure of Cerium in Aluminophosphate and Silicophosphate Glasses

    SciTech Connect

    Rygel, Jennifer L.; Chen, Yongsheng; Pantano, Carlo G.; Shibata, Tomohiro; Du, Jincheng; Kokou, Leopold; Woodman, Robert; Belcher, James

    2011-09-20

    The local structure of cerium in two systematic compositional series of glasses, nominally CeP{sub 3}O{sub 9}-AlP{sub 3}O{sub 9} and CeP{sub 3}O{sub 9}-SiP{sub 2}O{sub 7}, was interrogated using X-ray photoelectron spectroscopy (XPS) and X-ray absorption fine structure (XAFS) spectroscopy. XPS revealed that, for glasses melted in air, {>=}95% of cerium ions are Ce{sup 3+}. This was independently confirmed using X-ray absorption near edge spectroscopy (XANES). Ce K-edge extended X-ray absorption fine structure (EXAFS) has been used to determine the local structure of Ce{sup 3+}. Near the metaphosphate composition, cerium was found to have an average cerium coordination number of {approx}7.0 and an average cerium-oxygen bond length of 2.41 {angstrom}. The average cerium coordination number and average cerium-oxygen bond distance were found to increase with decreasing cerium concentration in both compositional series. Rare-earth clustering is suggested based on numerical calculations for glasses containing {>=}14 and {>=}15 mol% Ce{sub 2}O{sub 3} for the aluminophosphate and silicophosphate series, respectively.

  12. Eliminating Bias

    EPA Pesticide Factsheets

    Learn how to eliminate bias from monitoring systems by instituting appropriate installation, operation, and quality assurance procedures. Provides links to download An Operator's Guide to Eliminating Bias in CEM Systems.

  13. Localization and structure of carbonaceous deposits on reforming catalysts

    SciTech Connect

    Espinat, D.; Freund, E.; Martino, G. ); Dexpert, H. , Orsay )

    1990-12-01

    The aging of alumina-supported Pt-containing reforming catalysts by coke deposition has previously been extensively investigated. In the present work, a large number of techniques including optical and electron microscopy have been used to determine both the localization and the structure of the so-called coke (carbonaceous deposits) formed during the normal operation of these catalysts. The coke is not uniformly deposited on the surface of the catalysts. Its structure is not uniform for a given catalyst, and depends on the operating condition (especially the H{sub 2}/hydrocarbon ratio) as well as the composition of the metallic phase (pure platinum or multimetallic alloy). The structure is always rather well organized (pregraphitic) even at the onset of coke deposition.

  14. Electronic-structure calculation for metals by local optimization

    NASA Astrophysics Data System (ADS)

    Woodward, C.; Min, B. I.; Benedek, R.; Garner, J.

    1989-03-01

    Recent work by Car and Parrinello has generated considerable interest in the calculation of electronic structure by nonlinear optimization. The technique introduced by these authors, dynamical simulated annealing, is designed for problems that involve energy barriers. When local optimization suffices to determine the energy minimum, more direct methods are available. In this paper we apply the algorithm suggested by Williams and Soler to calculate the electronic structure of metals, using a plane-wave expansion for the electronic orbitals and an electron-ion pseudopotential of the Kleinman-Bylander form. Radial pseudopotentials were taken from the compilation of Bachelet, Hamann, and Schlüter. Calculations are performed to optimize the electronic structure (i) with fixed atomic configuration, or (ii) with the atomic volume being optimized simultaneously. It is found that the dual optimization (ii) converges in essentially the same number of steps as the static lattice optimization (i). Numerical results are presented for Li, K, Al, and simple-cubic P.

  15. Off-easy-plane antiferromagnetic spin canting in coupled FePt/NiO bilayer structure with perpendicular exchange bias

    NASA Astrophysics Data System (ADS)

    Gao, Tenghua; Itokawa, Nobuhide; Wang, Jian; Yu, Youxing; Harumoto, Takashi; Nakamura, Yoshio; Shi, Ji

    2016-08-01

    We report on the investigation of perpendicular exchange bias in FePt (001 ) /NiO (1 ¯1 ¯1 ) orthogonal exchange couple with FePt partially L 10 ordered. From initial magnetization curve measurement and magnetic domain imaging, we find that, for the as-grown bilayer structure, the FePt layer experiences a small-angle magnetization rotation when it is magnetized near to saturation in film normal direction. After field cooling, the bilayer structure shows a significant enhancement of perpendicular magnetic anisotropy, indicating the field mediated coupling between the spins across the FePt/NiO interface. According to Koon's theoretical calculation on the basis of lowest energy ferromagnetic/antiferromagnetic coupling configuration for compensated spins at antiferromagnetic side, we consider slightly slanted Ni spins at the interface off the (1 ¯1 ¯1 ) easy plane can stabilize the spin coupling between FePt and NiO and result in the observed exchange bias in this paper. This consideration was further confirmed by stripe domain width calculation.

  16. Electron-beam-induced current measurements with applied bias provide insight to locally resolved acceptor concentrations at p-n junctions

    SciTech Connect

    Abou-Ras, D. Schäfer, N.; Baldaz, N.; Brunken, S.; Boit, C.

    2015-07-15

    Electron-beam-induced current (EBIC) measurements have been employed for the investigation of the local electrical properties existing at various types of electrical junctions during the past decades. In the standard configuration, the device under investigation is analyzed under short-circuit conditions. Further insight into the function of the electrical junction can be obtained when applying a bias voltage. The present work gives insight into how EBIC measurements at applied bias can be conducted at the submicrometer level, at the example of CuInSe{sub 2} solar cells. From the EBIC profiles acquired across ZnO/CdS/CuInSe{sub 2}/Mo stacks exhibiting p-n junctions with different net doping densities in the CuInSe{sub 2} layers, values for the width of the space-charge region, w, were extracted. For all net doping densities, these values decreased with increasing applied voltage. Assuming a linear relationship between w{sup 2} and the applied voltage, the resulting net doping densities agreed well with the ones obtained by means of capacitance-voltage measurements.

  17. Role of nonlinear localized structures and turbulence in magnetized plasma

    NASA Astrophysics Data System (ADS)

    Pathak, Neha; Yadav, Nitin; Uma, R.; Sharma, R. P.

    2016-09-01

    In the present study, we have analyzed the field localization of kinetic Alfvén wave (KAW) due to the presence of background density perturbation, which are assumed to be originated by the three dimensionally propagating low frequency KAW. These localized structures play an important role for energy transportation at smaller scales in the dispersion range of magnetic power spectrum. For the present model, governing dynamic equations of high frequency pump KAW and low frequency KAW has been derived by considering ponderomotive nonlinearity. Further, these coupled equations have been numerically solved to analyze the resulting localized structures of pump KAW and magnetic power spectrum in the magnetopause regime. Numerically calculated spectrum exhibits inertial range having spectral index of -3/2 followed by steeper scaling; this steepening in the turbulent spectrum is a signature of energy transportation from larger to smaller scales. In this way, the proposed mechanism, which is based on nonlinear wave-wave interaction, may be useful for understanding the particle acceleration and turbulence in magnetopause.

  18. The local electronic structure of alpha-Li3N.

    PubMed

    Fister, T T; Seidler, G T; Shirley, E L; Vila, F D; Rehr, J J; Nagle, K P; Linehan, J C; Cross, J O

    2008-07-28

    New theoretical and experimental investigations of the occupied and unoccupied local electronic densities of states (DOS) are reported for alpha-Li(3)N. Band-structure and density-functional theory calculations confirm the absence of covalent bonding character. However, real-space full-multiple-scattering (RSFMS) calculations of the occupied local DOS find less extreme nominal valences than have previously been proposed. Nonresonant inelastic x-ray scattering, RSFMS calculations, and calculations based on the Bethe-Salpeter equation are used to characterize the unoccupied electronic final states local to both the Li and N sites. There is a good agreement between experiment and theory. Throughout the Li 1s near-edge region, both experiment and theory find strong similarities in the s-and p-type components of the unoccupied local final DOS projected onto an orbital angular momentum basis (l-DOS). An unexpected, significant correspondence exists between the near-edge spectra for the Li 1s and N 1s initial states. We argue that both spectra are sampling essentially the same final DOS due to the combination of long core-hole lifetimes, long photoelectron lifetimes, and the fact that orbital angular momentum is the same for all relevant initial states. Such considerations may be generally applicable for low atomic number compounds.

  19. Localizing target structures in ultrasound video - a phantom study.

    PubMed

    Kwitt, R; Vasconcelos, N; Razzaque, S; Aylward, S

    2013-10-01

    The problem of localizing specific anatomic structures using ultrasound (US) video is considered. This involves automatically determining when an US probe is acquiring images of a previously defined object of interest, during the course of an US examination. Localization using US is motivated by the increased availability of portable, low-cost US probes, which inspire applications where inexperienced personnel and even first-time users acquire US data that is then sent to experts for further assessment. This process is of particular interest for routine examinations in underserved populations as well as for patient triage after natural disasters and large-scale accidents, where experts may be in short supply. The proposed localization approach is motivated by research in the area of dynamic texture analysis and leverages several recent advances in the field of activity recognition. For evaluation, we introduce an annotated and publicly available database of US video, acquired on three phantoms. Several experiments reveal the challenges of applying video analysis approaches to US images and demonstrate that good localization performance is possible with the proposed solution. Copyright © 2013 Elsevier B.V. All rights reserved.

  20. Protein structure prediction with local adjust tabu search algorithm

    PubMed Central

    2014-01-01

    Background Protein folding structure prediction is one of the most challenging problems in the bioinformatics domain. Because of the complexity of the realistic protein structure, the simplified structure model and the computational method should be adopted in the research. The AB off-lattice model is one of the simplification models, which only considers two classes of amino acids, hydrophobic (A) residues and hydrophilic (B) residues. Results The main work of this paper is to discuss how to optimize the lowest energy configurations in 2D off-lattice model and 3D off-lattice model by using Fibonacci sequences and real protein sequences. In order to avoid falling into local minimum and faster convergence to the global minimum, we introduce a novel method (SATS) to the protein structure problem, which combines simulated annealing algorithm and tabu search algorithm. Various strategies, such as the new encoding strategy, the adaptive neighborhood generation strategy and the local adjustment strategy, are adopted successfully for high-speed searching the optimal conformation corresponds to the lowest energy of the protein sequences. Experimental results show that some of the results obtained by the improved SATS are better than those reported in previous literatures, and we can sure that the lowest energy folding state for short Fibonacci sequences have been found. Conclusions Although the off-lattice models is not very realistic, they can reflect some important characteristics of the realistic protein. It can be found that 3D off-lattice model is more like native folding structure of the realistic protein than 2D off-lattice model. In addition, compared with some previous researches, the proposed hybrid algorithm can more effectively and more quickly search the spatial folding structure of a protein chain. PMID:25474708

  1. Clinal resistance structure and pathogen local adaptation in a serpentine flax-flax rust interaction.

    PubMed

    Springer, Yuri P

    2007-08-01

    Because disease resistance is a hallmark signature of pathogen-mediated selection pressure on hosts, studies of resistance structure (the spatial distribution of disease resistance genes among conspecific host populations) can provide valuable insights into the influence of pathogens on host evolution and spatial variation in the magnitude of their effects. To date few studies of wild plant-pathogen interactions have characterized resistance structure by sampling across the host's biogeographic range, and only a handful have paired such investigations with studies of disease levels under natural conditions. I used a greenhouse cross-inoculation experiment to characterize genetic resistance of 16 populations of California dwarf flax (Hesperolinon californicum) to attack by multiple samples of the rust fungus Melampsora lini. I documented a latitudinal cline in resistance structure, manifest across the host's biogeographic range, which mirrored almost identically a cline in infection prevalence documented through field surveys of disease in study populations. These results provide empirical evidence for clinal patterns of antagonistic selection pressure, demonstrate that such patterns can be manifest across broad biogeographic scales, and suggest that rates of disease prevalence in wild plant populations may be tightly linked to the distribution of host resistance genes. Tests for local adaptation of the fungus revealed evidence of the phenomenon (significantly greater infection in sympatric plant-fungal pairings) as well as the potential for substantial bias to be introduced into statistical analyses by spatial patterns of host resistance structure.

  2. Synonymous codon usage influences the local protein structure observed

    PubMed Central

    Saunders, Rhodri; Deane, Charlotte M.

    2010-01-01

    Translation of mRNA into protein is a unidirectional information flow process. Analysing the input (mRNA) and output (protein) of translation, we find that local protein structure information is encoded in the mRNA nucleotide sequence. The Coding Sequence and Structure (CSandS) database developed in this work provides a detailed mapping between over 4000 solved protein structures and their mRNA. CSandS facilitates a comprehensive analysis of codon usage over many organisms. In assigning translation speed, we find that relative codon usage is less informative than tRNA concentration. For all speed measures, no evidence was found that domain boundaries are enriched with slow codons. In fact, genes seemingly avoid slow codons around structurally defined domain boundaries. Translation speed, however, does decrease at the transition into secondary structure. Codons are identified that have structural preferences significantly different from the amino acid they encode. However, each organism has its own set of ‘significant codons’. Our results support the premise that codons encode more information than merely amino acids and give insight into the role of translation in protein folding. PMID:20530529

  3. Change of Electronic Structures by Dopant-Induced Local Strain

    NASA Astrophysics Data System (ADS)

    Hyeong Kim, Gyu; Jeong, Sukmin

    2015-06-01

    Ag-induced Si(111)- surfaces (-Ag) exhibit unusual electronic structures that cannot be explained by the conventional rigid band model and charge transfer model. The (-Ag surfaces feature a free-electron-like parabolic band, the S1 band, that selectively shifts downward upon the adsorption of noble metal or alkali metal adatoms. Furthermore, the downward shift of S1 is independent of the type of dopants, Au, Ag, and Na. According to charge transfer analysis, Au adatoms accumulate electrons from the substrate and become negatively charged, whereas Na adatoms become positively charged, which indicates that S1 should shift in the opposite direction for both the adatoms. Investigation of calculated structures, calculation of model structures, and tight-binding analysis disclose that the changes in the electronic structure are closely related to the average Ag-Ag distance in the substrate and have their origin in the local strain induced by dopants (adatoms). This explanation implies that the electronic structure is irrespective of the dopant characters itself and paves a new way for understanding the electronic structures associated with the presence of dopants.

  4. Support for a link between the local processing bias and social deficits in autism: an investigation of embedded figures test performance in non-clinical individuals.

    PubMed

    Russell-Smith, Suzanna N; Maybery, Murray T; Bayliss, Donna M; Sng, Adelln A H

    2012-11-01

    The aim of this investigation was to explore the degree to which specific subsets of autistic-like traits relate to performance on the Embedded Figures Test (Witkin et al. in A manual for the embedded figures test. Consulting Psychologists Press, Palo Alto, CA, 1971). In the first group-based investigation with this focus, students were selected for their extreme scores (either high or low) on each of the 'Social Skills' and 'Details/Patterns' factors of the Autism Spectrum Quotient (Baron-Cohen et al. in J Austim Dev Disord 31:5-17, 2001). The resulting 2 × 2 factorial design permitted examination of the degree to which the social and non-social autistic-like traits separately relate to EFT performance. Surprisingly, in two studies, superior EFT performance was found to relate only to greater social difficulty, suggesting that the local processing bias in autism may be linked specifically to the social deficits.

  5. What is the difference between OASIS and OPERA? Roughly five pixels: orthographic structure biases the perceived length of letter strings.

    PubMed

    Chetail, Fabienne; Content, Alain

    2014-01-01

    A thorough understanding of monosyllabic-word-recognition processes, in contrast with multisyllabic-word processing, has accumulated over the past decades. One fundamental challenge regarding multisyllabic words concerns their parsing into smaller units and the nature of the cues determining the parsing. We propose that the organization of consonant and vowel letters provides powerful cues for parsing, and we present data from a new task showing that a word's orthographic structure, as determined by the number of vowel-letter clusters, influences estimations of its length. Words were briefly presented on a computer screen, and participants had to estimate word length by drawing a line on the screen with the mouse. In three experiments, participants estimated words comprising fewer orthographic units as shorter than words comprising more units even though the words matched for number of letters. Further results demonstrated that the length bias was driven by orthographic information and not by phonological structure.

  6. Measuring capital market efficiency: Global and local correlations structure

    NASA Astrophysics Data System (ADS)

    Kristoufek, Ladislav; Vosvrda, Miloslav

    2013-01-01

    We introduce a new measure for capital market efficiency. The measure takes into consideration the correlation structure of the returns (long-term and short-term memory) and local herding behavior (fractal dimension). The efficiency measure is taken as a distance from an ideal efficient market situation. The proposed methodology is applied to a portfolio of 41 stock indices. We find that the Japanese NIKKEI is the most efficient market. From a geographical point of view, the more efficient markets are dominated by the European stock indices and the less efficient markets cover mainly Latin America, Asia and Oceania. The inefficiency is mainly driven by a local herding, i.e. a low fractal dimension.

  7. Correlation Between Local Structure and Boson Peak in Metallic Glasses

    NASA Astrophysics Data System (ADS)

    Ahmad, Azkar Saeed; Zhao, Xiangnan; Xu, Mingxiang; Zhang, Dongxian; Hu, Junwen; Fecht, Hans J.; Wang, Xiaodong; Cao, Qingping; Jiang, J. Z.

    2017-01-01

    We made a systematic study of the boson peak for six different Zr-based metallic glasses and found a universal correlation between average local atomic structure and boson peak. It is found that the boson peak can be decomposed into six characteristic vibratory modes, i.e., Debye's vibratory mode and five Einstein's vibratory modes. By using the Ioffe-Regel condition over all studied Zr-based metallic glasses, we reveal that atomic pair correlation function exactly maps on the low-temperature dynamics and the origin of the boson peak, which is the sum of vibrations of local density fluctuation domains in the glasses. In addition, it is found that the Debye's type oscillators are the major contributors to the low-temperature specific heat capacities. This study opens a new way of understanding the relationship of the physical properties with the atomic arrangements in glasses.

  8. CONDENSED MATTER: ELECTRONIC STRUCTURE, ELECTRICAL, MAGNETIC, AND OPTICAL PROPERTIES Electronic Transport Calculations Using Maximally-Localized Wannier Functions

    NASA Astrophysics Data System (ADS)

    Wang, Neng-Ping

    2011-01-01

    I present a method to calculate the ballistic transport properties of atomic-scale structures under bias. The electronic structure of the system is calculated using the Kohn-Sham scheme of density functional theory (DFT). The DFT eigenvectors are then transformed into a set of maximally localized Wannier functions (MLWFs) [N. Marzari and D. Vanderbilt, Phys. Rev. B 56 (1997) 12847]. The MLWFs are used as a minimal basis set to obtain the Hamitonian matrices of the scattering region and the adjacent leads, which are needed for transport calculation using the nonequilibrium Green's function formalism. The coupling of the scattering region to the semi-infinite leads is described by the self-energies of the leads. Using the nonequilibrium Green's function method, one calculates self-consistently the charge distribution of the system under bias and evaluates the transmission and current through the system. To solve the Poisson equation within the scheme of MLWFs I introduce a computationally efficient method. The method is applied to a molecular hydrogen contact in two transition metal monatomic wires (Cu and Pt). It is found that for Pt the I-V characteristics is approximately linear dependence, however, for Cu the I-V characteristics manifests a linear dependence at low bias voltages and exhibits apparent nonlinearity at higher bias voltages. I have also calculated the transmission in the zero bias voltage limit for a single CO molecule adsorbed on Cu and Pt monatomic wires. While a chemical scissor effect occurs for the Cu monatomic wire with an adsorbed CO molecule, it is absent for the Pt monatomic wire due to the contribution of d-orbitals at the Fermi energy.

  9. Attention Orienting in Response to Non-conscious Hierarchical Arrows: Individuals with Higher Autistic Traits Differ in Their Global/Local Bias

    PubMed Central

    Laycock, Robin; Chan, Daniel; Crewther, Sheila G.

    2017-01-01

    One aspect of the social communication impairments that characterize autism spectrum disorder (ASD) include reduced use of often subtle non-verbal social cues. People with ASD, and those with self-reported sub-threshold autistic traits, also show impairments in rapid visual processing of stimuli unrelated to social or emotional properties. Hence, this study sought to investigate whether perceptually non-conscious visual processing is related to autistic traits. A neurotypical sample of thirty young adults completed the Subthreshold Autism Trait Questionnaire and a Posner-like attention cueing task. Continuous Flash Suppression (CFS) was employed to render incongruous hierarchical arrow cues perceptually invisible prior to consciously presented targets. This was achieved via a 10 Hz masking stimulus presented to the dominant eye that suppressed information presented to the non-dominant eye. Non-conscious arrows consisted of local arrow elements pointing in one direction, and forming a global arrow shape pointing in the opposite direction. On each trial, the cue provided either a valid or invalid cue for the spatial location of the subsequent target, depending on which level (global or local) received privileged attention. A significant autism-trait group by global cue validity interaction indicated a difference in the extent of non-conscious local/global cueing between groups. Simple effect analyses revealed that whilst participants with lower autistic traits showed a global arrow cueing effect, those with higher autistic traits demonstrated a small local arrow cueing effect. These results suggest that non-conscious processing biases in local/global attention may be related to individual differences in autistic traits. PMID:28149288

  10. A Phenomenological Theory of Spatially Structured Local Synaptic Connectivity

    PubMed Central

    Amirikian, Bagrat

    2005-01-01

    The structure of local synaptic circuits is the key to understanding cortical function and how neuronal functional modules such as cortical columns are formed. The central problem in deciphering cortical microcircuits is the quantification of synaptic connectivity between neuron pairs. I present a theoretical model that accounts for the axon and dendrite morphologies of pre- and postsynaptic cells and provides the average number of synaptic contacts formed between them as a function of their relative locations in three-dimensional space. An important aspect of the current approach is the representation of a complex structure of an axonal/dendritic arbor as a superposition of basic structures—synaptic clouds. Each cloud has three structural parameters that can be directly estimated from two-dimensional drawings of the underlying arbor. Using empirical data available in literature, I applied this theory to three morphologically different types of cell pairs. I found that, within a wide range of cell separations, the theory is in very good agreement with empirical data on (i) axonal–dendritic contacts of pyramidal cells and (ii) somatic synapses formed by the axons of inhibitory interneurons. Since for many types of neurons plane arborization drawings are available from literature, this theory can provide a practical means for quantitatively deriving local synaptic circuits based on the actual observed densities of specific types of neurons and their morphologies. It can also have significant implications for computational models of cortical networks by making it possible to wire up simulated neural networks in a realistic fashion. PMID:16103900

  11. Local structure in hard-sphere chain-molecule fluids

    NASA Astrophysics Data System (ADS)

    Wasti, Sambid; Taylor, Mark

    2012-04-01

    The conformation of a polymer chain in solvent is coupled to the local structure of the solvent environment. For hard-sphere systems, a monomeric solvent acts to compress a flexible hard-sphere-solute chain and, for a dense system, the local solvent structure is imprinted onto the chain. Here we use Monte Carlo simulation, including bond-rebridging moves, to study the size and conformation of a hard sphere chain in a hard-sphere solvent as a function of both solvent density and solvent diameter. We also study the structure of a hard-sphere-chain solute in a hard-sphere-chain solvent. In the case of a 5-mer chain in 5-mer solvent we show that the effects of solvent can be mapped to a set of two-body solvation potentials. Following our previous work on hard-sphere chains in monomeric solvent [1], we explore the application of these short chain potentials to the study of longer chain-molecule fluids. [4pt] [1] M.P. Taylor and S. Ichida, J. Polym. Sci. B: Polym. Phys. 45, 3319 (2007).

  12. Local structure in hard-sphere chain-molecule fluids

    NASA Astrophysics Data System (ADS)

    Wasti, Sambid; Taylor, Mark

    2011-10-01

    The conformation of a polymer chain in solvent is coupled to the local structure of the solvent environment. For hard-sphere systems, a monomeric solvent acts to compress a flexible hard-sphere-solute chain and, for a dense system, the local solvent structure is imprinted onto the chain. Here we use Monte Carlo simulation, including bond-rebridging moves, to study the size and conformation of a hard sphere chain in a hard-sphere solvent as a function of both solvent density and solvent diameter. We also study the structure of a hard-sphere-chain solute in a hard-sphere-chain solvent. In the case of a 5-mer chain in 5-mer solvent we show that the effects of solvent can be mapped to a set of two-body solvation potentials. Following our previous work on hard-sphere chains in monomeric solvent [1], we explore the application of these short chain potentials to the study of longer chain-molecule fluids. [4pt] [1] M.P. Taylor and S. Ichida, J. Polym. Sci. B: Polym. Phys. 45, 3319 (2007).

  13. Effect of negative bias voltage on CrN films deposited by arc ion plating. II. Film composition, structure, and properties

    SciTech Connect

    Wang Qimin; Kim, Kwang Ho

    2008-09-15

    Chromium nitride (CrN) films were deposited on Si wafers by arc ion plating at various negative bias voltages and several groups of N{sub 2}/Ar gas flux ratios and chamber gas pressures. The authors systematically investigated the influence of negative bias voltage on the synthesis, composition, microstructure, and properties of the arc ion plating (AIP) CrN films. In this article, the authors investigated the influence of negative bias voltage on the chemical composition, structure, and mechanical properties of the CrN films. The results showed that the chemical composition and phase structure of the AIP CrN films were greatly altered by application of negative bias voltage. Due to the selective resputtering effect, substoichiometric CrN films were obtained. With increase in bias voltages, the main phases in the films transformed from Cr+CrN to Cr{sub 2}N at low N{sub 2}/Ar flow ratios, whereas the films at high N{sub 2}/Ar flow ratios retained the CrN phase structure. The CrN films experienced texture transformation from CrN (200) to CrN (220), and Cr{sub 2}N (300) to Cr{sub 2}N(300)+Cr{sub 2}N(110). Increase in negative bias voltage also resulted in microstructure evolution of coarse columnar grains{yields}fine columnar grains{yields}quasiamorphous microstructure{yields}recrystallized structures. From the experimental results, the authors proposed a new structure zone model based on enhanced bombardment of incident ions by application of negative bias voltage. The influence of negative bias voltage on the microhardness and residual stresses of the films and the inherent mechanisms were also explored.

  14. Local pulmonary structure classification for computer-aided nodule detection

    NASA Astrophysics Data System (ADS)

    Bahlmann, Claus; Li, Xianlin; Okada, Kazunori

    2006-03-01

    We propose a new method of classifying the local structure types, such as nodules, vessels, and junctions, in thoracic CT scans. This classification is important in the context of computer aided detection (CAD) of lung nodules. The proposed method can be used as a post-process component of any lung CAD system. In such a scenario, the classification results provide an effective means of removing false positives caused by vessels and junctions thus improving overall performance. As main advantage, the proposed solution transforms the complex problem of classifying various 3D topological structures into much simpler 2D data clustering problem, to which more generic and flexible solutions are available in literature, and which is better suited for visualization. Given a nodule candidate, first, our solution robustly fits an anisotropic Gaussian to the data. The resulting Gaussian center and spread parameters are used to affine-normalize the data domain so as to warp the fitted anisotropic ellipsoid into a fixed-size isotropic sphere. We propose an automatic method to extract a 3D spherical manifold, containing the appropriate bounding surface of the target structure. Scale selection is performed by a data driven entropy minimization approach. The manifold is analyzed for high intensity clusters, corresponding to protruding structures. Techniques involve EMclustering with automatic mode number estimation, directional statistics, and hierarchical clustering with a modified Bhattacharyya distance. The estimated number of high intensity clusters explicitly determines the type of pulmonary structures: nodule (0), attached nodule (1), vessel (2), junction (>3). We show accurate classification results for selected examples in thoracic CT scans. This local procedure is more flexible and efficient than current state of the art and will help to improve the accuracy of general lung CAD systems.

  15. Characterizing structural transitions using localized free energy landscape analysis.

    PubMed

    Banavali, Nilesh K; Mackerell, Alexander D

    2009-01-01

    Structural changes in molecules are frequently observed during biological processes like replication, transcription and translation. These structural changes can usually be traced to specific distortions in the backbones of the macromolecules involved. Quantitative energetic characterization of such distortions can greatly advance the atomic-level understanding of the dynamic character of these biological processes. Molecular dynamics simulations combined with a variation of the Weighted Histogram Analysis Method for potential of mean force determination are applied to characterize localized structural changes for the test case of cytosine (underlined) base flipping in a GTCAGCGCATGG DNA duplex. Free energy landscapes for backbone torsion and sugar pucker degrees of freedom in the DNA are used to understand their behavior in response to the base flipping perturbation. By simplifying the base flipping structural change into a two-state model, a free energy difference of upto 14 kcal/mol can be attributed to the flipped state relative to the stacked Watson-Crick base paired state. This two-state classification allows precise evaluation of the effect of base flipping on local backbone degrees of freedom. The calculated free energy landscapes of individual backbone and sugar degrees of freedom expectedly show the greatest change in the vicinity of the flipping base itself, but specific delocalized effects can be discerned upto four nucleotide positions away in both 5' and 3' directions. Free energy landscape analysis thus provides a quantitative method to pinpoint the determinants of structural change on the atomic scale and also delineate the extent of propagation of the perturbation along the molecule. In addition to nucleic acids, this methodology is anticipated to be useful for studying conformational changes in all macromolecules, including carbohydrates, lipids, and proteins.

  16. The perceived effectiveness of persuasive messages: questions of structure, referent, and bias.

    PubMed

    Dillard, James Price; Ye, Sun

    2008-03-01

    To gain a sense of the persuasive efficacy of a message prior to implementation of a campaign, researchers often gather judgments of perceived effectiveness (PE). At present, they do so without much knowledge of the conceptual meaning or empirical properties of PE. In the spirit of construct explication, we report a study intended to address a series of questions about PE. Using student (N = 155) and community samples (N = 100), we found the following: (a) PE is a two-dimensional judgment involving global evaluations of message impact and specific judgments of message attributes, but it may be reducible to a single second-order factor, (b) most individuals reported using more than one referent (i.e., person or group) when making PE judgments, but the choice of referents varies by message and judge, and (c) judgments of PE are biased upward as a function of the number of referents chosen. Suggestions are offered for enhancing the validity of PE judgments in formative campaign research.

  17. Origin of spontaneous exchange bias in Co/NiMn bilayer structure

    NASA Astrophysics Data System (ADS)

    Akbulut, A.; Akbulut, S.; Yildiz, F.

    2016-11-01

    Spontaneous exchange bias (EB) is reported for as deposited Si/Pt(tPt)/Ni45Mn55(tAFM/Co(tFM)/Pt(30 Å) thin film system without requiring any post annealing, deposition with field or field cooling procedures. Magnetic properties of this system were investigated with respect to thicknesses of buffer Pt layer (tPt), antiferromagnetic NiMn layer (tAFM) and ferromagnetic Co layer (tFM). Exchange coupling between NiMn and Co layers enhanced considerably by increasing tPt. In order to observe a spontaneous EB in the system, Pt buffer layer must be thicker than a certain thickness, and NiMn layer must be grown directly on the buffer layer. On the other hand, significant increments in the coercive fields (HC) were reported for thinner Pt buffer layers. The thickness ranges for Co and NiMn layers were also determined to obtain spontaneous EB. This spontaneous EB is discussed to be a result of NiMn (111) texture which is induced by Pt buffer layer. Greater EB fields (HEB) are measured for the samples in the negative field direction by the effect of annealing and field cooling (from 400 K to 300 K at 2 kOe).

  18. Structural complexity, movement bias, and metapopulation extinction risk in dendritic ecological networks

    USGS Publications Warehouse

    Campbell Grant, Evan H.

    2011-01-01

    Spatial complexity in metacommunities can be separated into 3 main components: size (i.e., number of habitat patches), spatial arrangement of habitat patches (network topology), and diversity of habitat patch types. Much attention has been paid to lattice-type networks, such as patch-based metapopulations, but interest in understanding ecological networks of alternative geometries is building. Dendritic ecological networks (DENs) include some increasingly threatened ecological systems, such as caves and streams. The restrictive architecture of dendritic ecological networks might have overriding implications for species persistence. I used a modeling approach to investigate how number and spatial arrangement of habitat patches influence metapopulation extinction risk in 2 DENs of different size and topology. Metapopulation persistence was higher in larger networks, but this relationship was mediated by network topology and the dispersal pathways used to navigate the network. Larger networks, especially those with greater topological complexity, generally had lower extinction risk than smaller and less-complex networks, but dispersal bias and magnitude affected the shape of this relationship. Applying these general results to real systems will require empirical data on the movement behavior of organisms and will improve our understanding of the implications of network complexity on population and community patterns and processes.

  19. Local and Average Structures in Ferroelectrics under Perturbing Fields

    NASA Astrophysics Data System (ADS)

    Usher, Tedi-Marie

    Ferroelectric and dielectric ceramics are used in a multitude of applications including sonar, micro-positioning, actuators, transducers, and capacitors. The most widely used compositions are lead (Pb)-based, however there is an ongoing effort to reduce lead-based materials in consumer applications. Many lead-free compositions are under investigation; some are already in production and others have been identified as suitable for certain applications. For any such material system, there is a need to thoroughly characterize the structure in order to develop robust structure-property relationships, particularly during in situ application of different stimuli (e.g. electric field and mechanical stress). This work investigates two lead-free material systems of interest, (1-x)Na1/2Bi1/2TiO3 - (x)BaTiO3 (NBT-xBT) and (1-x)BaTiO3 - (x)Bi(Zn1/2Ti1/2)O3 (BT-xBZT), as well as the constituent compounds Na1/2Bi1/2TiO3 and BaTiO3. Both systems exhibit compositional boundaries between unique phases exhibiting different functional properties. Advanced scattering techniques are used to characterize the atomic structures and how they change during in situ application of different stimuli. The long-range, average structures are probed using high-resolution X-ray diffraction (HRXRD) and neutron diffraction (ND) and local scale structures are probed using X-ray or neutron total scattering, which are converted to pair distribution functions (PDFs). First, two in situ ND experiments which investigate structural changes to NBT-xBT in response to uniaxial stresses and electric fields are presented. In response to stresses, different crystallographic directions strain differently. The elastic anisotropy, (i.e., the orientation-dependence of elastic stiffness) for the studied compositions is characterized. A general inverse relationship between elastic anisotropy and piezoelectric anisotropy is demonstrated for three common ferroelectric point groups. In response to electric fields

  20. Intergroup bias.

    PubMed

    Hewstone, Miles; Rubin, Mark; Willis, Hazel

    2002-01-01

    This chapter reviews the extensive literature on bias in favor of in-groups at the expense of out-groups. We focus on five issues and identify areas for future research: (a) measurement and conceptual issues (especially in-group favoritism vs. out-group derogation, and explicit vs. implicit measures of bias); (b) modern theories of bias highlighting motivational explanations (social identity, optimal distinctiveness, uncertainty reduction, social dominance, terror management); (c) key moderators of bias, especially those that exacerbate bias (identification, group size, status and power, threat, positive-negative asymmetry, personality and individual differences); (d) reduction of bias (individual vs. intergroup approaches, especially models of social categorization); and (e) the link between intergroup bias and more corrosive forms of social hostility.

  1. Structure and chromosomal localization of the human thrombospondin gene.

    PubMed

    Wolf, F W; Eddy, R L; Shows, T B; Dixit, V M

    1990-04-01

    Thrombospondin (THBS1) is a large modular glycoprotein component of the extracellular matrix and contains a variety of distinct domains, including three repeating subunits (types I, II, and III) that share homology to an assortment of other proteins. Determination of THBS1 gene structure has revealed that the type I repeat modules are encoded by symmetrical exons and that the heparin-binding domain is encoded by a single exon. To further elucidate the higher level organization of THBS1, the gene was localized to the q11-qter region of chromosome 15.

  2. Localization-Based Super-Resolution Imaging of Cellular Structures

    PubMed Central

    Kanchanawong, Pakorn; Waterman, Clare M.

    2013-01-01

    Fluorescence microscopy allows direct visualization of fluorescently tagged proteins within cells. However, the spatial resolution of conventional fluorescence microscopes is limited by diffraction to ~250 nm, prompting the development of super-resolution microscopy which offers resolution approaching the scale of single proteins, i.e., ~20 nm. Here, we describe protocols for single molecule localization-based super-resolution imaging, using focal adhesion proteins as an example and employing either photoswitchable fluorophores or photoactivatable fluorescent proteins. These protocols should also be easily adaptable to imaging a broad array of macromolecular assemblies in cells whose components can be fluorescently tagged and assemble into high density structures. PMID:23868582

  3. Local structure probes of nanoscale heterogeneity in crystalline materials.

    PubMed

    Conradson, S; Espinosa, F; Villella, P

    2001-03-01

    In the conventional model of condensed matter increasing numbers of defects break down the order and ultimately convert perfect periodic crystals into aperiodic glasses. Local structure probes of a variety of materials with non-stoichiometric compositions, multiple degenerate ordering modes, or other symmetry breaking factors identify multiple ordered arrangements of atoms that render the materials heterogeneous on the nanometer scale. While exerting apparently negligible effects on bulk properties, this heterogeneity or phase separation does influence correlated or collective properties such as magnetism and phase stability.

  4. Localized structures in dissipative media: from optics to plant ecology

    PubMed Central

    Tlidi, M.; Staliunas, K.; Panajotov, K.; Vladimirov, A. G.; Clerc, M. G.

    2014-01-01

    Localized structures (LSs) in dissipative media appear in various fields of natural science such as biology, chemistry, plant ecology, optics and laser physics. The proposal for this Theme Issue was to gather specialists from various fields of nonlinear science towards a cross-fertilization among active areas of research. This is a cross-disciplinary area of research dominated by nonlinear optics due to potential applications for all-optical control of light, optical storage and information processing. This Theme Issue contains contributions from 18 active groups involved in the LS field and have all made significant contributions in recent years. PMID:25246688

  5. Investigation of nanogap localized field enhancement in gold plasmonic structures

    NASA Astrophysics Data System (ADS)

    Debu, Desalegn Tadesse; Bauman, Stephen; Saylor, Cameron; Novak, Eric; French, David; Herzog, Joseph

    2015-03-01

    Nanogaps between plasmonic structures allow confining the localized electric field with moreenhancements. Based on previously implemented two-step lithography process, we introducea nano-masking technique to fabricate nanostructrues and nanogaps for various geometrical patterns. This new method can fabricate gold nanostructures as well as nanogaps that are less than 10nm, below the limiting scale of lithography. Simulation from finite element method (FEM) shows strong gap dependence of optical properties and peak enhancement of these devices. The fabricated plasmonic nanostructure provides wide range of potential future application including highly sensitive optical antenna, surface enhanced Raman spectroscopy and biosensing.

  6. Lack of sex-biased dispersal promotes fine-scale genetic structure in alpine ungulates

    Treesearch

    Gretchen H. Roffler; Sandra L. Talbot; Gordon Luikart; George K. Sage; Kristy L. Pilgrim; Layne G. Adams; Michael K. Schwartz

    2014-01-01

    Identifying patterns of fine-scale genetic structure in natural populations can advance understanding of critical ecological processes such as dispersal and gene flow across heterogeneous landscapes. Alpine ungulates generally exhibit high levels of genetic structure due to female philopatry and patchy configuration of mountain habitats. We assessed the spatial scale...

  7. Local structure and structural signature underlying properties in metallic glasses and supercooled liquids

    NASA Astrophysics Data System (ADS)

    Ding, Jun

    Metallic glasses (MGs), discovered five decades ago as a newcomer in the family of glasses, are of current interest because of their unique structures and properties. There are also many fundamental materials science issues that remain unresolved for metallic glasses, as well as their predecessor above glass transition temperature, the supercooled liquids. In particular, it is a major challenge to characterize the local structure and unveil the structure-property relationship for these amorphous materials. This thesis presents a systematic study of the local structure of metallic glasses as well as supercooled liquids via classical and ab initio molecular dynamics simulations. Three typical MG models are chosen as representative candidate, Cu64 Zr36, Pd82Si18 and Mg65Cu 25Y10 systems, while the former is dominant with full icosahedra short-range order and the prism-type short-range order dominate for latter two. Furthermore, we move to unravel the underlying structural signature among several properties in metallic glasses. Firstly, the temperature dependence of specific heat and liquid fragility between Cu-Zr and Mg-Cu-Y (also Pd-Si) in supercooled liquids are quite distinct: gradual versus fast evolution of specific heat and viscosity/relaxation time with undercooling. Their local structural ordering are found to relate with the temperature dependence of specific heat and relaxation time. Then elastic heterogeneity has been studied to correlate with local structure in Cu-Zr MGs. Specifically, this part covers how the degree of elastic deformation correlates with the internal structure at the atomic level, how to quantitatively evaluate the local solidity/liquidity in MGs and how the network of interpenetrating connection of icosahedra determine the corresponding shear modulus. Finally, we have illustrated the structure signature of quasi-localized low-frequency vibrational normal modes, which resides the intriguing vibrational properties in MGs. Specifically, the

  8. Local thermal properties of the crust and thermochronometric data - how much can we bias the calculated denudation amount?

    NASA Astrophysics Data System (ADS)

    Łuszczak, Katarzyna; Persano, Cristina; Braun, Jean; Stuart, Finlay

    2016-04-01

    Low temperature thermochronometers are mainly used to decipher crustal denudation histories. However, these methods provide cooling paths that can be confidently translated into denudation rates only if the geothermal gradient at the time of cooling is known. As past geothermal gradients cannot be directly measured, they can be sometimes estimated from the thermochronometric data, when borehole data or vertical profiles are available. In all the other cases, our knowledge of the spatial and temporal variation of the geothermal gradient is limited. It is common practice in many thermochronometric studies to calculate the amounts and rates of denudation through time assuming a constant, average present-day value for the geothermal gradient. In this study, using 1D and 3D (Pecube) models, we have investigated the impact of crustal heat production and thermal conductivity (κ) on the estimated values of denudation, taking central west Britain as our case study. In this region, the apatite fission track (AFT) ages describe a characteristic U-shape pattern with early Cenozoic ages in the English Lake District and older, up to 200 Ma ages northwards in S Scotland, and southwards in N Wales. This pattern, which could be referred to a difficult to justify localized, differential denudation, can actually be best explained as an effect of the spatially variable heat production. The insulating effect of low thermal conductivity Upper Mesozoic sedimentary rocks, composed largely by chalk, increases the palaeogeothermal gradient and reduces the amounts of denudation, especially in the Lake District, where a heat productive granite batholith increases the local heat flow. The observed AFT age pattern may be, therefore, explained without any significant variation of early Cenozoic denudation across central west Britain. If the thermal proprieties of the crust are not taken into account, denudation in the Lake District will be overestimated by a factor of 1.5-2.0 and the mechanisms

  9. Local Tomography and the Jordan Structure of Quantum Theory

    NASA Astrophysics Data System (ADS)

    Barnum, Howard; Wilce, Alexander

    2014-02-01

    Using a result of H. Hanche-Olsen, we show that (subject to fairly natural constraints on what constitutes a system, and on what constitutes a composite system), orthodox finite-dimensional complex quantum mechanics with superselection rules is the only non-signaling probabilistic theory in which (i) individual systems are Jordan algebras (equivalently, their cones of unnormalized states are homogeneous and self-dual), (ii) composites are locally tomographic (meaning that states are determined by the joint probabilities they assign to measurement outcomes on the component systems) and (iii) at least one system has the structure of a qubit. Using this result, we also characterize finite dimensional quantum theory among probabilistic theories having the structure of a dagger-monoidal category.

  10. Imaging biological structures with fluorescence photoactivation localization microscopy

    PubMed Central

    Gould, Travis J; Verkhusha, Vladislav V; Hess, Samuel T

    2010-01-01

    Fluorescence photoactivation localization microscopy (FPALM) images biological structures with subdiffraction-limited resolution. With repeated cycles of activation, readout and bleaching, large numbers of photoactivatable probes can be precisely localized to obtain a map (image) of labeled molecules with an effective resolution of tens of nanometers. FPALM has been applied to a variety of biological imaging applications, including membrane, cytoskeletal and cytosolic proteins in fixed and living cells. Molecular motions can be quantified. FPALM can also be applied to nonbiological samples, which can be labeled with photoactivatable probes. With emphasis on cellular imaging, we describe here the adaptation of a conventional widefield fluorescence microscope for FPALM and present step-by-step procedures to successfully obtain and analyze FPALM images. The fundamentals of this protocol may also be applicable to users of similar imaging techniques that apply localization of photoactivatable probes to achieve super-resolution. Once alignment of the setup has been completed, data acquisitions can be obtained in approximately 1–30 min and analyzed in approximately 0.5–4 h. PMID:19214181

  11. Imaging biological structures with fluorescence photoactivation localization microscopy.

    PubMed

    Gould, Travis J; Verkhusha, Vladislav V; Hess, Samuel T

    2009-01-01

    Fluorescence photoactivation localization microscopy (FPALM) images biological structures with subdiffraction-limited resolution. With repeated cycles of activation, readout and bleaching, large numbers of photoactivatable probes can be precisely localized to obtain a map (image) of labeled molecules with an effective resolution of tens of nanometers. FPALM has been applied to a variety of biological imaging applications, including membrane, cytoskeletal and cytosolic proteins in fixed and living cells. Molecular motions can be quantified. FPALM can also be applied to nonbiological samples, which can be labeled with photoactivatable probes. With emphasis on cellular imaging, we describe here the adaptation of a conventional widefield fluorescence microscope for FPALM and present step-by-step procedures to successfully obtain and analyze FPALM images. The fundamentals of this protocol may also be applicable to users of similar imaging techniques that apply localization of photoactivatable probes to achieve super-resolution. Once alignment of the setup has been completed, data acquisitions can be obtained in approximately 1-30 min and analyzed in approximately 0.5-4 h.

  12. The local structure of topological charge fluctuations in QCD

    SciTech Connect

    I. Horvath; S.J. Dong; T. Draper; Frank Lee; K.F. Liu; J.B. Zhang; H.B. Thacker

    2002-06-01

    We introduce the Dirac eigenmode filtering of topological charge density associated with Ginsparg-Wilson fermions as a tool to investigate the local structure of topological charge fluctuations in QCD. The resulting framework is used to demonstrate that the bulk of topological charge in QCD does not appear in the form of unit quantized lumps. This means that the mixing of ''would-be'' zeromodes associated with such lumps is probably not the prevalent microscopic mechanism for spontaneous chiral symmetry breaking in QCD. To characterize the coherent local behavior in topological charge density at low energy, we compute the charges contained in maximal coherent spheres enclosing non-overlapping peaks. We find a continuous distribution essentially ending at {approx}0.5. Finally, we study, for the first time, the overlap-operator topological-charge-density correlators and find consistency with non-positivity at nonzero physical distance. This represents a non-trivial check on the locality (in gauge paths) of the overlap Dirac operator for realistic gauge backgrounds.

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

    NASA Technical Reports Server (NTRS)

    Dong, Stanley B.

    1989-01-01

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

  14. Accounting for selection bias in species distribution models: An econometric approach on forested trees based on structural modeling

    NASA Astrophysics Data System (ADS)

    Ay, Jean-Sauveur; Guillemot, Joannès; Martin-StPaul, Nicolas K.; Doyen, Luc; Leadley, Paul

    2015-04-01

    Species distribution models (SDMs) are widely used to study and predict the outcome of global change on species. In human dominated ecosystems the presence of a given species is the result of both its ecological suitability and human footprint on nature such as land use choices. Land use choices may thus be responsible for a selection bias in the presence/absence data used in SDM calibration. We present a structural modelling approach (i.e. based on structural equation modelling) that accounts for this selection bias. The new structural species distribution model (SSDM) estimates simultaneously land use choices and species responses to bioclimatic variables. A land use equation based on an econometric model of landowner choices was joined to an equation of species response to bioclimatic variables. SSDM allows the residuals of both equations to be dependent, taking into account the possibility of shared omitted variables and measurement errors. We provide a general description of the statistical theory and a set of application on forested trees over France using databases of climate and forest inventory at different spatial resolution (from 2km to 8 km). We also compared the output of the SSDM with outputs of a classical SDM in term of bioclimatic response curves and potential distribution under current climate. According to the species and the spatial resolution of the calibration dataset, shapes of bioclimatic response curves the modelled species distribution maps differed markedly between the SSDM and classical SDMs. The magnitude and directions of these differences were dependent on the correlations between the errors from both equations and were highest for higher spatial resolutions. A first conclusion is that the use of classical SDMs can potentially lead to strong miss-estimation of the actual and future probability of presence modelled. Beyond this selection bias, the SSDM we propose represents a crucial step to account for economic constraints on tree

  15. [Biases on community structure during DNA extraction of shrimp intestinal microbiota revealed by high-throughput sequencing].

    PubMed

    Wen, Chongqing; He, Yaoyao; Xue, Ming; Liang, Huafang; Dong, Junde

    2016-01-04

    High-throughput sequencing technology is increasingly applied in intestinal microbiota of aquatic animals including shrimp. However, there is a lack of standard method or kit for DNA isolation from shrimp intestinal microbiota, and little is known about the effectiveness and biases regarding DNA extraction based on high-throughput sequencing. The aim of this study was to study the biases of different DNA extraction kits on community structure of shrimp intestinal microbiota through high-throughput sequencing, and to better understand the structure and composition of bacterial flora associated with healthy Litopenaeus vannamei. We extracted the total DNA of intestinal microbiota from L. vannamei with three commercial kits designed for DNA extraction from bacteria, stool and tissue (Omega, USA). DNA quality was evaluated based on the absorbance ratios of 260/280 nm by NanoDrop, while DNA concentration was quantified using PicoGreen. Then Illumina MiSeq high-throughput sequencing was used to examine the intestinal bacterial communities following PCR amplification of 16S rDNA V4 region. The yield and purity of the DNA from the Bacterial Kit (SIB) were superior to those from the Stool Kit (SIS), whereas the DNA from Tissue Kit (SIT) presented too small amount to be amplified efficiently. The average sequence reads obtained from SIB and SIS samples were 52151 ± 5085 and 55296 ± 5147 respectively. After resampling at the same depth of 46800 reads, the operational taxonomic unit (OTU) number and Shannon diversity index of SIS samples were significantly higher than those of SIB samples. By contrast, the reproducibility of OTU among SIB replicates was higher than that among SIS replicates. The dominant phyla of SIS and SIB samples were identical, including Proteobacteria, Firmicutes, Bacteroidetes, Planctomycetes, Actinobacteria, and Cyanobacteria. However, the relative abundances of almost all the dominant groups at various taxonomic levels differed greatly between these

  16. Local structures surrounding Zr in nanostructurally stabilized cubic zirconia: Structural origin of phase stability

    SciTech Connect

    Soo, Y. L.; Chen, P. J.; Huang, S. H.; Shiu, T. J.; Tsai, T. Y.; Chow, Y. H.; Lin, Y. C.; Weng, S. C.; Chang, S. L.; Wang, G.; Cheung, C. L.; Sabirianov, R. F.; Mei, W. N.; Namavar, F.; Haider, H.; Garvin, K. L.; Lee, J. F.; Lee, H. Y.; Chu, P. P.

    2008-12-01

    Local environment surrounding Zr atoms in the thin films of nanocrystalline zirconia (ZrO{sub 2}) has been investigated by using the extended x-ray absorption fine structure (EXAFS) technique. These films prepared by the ion beam assisted deposition exhibit long-range structural order of cubic phase and high hardness at room temperature without chemical stabilizers. The local structure around Zr probed by EXAFS indicates a cubic Zr sublattice with O atoms located on the nearest tetragonal sites with respect to the Zr central atoms, as well as highly disordered locations. Similar Zr local structure was also found in a ZrO{sub 2} nanocrystal sample prepared by a sol-gel method. Variations in local structures due to thermal annealing were observed and analyzed. Most importantly, our x-ray results provide direct experimental evidence for the existence of oxygen vacancies arising from local disorder and distortion of the oxygen sublattice in nanocrystalline ZrO{sub 2}. These oxygen vacancies are regarded as the essential stabilizing factor for the nanostructurally stabilized cubic zirconia.

  17. Lack of sex-biased dispersal promotes fine-scale genetic structure in alpine ungulates

    USGS Publications Warehouse

    Roffler, Gretchen H.; Talbot, Sandra L.; Luikart, Gordon; Sage, George K.; Pilgrim, Kristy L.; Adams, Layne G.; Schwartz, Michael K.

    2014-01-01

    Identifying patterns of fine-scale genetic structure in natural populations can advance understanding of critical ecological processes such as dispersal and gene flow across heterogeneous landscapes. Alpine ungulates generally exhibit high levels of genetic structure due to female philopatry and patchy configuration of mountain habitats. We assessed the spatial scale of genetic structure and the amount of gene flow in 301 Dall’s sheep (Ovis dalli dalli) at the landscape level using 15 nuclear microsatellites and 473 base pairs of the mitochondrial (mtDNA) control region. Dall’s sheep exhibited significant genetic structure within contiguous mountain ranges, but mtDNA structure occurred at a broader geographic scale than nuclear DNA within the study area, and mtDNA structure for other North American mountain sheep populations. No evidence of male-mediated gene flow or greater philopatry of females was observed; there was little difference between markers with different modes of inheritance (pairwise nuclear DNA F ST = 0.004–0.325; mtDNA F ST = 0.009–0.544), and males were no more likely than females to be recent immigrants. Historical patterns based on mtDNA indicate separate northern and southern lineages and a pattern of expansion following regional glacial retreat. Boundaries of genetic clusters aligned geographically with prominent mountain ranges, icefields, and major river valleys based on Bayesian and hierarchical modeling of microsatellite and mtDNA data. Our results suggest that fine-scale genetic structure in Dall’s sheep is influenced by limited dispersal, and structure may be weaker in populations occurring near ancestral levels of density and distribution in continuous habitats compared to other alpine ungulates that have experienced declines and marked habitat fragmentation.

  18. Electron transport in electrically biased inverse parabolic double-barrier structure

    NASA Astrophysics Data System (ADS)

    M, Bati; S, Sakiroglu; I, Sokmen

    2016-05-01

    A theoretical study of resonant tunneling is carried out for an inverse parabolic double-barrier structure subjected to an external electric field. Tunneling transmission coefficient and density of states are analyzed by using the non-equilibrium Green’s function approach based on the finite difference method. It is found that the resonant peak of the transmission coefficient, being unity for a symmetrical case, reduces under the applied electric field and depends strongly on the variation of the structure parameters.

  19. Pulse-biased etching of Si3N4-layer in capacitively-coupled plasmas for nano-scale patterning of multi-level resist structures.

    PubMed

    Lee, Hyelim; Kim, Sechan; Choi, Gyuhyun; Lee, Nae-Eung

    2014-12-01

    Pulse-biased plasma etching of various dielectric layers is investigated for patterning nano-scale, multi-level resist (MLR) structures composed of multiple layers via dual-frequency, capacitively-coupled plasmas (CCPs). We compare the effects of pulse and continuous-wave (CW) biasing on the etch characteristics of a Si3N4 layer in CF4/CH2F2/O2/Aretch chemistries using a dual-frequency, superimposed CCP system. Pulse-biasing conditions using a low-frequency power source of 2 MHz were varied by controlling duty ratio, period time, power, and the gas flow ratio in the plasmas generated by the 27.12 MHz high-frequency power source. Application of pulse-biased plasma etching significantly affected the surface chemistry of the etched Si3N4 surfaces, and thus modified the etching characteristics of the Si3N4 layer. Pulse-biased etching was successfully applied to patterning of the nano-scale line and space pattern of Si3N4 in the MLR structure of KrF photoresist/bottom anti-reflected coating/SiO2/amorphous carbon layer/Si3N4. Pulse-biased etching is useful for tuning the patterning of nano-scale dielectric hard-mask layers in MLR structures.

  20. A local immunization strategy for networks with overlapping community structure

    NASA Astrophysics Data System (ADS)

    Taghavian, Fatemeh; Salehi, Mostafa; Teimouri, Mehdi

    2017-02-01

    Since full coverage treatment is not feasible due to limited resources, we need to utilize an immunization strategy to effectively distribute the available vaccines. On the other hand, the structure of contact network among people has a significant impact on epidemics of infectious diseases (such as SARS and influenza) in a population. Therefore, network-based immunization strategies aim to reduce the spreading rate by removing the vaccinated nodes from contact network. Such strategies try to identify more important nodes in epidemics spreading over a network. In this paper, we address the effect of overlapping nodes among communities on epidemics spreading. The proposed strategy is an optimized random-walk based selection of these nodes. The whole process is local, i.e. it requires contact network information in the level of nodes. Thus, it is applicable to large-scale and unknown networks in which the global methods usually are unrealizable. Our simulation results on different synthetic and real networks show that the proposed method outperforms the existing local methods in most cases. In particular, for networks with strong community structures, high overlapping membership of nodes or small size communities, the proposed method shows better performance.

  1. Embrittlement and Flow Localization in Reactor Structural Materials

    SciTech Connect

    Xianglin Wu; Xiao Pan; James Stubbins

    2006-10-06

    Many reactor components and structural members are made from metal alloys due, in large part, to their strength and ability to resist brittle fracture by plastic deformation. However, brittle fracture can occur when structural material cannot undergo extensive, or even limited, plastic deformation due to irradiation exposure. Certain irradiation conditions lead to the development of a damage microstructure where plastic flow is limited to very small volumes or regions of material, as opposed to the general plastic flow in unexposed materials. This process is referred to as flow localization or plastic instability. The true stress at the onset of necking is a constant regardless of the irradiation level. It is called 'critical stress' and this critical stress has strong temperature dependence. Interrupted tensile testes of 316L SS have been performed to investigate the microstructure evolution and competing mechanism between mechanic twinning and planar slip which are believed to be the controlling mechanism for flow localization. Deformation twinning is the major contribution of strain hardening and good ductility for low temperatures, and the activation of twinning system is determined by the critical twinning stress. Phases transform and texture analyses are also discussed in this study. Finite element analysis is carried out to complement the microstructural analysis and for the prediction of materaials performance with and without stress concentration and irradiation.

  2. Mapping Milky Way and Local Volume Structure With LSST

    NASA Astrophysics Data System (ADS)

    Willman, Beth; Bochanski, J. J.; Bullock, J. S.; de Jong, R.; Debattista, V. P.; Finkbeiner, D.; Grillmair, C. J.; Henry, T. J.; Ivezić, Ž.; Johnston, K. V.; Jurić, M.; Kalirai, J.; McGehee, P. M.; Minniti, D.; Roškar, R.; Sarajedini, A.; Simon, J. D.; Strader, J.; Strauss, M. A.

    2010-01-01

    The last decade has seen a renaissance in the study of our own and other galaxies in the Local Volume, based in large part on the multi-dimensional maps provided by the vast numbers of stars cataloged by surveys such as 2MASS and SDSS. This renaissance has revolutionized our view of the Milky Way (MW) by facilitating tomographic studies of its global structure and by revealing a vast menagerie of substructures, including a new population of satellite galaxies with a millionth the luminosity of the MW and a halo replete with lumps and streams that betray the formation history of the MW. With LSST's 6 bands, 1000 epochs, and a final a limiting magnitude of r=27.6 (AB mag; 5-sigma), it will provide an excellent resource for mapping the structure and accretion history of the MW and beyond in a way that the present generation of surveys has only hinted at. LSST is anticipated to catalog 10 billion stars, including photometric abundances for the 200 million F/G stars within 100 kpc and proper motion/parallax measurements for stars brighter than r = 24 mag. Specific MW and Local Volume science to be enabled by LSST includes: mapping the 3D distribution of dust throughout the MW's disk, including variations in R_V; understanding the smooth distribution of stars in the MW and other nearby galaxies; understanding large-scale chemical gradients in the MW; discovering lumps and streams in metallicity and phase-space; inferring the mass distribution in the MW; discovering ultra-faint galaxies throughout the Local Volume as overdensities of resolved stars.

  3. Local structural ordering in surface-confined liquid crystals

    NASA Astrophysics Data System (ADS)

    Śliwa, I.; Jeżewski, W.; Zakharov, A. V.

    2017-06-01

    The effect of the interplay between attractive nonlocal surface interactions and attractive pair long-range intermolecular couplings on molecular structures of liquid crystals confined in thin cells with flat solid surfaces has been studied. Extending the McMillan mean field theory to include finite systems, it has been shown that confining surfaces can induce complex orientational and translational ordering of molecules. Typically, local smectic A, nematic, and isotropic phases have been shown to coexist in certain temperature ranges, provided that confining cells are sufficiently thick, albeit finite. Due to the nonlocality of surface interactions, the spatial arrangement of these local phases can display, in general, an unexpected complexity along the surface normal direction. In particular, molecules located in the vicinity of surfaces can still be organized in smectic layers, even though nematic and/or isotropic order can simultaneously appear in the interior of cells. The resulting surface freezing of smectic layers has been confirmed to occur even for rather weak surface interactions. The surface interactions cannot, however, prevent smectic layers from melting relatively close to system boundaries, even when molecules are still arranged in layers within the central region of the system. The internal interfaces, separating individual liquid-crystal phases, are demonstrated here to form fronts of local finite-size transitions that move across cells under temperature changes. Although the complex molecular ordering in surface confined liquid-crystal systems can essentially be controlled by temperature variations, specific thermal properties of these systems, especially the nature of the local transitions, are argued to be strongly conditioned to the degree of molecular packing.

  4. GaAs quantum well structures investigation by local cathodoluminescence

    NASA Astrophysics Data System (ADS)

    Shakhmin, A. A.; Zamoryanskaya, M. V.; Arsentyev, I. N.; Konnikov, S. G.; Vinokurov, D. A.; Stankevich, A. L.; Tarasov, I. S.

    2009-04-01

    The article shows the cathodoluminescence technique application to a quality analysis of a semiconductor multilayer heterostructures. Two structures with a GaAs quantum well embedded between the AlGaAs and GaInP barriers were investigated. The AlGaAs/GaAs/GaInP and GaInP/GaAs/AlGaAs structures were grown by MOCVD on a GaAs substrate. In this work we study the interface quality of quantum-dimensional GaAs layer by means of the local cathodoluminescence. Degradation and broadening of GaAs/GaInP interface occurring during the growth process of GaAs on GaInP layer was assumed to result in the formation of a layer with mixed composition at the interface. In addition, the presence of the layer prevented the formation of a quantum well in the GaAs layer. The transition layer was clearly observed by the cathodoluminescence. In the other case it was found that the growth of a structure with GaAs layer on top of AlGaAs produced a quantum well with a 10 nm thickness. The interface quality and layer thicknesses were also confirmed by the X-ray diffraction investigation of these structures.

  5. Origin of the vertebrate body plan via mechanically biased conservation of regular geometrical patterns in the structure of the blastula.

    PubMed

    Edelman, David B; McMenamin, Mark; Sheesley, Peter; Pivar, Stuart

    2016-09-01

    We present a plausible account of the origin of the archetypal vertebrate bauplan. We offer a theoretical reconstruction of the geometrically regular structure of the blastula resulting from the sequential subdivision of the egg, followed by mechanical deformations of the blastula in subsequent stages of gastrulation. We suggest that the formation of the vertebrate bauplan during development, as well as fixation of its variants over the course of evolution, have been constrained and guided by global mechanical biases. Arguably, the role of such biases in directing morphology-though all but neglected in previous accounts of both development and macroevolution-is critical to any substantive explanation for the origin of the archetypal vertebrate bauplan. We surmise that the blastula inherently preserves the underlying geometry of the cuboidal array of eight cells produced by the first three cleavages that ultimately define the medial-lateral, dorsal-ventral, and anterior-posterior axes of the future body plan. Through graphical depictions, we demonstrate the formation of principal structures of the vertebrate body via mechanical deformation of predictable geometrical patterns during gastrulation. The descriptive rigor of our model is supported through comparisons with previous characterizations of the embryonic and adult vertebrate bauplane. Though speculative, the model addresses the poignant absence in the literature of any plausible account of the origin of vertebrate morphology. A robust solution to the problem of morphogenesis-currently an elusive goal-will only emerge from consideration of both top-down (e.g., the mechanical constraints and geometric properties considered here) and bottom-up (e.g., molecular and mechano-chemical) influences. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

  6. Influence of 8-Oxoguanosine on the Fine Structure of DNA Studied with Biasing-Potential Replica Exchange Simulations

    SciTech Connect

    Kara, Mahmut; Zacharias, Martin W.

    2013-03-05

    Chemical modification or radiation can cause DNA damage, which plays a crucial role for mutagenesis of DNA, carcinogenesis, and aging. DNA damage can also alter the fine structure of DNA that may serve as a recognition signal for DNA repair enzymes. A new, advanced sampling replica-exchange method has been developed to specifically enhance the sampling of conformational substates in duplex DNA during molecular dynamics (MD) simulations. The approach employs specific biasing potentials acting on pairs of pseudodihedral angles of the nucleic acid backbone that are added in the replica simulations to promote transitions of the most common substates of the DNA backbone. The sampled states can exchange with a reference simulation under the control of the original force field. The application to 7,8-dihydro-8oxo-guanosine, one of the most common oxidative damage in DNA indicated better convergence of sampled states during 10 ns simulations compared to 20 times longer standard MD simulations. It is well suited to study systematically the fine structure and dynamics of large nucleic acids under realistic conditions, including explicit solvent and ions. The biasing potential-replica exchange MD simulations indicated significant differences in the population of nucleic acid backbone substates in the case of 7,8-dihydro-8oxo-guanosine compared to a regular guanosine in the same sequence context. This concerns both the ratio of the B-DNA substates BI and BII associated with the backbone dihedral angles ε and z but also coupled changes in the backbone dihedral angles a and g. Such differences may play a crucial role in the initial recognition of damaged DNA by repair enzymes.

  7. Bias and Efficiency in Structural Equation Modeling: Maximum Likelihood versus Robust Methods

    ERIC Educational Resources Information Center

    Zhong, Xiaoling; Yuan, Ke-Hai

    2011-01-01

    In the structural equation modeling literature, the normal-distribution-based maximum likelihood (ML) method is most widely used, partly because the resulting estimator is claimed to be asymptotically unbiased and most efficient. However, this may not hold when data deviate from normal distribution. Outlying cases or nonnormally distributed data,…

  8. Bias and Efficiency in Structural Equation Modeling: Maximum Likelihood versus Robust Methods

    ERIC Educational Resources Information Center

    Zhong, Xiaoling; Yuan, Ke-Hai

    2011-01-01

    In the structural equation modeling literature, the normal-distribution-based maximum likelihood (ML) method is most widely used, partly because the resulting estimator is claimed to be asymptotically unbiased and most efficient. However, this may not hold when data deviate from normal distribution. Outlying cases or nonnormally distributed data,…

  9. Sample Size Requirements for Structural Equation Models: An Evaluation of Power, Bias, and Solution Propriety

    ERIC Educational Resources Information Center

    Wolf, Erika J.; Harrington, Kelly M.; Clark, Shaunna L.; Miller, Mark W.

    2013-01-01

    Determining sample size requirements for structural equation modeling (SEM) is a challenge often faced by investigators, peer reviewers, and grant writers. Recent years have seen a large increase in SEMs in the behavioral science literature, but consideration of sample size requirements for applied SEMs often relies on outdated rules-of-thumb.…

  10. Sample Size Requirements for Structural Equation Models: An Evaluation of Power, Bias, and Solution Propriety

    ERIC Educational Resources Information Center

    Wolf, Erika J.; Harrington, Kelly M.; Clark, Shaunna L.; Miller, Mark W.

    2013-01-01

    Determining sample size requirements for structural equation modeling (SEM) is a challenge often faced by investigators, peer reviewers, and grant writers. Recent years have seen a large increase in SEMs in the behavioral science literature, but consideration of sample size requirements for applied SEMs often relies on outdated rules-of-thumb.…

  11. Diversity of Secondary Structure in Catalytic Peptides with β-Turn-Biased Sequences

    PubMed Central

    2016-01-01

    X-ray crystallography has been applied to the structural analysis of a series of tetrapeptides that were previously assessed for catalytic activity in an atroposelective bromination reaction. Common to the series is a central Pro-Xaa sequence, where Pro is either l- or d-proline, which was chosen to favor nucleation of canonical β-turn secondary structures. Crystallographic analysis of 35 different peptide sequences revealed a range of conformational states. The observed differences appear not only in cases where the Pro-Xaa loop-region is altered, but also when seemingly subtle alterations to the flanking residues are introduced. In many instances, distinct conformers of the same sequence were observed, either as symmetry-independent molecules within the same unit cell or as polymorphs. Computational studies using DFT provided additional insight into the analysis of solid-state structural features. Select X-ray crystal structures were compared to the corresponding solution structures derived from measured proton chemical shifts, 3J-values, and 1H–1H-NOESY contacts. These findings imply that the conformational space available to simple peptide-based catalysts is more diverse than precedent might suggest. The direct observation of multiple ground state conformations for peptides of this family, as well as the dynamic processes associated with conformational equilibria, underscore not only the challenge of designing peptide-based catalysts, but also the difficulty in predicting their accessible transition states. These findings implicate the advantages of low-barrier interconversions between conformations of peptide-based catalysts for multistep, enantioselective reactions. PMID:28029251

  12. Structure and local charging of electromigrated Au nanocontacts

    NASA Astrophysics Data System (ADS)

    Arnold, D.; Marz, M.; Schneider, S.; Hoffmann-Vogel, R.

    2017-02-01

    We study the structure and the electronic properties of Au nanocontacts created by controlled electromigration of thin film devices, a method frequently used to contact molecules. In contrast to electromigration testing, a current is applied in a cyclic fashion and during each cycle the resistance increase of the metal upon heating is used to avoid thermal runaway. In this way, nanometer sized-gaps are obtained. The thin film devices with an optimized structure at the origin of the electromigration process are made by shadow evaporation without contamination by organic materials. Defining rounded edges and a thinner area in the center of the device allow to pre-determine the location where the electromigration takes place. Scanning force microscopy images of the pristine Au film and electromigrated contact show its grainy structure. Through electromigration, a 1.5 μm-wide slit is formed, with extensions only on the anode side that had previously not been observed in narrower structures. It is discussed whether this could be explained by asymmetric heating of both electrodes. New grains are formed in the slit and on the extensions on both, the anode and the cathode side. The smaller structures inside the slit lead to an electrode distance below 150 nm. Kelvin probe force microscopy images show a local work function difference with fluctuations of 70 mV on the metal before electromigration. Between the electrodes, disconnected through electromigration, a work function difference of 3.2 V is observed due to charging. Some of the grains newly formed by electromigration are electrically disconnected from the electrodes.

  13. Structure and local charging of electromigrated Au nanocontacts.

    PubMed

    Arnold, D; Marz, M; Schneider, S; Hoffmann-Vogel, R

    2017-02-03

    We study the structure and the electronic properties of Au nanocontacts created by controlled electromigration of thin film devices, a method frequently used to contact molecules. In contrast to electromigration testing, a current is applied in a cyclic fashion and during each cycle the resistance increase of the metal upon heating is used to avoid thermal runaway. In this way, nanometer sized-gaps are obtained. The thin film devices with an optimized structure at the origin of the electromigration process are made by shadow evaporation without contamination by organic materials. Defining rounded edges and a thinner area in the center of the device allow to pre-determine the location where the electromigration takes place. Scanning force microscopy images of the pristine Au film and electromigrated contact show its grainy structure. Through electromigration, a 1.5 μm-wide slit is formed, with extensions only on the anode side that had previously not been observed in narrower structures. It is discussed whether this could be explained by asymmetric heating of both electrodes. New grains are formed in the slit and on the extensions on both, the anode and the cathode side. The smaller structures inside the slit lead to an electrode distance below 150 nm. Kelvin probe force microscopy images show a local work function difference with fluctuations of 70 mV on the metal before electromigration. Between the electrodes, disconnected through electromigration, a work function difference of 3.2 V is observed due to charging. Some of the grains newly formed by electromigration are electrically disconnected from the electrodes.

  14. Flexible structural protein alignment by a sequence of local transformations

    PubMed Central

    Rocha, Jairo; Segura, Joan; Wilson, Richard C.; Dasgupta, Swagata

    2009-01-01

    Motivation: Throughout evolution, homologous proteins have common regions that stay semi-rigid relative to each other and other parts that vary in a more noticeable way. In order to compare the increasing number of structures in the PDB, flexible geometrical alignments are needed, that are reliable and easy to use. Results: We present a protein structure alignment method whose main feature is the ability to consider different rigid transformations at different sites, allowing for deformations beyond a global rigid transformation. The performance of the method is comparable with that of the best ones from 10 aligners tested, regarding both the quality of the alignments with respect to hand curated ones, and the classification ability. An analysis of some structure pairs from the literature that need to be matched in a flexible fashion are shown. The use of a series of local transformations can be exported to other classifiers, and a future golden protein similarity measure could benefit from it. Availability: A public server for the program is available at http://dmi.uib.es/ProtDeform/. Contact: jairo@uib.es Supplementary information: All data used, results and examples are available at http://dmi.uib.es/people/jairo/bio/ProtDeform.Supplementary data are available at Bioinformatics online. PMID:19417057

  15. Structuring Lecture Videos by Automatic Projection Screen Localization and Analysis.

    PubMed

    Li, Kai; Wang, Jue; Wang, Haoqian; Dai, Qionghai

    2015-06-01

    We present a fully automatic system for extracting the semantic structure of a typical academic presentation video, which captures the whole presentation stage with abundant camera motions such as panning, tilting, and zooming. Our system automatically detects and tracks both the projection screen and the presenter whenever they are visible in the video. By analyzing the image content of the tracked screen region, our system is able to detect slide progressions and extract a high-quality, non-occluded, geometrically-compensated image for each slide, resulting in a list of representative images that reconstruct the main presentation structure. Afterwards, our system recognizes text content and extracts keywords from the slides, which can be used for keyword-based video retrieval and browsing. Experimental results show that our system is able to generate more stable and accurate screen localization results than commonly-used object tracking methods. Our system also extracts more accurate presentation structures than general video summarization methods, for this specific type of video.

  16. Strain localization driven by structural relaxation in sheared amorphous solids.

    PubMed

    Jagla, E A

    2007-10-01

    A two dimensional amorphous material is modeled as an assembly of mesoscopic elemental pieces coupled together to form an elastically coherent structure. Plasticity is introduced as the existence of different minima in the energy landscape of the elemental constituents. Upon the application of an external strain rate, the material shears through the appearance of elemental slip events with quadrupolar symmetry. When the energy landscape of the elemental constituents is kept fixed, the slip events distribute uniformly throughout the sample, producing on average a uniform deformation. However, when the energy landscape at different spatial positions can be rearranged dynamically to account for structural relaxation, the system develops inhomogeneous deformation in the form of shear bands at low shear rates, and stick-slip-like motion at the shear bands for the lowest shear rates. The origin of strain localization is traced back to a region of negative correlation between strain rate and stress, which appears only if structural relaxation is present. The model also reproduces other well known effects in the rheology of amorphous materials, as a stress peak in a strain rate controlled experiment staring from rest, and the increase of the maximum of this peak with sample age.

  17. Local structure of solid Rb at megabar pressures

    SciTech Connect

    De Panfilis, S.; Gorelli, F.; Santoro, M.; Ulivi, L.; Gregoryanz, E.; Irifune, T.; Shinmei, T.; Kantor, I.; Mathon, O.; Pascarelli, S.

    2015-06-07

    We have investigated the local and electronic structure of solid rubidium by means of x-ray absorption spectroscopy up to 101.0 GPa, thus doubling the maximum investigated experimental pressure. This study confirms the predicted stability of phase VI and was completed by the combination of two pivotal instrumental solutions. On one side, we made use of nanocrystalline diamond anvils, which, contrary to the more commonly used single crystal diamond anvils, do not generate sharp Bragg peaks (glitches) at specific energies that spoil the weak fine structure oscillations in the x-ray absorption cross section. Second, we exploited the performance of a state-of-the-art x-ray focussing device yielding a beam spot size of 5 × 5 μm{sup 2}, spatially stable over the entire energy scan. An advanced data analysis protocol was implemented to extract the pressure dependence of the structural parameters in phase VI of solid Rb from 51.2 GPa up to the highest pressure. A continuous reduction of the nearest neighbour distances was observed, reaching about 6% over the probed pressure range. We also discuss a phenomenological model based on the Einstein approximation to describe the pressure behaviour of the mean-square relative displacement. Within this simplified scheme, we estimate the Grüneisen parameter for this high pressure Rb phase to be in the 1.3–1.5 interval.

  18. Local atomic structures of single-component metallic glasses

    NASA Astrophysics Data System (ADS)

    Trady, Salma; Hasnaoui, Abdellatif; Mazroui, M.'hammed; Saadouni, Khalid

    2016-10-01

    In this study we examine the structural properties of single-component metallic glasses of aluminum. We use a molecular dynamics simulation based on semi-empirical many-body potential, derived from the embedded atom method (EAM). The radial distribution function (RDF), common neighbors analysis method (CNA), coordination number analysis (CN) and Voronoi tessellation are used to characterize the metal's local structure during the heating and cooling (quenching). The simulation results reveal that the melting temperature depends on the heating rate. In addition, atomic visualization shows that the structure of aluminum after fast quenching is in a glassy state, confirmed quantitatively by the splitting of the second peak of the radial distribution function, and by the appearance of icosahedral clusters observed via CNA technique. On the other hand, the Wendt-Abraham parameters are calculated to determine the glass transition temperature (Tg), which depends strongly on the cooling rate; it increases while the cooling rate increases. On the basis of CN analysis and Voronoi tessellation, we demonstrate that the transition from the Al liquid to glassy state is mainly due to the formation of distorted and perfect icosahedral clusters.

  19. Revealing strong bias in common measures of galaxy properties using new inclination-independent structures

    NASA Astrophysics Data System (ADS)

    Devour, Brian M.; Bell, Eric F.

    2017-06-01

    Accurate measurement of galaxy structures is a prerequisite for quantitative investigation of galaxy properties or evolution. Yet, the impact of galaxy inclination and dust on commonly used metrics of galaxy structure is poorly quantified. We use infrared data sets to select inclination-independent samples of disc and flattened elliptical galaxies. These samples show strong variation in Sérsic index, concentration and half-light radii with inclination. We develop novel inclination-independent galaxy structures by collapsing the light distribution in the near-infrared on to the major axis, yielding inclination-independent 'linear' measures of size and concentration. With these new metrics we select a sample of Milky Way analogue galaxies with similar stellar masses, star formation rates, sizes and concentrations. Optical luminosities, light distributions and spectral properties are all found to vary strongly with inclination: When inclining to edge-on, r-band luminosities dim by >1 magnitude, sizes decrease by a factor of 2, 'dust-corrected' estimates of star formation rate drop threefold, metallicities decrease by 0.1 dex and edge-on galaxies are half as likely to be classified as star forming. These systematic effects should be accounted for in analyses of galaxy properties.

  20. Efficient reanalysis of structures by a direct modification method. [local stiffness modifications of large structures

    NASA Technical Reports Server (NTRS)

    Raibstein, A. I.; Kalev, I.; Pipano, A.

    1976-01-01

    A procedure for the local stiffness modifications of large structures is described. It enables structural modifications without an a priori definition of the changes in the original structure and without loss of efficiency due to multiple loading conditions. The solution procedure, implemented in NASTRAN, involved the decomposed stiffness matrix and the displacement vectors of the original structure. It solves the modified structure exactly, irrespective of the magnitude of the stiffness changes. In order to investigate the efficiency of the present procedure and to test its applicability within a design environment, several real and large structures were solved. The results of the efficiency studies indicate that the break-even point of the procedure varies between 8% and 60% stiffness modifications, depending upon the structure's characteristics and the options employed.

  1. Using Local Born and Local Rytov Fourier Modeling and Migration Methods for Investigation of Heterogeneous Structures

    SciTech Connect

    Fehler, M.C.; Huang, L.-J.

    1998-12-10

    During the past few years, there has been interest in developing migration and forward modeling approaches that are both fast and reliable particularly in regions that have rapid spatial variations in structure. The authors have been investigating a suite of modeling and migration methods that are implemented in the wavenumber-space domains and operate on data in the frequency domain. The best known example of these methods is the split-step Fourier method (SSF). Two of the methods that the authors have developed are the extended local Born Fourier (ELBF) approach and the extended local Rytov Fourier (ELRF) approach. Both methods are based on solutions of the scalar (constant density) wave equation, are computationally fast and can reliably model effects of both deterministic and random structures. The authors have investigated their reliability for migrating both 2D synthetic data and real 2D field data. The authors have found that the methods give images that are better than those that can be obtained using other methods like the SSF and Kirchhoff migration approaches. More recently, the authors have developed an approach for solving the acoustic (variable density) wave equation and have begun to investigate its applicability for modeling one-way wave propagation. The methods will be introduced and their ability to model seismic wave propagation and migrate seismic data will be investigated. The authors will also investigate their capability to model forward wave propagation through random media and to image zones of small scale heterogeneity such as those associated with zones of high permeability.

  2. Ligand-biased ensemble receptor docking (LigBEnD): a hybrid ligand/receptor structure-based approach

    NASA Astrophysics Data System (ADS)

    Lam, Polo C.-H.; Abagyan, Ruben; Totrov, Maxim

    2017-09-01

    Ligand docking to flexible protein molecules can be efficiently carried out through ensemble docking to multiple protein conformations, either from experimental X-ray structures or from in silico simulations. The success of ensemble docking often requires the careful selection of complementary protein conformations, through docking and scoring of known co-crystallized ligands. False positives, in which a ligand in a wrong pose achieves a better docking score than that of native pose, arise as additional protein conformations are added. In the current study, we developed a new ligand-biased ensemble receptor docking method and composite scoring function which combine the use of ligand-based atomic property field (APF) method with receptor structure-based docking. This method helps us to correctly dock 30 out of 36 ligands presented by the D3R docking challenge. For the six mis-docked ligands, the cognate receptor structures prove to be too different from the 40 available experimental Pocketome conformations used for docking and could be identified only by receptor sampling beyond experimentally explored conformational subspace.

  3. Optical fingerprint recognition based on local minutiae structure coding.

    PubMed

    Yi, Yao; Cao, Liangcai; Guo, Wei; Luo, Yaping; Feng, Jianjiang; He, Qingsheng; Jin, Guofan

    2013-07-15

    A parallel volume holographic optical fingerprint recognition system robust to fingerprint translation, rotation and nonlinear distortion is proposed. The optical fingerprint recognition measures the similarity by using the optical filters of multiplexed holograms recorded in the holographic media. A fingerprint is encoded into multiple template data pages based on the local minutiae structure coding method after it is adapted for the optical data channel. An improved filter recording time schedule and a post-filtering calibration technology are combined to suppress the calculating error from the large variations in data page filling ratio. Experimental results tested on FVC2002 DB1 and a forensic database comprising 270,216 fingerprints demonstrate the robustness and feasibility of the system.

  4. Balancing Newtonian gravity and spin to create localized structures

    NASA Astrophysics Data System (ADS)

    Bush, Michael; Lindner, John

    2015-03-01

    Using geometry and Newtonian physics, we design localized structures that do not require electromagnetic or other forces to resist implosion or explosion. In two-dimensional Euclidean space, we find an equilibrium configuration of a rotating ring of massive dust whose inward gravity is the centripetal force that spins it. We find similar solutions in three-dimensional Euclidean and hyperbolic spaces, but only in the limit of vanishing mass. Finally, in three-dimensional Euclidean space, we generalize the two-dimensional result by finding an equilibrium configuration of a spherical shell of massive dust that supports itself against gravitational collapse by spinning isoclinically in four dimensions so its three-dimensional acceleration is everywhere inward. These Newtonian ``atoms'' illuminate classical physics and geometry.

  5. Characterization of localized transverse structures in wide-aperture lasers

    NASA Astrophysics Data System (ADS)

    Rosanov, N. N.; Fedorov, A. V.; Fedorov, S. V.; Khodova, G. V.

    The problem of characterization of spatio-temporal patterns is discussed for the case of wide-aperture lasers with nonlinear losses where variety of such patterns is especially rich. Laser autosolitons (LASs)-localized transverse structures representing “islands of lasing” on a background of the nonlasing mode on the laser aperture-are studied. Existence of stable single LASs which are motionless or moving in the transverse direction with constant linear velocity is shown. Described are also LASs with regular wavefronts, those with screw dislocations (defects) of wavefronts with different topological indices, and those with axially symmetric and asymmetric intensity distributions rotating with constant angular velocity around the LAS center. An approach is given for qualitative and quantitative characterization of a single LAS by its linear and angular velocities and frequency shift, based on a combination of analytical methods and computer simulations. Results of investigations of weak and strong interactions among the LASs are presented.

  6. Localized structures in dissipative media: from optics to plant ecology.

    PubMed

    Tlidi, M; Staliunas, K; Panajotov, K; Vladimirov, A G; Clerc, M G

    2014-10-28

    Localized structures (LSs) in dissipative media appear in various fields of natural science such as biology, chemistry, plant ecology, optics and laser physics. The proposal for this Theme Issue was to gather specialists from various fields of nonlinear science towards a cross-fertilization among active areas of research. This is a cross-disciplinary area of research dominated by nonlinear optics due to potential applications for all-optical control of light, optical storage and information processing. This Theme Issue contains contributions from 18 active groups involved in the LS field and have all made significant contributions in recent years. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

  7. Polariton Local States in Periodic Bragg Multiple Quantum Well Structures

    NASA Astrophysics Data System (ADS)

    Deych, Lev; Yamilov, Alexey; Lisyansky, Alexander

    2000-11-01

    We analytically study defect polariton states in Bragg MQW structures, and defect induced changes in transmission and reflection spectra. Defect layers can differ from the host layers in three different ways: in the exciton-light coupling strength, in the exciton resonance frequency, and in interwell spacing. We show that a single defect leads to two local polariton modes in the photonic band gap. These modes lead to peculiarities in reflection and transmission spectra. Each type of defect can be reproduced experimentally, and we show that each of them play distinctly different roles in the optical properties of the system. We obtain closed analytical expressions for respective local frequencies, as well as for reflection and transmission coefficients. On the basis of the results obtained, we give practical recommendation for experimental observation of the studied effects in samples used in Refs. [1,2]. [1] M.Hübner, J. Kuhl, T. Stroucken, A. Knorr, S.W. Koch, R. Hey, K. Ploog, Phys. Rev. Lett. 76, 4199 (1996). [2] M.Hübner, J.P. Prineas, C. Ell, P. Brick, E.S. Lee, G. Khitrova, H.M. Gibbs, S.W. Koch, Phys. Rev. Lett. 83, 2841 (1999).

  8. The local electronic structure of α-Li3N

    SciTech Connect

    Fister, Timothy T.; Siedler, Gerald T.; Shirley, E. L.; Vila, Fernando D.; Nagle, Kenneth P.; Rehr, John J.; Linehan, John C.; Cross, Julie O.

    2008-07-28

    We investigate the local electronic structure of α-Li3N by the combination of nonresonant inelastic x-ray scattering measurements and three independent ab initio theoretical treatments. Experimental determination of the local final density of states projected onto an orbital angular momentum basis (l-DOS) for Li 1s initial states finds strong similarities in the s- and p-DOS throughout the near-edge region, which we attribute to the 3-fold rotational symmetry about Li sites in the Li2N sheets of α-Li3N. We also find a significant correspondence between the near-edge spectra for the Li 1s and N 1s contributions to the NRIXS signal. This is unexpected, as such behavior is typically associated with covalent materials whereas α-Li3N is strongly ionic. We explain that such similarity in the DOS at different sites in either ionic or covalent systems may occur when the core-hole lifetimes are very long, so that the lifetime of the photoelectron is the dominant factor in cutting off high-order multiple scattering in the near-edge regime. This work was supported by the U.S. Department of Energy's Office of Basic Energy Sciences. The Pacific Northwest National Laboratory is operated by Battelle for DOE.

  9. Studies of local magnetism and local structure in La(2-x)Sr(x)CuO4

    NASA Technical Reports Server (NTRS)

    Budnick, J. I.; Tan, Z.; Filipkowski, M.

    1991-01-01

    The muon spin rotation (MUSR) study of local magnetism of Sr-doped La2CrO4 is reviewed. Emphasis is placed on magnetic order as detected by local and bulk probes with local atomic environments studies by x ray absorption fine structure (XAFS). Correlations between the MUSR study of local magnetic ordering and the bulk magnetization study are presented along with a discussion of the dependence upon oxygen stoichiometry. Results are presented for both superconducting phases and magnetic phases. Recent data which reveals the existence of local magnetic ordering in the hydrogen-doped YBa2Cu3O7 system are also discussed.

  10. Pressure dependence of the local structure of iridium ditelluride across the structural phase transition

    NASA Astrophysics Data System (ADS)

    Paris, E.; Joseph, B.; Iadecola, A.; Marini, C.; Ishii, H.; Kudo, K.; Pascarelli, S.; Nohara, M.; Mizokawa, T.; Saini, N. L.

    2016-04-01

    The local structure of IrTe2 has been studied by iridium L3-edge x-ray absorption spectroscopy (XAS) measurements as a function of pressure, performed at two temperatures (100 and 295 K) across the structural phase transition at ˜270 K. Extended x-ray absorption fine structure (EXAFS) and x-ray absorption near-edge structure (XANES) spectra show pressure-dependent anomalies, suggesting phase transitions that are characterized by different local atomic displacements. The high-temperature phase of IrTe2 (trigonal at 295 K) reveals a clear anomaly in the Ir-Te correlations at ˜4 GPa, while the low-temperature phase (at 100 K) shows a smaller change at ˜6 GPa, likely to be associated with transitions in lower-symmetry phases. XANES spectra, measuring higher-order atomic correlations, also show nonlinear pressure dependence in the local geometry at the anomalous pressures. These nonlinear changes suggest that IrTe2 goes through lower local symmetry phases with increasing pressure.

  11. Peculiar velocities into the next generation: cosmological parameters from large surveys without bias from non-linear structure

    NASA Astrophysics Data System (ADS)

    Abate, Alexandra; Bridle, Sarah; Teodoro, Luis F. A.; Warren, Michael S.; Hendry, Martin

    2008-10-01

    We investigate methods to best estimate the normalization of the mass density fluctuation power spectrum (σ8) using peculiar velocity data from a survey like the six-degree Field Galaxy Velocity Survey (6dFGSv). We focus on two potential problems: (i) biases from non-linear growth of structure and (ii) the large number of velocities in the survey. Simulations of ΛCDM-like models are used to test the methods. We calculate the likelihood from a full covariance matrix of velocities averaged in grid cells. This simultaneously reduces the number of data points and smoothes out non-linearities which tend to dominate on small scales. We show how the averaging can be taken into account in the predictions in a practical way, and show the effect of the choice of cell size. We find that a cell size can be chosen that significantly reduces the non-linearities without significantly increasing the error bars on cosmological parameters. We compare our results with those from a principal components analysis following Watkins et al. and Feldman et al. to select a set of optimal moments constructed from linear combinations of the peculiar velocities that are least sensitive to the non-linear scales. We conclude that averaging in grid cells performs equally well. We find that for a survey such as 6dFGSv we can estimate σ8 with less than 3 per cent bias from non-linearities. The expected error on σ8 after marginalizing over Ωm is approximately 16 per cent.

  12. Thresholds of surface codes on the general lattice structures suffering biased error and loss

    SciTech Connect

    Tokunaga, Yuuki; Fujii, Keisuke

    2014-12-04

    A family of surface codes with general lattice structures is proposed. We can control the error tolerances against bit and phase errors asymmetrically by changing the underlying lattice geometries. The surface codes on various lattices are found to be efficient in the sense that their threshold values universally approach the quantum Gilbert-Varshamov bound. We find that the error tolerance of the surface codes depends on the connectivity of the underlying lattices; the error chains on a lattice of lower connectivity are easier to correct. On the other hand, the loss tolerance of the surface codes exhibits an opposite behavior; the logical information on a lattice of higher connectivity has more robustness against qubit loss. As a result, we come upon a fundamental trade-off between error and loss tolerances in the family of surface codes with different lattice geometries.

  13. Thresholds of surface codes on the general lattice structures suffering biased error and loss

    NASA Astrophysics Data System (ADS)

    Tokunaga, Yuuki; Fujii, Keisuke

    2014-12-01

    A family of surface codes with general lattice structures is proposed. We can control the error tolerances against bit and phase errors asymmetrically by changing the underlying lattice geometries. The surface codes on various lattices are found to be efficient in the sense that their threshold values universally approach the quantum Gilbert-Varshamov bound. We find that the error tolerance of the surface codes depends on the connectivity of the underlying lattices; the error chains on a lattice of lower connectivity are easier to correct. On the other hand, the loss tolerance of the surface codes exhibits an opposite behavior; the logical information on a lattice of higher connectivity has more robustness against qubit loss. As a result, we come upon a fundamental trade-off between error and loss tolerances in the family of surface codes with different lattice geometries.

  14. Local field enhancement and thermoplasmonics in multimodal aluminum structures

    NASA Astrophysics Data System (ADS)

    Wiecha, Peter R.; Mennemanteuil, Marie-Maxime; Khlopin, Dmitry; Martin, Jérôme; Arbouet, Arnaud; Gérard, Davy; Bouhelier, Alexandre; Plain, Jérôme; Cuche, Aurélien

    2017-07-01

    Aluminum nanostructures have recently been at the focus of numerous studies due to their properties including oxidation stability and surface plasmon resonances covering the ultraviolet and visible spectral windows. In this article, we reveal a facet of this metal relevant for both plasmonic purposes and photothermal conversion. The field distribution of high-order plasmonic resonances existing in two-dimensional Al structures is studied by nonlinear photoluminescence microscopy in a spectral region where electronic interband transitions occur. The polarization sensitivity of the field intensity maps shows that the electric field concentration can be addressed and controlled on demand. We use a numerical tool based on the Green dyadic method to analyze our results and to simulate the absorbed energy that is locally converted into heat. The polarization-dependent temperature increase of the Al structures is experimentally quantitatively measured, and is in an excellent agreement with theoretical predictions. Our work highlights Al as a promising candidate for designing thermal nanosources integrated in coplanar geometries for thermally assisted nanomanipulation or biophysical applications.

  15. Band gaps in grid structure with periodic local resonator subsystems

    NASA Astrophysics Data System (ADS)

    Zhou, Xiaoqin; Wang, Jun; Wang, Rongqi; Lin, Jieqiong

    2017-09-01

    The grid structure is widely used in architectural and mechanical field for its high strength and saving material. This paper will present a study on an acoustic metamaterial beam (AMB) based on the normal square grid structure with local resonators owning both flexible band gaps and high static stiffness, which have high application potential in vibration control. Firstly, the AMB with variable cross-section frame is analytically modeled by the beam-spring-mass model that is provided by using the extended Hamilton’s principle and Bloch’s theorem. The above model is used for computing the dispersion relation of the designed AMB in terms of the design parameters, and the influences of relevant parameters on band gaps are discussed. Then a two-dimensional finite element model of the AMB is built and analyzed in COMSOL Multiphysics, both the dispersion properties of unit cell and the wave attenuation in a finite AMB have fine agreement with the derived model. The effects of design parameters of the two-dimensional model in band gaps are further examined, and the obtained results can well verify the analytical model. Finally, the wave attenuation performances in three-dimensional AMBs with equal and unequal thickness are presented and discussed.

  16. Identification of ligand templates using local structure alignment for structure-based drug design.

    PubMed

    Lee, Hui Sun; Im, Wonpil

    2012-10-22

    With a rapid increase in the number of high-resolution protein-ligand structures, the known protein-ligand structures can be used to gain insight into ligand-binding modes in a target protein. On the basis of the fact that the structurally similar binding sites share information about their ligands, we have developed a local structure alignment tool, G-LoSA (graph-based local structure alignment). The known protein-ligand binding-site structure library is searched by G-LoSA to detect binding-site structures with similar geometry and physicochemical properties to a query binding-site structure regardless of sequence continuity and protein fold. Then, the ligands in the identified complexes are used as templates (i.e., template ligands) to predict/design a ligand for the target protein. The performance of G-LoSA is validated against 76 benchmark targets from the Astex diverse set. Using the currently available protein-ligand structure library, G-LoSA is able to identify a single template ligand (from a nonhomologous protein complex) that is highly similar to the target ligand in more than half of the benchmark targets. In addition, our benchmark analyses show that an assembly of structural fragments from multiple template ligands with partial similarity to the target ligand can be used to design novel ligand structures specific to the target protein. This study clearly indicates that a template-based ligand modeling has potential for de novo ligand design and can be a complementary approach to the receptor structure based methods.

  17. Identification of Ligand Templates using Local Structure Alignment for Structure-based Drug Design

    PubMed Central

    Lee, Hui Sun; Im, Wonpil

    2012-01-01

    With a rapid increase in the number of high-resolution protein-ligand structures, the known protein-ligand structures can be used to gain insight into ligand-binding modes in a target protein. Based on the fact that the structurally similar binding sites share information about their ligands, we have developed a local structure alignment tool, G-LoSA (Graph-based Local Structure Alignment). In G-LoSA, the known protein-ligand binding-site structure library is searched to detect binding-site structures with similar geometry and physicochemical properties to a query binding-site structure regardless of sequence continuity and protein fold. Then, the ligands in the identified complexes are used as templates (i.e., template ligands) to predict/design a ligand for the target protein. The performance of G-LoSA is validated against 76 benchmark targets from the Astex diverse set. Using the currently available protein-ligand structure library, G-LoSA is able to identify a single template ligand (from a non-homologous protein complex) that is highly similar to the target ligand in more than half of the benchmark targets. In addition, our benchmark analyses show that an assembly of structural fragments from multiple template ligands with partial similarity to the target ligand can be used to design novel ligand structures specific to the target protein. This study clearly indicates that a template-based ligand modeling has potential for de novo ligand design and can be a complementary approach to the receptor structure based methods. PMID:22978550

  18. Hydroxyl radicals in ice: insights into local structure and dynamics.

    PubMed

    Codorniu-Hernández, Edelsys; Kusalik, Peter G

    2012-09-07

    The hydroxyl radical and its reactivity within ice environments are crucial to many important atmospheric reactions. The associated molecular mechanisms are largely unknown due to challenges posed by direct experimental measurements and computational studies of this transient species. Here we report insights into the local structure and behaviour of the hydroxyl radical in bulk ice through an extensive study utilizing Car-Parrinello molecular dynamics simulations. Interstitial and in-lattice hydroxyl radicals in hexagonal ice were investigated at primarily 190 K. Our findings, utilizing both HCTH/120 and BLYP functionals, show that OH* can exhibit greater mobility than other ice defects (the trapping energy estimated to be only 0.09 eV). We observe the formation of a two-center three-electron hemibond structure between the hydroxyl radical and an in-lattice water molecule; while controversial, such a structure in ice may be amenable to experimental detection due to its relative stability. Our results show that interstitial water molecules can strongly influence the mobility of the hydroxyl radical in bulk ice through the displacement of the radical to an interstitial location. We also demonstrate that the H-transfer reaction from an interstitial water to the radical is a rare event in ice. Together, these results predict that the radical can be a reactive species in bulk ice, as both interstitial and in-lattice OH* can be available for reactions with other species. These microscopic insights should contribute to our understanding of the reactivity of OH* in ice and its implications to atmospheric reactions.

  19. The brain structure and spontaneous activity baseline of the behavioral bias in trait anxiety.

    PubMed

    Yin, Ping; Zhang, Meng; Hou, Xin; Tan, Yafei; Fu, Yixiao; Qiu, Jiang

    2016-10-01

    Individuals with trait anxiety are often considered to be predisposed to psychiatric disorders. However, there is great heterogeneity in the development of psychiatric disorders in this group of people and the nature of the trait anxiety is still unclear. So, we decided to explore the correlations of brain structure and brain activity with trait anxiety in normal individuals. Specifically, we investigated the correlations between trait anxiety and regional grey matter volume (rGMV) and regional BOLD, using the Amplitude of Low Frequency Fluctuations (ALFF) as an index in 382 university students. The results showed that the level of trait anxiety was negatively correlated with rGMV in the right middle occipital gyrus. This result indicates that individuals with high trait anxiety tend to have less image processing on conscious level. Furthermore, we found that trait anxiety was positively correlated with the ALFF in the bilateral superior frontal gyrus and the right supplementary motor area, and negatively correlated with the ALFF in the cerebellum and the thalamus. These results indicate that individuals with high trait anxiety may be more sensitive to relationships and sensory information. Overall, this study's findings suggest that individuals with high trait anxiety have attenuated image processing on the conscious level, and exhibit stronger induced sensibility and over-processing of relationships, which is a brain imaging precondition for psychiatric disorders. Copyright © 2016 Elsevier B.V. All rights reserved.

  20. Dynamic behavior of acoustic metamaterials and metaconfigured structures with local oscillators

    NASA Astrophysics Data System (ADS)

    Manimala, James Mathew

    in locally dissipative AM with various damped oscillator microstructures was studied using mechanical lattice models. The presence of damping was represented by a complex effective-mass. Analytical transmissibilities and numerical verifications were obtained for Kelvin-Voigt-type, Maxwell-type and Zener-type oscillators. Although peak attenuation at resonance is diminished, broadband attenuation was found to be achievable without increasing mass ratio, obviating the bandgap width limitations of locally resonant AM. Static and frequency-dependent measures of optimal damping that maximize the attenuation characteristics were established. A transitional value for the excitation frequency was identified within the locally resonant bandgap, above which there always exists an optimal amount of damping that renders the attenuation for the dissipative AM greater than that for the locally resonant case. AM with nonlinear stiffnesses were also investigated. For a base-excited two degree of freedom system consisting of a master structure and a Duffing-type oscillator, approximate transmissibility was derived, verified using simulations and compared to its equivalent damped model. Analytical solutions for dispersion curve shifts in nonlinear chains with linear resonators and in linear chains with nonlinear oscillators were obtained using perturbation analysis and first order approximations for cubic hardening and softening cases. Amplitude-activated alterations in bandgap width and the possibility of phenomena such as branch curling and overtaking were observed. Device implications of nonlinear AM as amplitude-dependent filters and direction-biased waveguides were examined using simulations.

  1. Predicting continuous local structure and the effect of its substitution for secondary structure in fragment-free protein structure prediction.

    PubMed

    Faraggi, Eshel; Yang, Yuedong; Zhang, Shesheng; Zhou, Yaoqi

    2009-11-11

    Local structures predicted from protein sequences are used extensively in every aspect of modeling and prediction of protein structure and function. For more than 50 years, they have been predicted at a low-resolution coarse-grained level (e.g., three-state secondary structure). Here, we combine a two-state classifier with real-value predictor to predict local structure in continuous representation by backbone torsion angles. The accuracy of the angles predicted by this approach is close to that derived from NMR chemical shifts. Their substitution for predicted secondary structure as restraints for ab initio structure prediction doubles the success rate. This result demonstrates the potential of predicted local structure for fragment-free tertiary-structure prediction. It further implies potentially significant benefits from using predicted real-valued torsion angles as a replacement for or supplement to the secondary-structure prediction tools used almost exclusively in many computational methods ranging from sequence alignment to function prediction.

  2. Localized and chaotic folding: the role of axial plane structures.

    PubMed

    Hobbs, Bruce E; Ord, Alison

    2012-04-28

    Most natural fold systems are not sinusoidal in profile. A widely held view is that such irregularity derives solely from inherited initial geometrical perturbations. Although, undoubtedly, initial perturbations can contribute to irregularity, we explore a different (but complementary) view in which the irregular geometry results from some material or system softening process. This arises because the buckling response of a layer (or layers) embedded in a weaker matrix is controlled in a sensitive manner by the nature of the reaction forces exerted by the deforming matrix on the layer. In many theoretical treatments of the folding problem, this reaction force is assumed to be a linear function of some measure of the deformation or deformation rate. This paper is concerned with the influence of nonlinear reaction forces such as arise from nonlinear elasticity or viscosity. Localized folds arising from nonlinearity form in a fundamentally different way than the Biot wavelength selection process. As a particular example of nonlinear behaviour, we examine the influence of axial plane structures made up of layers of different mineralogy formed by chemical differentiation processes accompanying the deformation; they are referred to as metamorphic layering. The alternating mineralogical composition in the metamorphic layers means that the embedding matrix exerts a reaction force on the folded layers that varies not only with the deflection or the velocity of deflection of the layer, but also in a periodic manner along the length of the folded layers. The influence of this spatially periodic reaction force on the development of localized and chaotic folding is explored numerically.

  3. Probing the band structure and local electronic properties of low-dimensional semiconductor structures

    NASA Astrophysics Data System (ADS)

    Walrath, Jenna Cherie

    Low-dimensional semiconductor structures are important for a wide variety of applications, and recent advances in nanoscale fabrication are paving the way for increasingly precise nano-engineering of a wide range of materials. It is therefore essential that the physics of materials at the nanoscale are thoroughly understood to unleash the full potential of nanotechnology, requiring the development of increasingly sophisticated instrumentation and modeling. Of particular interest is the relationship between the local density of states (LDOS) of low-dimensional structures and the band structure and local electronic properties. This dissertation presents the investigation of the band structure, LDOS, and local electronic properties of nanostructures ranging from zero-dimensional (0D) quantum dots (QDs) to two-dimensional (2D) thin films, synthesizing computational and experimental approaches including Poisson-Schrodinger band structure calculations, scanning tunneling microscopy (STM), scanning tunneling spectroscopy (STS), and scanning thermoelectric microscopy (SThEM). A method is presented for quantifying the local Seebeck coefficient (S) with SThEM, using a quasi-3D conversion matrix approach to directly convert temperature gradient-induced voltages S. For a GaAs p-n junction, the resulting S-profile is consistent with that computed using the free carrier concentration profile. This combined computational-experimental approach is expected to enable nanoscale measurements of S across a wide variety of heterostructure interfaces. The local carrier concentration, n, is profiled across epitaxial InAs/GaAs QDs, where SThEM is used to profile the temperature gradient-induced voltage, which is converted to a profile of the local S and finally to an n profile. The S profile is converted to a conduction band-edge profile and compared with Poisson-Schrodinger band-edge simulations. The combined computational-experimental approach suggests a reduced n in the QD center in

  4. The model of local mode analysis for structural acoustics of box structures

    NASA Astrophysics Data System (ADS)

    Ngai, King-Wah

    Structure-borne noise is a new noise pollution problem emerging from railway concrete box structures in Hong Kong. Its low frequency noise with intermittent effect can cause considerable nuisance to neighborhoods. The tonal noise peaks in this low frequency range should be one of the important factors in structure-borne noise analysis. In the acoustic field, the deterministic analysis of all the resonant modes of vibration is generally considered as not practical. Many acoustic experts use the statistical energy analysis as the main tool for the noise investigation whereas the application of the experimental modal analysis in the structural acoustic problem is comparatively rare. In the past, most studies mainly focused on the structure-borne noise measurement and analysis. The detail study of the cause of structure-borne noise is lack, especially for the rectangular concrete box structure. In this dissertation, an experimental and analytical approach is adopted to study a typical concrete box model. This thesis aims at confirming the importance of modal analysis in the structure-borne noise study and then at identifying the local vibration modes along the cross-section of box structure. These local modes are responsible for the structure-borne noise radiation. The findings of this study suggest that the web of viaduct cross-section is not as rigid as assumed in the conventional viaduct design and the web face is likely to be more flexible in the vertical displacement of the concrete viaduct. Two types of local vibration modes along the cross-section are identified: the centre mode and the web mode. At the top panel of the viaduct, the centre mode has movement in the middle but not at the edges. The web mode has movement at the edges with the middle fixed. The combined centre and web mode has been found to be important in the structural acoustics of the concrete box structure. In the actual concrete viaduct, the coincidence frequency is especially low (often around

  5. Biased predecision processing.

    PubMed

    Brownstein, Aaron L

    2003-07-01

    Decision makers conduct biased predecision processing when they restructure their mental representation of the decision environment to favor one alternative before making their choice. The question of whether biased predecision processing occurs has been controversial since L. Festinger (1957) maintained that it does not occur. The author reviews relevant research in sections on theories of cognitive dissonance, decision conflict, choice certainty, action control, action phases, dominance structuring, differentiation and consolidation, constructive processing, motivated reasoning, and groupthink. Some studies did not find evidence of biased predecision processing, but many did. In the Discussion section, the moderators are summarized and used to assess the theories.

  6. Local Structural Distortion Induced Uniaxial Negative Thermal Expansion in Nanosized Semimetal Bismuth.

    PubMed

    Li, Qiang; Zhu, He; Zheng, Lirong; Fan, Longlong; Ren, Yang; Chen, Jun; Deng, Jinxia; Xing, Xianran

    2016-11-01

    The corrugated layer structure bismuth has been successfully tailored into negative thermal expansion along c axis by size effect. Pair distribution function and extended X-ray absorption fine structure are combined to reveal the local structural distortion for nanosized bismuth. The comprehensive method to identify the local structure of nanomaterials can benefit the regulating and controlling of thermal expansion in nanodivices.

  7. Berkson’s bias, selection bias, and missing data

    PubMed Central

    Westreich, Daniel

    2011-01-01

    While Berkson’s bias is widely recognized in the epidemiologic literature, it remains underappreciated as a model of both selection bias and bias due to missing data. Simple causal diagrams and 2×2 tables illustrate how Berkson’s bias connects to collider bias and selection bias more generally, and show the strong analogies between Berksonian selection bias and bias due to missing data. In some situations, considerations of whether data are missing at random or missing not at random is less important than the causal structure of the missing-data process. While dealing with missing data always relies on strong assumptions about unobserved variables, the intuitions built with simple examples can provide a better understanding of approaches to missing data in real-world situations. PMID:22081062

  8. Local structure in anisotropic systems determined by molecular dynamics simulation

    NASA Astrophysics Data System (ADS)

    Komolkin, Andrei V.; Maliniak, Arnold

    In the present communication we describe the investigation of local structure using a new visualization technique. The approach is based on two-dimensional pair correlation functions derived from a molecular dynamics computer simulation. We have used this method to analyse a trajectory produced in a simulation of a nematic liquid crystal of 4-n-pentyl-4'-cyanobiphenyl (5CB) (Komolkin et al., 1994, J. chem. Phys., 101, 4103). The molecule is assumed to have cylindrical symmetry, and the liquid crystalline phase is treated as uniaxial. The pair correlation functions or cylindrical distribution functions (CDFs) are calculated in the molecular (m) and laboratory (l) frames, gm2(z1 2, d1 2) and g12(Z1 2, D1 2). Anisotropic molecular organization in the liquid crystal is reflected in laboratory frame CDFs. The molecular excluded volume is determined and the effect of the fast motion in the alkyl chain is observed. The intramolecular distributions are included in the CDFs and indicate the size of the motional amplitude in the chain. Absence of long range order was confirmed, a feature typical for a nematic liquid crystal.

  9. Historic timber skeleton structures and the local seismic culture

    NASA Astrophysics Data System (ADS)

    Bostenaru, M.

    2009-04-01

    This presentation deals with the employment of timber skeleton structure and the local seismic culture. After the 1755 earthquake in the reconstruction of Lisbon a type of building with timber skeleton and masonry infill called "gaiola pombalina" was promoted, since this was designed to better resists earthquakes. "Gaiola" means cage, and it was also named after the Marques de Pombal who introduced it in the reconstruction following the earthquake. The „gaiola pombalina" presents a timber skeleton with Saint Andrew crosses in the interior walls with masonry infill and thick masonry load bearing walls loosing in thickness to the upper floors in the exterior walls. The masonry can fall out during earthquakes but the building remains staying given the interior timber skeleton. The type of buildings with timber structure and (masonry) infill behaved well in earthquakes in various parts of the earth, like Nepal (the dhaji dewary type), Pakistan, Turkey (the himiş type after the 1999 earthquake) [both latter types were researched by Langenbach, www.conservationtech.com and www.traditional-is-modern.net] and also in Germany after the 1356 earthquake (the Southern German subtype of Fachwerk). Also in Italy a subtype called "casa baraccata" was promoted in a construction code to a similar time (following the 1783 earthquake in Southern Italy, see Tobriner 1983) as that of the "gaiola pombalina", the time of the Baroque, when town planning acquired another status. Unlike at the "gaiola pombalina" the "casa baraccata" the timber skeleton is at the exterior walls. For this reason this type of buildings is considered to be an expression of the local seismic culture. However, this type of buildings is common also for areas where seismic risk is not an issue, like half-timbered in England and the northern subtype of Fachwerk in Northern Germany, and in some high seismic risk regions with mountains and timber resources like Romania is not spread. Given these premises the author

  10. Crustal structure beneath the southern Korean Peninsula from local earthquakes

    NASA Astrophysics Data System (ADS)

    Kim, Kwang-Hee; Park, Jung-Ho; Park, Yongcheol; Hao, Tian-Yao; Kim, Han-Joon

    2017-02-01

    The three-dimensional subsurface structure beneath the southern Korean Peninsula is poorly known, even though such information could be key in verifying or rejecting several competing models of the tectonic evolution of East Asia. We constructed a three-dimensional velocity model of the upper crust beneath the southern Korean Peninsula using 19,935 P-wave arrivals from 747 earthquakes recorded by high-density local seismic networks. Results show significant lateral and vertical variations: velocity increases from northwest to southeast at shallow depths, and significant velocity variations are observed across the South Korea Tectonic Line between the Okcheon Fold Belt and the Youngnam Massif. Collision between the North China and South China blocks during the Early Cretaceous might have caused extensive deformation and the observed negative velocity anomalies in the region. The results of the tomographic inversion, combined with the findings of previous studies of Bouguer and isostatic gravity anomalies, indicate the presence of high-density material in the upper and middle crust beneath the Gyeongsang Basin in the southeastern Korean Peninsula. Although our results partially support the indentation tectonic model, it is still premature to discard other tectonic evolution models because our study only covers the southern half of the peninsula.

  11. Local genetic structure in a white-bearded manakin population.

    PubMed

    Höglund, Jacob; Shorey, Lisa

    2003-09-01

    Local genetic structure was studied in lekking white-bearded manakins in a study area on northern Trinidad, West Indies. The study population consisted of nine leks, at which a total of 238 birds were caught. By genotyping the individuals at eight polymorphic microsatellite loci we inferred some males on leks to be related (r = 0.25) as we found an average number of 14.8 half-sib relationships and two full-sib relationships per lek. We found that the sampled birds belonged to one genetic population that was slightly inbred (FIS and FIT = 0.02). Kinship coefficients decreased with increasing geographical distance, indicating that related birds displayed at the same or nearby leks. However, leks did not consist of only one family group because the average genetic distance (aij) between males within leks was higher than when comparing males on leks within close proximity. These patterns suggest limited male dispersal, that some type of kin recognition process between individuals may exist in this species and that males on leks may be more likely to establish themselves as territory-holding birds if a relative is already present.

  12. Crustal structure beneath the southern Korean Peninsula from local earthquakes

    NASA Astrophysics Data System (ADS)

    Kim, Kwang-Hee; Park, Jung-Ho; Park, Yongcheol; Hao, Tian-Yao; Kim, Han-Joon

    2017-05-01

    The 3-D subsurface structure beneath the southern Korean Peninsula is poorly known, even though such information could be key in verifying or rejecting several competing models of the tectonic evolution of East Asia. We constructed a 3-D velocity model of the upper crust beneath the southern Korean Peninsula using 19 935 P-wave arrivals from 747 earthquakes recorded by high-density local seismic networks. Results show significant lateral and vertical variations: velocity increases from northwest to southeast at shallow depths, and significant velocity variations are observed across the South Korea Tectonic Line between the Okcheon Fold Belt and the Youngnam Massif. Collision between the North and South China blocks during the Early Cretaceous might have caused extensive deformation and the observed negative velocity anomalies in the region. The results of the tomographic inversion, combined with the findings of previous studies of Bouguer and isostatic gravity anomalies, indicate the presence of high-density material in the upper and middle crust beneath the Gyeongsang Basin in the southeastern Korean Peninsula. Although our results partially support the indentation tectonic model, it is still premature to discard other tectonic evolution models because our study only covers the southern half of the peninsula.

  13. Spatial-temporal structures of human alpha rhythms: theory, microcurrent sources, multiscale measurements, and global binding of local networks.

    PubMed

    Nunez, P L; Wingeier, B M; Silberstein, R B

    2001-07-01

    A theoretical framework supporting experimental measures of dynamic properties of human EEG is proposed with emphasis on distinct alpha rhythms. Robust relationships between measured dynamics and cognitive or behavioral conditions are reviewed, and proposed physiological bases for EEG at cellular levels are considered. Classical EEG data are interpreted in the context of a conceptual framework that distinguishes between locally and globally dominated dynamic processes, as estimated with coherence or other measures of phase synchronization. Macroscopic (scalp) potentials generated by cortical current sources are described at three spatial scales, taking advantage of the columnar structure of neocortex. New EEG data demonstrate that both globally coherent and locally dominated behavior can occur within the alpha band, depending on narrow band frequency, spatial measurement scale, and brain state. Quasi-stable alpha phase structures consistent with global standing waves are observed. At the same time, alpha and theta phase locking between cortical regions during mental calculations is demonstrated, consistent with neural network formation. The brain-binding problem is considered in the context of EEG dynamic behavior that generally exhibits both of these local and global aspects. But specific experimental designs and data analysis methods may severely bias physiological interpretations in either local or global directions.

  14. Local structure analysis of materials for increased energy efficiency

    NASA Astrophysics Data System (ADS)

    Medling, Scott

    In this dissertation, a wide range of materials which exhibit interesting properties with potential for energy efficiency applications are investigated. The bulk of the research was conducted using the Extended X-ray Absorption Fine Structure (EXAFS) technique. EXAFS is a powerful tool for elucidating the local structure of novel materials, and it's advantages are presented in Chapter 2. In Chapter 3, I present details on two new techniques which are used in studies later in this dissertation, but are also promising for other, unrelated studies and, therefore, warrant being discussed generally. I explain the presence of and present a method for subtracting the X-ray Raman background in the fluorescence window when collecting fluorescence EXAFS data of a dilute dopant Z in a Z+1 host. I introduce X-ray magnetic circular dichroism (XMCD) and discuss the process to reduce XMCD data, including the self-absorption corrections for low energy K-edges. In Chapter 4, I present a series of investigations on ZnS:Cu electroluminescent phosphors. Optical microscopy indicates that the emission centers do not degrade uniformly or monotonically, but rather, most of the emission centers blink on and off during degradation. The effect of this on various proposed degradation mechanisms is discussed. EXAFS data of ZnS:Cu phosphors ground to enable thinner, lower-voltage devices indicate that grinding preferentially causes damage to the CuS nanoprecipitates, quenching electroluminescence (EL) and concluding that smaller particles must be built up from nanoparticles instead. EXAFS data of nanoparticles show that adding a ZnS shell outside a ZnS:Cu core provides significant additional encapsulation of the Cu, increasing photoluminescence and indicating that this may increase EL if devices can be fabricated. Data from extremely dilute (0.02% Cu) ZnS:Cu nanoparticles is presented in order to specifically study the non-precipitate and suggests that the Cu dopant substitutes for Zn and is

  15. Exchange bias and crystal structure of epitaxial (111) FePt/BiFeO3 sputtered thin films

    NASA Astrophysics Data System (ADS)

    Chiu, Shang-Jui; Huang, Li-Chun; Hsiao, Shih-Nan; Chang, Huang-Wei; Yu, Ge-Ping; Lee, Hsin-Yi

    2014-05-01

    Crystallographic structure and magnetic properties of the epitaxial FePt (10 nm)/BiFeO3 (BFO) (10 nm) bilayer films grown on (111) SrTiO3 (STO) substrates with different deposition temperatures of FePt layers (Td) have been investigated using magnetron sputtering. Out-of-plane radial scan along (111) direction and off-normal (002) azimuthal scan, determined by synchrotron radiation x-ray diffractometry, evidence that the FePt layers were well epitaxially grown on the (111) epitaxial BFO layers for the samples with Td = 300 and 700 °C. On the contrary, for the bilayer films with Td = 500 °C, the FePt and BFO layers exhibit low epitaxial quality. Large in-plane exchange bias field (Heb) values of 45-412 Oe are obtained for the L10-FePt/BFO bilayer films measured with applied field of 12 kOe at room temperature. The change of effective interfacial area, observed by scanning electron microscopy, between FePt island-like particles and BFO continuous layers, and epitaxiality of the bilayer were correlated with the evolution of Heb.

  16. Population genetic structure of Cichla pleiozona (Perciformes: Cichlidae) in the Upper Madera basin (Bolivian Amazon): sex-biased dispersal?

    PubMed

    Carvajal-Vallejos, F M; Duponchelle, F; Ballivian, J P Torrico; Hubert, Nicolas; Rodríguez, J Nuñez; Berrebi, P; Cornejo, S Sirvas; Renno, J-F

    2010-12-01

    This study investigates the population structure of the Tucunaré (Cichla pleiozona) in the Bolivian Amazon (Upper Madera) by using nuclear (EPIC-PCR, 67 individuals) and mitochondrial (Control Region, 41 published and 76 new sequences) DNA analyses, in relation with ecological (water quality: muddy, clear and mix) and geographic factors. Our analyses of both markers showed the highest diversity in clear waters (Yata, Middle and Upper Iténez), and the existence of two populations in muddy waters (Sécure and Ichilo) and one in mix waters (Manuripi). On the other hand, mitochondrial analyses identified three populations in clear waters where nuclear analyses identified a panmictic population. The highest diversity observed in the Yata-Iténez system suggests that an aquatic refuge occurred during the past in this area. The possible explanations for the observed discrepancy between nuclear and mitochondrial markers are discussed, and a sex-biased dispersal seems to be the most plausible hypothesis in the light of the available information and field observations. Copyright © 2010 Elsevier Inc. All rights reserved.

  17. Exchange bias and crystal structure of epitaxial (111) FePt/BiFeO{sub 3} sputtered thin films

    SciTech Connect

    Chiu, Shang-Jui; Hsiao, Shih-Nan Lee, Hsin-Yi; Huang, Li-Chun; Yu, Ge-Ping; Chang, Huang-Wei

    2014-05-07

    Crystallographic structure and magnetic properties of the epitaxial FePt (10 nm)/BiFeO{sub 3} (BFO) (10 nm) bilayer films grown on (111) SrTiO{sub 3} (STO) substrates with different deposition temperatures of FePt layers (T{sub d}) have been investigated using magnetron sputtering. Out-of-plane radial scan along (111) direction and off-normal (002) azimuthal scan, determined by synchrotron radiation x-ray diffractometry, evidence that the FePt layers were well epitaxially grown on the (111) epitaxial BFO layers for the samples with T{sub d} = 300 and 700 °C. On the contrary, for the bilayer films with T{sub d} = 500 °C, the FePt and BFO layers exhibit low epitaxial quality. Large in-plane exchange bias field (H{sub eb}) values of 45–412 Oe are obtained for the L1{sub 0}-FePt/BFO bilayer films measured with applied field of 12 kOe at room temperature. The change of effective interfacial area, observed by scanning electron microscopy, between FePt island-like particles and BFO continuous layers, and epitaxiality of the bilayer were correlated with the evolution of H{sub eb}.

  18. Strength through structure: visualization and local assessment of the trabecular bone structure

    NASA Astrophysics Data System (ADS)

    Räth, C.; Monetti, R.; Bauer, J.; Sidorenko, I.; Müller, D.; Matsuura, M.; Lochmüller, E.-M.; Zysset, P.; Eckstein, F.

    2008-12-01

    The visualization and subsequent assessment of the inner human bone structures play an important role for better understanding the disease- or drug-induced changes of bone in the context of osteoporosis giving prospect for better predictions of bone strength and thus of the fracture risk of osteoporotic patients. In this work, we show how the complex trabecular bone structure can be visualized using μCT imaging techniques at an isotropic resolution of 26 μm. We quantify these structures by calculating global and local topological and morphological measures, namely Minkowski functionals (MFs) and utilizing the (an-)isotropic scaling index method (SIM) and by deriving suitable texture measures based on MF and SIM. Using a sample of 151 specimens taken from human vertebrae in vitro, we correlate the texture measures with the mechanically measured maximum compressive strength (MCS), which quantifies the strength of the bone probe, by using Pearson's correlation coefficient. The structure parameters derived from the local measures yield good correlations with the bone strength as measured in mechanical tests. We investigate whether the performance of the texture measures depends on the MCS value by selecting different subsamples according to MCS. Considering the whole sample the results for the newly defined parameters are better than those obtained for the standard global histomorphometric parameters except for bone volume/total volume (BV/TV). If a subsample consisting only of weak bones is analysed, the local structural analysis leads to similar and even better correlations with MCS as compared to BV/TV. Thus, the MF and SIM yield additional information about the stability of the bone especially in the case of weak bones, which corroborates the hypothesis that the bone structure (and not only its mineral mass) constitutes an important component of bone stability.

  19. Expectation and Locality Effects in German Verb-final Structures.

    PubMed

    Levy, Roger P; Keller, Frank

    2013-02-01

    Probabilistic expectations and memory limitations are central factors governing the real-time comprehension of natural language, but how the two factors interact remains poorly understood. One respect in which the two factors have come into theoretical conflict is the documentation of both locality effects, in which more dependents preceding a governing verb increase processing difficulty at the verb, and anti-locality effects, in which more preceding dependents facilitate processing at the verb. However, no controlled study has previously demonstrated both locality and anti-locality effects in the same type of dependency relation within the same language. Additionally, many previous demonstrations of anti-locality effects have been potentially confounded with lexical identity, plausibility, and sentence position. Here, we provide new evidence of both locality and anti-locality effects in the same type of dependency relation in a single language-verb-final constructions in German-while controlling for lexical identity, plausibility, and sentence position. In main clauses, we find clear anti-locality effects, with the presence of a preceding dative argument facilitating processing at the final verb; in subject-extracted relative clauses with identical linear ordering of verbal dependents, we find both anti-locality and locality effects, with processing facilitated when the verb is preceded by a dative argument alone, but hindered when the verb is preceded by both the dative argument and an adjunct. These results indicate that both expectations and memory limitations need to be accounted for in any complete theory of online syntactic comprehension.

  20. Long-distance correlation and zonal flow structures induced by mean ExB shear flows in the biasing H-mode at TEXTOR

    SciTech Connect

    Xu, Y.; Jachmich, S.; Weynants, R. R.; Schoor, M. van; Vergote, M.; Kraemer-Flecken, A.; Schmitz, O.; Unterberg, B.

    2009-11-15

    Long-distance toroidal correlations of potential and density fluctuations have been investigated at the TEXTOR tokamak [H. Soltwisch et al., Plasma Phys. Controlled Fusion 26, 23 (1984)] in edge electrode-biasing experiments. During the biasing-induced H-mode, the dc ExB shear flow triggers a zonal flow structure and hence long-distance correlation in potential fluctuations, whereas for density fluctuations there is nearly no correlation. These results indicate an intimate interaction between the mean and zonal flows, and the significance of long range correlations in improved-confinement regimes.

  1. Superpose3D: A Local Structural Comparison Program That Allows for User-Defined Structure Representations

    PubMed Central

    Gherardini, Pier Federico; Ausiello, Gabriele; Helmer-Citterich, Manuela

    2010-01-01

    Local structural comparison methods can be used to find structural similarities involving functional protein patches such as enzyme active sites and ligand binding sites. The outcome of such analyses is critically dependent on the representation used to describe the structure. Indeed different categories of functional sites may require the comparison program to focus on different characteristics of the protein residues. We have therefore developed superpose3D, a novel structural comparison software that lets users specify, with a powerful and flexible syntax, the structure description most suited to the requirements of their analysis. Input proteins are processed according to the user's directives and the program identifies sets of residues (or groups of atoms) that have a similar 3D position in the two structures. The advantages of using such a general purpose program are demonstrated with several examples. These test cases show that no single representation is appropriate for every analysis, hence the usefulness of having a flexible program that can be tailored to different needs. Moreover we also discuss how to interpret the results of a database screening where a known structural motif is searched against a large ensemble of structures. The software is written in C++ and is released under the open source GPL license. Superpose3D does not require any external library, runs on Linux, Mac OSX, Windows and is available at http://cbm.bio.uniroma2.it/superpose3D. PMID:20700534

  2. Bias-induced offset effect overlapped on bipolar-resistance effect based on Co/SiO{sub 2}/Si structure

    SciTech Connect

    Yu Chongqi; Wang Hui

    2010-07-26

    Recent study shows the resistance of a metal-oxide-semiconductor (MOS) structure can be controlled by a laser via a bipolar-resistance effect (BRE). Based on this BRE phenomenon, we find an overlapped offset effect which is induced by an external bias applying to the structure. This offset effect features with a moveable equilibrium point of BRE, suggesting a combined control to the resistance and adding functionality to the MOS-based photoelectric devices.

  3. Comparison of codon usage bias across Leishmania and Trypanosomatids to understand mRNA secondary structure, relative protein abundance and pathway functions.

    PubMed

    Subramanian, Abhishek; Sarkar, Ram Rup

    2015-10-01

    Understanding the variations in gene organization and its effect on the phenotype across different Leishmania species, and to study differential clinical manifestations of parasite within the host, we performed large scale analysis of codon usage patterns between Leishmania and other known Trypanosomatid species. We present the causes and consequences of codon usage bias in Leishmania genomes with respect to mutational pressure, translational selection and amino acid composition bias. We establish GC bias at wobble position that governs codon usage bias across Leishmania species, rather than amino acid composition bias. We found that, within Leishmania, homogenous codon context coding for less frequent amino acid pairs and codons avoiding formation of folding structures in mRNA are essentially chosen. We predicted putative differences in global expression between genes belonging to specific pathways across Leishmania. This explains the role of evolution in shaping the otherwise conserved genome to demonstrate species-specific function-level differences for efficient survival. Copyright © 2015 Elsevier Inc. All rights reserved.

  4. The structure of locally bounded finite-dimensional representations of connected locally compact groups

    SciTech Connect

    Shtern, A. I.

    2014-04-30

    An analogue of a Lie theorem is obtained for (not necessarily continuous) finite-dimensional representations of soluble finite-dimensional locally compact groups with connected quotient group by the centre. As a corollary, the following automatic continuity proposition is obtained for locally bounded finite-dimensional representations of connected locally compact groups: if G is a connected locally compact group, N is a compact normal subgroup of G such that the quotient group G/N is a Lie group, N{sub 0} is the connected identity component in N, H is the family of elements of G commuting with every element of N{sub 0}, and π is a (not necessarily continuous) locally bounded finite-dimensional representation of G, then π is continuous on the commutator subgroup of H (in the intrinsic topology of the smallest analytic subgroup of G containing this commutator subgroup). Bibliography: 23 titles. (paper)

  5. Local structure and dynamics of hemeproteins by X-ray absorption near edge structure spectroscopy.

    PubMed

    Arcovito, Alessandro; della Longa, Stefano

    2012-07-01

    X-ray absorption near edge structure (XANES) spectroscopy is a synchrotron radiation technique sensitive to the local structure and dynamics around the metal site of a heme containing protein. Advances in detection techniques and theoretical/computational platforms in the last 15 years allowed the use of XANES as a quantitative probe of the key structural determinants driving functional changes, both in a concerted way with protein crystallography and EXAFS (extended X-ray absorption fine structure), or as a stand-alone method to apply in the crystal state as well as in solution. Moreover, the local dynamics of the heme site has been deeply investigated, on one hand, coupling XANES to classical photolysis experiments at cryogenic temperatures; on the other hand, the intrinsic property of the synchrotron radiation to induce radiolysis events, has been exploited to investigate specific cryotrapped intermediates, using X-rays both as a pump and a probe. Insights on the XANES method and some specific examples are presented to illustrate these topics. Copyright © 2012 Elsevier Inc. All rights reserved.

  6. A special kind of local structure in the CMB intensity maps: duel peak structure

    NASA Astrophysics Data System (ADS)

    Liu, Hao; Li, Ti-Pei

    2009-03-01

    We study the local structure of Cosmic Microwave Background (CMB) temperature maps released by the Wilkinson Microwave Anisotropy Probe (WMAP) team, and find a new kind of structure, which can be described as follows: a peak (or valley) of average temperature is often followed by a peak of temperature fluctuation that is 4° away. This structure is important for the following reasons: both the well known cold spot detected by Cruz et al. and the hot spot detected by Vielva et al. with the same technology (the third spot in their article) have such structure; more spots that are similar to them can be found on CMB maps and they also tend to be significant cold/hot spots; if we change the 4° characteristic into an artificial one, such as 3° or 5°, there will be less 'similar spots', and the temperature peaks or valleys will be less significant. The presented 'similar spots' have passed a strict consistency test which requires them to be significant on at least three different CMB temperature maps. We hope that this article could arouse some interest in the relationship of average temperature with temperature fluctuation in local areas; meanwhile, we are also trying to find an explanation for it which might be important to CMB observation and theory.

  7. Female philopatry and male-biased dispersal in a direct-developing salamander, Plethodon cinereus.

    PubMed

    Liebgold, Eric B; Brodie, Edmund D; Cabe, Paul R

    2011-01-01

    The local resource competition hypothesis and the local mate competition hypothesis were developed based on avian and mammalian systems to explain sex-biased dispersal. Most avian species show a female bias in dispersal, ostensibly due to resource defence, and most mammals show a male bias, ostensibly due to male-male competition. These findings confound phylogeny with mating strategy; little is known about sex-biased dispersal in other taxa. Resource defence and male-male competition are both intense in Plethodon cinereus, a direct-developing salamander, so we tested whether sex-biased dispersal in this amphibian is consistent with the local resource competition hypothesis (female-biased) or the local mate competition hypothesis (male-biased). Using fine-scale genetic spatial autocorrelation analyses, we found that females were philopatric, showing significant positive genetic structure in the shortest distance classes, with stronger patterns apparent when only territorial females were tested. Males showed no spatial genetic structure over the shortest distances. Mark-recapture observations of P. cinereus over 5 years were consistent with the genetic data: males dispersed farther than females during natal dispersal and 44% of females were recaptured within 1 m of their juvenile locations. We conclude that, in this population of a direct-developing amphibian, females are philopatric and dispersal is male-biased, consistent with the local mate competition hypothesis. © 2010 Blackwell Publishing Ltd.

  8. Bias-polarity-dependent resistance switching in W/SiO2/Pt and W/SiO2/Si/Pt structures.

    PubMed

    Jiang, Hao; Li, Xiang Yuan; Chen, Ran; Shao, Xing Long; Yoon, Jung Ho; Hu, Xiwen; Hwang, Cheol Seong; Zhao, Jinshi

    2016-02-26

    SiO2 is the most significantly used insulator layer in semiconductor devices. Its functionality was recently extended to resistance switching random access memory, where the defective SiO2 played an active role as the resistance switching (RS) layer. In this report, the bias-polarity-dependent RS behaviours in the top electrode W-sputtered SiO2-bottom electrode Pt (W/SiO2/Pt) structure were examined based on the current-voltage (I-V) sweep. When the memory cell was electroformed with a negative bias applied to the W electrode, the memory cell showed a typical electronic switching mechanism with a resistance ratio of ~100 and high reliability. For electroforming with opposite bias polarity, typical ionic-defect-mediated (conducting filament) RS was observed with lower reliability. Such distinctive RS mechanisms depending on the electroforming-bias polarity could be further confirmed using the light illumination study. Devices with similar electrode structures with a thin intervening Si layer between the SiO2 and Pt electrode, to improve the RS film morphology (root-mean-squared roughness of ~1.7 nm), were also fabricated. Their RS performances were almost identical to that of the single-layer SiO2 sample with very high roughness (root-mean-squared roughness of ~10 nm), suggesting that the reported RS behaviours were inherent to the material property.

  9. Imitating intrinsic alignments: a bias to the CMB lensing-galaxy shape cross-correlation power spectrum induced by the large-scale structure bispectrum

    NASA Astrophysics Data System (ADS)

    Merkel, Philipp M.; Schäfer, Björn Malte

    2017-10-01

    Cross-correlating the lensing signals of galaxies and comic microwave background (CMB) fluctuations is expected to provide valuable cosmological information. In particular, it may help tighten constraints on parameters describing the properties of intrinsically aligned galaxies at high redshift. To access the information conveyed by the cross-correlation signal, its accurate theoretical description is required. We compute the bias to CMB lensing-galaxy shape cross-correlation measurements induced by non-linear structure growth. Using tree-level perturbation theory for the large-scale structure bispectrum, we find that the bias is negative on most angular scales, therefore mimicking the signal of intrinsic alignments. Combining Euclid-like galaxy lensing data with a CMB experiment comparable to the Planck satellite mission, the bias becomes significant only on smallest scales (ℓ ≳ 2500). For improved CMB observations, however, the corrections amount to 10-15 per cent of the CMB lensing-intrinsic alignment signal over a wide multipole range (10 ≲ ℓ ≲ 2000). Accordingly, the power spectrum bias, if uncorrected, translates into 2σ and 3σ errors in the determination of the intrinsic alignment amplitude in the case of CMB stage III and stage IV experiments, respectively.

  10. Bias-polarity-dependent resistance switching in W/SiO2/Pt and W/SiO2/Si/Pt structures

    PubMed Central

    Jiang, Hao; Li, Xiang Yuan; Chen, Ran; Shao, Xing Long; Yoon, Jung Ho; Hu, Xiwen; Hwang, Cheol Seong; Zhao, Jinshi

    2016-01-01

    SiO2 is the most significantly used insulator layer in semiconductor devices. Its functionality was recently extended to resistance switching random access memory, where the defective SiO2 played an active role as the resistance switching (RS) layer. In this report, the bias-polarity-dependent RS behaviours in the top electrode W-sputtered SiO2-bottom electrode Pt (W/SiO2/Pt) structure were examined based on the current-voltage (I-V) sweep. When the memory cell was electroformed with a negative bias applied to the W electrode, the memory cell showed a typical electronic switching mechanism with a resistance ratio of ~100 and high reliability. For electroforming with opposite bias polarity, typical ionic-defect-mediated (conducting filament) RS was observed with lower reliability. Such distinctive RS mechanisms depending on the electroforming-bias polarity could be further confirmed using the light illumination study. Devices with similar electrode structures with a thin intervening Si layer between the SiO2 and Pt electrode, to improve the RS film morphology (root-mean-squared roughness of ~1.7 nm), were also fabricated. Their RS performances were almost identical to that of the single-layer SiO2 sample with very high roughness (root-mean-squared roughness of ~10 nm), suggesting that the reported RS behaviours were inherent to the material property. PMID:26916050

  11. A room temperature strategy towards enhanced performance and bias stability of oxide thin film transistor with a sandwich structure channel layer

    NASA Astrophysics Data System (ADS)

    Zeng, Yong; Ning, Honglong; Zheng, Zeke; Zhang, Hongke; Fang, Zhiqiang; Yao, Rihui; Xu, Miao; Wang, Lei; Lan, Linfeng; Peng, Junbiao; Lu, Xubing

    2017-04-01

    Thermal annealing is a conventional and effective way to improve the bias stress stability of oxide thin film transistors (TFT) on solid substrates. However, it is still a challenge for enhancing the bias stress stability of oxide TFTs on flexible substrates by high-temperature post-treatment due to the thermal sensitivity of flexible substrates. Here, a room temperature strategy is presented towards enhanced performance and bias stability of oxide TFTs by intentionally engineering a sandwich structure channel layer consisting of a superlattice with aluminum doped zinc oxide (AZO) and Al2O3 thin films. The Al2O3/AZO/Al2O3-TFTs not only exhibit a saturation mobility of 9.27 cm2 V-1 s-1 and a linear mobility of 11.38 cm2 V-1 s-1 but also demonstrate a better bias stress stability than AZO/Al2O3-TFT. Moreover, the underlying mechanism of this enhanced electrical performance of TFTs with a sandwich structure channel layer is that the bottom Al2O3 thin films can obviously improve the crystalline phase of AZO films while decreasing electrical trapping centers and adsorption sites for undesirable molecules such as water and oxygen.

  12. STRUCTURAL AND HIDDEN BARRIERS TO A LOCAL PRIMARY HEALTH CARE INFRASTRUCTURE: AUTONOMY, DECISIONS ABOUT PRIMARY HEALTH CARE, AND THE CENTRALITY AND SIGNIFICANCE OF POWER

    PubMed Central

    Freed, Christopher R.; Hansberry, Shantisha T.; Arrieta, Martha I.

    2014-01-01

    Purpose: To examine a local primary health care infrastructure and the reality of primary health care from the perspective of residents of a small, urban community in the southern United States. Methodology/approach: Data derive from 13 semi-structured focus groups, plus three semi-structured interviews, and were analyzed inductively consistent with a grounded theory approach. Findings: Structural barriers to the local primary health care infrastructure include transportation, clinic and appointment wait time, and co-payments and health insurance. Hidden barriers consist of knowledge about local health care services, non-physician gatekeepers, and fear of medical care. Community residents have used home remedies and the emergency department at the local academic medical center to manage these structural and hidden barriers. Research limitations/implications: Findings might not generalize to primary health care infrastructures in other communities, respondent perspectives can be biased, and the data are subject to various interpretations and conceptual and thematic frameworks. Nevertheless, the structural and hidden barriers to the local primary health care infrastructure have considerably diminished the autonomy community residents have been able to exercise over their decisions about primary health care, ultimately suggesting that efforts concerned with increasing the access of medically underserved groups to primary health care in local communities should recognize the centrality and significance of power. Originality/value: This study addresses a gap in the sociological literature regarding the impact of specific barriers to primary health care among medically underserved groups. PMID:24532864

  13. Structural modification of nanocrystalline diamond films via positive/negative bias enhanced nucleation and growth processes for improving their electron field emission properties

    SciTech Connect

    Saravanan, A.; Huang, B. R.; Sankaran, K. J.; Tai, N. H.; Keiser, G.; Kurian, J.; Lin, I. N.

    2015-06-07

    Electron field emission (EFE) properties of nanocrystalline diamond (NCD) films synthesized by the bias-enhanced growth (beg) process under different bias voltages were investigated. The induction of the nanographitic phases is presumed to be the prime factor in enhancing the EFE properties of negative biased NCD films. Transmission electron microscopic investigations reveal that a negative bias voltage of −300 V increases the rate of growth for NCD films with the size of the grains changing from nano to ultranano size. This effect also is accompanied by the induction of nanographitic filaments in the grain boundaries of the films. The turn-on field (E{sub 0}) for the EFE process then effectively gets reduced. The EFE process of the beg-NCD{sub −300V} films can be turned on at E{sub 0} = 3.86 V/μm, and the EFE current density achieved is 1.49 mA/cm{sup 2} at an applied field of 7.85 V/μm. On the other hand, though a positive-bias beg process (+200 V) results in the reduction of grain size, it does not induce sufficient nanographitic phases to lower the E{sub 0} value of the EFE process. Moreover, the optical emission spectroscopic investigation indicates that one of the primary causes that changes the granular structure of the NCD films is the increase in the proportion of C{sub 2} and CH species induced in the growing plasma. The polarity of the bias voltage is of less importance in the microstructural evolution of the films.

  14. Structural modification of nanocrystalline diamond films via positive/negative bias enhanced nucleation and growth processes for improving their electron field emission properties

    NASA Astrophysics Data System (ADS)

    Saravanan, A.; Huang, B. R.; Sankaran, K. J.; Keiser, G.; Kurian, J.; Tai, N. H.; Lin, I. N.

    2015-06-01

    Electron field emission (EFE) properties of nanocrystalline diamond (NCD) films synthesized by the bias-enhanced growth (beg) process under different bias voltages were investigated. The induction of the nanographitic phases is presumed to be the prime factor in enhancing the EFE properties of negative biased NCD films. Transmission electron microscopic investigations reveal that a negative bias voltage of -300 V increases the rate of growth for NCD films with the size of the grains changing from nano to ultranano size. This effect also is accompanied by the induction of nanographitic filaments in the grain boundaries of the films. The turn-on field (E0) for the EFE process then effectively gets reduced. The EFE process of the beg-NCD-300V films can be turned on at E0 = 3.86 V/μm, and the EFE current density achieved is 1.49 mA/cm2 at an applied field of 7.85 V/μm. On the other hand, though a positive-bias beg process (+200 V) results in the reduction of grain size, it does not induce sufficient nanographitic phases to lower the E0 value of the EFE process. Moreover, the optical emission spectroscopic investigation indicates that one of the primary causes that changes the granular structure of the NCD films is the increase in the proportion of C2 and CH species induced in the growing plasma. The polarity of the bias voltage is of less importance in the microstructural evolution of the films.

  15. Journal bias or author bias?

    PubMed

    Harris, Ian

    2016-01-01

    I read with interest the comment by Mark Wilson in the Indian Journal of Medical Ethics regarding bias and conflicts of interest in medical journals. Wilson targets one journal (the New England Journal of Medicine: NEJM) and one particular "scandal" to make his point that journals' decisions on publication are biased by commercial conflicts of interest (CoIs). It is interesting that he chooses the NEJM which, by his own admission, had one of the strictest CoI policies and had published widely on this topic. The feeling is that if the NEJM can be guilty, they can all be guilty.

  16. Effect of local structures on structural evolution during crystallization in undercooled metallic glass-forming liquids.

    PubMed

    Wu, Z W; Li, M Z; Wang, W H; Song, W J; Liu, K X

    2013-02-21

    The effect of local structures on structural evolution during the crystallization of undercooled ZrCu metallic glass-forming liquid was studied via molecular dynamics simulations. It is found that body-centered-cubic (bcc)-like clusters play a key role in structural evolution during crystallization. In contrast to previous speculations, the number of bcc-like crystal nuclei does not change much before the onset of crystallization. Instead, the development of a bcc-like critical nucleus during annealing leads to a strong spatial correlation with other nuclei in its surroundings, forming a crystalline structure template. It is also found that the size distribution of bcc-like nuclei follows a power-law form with an exponential cutoff in the early stage of annealing, but changes to a pure power-law behavior just before the onset of crystallization. This implies that the crystalline structure template has fractal feature and the undercooled liquids evolve to a self-organized critical state before the onset of crystallization, which might trigger the subsequent rapid crystallization. According to the graph theory analysis, it is also found that the observed large scatter of the onset time of crystallization in different liquid samples results from the connectivity of the bcc-like clusters.

  17. Optimistic bias, sexual assault, and fear.

    PubMed

    Chapin, John R; Pierce, Mari

    2012-01-01

    A survey of 431 adults documents optimistic bias regarding people's perceived risk of sexual victimization. The findings extend optimistic bias to crime victimization and contribute to the literature by considering a motivational factor, fear, as a predictor of optimistic bias. The study also yielded significant relationships between optimistic bias and demographic variables, including age, gender, and family structure.

  18. Giant low-frequency multipeak self-biased magnetoelectric properties in four-phase structure with stepped ultrasonic horn

    NASA Astrophysics Data System (ADS)

    Li, Jie; Lu, Caijiang

    2016-11-01

    This paper develops a self-biased magnetoelectric (ME) heterostructure FeCuNbSiB/terfenol-d/ultrasonic-horn/PZT by sandwiching a piezoelectric Pb(Zr,Ti)O3 (PZT) plate and a magnetization-graded FeCuNbSiB/terfenol-d layer on a rectangular-stepped ultrasonic horn substrate. The rectangular-stepped ultrasonic horn substrate severs as the resonance frequency determining element of the ME heterostructure, converges and amplifies the vibration excited by the magnetization-graded FeCuNbSiB/terfenol-d layer. The experiments show that fifteen large peaks of ME response with magnitudes of 0.2-7.5 V/(cm·Oe) in 0.5-50 kHz range are observed at zero-biased magnetic field. This demonstrates that the proposed multi-peak self-biased heterostructure may be useful for multifunctional devices for multi-frequency operation.

  19. Biased tracers and time evolution

    SciTech Connect

    Mirbabayi, Mehrdad; Zaldarriaga, Matias; Schmidt, Fabian E-mail: fabians@mpa-garching.mpg.de

    2015-07-01

    We study the effect of time evolution on galaxy bias. We argue that at any order in perturbations, the galaxy density contrast can be expressed in terms of a finite set of locally measurable operators made of spatial and temporal derivatives of the Newtonian potential. This is checked in an explicit third order calculation. There is a systematic way to derive a basis for these operators. This basis spans a larger space than the expansion in gravitational and velocity potentials usually employed, although new operators only appear at fourth order. The basis is argued to be closed under renormalization. Most of the arguments also apply to the structure of the counter-terms in the effective theory of large-scale structure.

  20. Local structure studies of some cobalt (II) complexes using extended X-ray absorption fine structure

    NASA Astrophysics Data System (ADS)

    Mishra, Ashutosh; Ninama, Samrath; Trivedi, Apurva

    2014-09-01

    Extended X-ray Absorption Fine Structure (EXAFS) analysis of Cobalt (II) complex as a ligand of 2 -methyl-3-[(bis-aniline(R) phenyl]-3H-l,5 benzodiazepine for finding local structure using conventional method .The Co(II) complexes were prepared by chemical root method. The EXAFS spectra were recorded at Cobalt K-edge i.e.; 7709 eV using Dispersive EXFAS beam line at 2.5GeV Indus-2 Synchrotron Radiation Source(SRS) at RRCAT, Indore, India. The recorded EXAFS data were analysed using the computer software Athena for determine the nearest neighbouring distances (bond lengths) of these complexes with conventional methods and it compared with Fourier transform(FT) analysis. The Fourier Transform convert EXAFS data signal into r-space or k-space. This is useful for visualizing the major contributions to the EXAFS spectrum.

  1. Non-Gaussian halo assembly bias

    SciTech Connect

    Reid, Beth A.; Verde, Licia; Dolag, Klaus; Matarrese, Sabino; Moscardini, Lauro E-mail: liciaverde@icc.ub.edu E-mail: sabino.matarrese@pd.infn.it

    2010-07-01

    The strong dependence of the large-scale dark matter halo bias on the (local) non-Gaussianity parameter, f{sub NL}, offers a promising avenue towards constraining primordial non-Gaussianity with large-scale structure surveys. In this paper, we present the first detection of the dependence of the non-Gaussian halo bias on halo formation history using N-body simulations. We also present an analytic derivation of the expected signal based on the extended Press-Schechter formalism. In excellent agreement with our analytic prediction, we find that the halo formation history-dependent contribution to the non-Gaussian halo bias (which we call non-Gaussian halo assembly bias) can be factorized in a form approximately independent of redshift and halo mass. The correction to the non-Gaussian halo bias due to the halo formation history can be as large as 100%, with a suppression of the signal for recently formed halos and enhancement for old halos. This could in principle be a problem for realistic galaxy surveys if observational selection effects were to pick galaxies occupying only recently formed halos. Current semi-analytic galaxy formation models, for example, imply an enhancement in the expected signal of ∼ 23% and ∼ 48% for galaxies at z = 1 selected by stellar mass and star formation rate, respectively.

  2. Multiscale tomography of buried magnetic structures: its use in the localization and characterization of archaeological structures

    NASA Astrophysics Data System (ADS)

    Saracco, Ginette; Moreau, Frédérique; Mathé, Pierre-Etienne; Hermitte, Daniel; Michel, Jean-Marie

    2007-10-01

    We have previously developed a method for characterizing and localizing `homogeneous' buried sources, from the measure of potential anomalies at a fixed height above ground (magnetic, electric and gravity). This method is based on potential theory and uses the properties of the Poisson kernel (real by definition) and the continuous wavelet theory. Here, we relax the assumption on sources and introduce a method that we call the `multiscale tomography'. Our approach is based on the harmonic extension of the observed magnetic field to produce a complex source by use of a complex Poisson kernel solution of the Laplace equation for complex potential field. A phase and modulus are defined. We show that the phase provides additional information on the total magnetic inclination and the structure of sources, while the modulus allows us to characterize its spatial location, depth and `effective degree'. This method is compared to the `complex dipolar tomography', extension of the Patella method that we previously developed. We applied both methods and a classical electrical resistivity tomography to detect and localize buried archaeological structures like antique ovens from magnetic measurements on the Fox-Amphoux site (France). The estimates are then compared with the results of excavations.

  3. Expectation and Locality Effects in German Verb-Final Structures

    ERIC Educational Resources Information Center

    Levy, Roger P.; Keller, Frank

    2013-01-01

    Probabilistic expectations and memory limitations are central factors governing the real-time comprehension of natural language, but how the two factors interact remains poorly understood. One respect in which the two factors have come into theoretical conflict is the documentation of both "locality" effects, in which having more dependents…

  4. Illustrative bias

    NASA Astrophysics Data System (ADS)

    Zagoskin, Alexandre

    2017-08-01

    In response to Rebecca Holmes’ feature “Local realism is dead, long live local realism?” (June pp21-25), which describes the experiments that finally closed the long-standing loopholes in Bell tests, suggesting the end of the road for local realism.

  5. Direct imaging of thermally-activated grain-boundary diffusion in Cu/Co/IrMn/Pt exchange-bias structures using atom-probe tomography

    SciTech Connect

    Letellier, F.; Lardé, R.; Le Breton, J.-M.; Akmaldinov, K.; Auffret, S.; Dieny, B.; Baltz, V.

    2014-11-28

    Magnetic devices are often subject to thermal processing steps, such as field cooling to set exchange bias and annealing to crystallize amorphous magnetic electrodes. These processing steps may result in interdiffusion and the subsequent deterioration of magnetic properties. In this study, we investigated thermally-activated diffusion in Cu/Co/IrMn/Pt exchange biased polycrystalline thin-film structures using atom probe tomography. Images taken after annealing at 400 °C for 60 min revealed Mn diffusion into Co grains at the Co/IrMn interface and along Pt grain boundaries for the IrMn/Pt stack, i.e., a Harrison type C regime. Annealing at 500 °C showed further Mn diffusion into Co grains. At the IrMn/Pt interface, annealing at 500 °C led to a type B behavior since Mn diffusion was detected both along Pt grain boundaries and also into Pt grains. The deterioration of the films' exchange bias properties upon annealing was correlated to the observed diffusion. In particular, the topmost Pt capping layer thickness turned out to be crucial since a faster deterioration of the exchange bias properties for thicker caps was observed. This is consistent with the idea that Pt acts as a getter for Mn, drawing Mn out of the IrMn layer.

  6. Direct imaging of thermally-activated grain-boundary diffusion in Cu/Co/IrMn/Pt exchange-bias structures using atom-probe tomography

    NASA Astrophysics Data System (ADS)

    Letellier, F.; Lechevallier, L.; Lardé, R.; Le Breton, J.-M.; Akmaldinov, K.; Auffret, S.; Dieny, B.; Baltz, V.

    2014-11-01

    Magnetic devices are often subject to thermal processing steps, such as field cooling to set exchange bias and annealing to crystallize amorphous magnetic electrodes. These processing steps may result in interdiffusion and the subsequent deterioration of magnetic properties. In this study, we investigated thermally-activated diffusion in Cu/Co/IrMn/Pt exchange biased polycrystalline thin-film structures using atom probe tomography. Images taken after annealing at 400 °C for 60 min revealed Mn diffusion into Co grains at the Co/IrMn interface and along Pt grain boundaries for the IrMn/Pt stack, i.e., a Harrison type C regime. Annealing at 500 °C showed further Mn diffusion into Co grains. At the IrMn/Pt interface, annealing at 500 °C led to a type B behavior since Mn diffusion was detected both along Pt grain boundaries and also into Pt grains. The deterioration of the films' exchange bias properties upon annealing was correlated to the observed diffusion. In particular, the topmost Pt capping layer thickness turned out to be crucial since a faster deterioration of the exchange bias properties for thicker caps was observed. This is consistent with the idea that Pt acts as a getter for Mn, drawing Mn out of the IrMn layer.

  7. Optical and Electrical Performance of MOS-Structure Silicon Solar Cells with Antireflective Transparent ITO and Plasmonic Indium Nanoparticles under Applied Bias Voltage

    PubMed Central

    Ho, Wen-Jeng; Sue, Ruei-Siang; Lin, Jian-Cheng; Syu, Hong-Jang; Lin, Ching-Fuh

    2016-01-01

    This paper reports impressive improvements in the optical and electrical performance of metal-oxide-semiconductor (MOS)-structure silicon solar cells through the incorporation of plasmonic indium nanoparticles (In-NPs) and an indium-tin-oxide (ITO) electrode with periodic holes (perforations) under applied bias voltage. Samples were prepared using a plain ITO electrode or perforated ITO electrode with and without In-NPs. The samples were characterized according to optical reflectance, dark current voltage, induced capacitance voltage, external quantum efficiency, and photovoltaic current voltage. Our results indicate that induced capacitance voltage and photovoltaic current voltage both depend on bias voltage, regardless of the type of ITO electrode. Under a bias voltage of 4.0 V, MOS cells with perforated ITO and plain ITO, respectively, presented conversion efficiencies of 17.53% and 15.80%. Under a bias voltage of 4.0 V, the inclusion of In-NPs increased the efficiency of cells with perforated ITO and plain ITO to 17.80% and 16.87%, respectively. PMID:28773801

  8. Optical and Electrical Performance of MOS-Structure Silicon Solar Cells with Antireflective Transparent ITO and Plasmonic Indium Nanoparticles under Applied Bias Voltage.

    PubMed

    Ho, Wen-Jeng; Sue, Ruei-Siang; Lin, Jian-Cheng; Syu, Hong-Jang; Lin, Ching-Fuh

    2016-08-10

    This paper reports impressive improvements in the optical and electrical performance of metal-oxide-semiconductor (MOS)-structure silicon solar cells through the incorporation of plasmonic indium nanoparticles (In-NPs) and an indium-tin-oxide (ITO) electrode with periodic holes (perforations) under applied bias voltage. Samples were prepared using a plain ITO electrode or perforated ITO electrode with and without In-NPs. The samples were characterized according to optical reflectance, dark current voltage, induced capacitance voltage, external quantum efficiency, and photovoltaic current voltage. Our results indicate that induced capacitance voltage and photovoltaic current voltage both depend on bias voltage, regardless of the type of ITO electrode. Under a bias voltage of 4.0 V, MOS cells with perforated ITO and plain ITO, respectively, presented conversion efficiencies of 17.53% and 15.80%. Under a bias voltage of 4.0 V, the inclusion of In-NPs increased the efficiency of cells with perforated ITO and plain ITO to 17.80% and 16.87%, respectively.

  9. The role of anxiety sensitivity, behavioral inhibition, and cognitive biases in anxiety symptoms: structural equation modeling of direct and indirect pathways.

    PubMed

    Viana, Andres G; Gratz, Kim L

    2012-10-01

    Limited research has examined how temperamental (i.e., behavioral inhibition, anxiety sensitivity) and cognitive (i.e., interpretive and judgment biases) risks for the development anxiety covary to influence anxiety symptoms. Thus, the present study aimed to advance understanding of the direct and indirect links between anxiety sensitivity, behavioral inhibition, and interpretive biases, and judgment biases (in the form of perceived control) to anxiety outcomes (i.e., worry and trait anxiety symptoms). 842 emerging adults (mean = 18.75 years, standard deviation = 1.05; age range = 18-24; 70% women) recruited from a university in the northeast participated in this study. Participants completed a battery of self-report measures assessing risk factors and anxiety outcomes of interest. Structural equation modeling revealed anxiety sensitivity and behavioral inhibition were directly linked with anxiety outcomes. Anxiety sensitivity and behavioral inhibition were also indirectly linked with anxiety outcomes through interpretive and judgment biases. The hypothesized model was partially invariant across high-risk and low-risk groups for anxiety disorders. Results of this study provide preliminary support for theoretical models hypothesizing a developmental progression from temperamental to cognitive risks and culminating in the expression of anxiety symptoms. Limitations and clinical implications of this research are discussed. © 2012 Wiley Periodicals, Inc.

  10. An Approximate Bayesian Computation Approach to Overcome Biases That Arise When Using Amplified Fragment Length Polymorphism Markers to Study Population Structure

    PubMed Central

    Foll, Matthieu; Beaumont, Mark A.; Gaggiotti, Oscar

    2008-01-01

    There is great interest in using amplified fragment length polymorphism (AFLP) markers because they are inexpensive and easy to produce. It is, therefore, possible to generate a large number of markers that have a wide coverage of species genomes. Several statistical methods have been proposed to study the genetic structure using AFLPs but they assume Hardy–Weinberg equilibrium and do not estimate the inbreeding coefficient, FIS. A Bayesian method has been proposed by Holsinger and colleagues that relaxes these simplifying assumptions but we have identified two sources of bias that can influence estimates based on these markers: (i) the use of a uniform prior on ancestral allele frequencies and (ii) the ascertainment bias of AFLP markers. We present a new Bayesian method that avoids these biases by using an implementation based on the approximate Bayesian computation (ABC) algorithm. This new method estimates population-specific FIS and FST values and offers users the possibility of taking into account the criteria for selecting the markers that are used in the analyses. The software is available at our web site (http://www-leca.ujf-grenoble.fr/logiciels.htm). Finally, we provide advice on how to avoid the effects of ascertainment bias. PMID:18505879

  11. Localized surface plasmon enhanced cellular imaging using random metallic structures

    NASA Astrophysics Data System (ADS)

    Son, Taehwang; Lee, Wonju; Kim, Donghyun

    2017-02-01

    We have studied fluorescence cellular imaging with randomly distributed localized near-field induced by silver nano-islands. For the fabrication of nano-islands, a 10-nm silver thin film evaporated on a BK7 glass substrate with an adhesion layer of 2-nm thick chromium. Micrometer sized silver square pattern was defined using e-beam lithography and then the film was annealed at 200°C. Raw images were restored using electric field distribution produced on the surface of random nano-islands. Nano-islands were modeled from SEM images. 488-nm p-polarized light source was set to be incident at 60°. Simulation results show that localized electric fields were created among nano-islands and that their average size was found to be 135 nm. The feasibility was tested using conventional total internal reflection fluorescence microscopy while the angle of incidence was adjusted to maximize field enhancement. Mouse microphage cells were cultured on nano-islands, and actin filaments were selectively stained with FITC-conjugated phalloidin. Acquired images were deconvolved based on linear imaging theory, in which molecular distribution was sampled by randomly distributed localized near-field and blurred by point spread function of far-field optics. The optimum fluorophore distribution was probabilistically estimated by repetitively matching a raw image. The deconvolved images are estimated to have a resolution in the range of 100-150 nm largely determined by the size of localized near-fields. We also discuss and compare the results with images acquired with periodic nano-aperture arrays in various optical configurations to excite localized plasmonic fields and to produce super-resolved molecular images.

  12. Structural features of multiple nifH-like sequences and very biased codon usage in nitrogenase genes of Clostridium pasteurianum.

    PubMed Central

    Chen, K C; Chen, J S; Johnson, J L

    1986-01-01

    The structural gene (nifH1) encoding the nitrogenase iron protein of Clostridium pasteurianum has been cloned and sequenced. It is located on a 4-kilobase EcoRI fragment (cloned into pBR325) that also contains a portion of nifD and another nifH-like sequence (nifH2). C. pasteurianum nifH1 encodes a polypeptide (273 amino acids) identical to that of the isolated iron protein, indicating that the smaller size of the C. pasteurianum iron protein does not result from posttranslational processing. The 5' flanking region of nifH1 or nifH2 does not contain the nif promoter sequences found in several gram-negative bacteria. Instead, a sequence resembling the Escherichia coli consensus promoter (TTGACA-N17-TATAAT) is present before C. pasteurianum nifH2, and a TATAAT sequence is present before C pasteurianum nifH1. Codon usage in nifH1, nifH2, and nifD (partial) is very biased. A preference for A or U in the third position of the codons is seen. nifH2 could encode a protein of 272 amino acid residues, which differs from the iron protein (nifH1 product) in 23 amino acid residues (8%). Another nifH-like sequence (nifH3) is located on a nonadjacent EcoRI fragment and has been partially sequenced. C. pasteurianum nifH2 and nifH3 may encode proteins having several amino acids that are conserved in other proteins but not in C. pasteurianum iron protein, suggesting a possible role for the multiple nifH-like sequences of C. pasteurianum in the evolution of nifH. Among the nine sequenced iron proteins, only the C. pasteurianum protein lacks a conserved lysine residue which is near the extended C terminus of the other iron proteins. The absence of this positive charge in the C. pasteurianum iron protein might affect the cross-reactivity of the protein in heterologous systems. Images PMID:3457003

  13. Global/local methods research using a common structural analysis framework

    NASA Technical Reports Server (NTRS)

    Knight, Norman F., Jr.; Ransom, Jonathan B.; Griffin, O. H., Jr.; Thompson, Danniella M.

    1991-01-01

    Methodologies for global/local stress analysis are described including both two- and three-dimensional analysis methods. These methods are being developed within a common structural analysis framework. Representative structural analysis problems are presented to demonstrate the global/local methodologies being developed.

  14. Global/local methods research using a common structural analysis framework

    NASA Technical Reports Server (NTRS)

    Knight, Norman F., Jr.; Ransom, Jonathan B.; Griffin, O. H., Jr.; Thompson, Danniella M.

    1991-01-01

    Methodologies for global/local stress analysis are described including both two- and three-dimensional analysis methods. These methods are being developed within a common structural analysis framework. Representative structural analysis problems are presented to demonstrate the global/local methodologies being developed.

  15. Structure-based Molecular Simulations Reveal the Enhancement of Biased Brownian Motions in Single-headed Kinesin

    PubMed Central

    Kanada, Ryo; Kuwata, Takeshi; Kenzaki, Hiroo; Takada, Shoji

    2013-01-01

    Kinesin is a family of molecular motors that move unidirectionally along microtubules (MT) using ATP hydrolysis free energy. In the family, the conventional two-headed kinesin was experimentally characterized to move unidirectionally through “walking” in a hand-over-hand fashion by coordinated motions of the two heads. Interestingly a single-headed kinesin, a truncated KIF1A, still can generate a biased Brownian movement along MT, as observed by in vitro single molecule experiments. Thus, KIF1A must use a different mechanism from the conventional kinesin to achieve the unidirectional motions. Based on the energy landscape view of proteins, for the first time, we conducted a set of molecular simulations of the truncated KIF1A movements over an ATP hydrolysis cycle and found a mechanism exhibiting and enhancing stochastic forward-biased movements in a similar way to those in experiments. First, simulating stand-alone KIF1A, we did not find any biased movements, while we found that KIF1A with a large friction cargo-analog attached to the C-terminus can generate clearly biased Brownian movements upon an ATP hydrolysis cycle. The linked cargo-analog enhanced the detachment of the KIF1A from MT. Once detached, diffusion of the KIF1A head was restricted around the large cargo which was located in front of the head at the time of detachment, thus generating a forward bias of the diffusion. The cargo plays the role of a diffusional anchor, or cane, in KIF1A “walking.” PMID:23459019

  16. Oscillation structure of localized perturbations in modulationally unstable media.

    PubMed

    Biondini, Gino; Li, Sitai; Mantzavinos, Dionyssios

    2016-12-01

    We characterize the properties of the asymptotic stage of modulational instability arising from localized perturbations of a constant background, including the number and location of the individual peaks in the oscillation region. We show that, for long times, the solution tends to an ensemble of classical (i.e., sech-shaped) solitons of the focusing nonlinear Schrödinger equation (as opposed to the various breatherlike solutions of the same equation with a nonzero background). We also confirm the robustness of the theoretical results by comparing the analytical predictions with careful numerical simulations with a variety of initial conditions, which confirm that the evolution of modulationally unstable media in the presence of localized initial perturbations is indeed described by the same asymptotic state.

  17. Oscillation structure of localized perturbations in modulationally unstable media

    NASA Astrophysics Data System (ADS)

    Biondini, Gino; Li, Sitai; Mantzavinos, Dionyssios

    2016-12-01

    We characterize the properties of the asymptotic stage of modulational instability arising from localized perturbations of a constant background, including the number and location of the individual peaks in the oscillation region. We show that, for long times, the solution tends to an ensemble of classical (i.e., sech-shaped) solitons of the focusing nonlinear Schrödinger equation (as opposed to the various breatherlike solutions of the same equation with a nonzero background). We also confirm the robustness of the theoretical results by comparing the analytical predictions with careful numerical simulations with a variety of initial conditions, which confirm that the evolution of modulationally unstable media in the presence of localized initial perturbations is indeed described by the same asymptotic state.

  18. Structural biomechanics modulate intramuscular distribution of locally delivered drugs.

    PubMed

    Wu, Peter I-Kung; Edelman, Elazer R

    2008-09-18

    As local drug delivery continues to emerge as a clinical force, so does understanding of its potentially narrow therapeutic window. Classic molecular transport studies are of value but do not typically account for the local nature of drug transport or the effects of regional dynamic function in target tissues like muscle that may undergo cyclical and variable mechanical motion and loading. We examined the impact of dynamic architecture on intramuscular drug distribution. We designed a tissue mounting technique and mechanical loading system that uniquely enables pharmacokinetics investigations in association with control of muscle biomechanics while preserving physiologic tissue architecture. The system was validated and used to elucidate the influence of architecture and controlled cyclic strain on intramuscular drug distribution. Rat soleus muscles underwent controlled deformations within a drug delivery chamber that preserved in vivo physiology. Penetration of 1mM 20 kDa FITC-dextran at planar surfaces of the soleus axial cross-section increased significantly from 0.52+/-0.09 mm under 80 min of static (0%) strain to 0.81+/-0.09 mm under cyclic (3 Hz, 0-20% peak-to-peak) strain, demonstrating the driving effect of cyclic loading on transport. Penetration at curved margins was 1.57- and 2.53-fold greater than at planar surfaces under static and cyclic strain, respectively, and was enhanced 1.6-fold more by cyclic strain, revealing architecturally dictated spatial heterogeneity in transport and modulation of motion dynamics. Architectural geometry and dynamics modulate the impact of mechanical loading on local drug penetration and intramuscular distribution. Future work will use the biomechanical test system to investigate mechanisms underlying transport effects of specific loading regimens. It is hoped that this work will initiate a broader understanding of intramuscular pharmacokinetics and guide local drug delivery strategies.

  19. The role of local structure in dynamical arrest

    NASA Astrophysics Data System (ADS)

    Royall, C. Patrick; Williams, Stephen R.

    2015-02-01

    Amorphous solids, or glasses, are distinguished from crystalline solids by their lack of long-range structural order. At the level of two-body structural correlations, glassformers show no qualitative change upon vitrifying from a supercooled liquid. Nonetheless the dynamical properties of a glass are so much slower that it appears to take on the properties of a solid. While many theories of the glass transition focus on dynamical quantities, a solid's resistance to flow is often viewed as a consequence of its structure. Here we address the viewpoint that this remains the case for a glass. Recent developments using higher-order measures show a clear emergence of structure upon dynamical arrest in a variety of glass formers and offer the tantalising hope of a structural mechanism for arrest. However a rigorous fundamental identification of such a causal link between structure and arrest remains elusive. We undertake a critical survey of this work in experiments, computer simulation and theory and discuss what might strengthen the link between structure and dynamical arrest. We move on to highlight the relationship between crystallisation and glass-forming ability made possible by this deeper understanding of the structure of the liquid state, and emphasise the potential to design materials with optimal glassforming and crystallisation ability, for applications such as phase-change memory. We then consider aspects of the phenomenology of glassy systems where structural measures have yet to make a large impact, such as polyamorphism (the existence of multiple liquid states), ageing (the time-evolution of non-equilibrium materials below their glass transition) and the response of glassy materials to external fields such as shear.

  20. Remote sensing image segmentation using local sparse structure constrained latent low rank representation

    NASA Astrophysics Data System (ADS)

    Tian, Shu; Zhang, Ye; Yan, Yimin; Su, Nan; Zhang, Junping

    2016-09-01

    Latent low-rank representation (LatLRR) has been attached considerable attention in the field of remote sensing image segmentation, due to its effectiveness in exploring the multiple subspace structures of data. However, the increasingly heterogeneous texture information in the high spatial resolution remote sensing images, leads to more severe interference of pixels in local neighborhood, and the LatLRR fails to capture the local complex structure information. Therefore, we present a local sparse structure constrainted latent low-rank representation (LSSLatLRR) segmentation method, which explicitly imposes the local sparse structure constraint on LatLRR to capture the intrinsic local structure in manifold structure feature subspaces. The whole segmentation framework can be viewed as two stages in cascade. In the first stage, we use the local histogram transform to extract the texture local histogram features (LHOG) at each pixel, which can efficiently capture the complex and micro-texture pattern. In the second stage, a local sparse structure (LSS) formulation is established on LHOG, which aims to preserve the local intrinsic structure and enhance the relationship between pixels having similar local characteristics. Meanwhile, by integrating the LSS and the LatLRR, we can efficiently capture the local sparse and low-rank structure in the mixture of feature subspace, and we adopt the subspace segmentation method to improve the segmentation accuracy. Experimental results on the remote sensing images with different spatial resolution show that, compared with three state-of-the-art image segmentation methods, the proposed method achieves more accurate segmentation results.

  1. Optical Activity Governed by Local Chiral Structures in Two-Dimensional Curved Metallic Nanostructures.

    PubMed

    Narushima, Tetsuya; Hashiyada, Shun; Okamoto, Hiromi

    2016-07-01

    Chiral nanostructures show macroscopic optical activity. Local optical activity and its handedness are not uniform in the nanostructure, and are spatially distributed depending on the shape of the nanostructure. In this study we fabricated curved chain nanostructures made of gold by connecting linearly two or more arc structures in a two-dimensional plane. Spatial features of local optical activity in the chain structures were evaluated with near-field circular dichroism (CD) imaging, and analyzed with the aid of classical electromagnetic simulation. The electromagnetic simulation predicted that local optical activity appears at inflection points where arc structures are connected. The handedness of the local optical activity was dependent on the handedness of the local chirality at the inflection point. Chiral chain structures have odd inflection points and the local optical activity distributed symmetrically with respect to structural centers. In contrast, achiral chain structures have even inflection points and showed antisymmetric distribution. In the near-field CD images of fabricated chain nanostructures, the symmetric and antisymmetric distributions of local CD were observed for chiral and achiral chain structures, respectively, consistent with the simulated results. The handedness of the local optical activity was found to be determined by the handedness of the inflection point, for the fabricated chain structures having two or more inflection points. The local optical activity was thus governed primarily by the local chirality of the inflection points for the gold chain structures. The total effect of all the inflection points in the chain structure is considered to be a predominant factor that determines the macroscopic optical activity. Chirality 28:540-544, 2016. © 2016 Wiley Periodicals, Inc.

  2. Magnetic field dependent zero-bias diffusive anomaly in Pb-oxide- n-InAs structures: Coexistence of 2D and 3D states

    NASA Astrophysics Data System (ADS)

    Minkov, G. M.; Germanenko, A. V.; Negachev, S. A.; Rut, O. E.; Sukhorukov, Eugene V.

    1998-12-01

    The results of experimental and theoretical studies of zero-bias anomaly (ZBA) in the Pb-oxide- n-InAs tunnel structures in magnetic field up to 6 T are presented. A specific feature of the structures is a coexistence of the 2D and 3D states at the Fermi energy near the semiconductor surface. Experimentally observed magnetic field dependence of the amplitude of ZBA for different orientations of the magnetic field is in agreement with the proposed theoretical model. According to this model, electrons tunnel into 2D states, and move diffusively in 2D layer, whereas the main contribution to the screening comes from 3D electrons.

  3. Local Crystalline Structure in an Amorphous Protein Dense Phase.

    PubMed

    Greene, Daniel G; Modla, Shannon; Wagner, Norman J; Sandler, Stanley I; Lenhoff, Abraham M

    2015-10-20

    Proteins exhibit a variety of dense phases ranging from gels, aggregates, and precipitates to crystalline phases and dense liquids. Although the structure of the crystalline phase is known in atomistic detail, little attention has been paid to noncrystalline protein dense phases, and in many cases the structures of these phases are assumed to be fully amorphous. In this work, we used small-angle neutron scattering, electron microscopy, and electron tomography to measure the structure of ovalbumin precipitate particles salted out with ammonium sulfate. We found that the ovalbumin phase-separates into core-shell particles with a core radius of ∼2 μm and shell thickness of ∼0.5 μm. Within this shell region, nanostructures comprised of crystallites of ovalbumin self-assemble into a well-defined bicontinuous network with branches ∼12 nm thick. These results demonstrate that the protein gel is comprised in part of nanocrystalline protein.

  4. Local Crystalline Structure in an Amorphous Protein Dense Phase

    PubMed Central

    Greene, Daniel G.; Modla, Shannon; Wagner, Norman J.; Sandler, Stanley I.; Lenhoff, Abraham M.

    2015-01-01

    Proteins exhibit a variety of dense phases ranging from gels, aggregates, and precipitates to crystalline phases and dense liquids. Although the structure of the crystalline phase is known in atomistic detail, little attention has been paid to noncrystalline protein dense phases, and in many cases the structures of these phases are assumed to be fully amorphous. In this work, we used small-angle neutron scattering, electron microscopy, and electron tomography to measure the structure of ovalbumin precipitate particles salted out with ammonium sulfate. We found that the ovalbumin phase-separates into core-shell particles with a core radius of ∼2 μm and shell thickness of ∼0.5 μm. Within this shell region, nanostructures comprised of crystallites of ovalbumin self-assemble into a well-defined bicontinuous network with branches ∼12 nm thick. These results demonstrate that the protein gel is comprised in part of nanocrystalline protein. PMID:26488663

  5. Identification of local variations within secondary structures of proteins.

    PubMed

    Kumar, Prasun; Bansal, Manju

    2015-05-01

    Secondary-structure elements (SSEs) play an important role in the folding of proteins. Identification of SSEs in proteins is a common problem in structural biology. A new method, ASSP (Assignment of Secondary Structure in Proteins), using only the path traversed by the C(α) atoms has been developed. The algorithm is based on the premise that the protein structure can be divided into continuous or uniform stretches, which can be defined in terms of helical parameters, and depending on their values the stretches can be classified into different SSEs, namely α-helices, 310-helices, π-helices, extended β-strands and polyproline II (PPII) and other left-handed helices. The methodology was validated using an unbiased clustering of these parameters for a protein data set consisting of 1008 protein chains, which suggested that there are seven well defined clusters associated with different SSEs. Apart from α-helices and extended β-strands, 310-helices and π-helices were also found to occur in substantial numbers. ASSP was able to discriminate non-α-helical segments from flanking α-helices, which were often identified as part of α-helices by other algorithms. ASSP can also lead to the identification of novel SSEs. It is believed that ASSP could provide a better understanding of the finer nuances of protein secondary structure and could make an important contribution to the better understanding of comparatively less frequently occurring structural motifs. At the same time, it can contribute to the identification of novel SSEs. A standalone version of the program for the Linux as well as the Windows operating systems is freely downloadable and a web-server version is also available at http://nucleix.mbu.iisc.ernet.in/assp/index.php.

  6. Photoconductivity and photoluminescence under bias in GaInNAs/GaAs MQW p-i-n structures

    NASA Astrophysics Data System (ADS)

    Khalil, Hagir M.; Royall, Ben; Mazzucato, Simone; Balkan, Naci

    2012-09-01

    The low temperature photoluminescence under bias (PLb) and the photoconductivity (PC) of a p-i-n GaInNAs/GaAs multiple quantum well sample have been investigated. Under optical excitation with photons of energy greater than the GaAs bandgap, PC and PLb results show a number of step-like increases when the sample is reverse biased. The nature of these steps, which depends upon the temperature, exciting wavelength and intensity and the number of quantum wells (QWs) in the device, is explained in terms of thermionic emission and negative charge accumulation due to the low confinement of holes in GaInNAs QWs. At high temperature, thermal escape from the wells becomes much more dominant and the steps smear out.

  7. Photoconductivity and photoluminescence under bias in GaInNAs/GaAs MQW p-i-n structures.

    PubMed

    Khalil, Hagir M; Royall, Ben; Mazzucato, Simone; Balkan, Naci

    2012-09-28

    The low temperature photoluminescence under bias (PLb) and the photoconductivity (PC) of a p-i-n GaInNAs/GaAs multiple quantum well sample have been investigated. Under optical excitation with photons of energy greater than the GaAs bandgap, PC and PLb results show a number of step-like increases when the sample is reverse biased. The nature of these steps, which depends upon the temperature, exciting wavelength and intensity and the number of quantum wells (QWs) in the device, is explained in terms of thermionic emission and negative charge accumulation due to the low confinement of holes in GaInNAs QWs. At high temperature, thermal escape from the wells becomes much more dominant and the steps smear out.

  8. Consequences of local Allee effects in spatially structured populations.

    PubMed

    Cassini, Marcelo H

    2011-03-01

    The ideal free distribution model incorporating the Allee effect was published by Fretwell and Lucas (1970), but went almost unnoticed within the ecological literature. The model is relevant to populations distributed among patchy habitats. It predicts a sporadic but substantial decline in populations at high densities, which in turn induces the rapid growth of new populations. In this paper, I show that the simple process explained by this model can be used to change our view of several phenomena within the field of population ecology, behavioural ecology and conservation. The ecological consequences of the model are well known. A key feature of Fretwell and Lucas's model is what I call the "Allee paradox:" there is a range of local population densities at which local individual fitness is less than the potential mean gain that could be obtained in the environment; however, individuals cannot disperse. This paradox can be used to explain why helping appears before suitable breeding areas are fully occupied, and why breeding females aggregate when male coercion is a reproductive cost. The model also predicts high clustering between related populations, and, in conservation biology, it can identify unfounded concerns about the dangers of extinction, delays in recolonisation processes after human-induced population decline, and latency periods in the initial phases of expansion of invasive species.

  9. Locally resonant periodic structures with low-frequency band gaps

    NASA Astrophysics Data System (ADS)

    Cheng, Zhibao; Shi, Zhifei; Mo, Y. L.; Xiang, Hongjun

    2013-07-01

    Presented in this paper are study results of dispersion relationships of periodic structures composited of concrete and rubber, from which the frequency band gap can be found. Two models with fixed or free boundary conditions are proposed to approximate the bound frequencies of the first band gap. Studies are conducted to investigate the low-frequency and directional frequency band gaps for their application to engineering. The study finds that civil engineering structures can be designed to block harmful waves, such as earthquake disturbance.

  10. Defect Structure of Localized Excitons in a WSe2 Monolayer

    NASA Astrophysics Data System (ADS)

    Zhang, Shuai; Wang, Chen-Guang; Li, Ming-Yang; Huang, Di; Li, Lain-Jong; Ji, Wei; Wu, Shiwei

    2017-07-01

    The atomic and electronic structure of intrinsic defects in a WSe2 monolayer grown on graphite was revealed by low temperature scanning tunneling microscopy and spectroscopy. Instead of chalcogen vacancies that prevail in other transition metal dichalcogenide materials, intrinsic defects in WSe2 arise surprisingly from single tungsten vacancies, leading to the hole (p -type) doping. Furthermore, we found these defects to dominate the excitonic emission of the WSe2 monolayer at low temperature. Our work provided the first atomic-scale understanding of defect excitons and paved the way toward deciphering the defect structure of single quantum emitters previously discovered in the WSe2 monolayer.

  11. The Local Job Bank Program: Performance, Structure, and Direction.

    ERIC Educational Resources Information Center

    Ullman, Joseph C.; Huber, George P.

    The book represents an effort to assess the performance, structure, and direction of the Job Bank Program of the Public Employment Service, a program meant to improve the functioning of the labor market information system in the United States. The research had three goals: to assess the relative goal achievement of job banks; to determine its…

  12. Judicial Structuring of Collective Bargaining in Local School Districts.

    ERIC Educational Resources Information Center

    Colton, David L.; Graber, Edith E.

    Collective bargaining relationships in school districts are affected by court actions in a variety of ways. Courts have acted as a "surrogate legislature" by providing legal structures where legislation is absent and by modifying legislation through the process of statutory construction. This paper examines the courts' role in structuring…

  13. The Local Job Bank Program: Performance, Structure, and Direction.

    ERIC Educational Resources Information Center

    Ullman, Joseph C.; Huber, George P.

    The book represents an effort to assess the performance, structure, and direction of the Job Bank Program of the Public Employment Service, a program meant to improve the functioning of the labor market information system in the United States. The research had three goals: to assess the relative goal achievement of job banks; to determine its…

  14. Influence of the substrate bias voltage on the crystallographic structure and mechanical properties of Ti6Al4V coatings deposited by rf magnetron

    NASA Astrophysics Data System (ADS)

    Alfonso, J. E.; Pacheco, Fernando; Castro P., Alvaro; Torres, J.

    2005-08-01

    Physical and mechanical properties of pure titanium are improved when the material is mixed with aluminum and vanadium at specific concentrations. Specifically, the alloy composed by 90% of titanium, 6% of aluminum and 4% of vanadium (Ti-6Al-4V) is highly resistant to fatigue and corrosion titanium and their alloys can be deposited by two techniques: Chemical Vapor Deposition (CVD) and Physical Vapor Deposition (PVD). However, some problems are generated when carbonated steel substrates are used under the CVD technique, mainly because those substrates lost its carbon as a result of the high substrate temperature used during the deposition process. Alternatively, PVD (magnetron sputtering, ion plating) is a low temperature substrate process and also has the advantage that substrate bias can promote structure refinement through resputtering effects.Substrate bias influence on the crystalline structure of Ti6Al4V thin films prepared by rf magnetron sputtering are presented in this work. Samples were grown onto common glass and AISI 420 steel substrates using a Ti6Al4V (99.9 %) target. Substrate bias was varied from -100 V to -200 V. Samples were characterized by X-ray Diffraction (XRD), Energy Dispersive X-ray Spectroscopy (EDXS), Scanning Electron Microscopy (SEM), and Atomic Force Microscopy (AFM). Thin films stoichiometry were studied by EDX in agreement with the Ti-6Al-4V target. Finally, the studies of the mechanical behavior of the films on steel showed that the hardness increased 1100 Knoop when the bias voltage is raised to -160 V.

  15. Novel method to detect a motif of local structures in different protein conformations.

    PubMed

    Wako, H; Yamato, T

    1998-11-01

    In order to detect a motif of local structures in different protein conformations, the Delaunay tessellation is applied to protein structures represented by C(alpha) atoms only. By the Delaunay tessellation the interior space of the protein is uniquely divided up into Delaunay tetrahedra whose vertices are the C(alpha) atom positions. Some edges of the tetrahedra are virtual bonds connecting adjacent residues' C(alpha) atoms along the polypeptide chain and others indicate interactions between residues nearest neighbouring in space. The rules are proposed to assign a code, i.e., a string of digits, to each tetrahedron to characterize the local structure constructed by the vertex residues of one relevant tetrahedron and four surrounding it. Many sets comprised of the local structures with the same code are obtained from 293 proteins, each of which has relatively low sequence similarity with the others. The local structures in each set are similar enough to each other to represent a motif. Some of them are parts of secondary or supersecondary structures, and others are irregular, but definite structures. The method proposed here can find motifs of local structures in the Protein Data Bank much more easily and rapidly than other conventional methods, because they are represented by codes. The motifs detected in this method can provide more detailed information about specific interactions between residues in the local structures, because the edges of the Delaunay tetrahedra are regarded to express interactions between residues nearest neighbouring in space.

  16. Molecular modeling of phosphorylation sites in proteins using a database of local structure segments.

    PubMed

    Plewczynski, Dariusz; Jaroszewski, Lukasz; Godzik, Adam; Kloczkowski, Andrzej; Rychlewski, Leszek

    2005-11-01

    A new bioinformatics tool for molecular modeling of the local structure around phosphorylation sites in proteins has been developed. Our method is based on a library of short sequence and structure motifs. The basic structural elements to be predicted are local structure segments (LSSs). This enables us to avoid the problem of non-exact local description of structures, caused by either diversity in the structural context, or uncertainties in prediction methods. We have developed a library of LSSs and a profile--profile-matching algorithm that predicts local structures of proteins from their sequence information. Our fragment library prediction method is publicly available on a server (FRAGlib), at http://ffas.ljcrf.edu/Servers/frag.html . The algorithm has been applied successfully to the characterization of local structure around phosphorylation sites in proteins. Our computational predictions of sequence and structure preferences around phosphorylated residues have been confirmed by phosphorylation experiments for PKA and PKC kinases. The quality of predictions has been evaluated with several independent statistical tests. We have observed a significant improvement in the accuracy of predictions by incorporating structural information into the description of the neighborhood of the phosphorylated site. Our results strongly suggest that sequence information ought to be supplemented with additional structural context information (predicted with our segment similarity method) for more successful predictions of phosphorylation sites in proteins.

  17. Local structure of liquid carbon controls diamond nucleation.

    PubMed

    Ghiringhelli, L M; Valeriani, C; Meijer, E J; Frenkel, D

    2007-08-03

    Diamonds melt at temperatures above 4000 K. There are no measurements of the steady-state rate of the reverse process, i.e., diamond nucleation from the melt, because experiments are difficult at these extreme temperatures and pressures. Using numerical simulations, we estimate the diamond nucleation rate and find that it increases by many orders of magnitude when the pressure is increased at constant supersaturation. The reason is that by increasing the pressure the local coordination of the liquid changes from threefold to fourfold, and we show that the free-energy cost to create a diamond-liquid interface is lower in the fourfold than in the threefold liquid. We speculate that this mechanism for nucleation control is relevant for crystallization in many network-forming liquids. We conclude that homogeneous diamond nucleation is likely in carbon-rich stars and unlikely in gaseous planets.

  18. Deformed relativity symmetries and the local structure of spacetime

    NASA Astrophysics Data System (ADS)

    Letizia, Marco; Liberati, Stefano

    2017-02-01

    A spacetime interpretation of deformed relativity symmetry groups was recently proposed by resorting to Finslerian geometries, seen as the outcome of a continuous limit endowed with first-order corrections from the quantum gravity regime. In this work, we further investigate such connections between deformed algebras and Finslerian geometries by showing that the Finsler geometries associated with the generalization of the Poincaré group (the so-called κ -Poincaré Hopf algebra) are maximally symmetric spacetimes which are also of the Berwald type: Finslerian spacetimes for which the connections are substantially Riemannian, belonging to the unique class for which the weak equivalence principle still holds. We also extend this analysis by considering a generalization of the de Sitter group (the so-called q -de Sitter group) and showing that its associated Finslerian geometry reproduces locally the one from the κ -Poincaré group, and that it itself can be recast in a Berwald form in an appropriate limit.

  19. CONDENSED MATTER: ELECTRONIC STRUCTURE, ELECTRICAL, MAGNETIC, AND OPTICAL PROPERTIES: Intraband dynamics and terahertz emission in biased semiconductor superlattices coupled to double far-infrared pulses

    NASA Astrophysics Data System (ADS)

    Li, Min; Mi, Xian-Wu

    2009-12-01

    This paper studies both the intraband polarization and terahertz emission of a semiconductor superlattice in combined dc and ac electric fields by using the superposition of two identical time delayed and phase shifted optical pulses. By adjusting the delay between these two optical pulses, our results show that the intraband polarization is sensitive to the time delay. The peak values appear again for the terahertz emission intensity due to the superposition of two optical pulses. The emission lines of terahertz blueshift and redshift in different ac electric fields and dynamic localization appears. The emission lines of THz only appear to blueshift when the biased superlattice is driven by a single optical pulse. Due to excitonic dynamic localization, the terahertz emission intensity decays with time in different dc and ac electric fields. These are features of this superlattice which distinguish it from a superlattice generated by a single optical pulse to drive it.

  20. Light Localization by Defects in Optically Induced Photonic Structures

    NASA Astrophysics Data System (ADS)

    Yang, Jianke; Wang, Xiaosheng; Wang, Jiandong; Chen, Zhigang

    In the past ten years, there has blossomed an interest in the study of collective behavior of wave propagation in periodic waveguide arrays and photonic lattices [1-3]. The unique bandgap structures of these periodic media, coupled with nonlinear effects, give rise to many types of novel soliton structures [1- 26]. On the other hand, it is well known that one of the unique and most interesting features of photonic band-gap structures is a fundamentally different way of waveguiding by defects in otherwise uniformly periodic structures. Such waveguiding has been demonstrated with an "air-hole" in photonic crystal fibers (PCF) for optical waves [27, 28], in an isolated defect in two-dimensional arrays of dielectric cylinders for microwaves [29-31], and recently in all-solid PCF with a lower-index core [32, 33]. In addition, laser emission based on photonic defect modes has been realized in a number of experiments [34-38]. In one-dimensional (1D) fabricated semiconductor waveguide arrays, previous experiments have investigated nonlinearity-induced escape from a defect state [39] and interactions of discrete solitons with structural defects [40] (see also [41]). Despite the above efforts, theoretical understanding on defect guiding was still limited, and experimental demonstrations of defect guiding was still scarce. In addition, when nonlinear effects are significant, how defect guiding is affected by nonlinearity is largely an open issue. Recently, in a series of theoretical and experimental studies, we optically induced 1D, 2D and ringlike photonic lattices with single-site negative defects in photorefractive crystals, and investigated their linear and nonlinear light guiding properties [42-48]. This work will be reviewed in this Chapter. In addition, we present the first experimental demonstration of nonlinear defect modes which undergoes nonlinear propagation through the defects. Our work not only has a direct link to technologically important systems of periodic

  1. Acute pulmonary embolism: impact of selection bias in prospective diagnostic studies. ANTELOPE Study Group. Advances in New Technologies Evaluating the Localization of Pulmonary Embolism.

    PubMed

    Hartmann, I J; Prins, M H; Büller, H R; Banga, J D

    2001-04-01

    We evaluated selection bias in a prospective study of 1,162 consecutive patients with suspected pulmonary embolism. Of these, 983 were eligible, and 627 could actually be included. During two months extensive data were collected on all non-included patients. Finally, our patient characteristics were compared with those of the PIOPED study (1990) and the study of Hull et al. (1994). Compared with included patients, the non-included patients had more often non-diagnostic V/Q scans (50% vs. 36%, p <0.01) and were more often already hospitalized (31% vs. 22%, P = 0.04). The subgroup of patients not included due to refusal or inability to give informed consent (IC) was older (mean age 61 vs. 53 years, P <0.01), more often suffered from malignancies (26% vs. 11%, P <0.01) and frequently had non-diagnostic V/Q scans (57%) as compared to included patients. In our study, 54% of all patients screened was eventually included versus 27% in the PIOPED study. In the PIOPED study patients who had contra-indications for pulmonary angiography were excluded, while in the study of Hull et al. those with inadequate cardiorespiratory reserve were excluded. In studies on new diagnostic technologies, patient selection bias does occur. The potential for such a selection bias should be taken into account when diagnostic strategies are devised to improve their generalizability and acceptability.

  2. Transcription inactivation through local refolding of the RNA polymerase structure

    SciTech Connect

    Belogurov, Georgiy A.; Vassylyeva, Marina N.; Sevostyanova, Anastasiya; Appleman, James R.; Xiang, Alan X.; Lira, Ricardo; Webber, Stephen E.; Klyuyev, Sergiy; Nudler, Evgeny; Artsimovitch, Irina; Vassylyev, Dmitry G.

    2009-02-12

    Structural studies of antibiotics not only provide a shortcut to medicine allowing for rational structure-based drug design, but may also capture snapshots of dynamic intermediates that become 'frozen' after inhibitor binding. Myxopyronin inhibits bacterial RNA polymerase (RNAP) by an unknown mechanism. Here we report the structure of dMyx - a desmethyl derivative of myxopyronin B - complexed with a Thermus thermophilus RNAP holoenzyme. The antibiotic binds to a pocket deep inside the RNAP clamp head domain, which interacts with the DNA template in the transcription bubble. Notably, binding of dMyx stabilizes refolding of the {beta}'-subunit switch-2 segment, resulting in a configuration that might indirectly compromise binding to, or directly clash with, the melted template DNA strand. Consistently, footprinting data show that the antibiotic binding does not prevent nucleation of the promoter DNA melting but instead blocks its propagation towards the active site. Myxopyronins are thus, to our knowledge, a first structurally characterized class of antibiotics that target formation of the pre-catalytic transcription initiation complex - the decisive step in gene expression control. Notably, mutations designed in switch-2 mimic the dMyx effects on promoter complexes in the absence of antibiotic. Overall, our results indicate a plausible mechanism of the dMyx action and a stepwise pathway of open complex formation in which core enzyme mediates the final stage of DNA melting near the transcription start site, and that switch-2 might act as a molecular checkpoint for DNA loading in response to regulatory signals or antibiotics. The universally conserved switch-2 may have the same role in all multisubunit RNAPs.

  3. Local identification of scalar hybrid models with tree structure

    NASA Astrophysics Data System (ADS)

    Fiedler, Bernold; Schuppert, Andreas

    2008-06-01

    Standard modelling approaches, e.g. in chemical engineering, suffer from two principal difficulties: the curse of dimension and a lack of extrapolability. We propose an approach via structured hybrid models (SHMs) to resolve both issues. For simplicity, we consider reactor models which can be written as a tree-like composition of scalar input-output (i/o) functions uj. The vertices j of the finite tree structure represent known or unknown subprocesses of the overall process. Known processes are modelled by white-box functions uj; unknown processes are represented by black boxes uj. Oriented edges of the tree indicate composition of the i/o relations uj in a feedforward structure. The tree structure of a mixture of black and white boxes constitutes what we call an SHM. Under certain assumptions on differentiability, genericity and monotonicity, we provide an inductive algorithm which uniquely identifies all black boxes in the SHM up to a trivial scaling calibration between adjacent black boxes. Our result does not require any extra measurements interior to the SHM. Instead, we only require global, overall i/o data clustered along a d-dimensional database of inputs. More precisely, information on partial derivatives of order up to 5 is required, in all directions, but only at base points within the d-dimensional database. The dimension d need not exceed the maximal input dimension of any individual black box in the SHM. Compared to the total input dimension n of the reactor, which may be much larger than d, this dimension reduction effectively avoids the curse of dimension: the complexity of our approach is polynomial in n and exponential in d, only, rather than exponential in n. Moreover, our unique identification of all black boxes accommodates a reliable global extrapolation, far beyond the original database, to input regions of full dimension. We illustrate our results with a model of an industrial continuous polymerization plant.

  4. Solving local structure around dopants in metal nanoparticles with ab initio modeling of X-ray absorption near edge structure

    DOE PAGES

    Timoshenko, J.; Shivhare, A.; Scott, R. W.; ...

    2016-06-30

    We adopted ab-initio X-ray Absorption Near Edge Structure (XANES) modelling for structural refinement of local environments around metal impurities in a large variety of materials. Our method enables both direct modelling, where the candidate structures are known, and the inverse modelling, where the unknown structural motifs are deciphered from the experimental spectra. We present also estimates of systematic errors, and their influence on the stability and accuracy of the obtained results. We illustrate our approach by following the evolution of local environment of palladium atoms in palladium-doped gold thiolate clusters upon chemical and thermal treatments.

  5. Solving local structure around dopants in metal nanoparticles with ab initio modeling of X-ray absorption near edge structure.

    PubMed

    Timoshenko, Janis; Shivhare, Atal; Scott, Robert W J; Lu, Deyu; Frenkel, Anatoly I

    2016-07-20

    We adopted ab initio X-ray absorption near edge structure (XANES) modeling for structural refinement of local environments around metal impurities in a large variety of materials. Our method enables both direct modeling, where the candidate structures are known, and the inverse modeling, where the unknown structural motifs are deciphered from the experimental spectra. We present also estimates of systematic errors, and their influence on the stability and accuracy of the obtained results. We illustrate our approach by revealing the evolution of local environment of palladium atoms in palladium-doped gold thiolate clusters upon chemical and thermal treatments.

  6. Local structures in computer-generated liquids and glasses: Classification of three-dimensional patterns

    NASA Astrophysics Data System (ADS)

    Gades, Heinrich; Mitus, Antoni C.

    1991-08-01

    Using probabilistic methods we work out mathematical tools for an identification of local close-packed structures (fcc, hcp, icosahedron) in a configuration of atoms undergoing (thermal) fluctuations. A structure is described by invariants constructed from standard and generalized local bond-order parameters and by laws of their fluctuations. We provide a detailed analysis of fluctuations of 13-atom close-packed clusters, find the most informative invariants for each of them and calculate the metric which quantifies a concept of similarity of fluctuating structures. A simple algorithm for an identification of close-packed clusters is proposed. As an example, we analyze local structures in hot fcc solid. We discuss the origin of the difficulties encountered by a classification of local structures in liquids and glasses (Voronoi-like or standard bond-order analysis) and suggest how they can be avoided.

  7. Study of local structure and magnetism in high-T(sub c) copper oxide superconductors

    NASA Technical Reports Server (NTRS)

    Budnick, J. I.; Tan, Z.; Filipkowski, M.; Niedermayer, CH.; Glueckler, H.; Simon, R.; Golnik, A.; Rauer, M.; Recknagel, E.; Weidinger, A.

    1990-01-01

    The muon spin rotation (MUSR) study of local magnetism of Sr-doped La2CuO4 is reviewed. Emphasis is placed on magnetic order as detected by local and bulk probes with local atomic environments studied by x ray absorption fine structure (XAFS). Correlations between the MUSR study of local magnetic ordering and the bulk magnetization study are presented along with a discussion of the dependence upon oxygen stoichiometry. Results are presented for both superconducting phases and magnetic phases. Recent data which reveals the existence of local magnetic ordering in the hydrogen-doped YBa2Cu3O7 system are also discussed.

  8. Amorphous FeCoSiB for exchange bias coupled and decoupled magnetoelectric multilayer systems: Real-structure and magnetic properties

    SciTech Connect

    Hrkac, V.; Strobel, J.; Kienle, L.; Lage, E.; Köppel, G.; McCord, J.; Quandt, E.; Meyners, D.

    2014-10-07

    The effect of field annealing for exchanged biased multilayer films is studied with respect to the resultant structural and magnetic film properties. The presented multilayer stacks comprise repeating sequences of Ta/Cu/(1 1 1) textured antiferromagnetic Mn₇₀Ir₃₀ /amorphous ferromagnetic Fe₇₀.₂Co₇.₈Si₂B₁₀. Within the ferromagnetic layers crystalline filaments are observed. An additional Ta layer between the antiferromagnet and ferromagnet is used in order to investigate and separate the influence of the common Mn₇₀Ir₃₀/Fe₇₀.₂Co₇.₈Si₁₂B₁₀ interface on the occurring filaments and structural changes. In situ and ex situ transmission electron microscopy is used for a comprehensive structure characterization of multilayer stacks for selected temperature stages. Up to 250 °C, the multilayers are structurally unaltered and preserve the as-deposited condition. A deliberate increase to 350 °C exhibits different crystallization processes for the films, depending on the presence of crystal nuclei within the amorphous ferromagnetic layer. The influence of volume-to-surface ratio of the multilayer stacks to the crystallization process is emphasized by the comparison of in situ and ex situ investigations as the respective specimen thickness is changed. Complementary magnetic studies reveal a defined exchange bias obtained at the first annealing step and a decrease of total anisotropy field with partial crystallization after the subsequent annealing at 350 °C.

  9. SPLASH: structural pattern localization analysis by sequential histograms.

    PubMed

    Califano, A

    2000-04-01

    The discovery of sparse amino acid patterns that match repeatedly in a set of protein sequences is an important problem in computational biology. Statistically significant patterns, that is patterns that occur more frequently than expected, may identify regions that have been preserved by evolution and which may therefore play a key functional or structural role. Sparseness can be important because a handful of non-contiguous residues may play a key role, while others, in between, may be changed without significant loss of function or structure. Similar arguments may be applied to conserved DNA patterns. Available sparse pattern discovery algorithms are either inefficient or impose limitations on the type of patterns that can be discovered. This paper introduces a deterministic pattern discovery algorithm, called Splash, which can find sparse amino or nucleic acid patterns matching identically or similarly in a set of protein or DNA sequences. Sparse patterns of any length, up to the size of the input sequence, can be discovered without significant loss in performances. Splash is extremely efficient and embarrassingly parallel by nature. Large databases, such as a complete genome or the non-redundant SWISS-PROT database can be processed in a few hours on a typical workstation. Alternatively, a protein family or superfamily, with low overall homology, can be analyzed to discover common functional or structural signatures. Some examples of biologically interesting motifs discovered by Splash are reported for the histone I and for the G-Protein Coupled Receptor families. Due to its efficiency, Splash can be used to systematically and exhaustively identify conserved regions in protein family sets. These can then be used to build accurate and sensitive PSSM or HMM models for sequence analysis. Splash is available to non-commercial research centers upon request, conditional on the signing of a test field agreement. acal@us.ibm.com, Splash main page http://www.research.ibm.com/splash

  10. Dynamics of galaxy structures in the Local Volume

    NASA Astrophysics Data System (ADS)

    Karachentsev, I. D.

    2016-10-01

    I consider a sample of `Updated Nearby Galaxy Catalog' that contains eight hundred objects within 11 Mpc. Environment of each galaxy is characterized by a tidal index Θ1 depending on separation and mass of the galaxy Main Disturber (=MD). The UNGC galaxies with a common MD are ascribed to its `suite' and ranked according to their Θ1. Fifteen the most populated suites contain more than half of the UNGC sample. The fraction of MDs among the brightest galaxies is almost 100% and drops to 50% at M_B = -18 mag. The observational properties of galaxies accumulated in UNGC are used to derive orbital masses of giant galaxies via motions of their satellites. The average orbital-to-stellar mass ratio for them is M orb M* ~= 30, corresponding to the mean local density of matter Ωm ~= 0.09, i.e 1/3 of the global cosmic one. The dark-to-stellar mass ratio for the Milky Way and M31 is typical for other neighboring giant galaxies.

  11. Local structure analysis of some Cu(II) theophylline complexes

    NASA Astrophysics Data System (ADS)

    David, L.; Cozar, O.; Forizs, E.; Cr ăciun, C.; Ristoiu, D.; B ălan, C.

    1999-10-01

    The CuT 2L 2·2H 2O complexes [T=Theophylline (1,3-dimethylxanthine); L=NH 3, n-propylamine (npa), 2-aminoethanol (ae)] were prepared and investigated by ESR spectroscopy. Powder ESR spectrum of CuT 2(NH 3) 2·2H 2O is axial ( g||=2.255, g⊥=2.059). ESR spectrum of CuT 2(npa) 2·2H 2O with ( g||=2.299, g⊥=2.081) is a superposition of one axial ( g||=2.299, g⊥=2.073) and one isotropic component ( g0≈2.089), in the same amount. The axial spectra of the former complexes are due to a static Jahn-Teller effect ( EJT≈2880 cm -1). ESR spectrum of CuT 2(ae) 2·2H 2O is orthorhombic ( g1c=2.199, g2c=2.095, g3c=2.037). The local symmetries around the Cu(II) ions remain unchanged by DMF solvating, by adsorbing these solutions on NaY zeolite or by lowering the temperature.

  12. Structural Damage Detection Using Frequency Domain Error Localization.

    DTIC Science & Technology

    1994-12-01

    113 rn ~l-,I T X ~oy Ul C 114 APPENDIX D. FE MODEL / COMPUTER CODES The following is a brief description of MATLAB routines employed in this thesis...R.R., Structural Dynamics, An Introduction to Computer Methods , pp. 383-387, John Wiley and Sons, Inc., 1981. 8. Guyan , R.J., "Reduction of Stiffness...official policy or position of the Department of Defense or the U.S. Government. 12a. DISTRIBUTION/AVAILABILITY STATEMENT 12b. DISTRIBUTION CODE

  13. Input clustering and the microscale structure of local circuits

    PubMed Central

    DeBello, William M.; McBride, Thomas J.; Nichols, Grant S.; Pannoni, Katy E.; Sanculi, Daniel; Totten, Douglas J.

    2014-01-01

    The recent development of powerful tools for high-throughput mapping of synaptic networks promises major advances in understanding brain function. One open question is how circuits integrate and s