Discrete square root filtering - A survey of current techniques.

NASA Technical Reports Server (NTRS)

Kaminskii, P. G.; Bryson, A. E., Jr.; Schmidt, S. F.

1971-01-01

Current techniques in square root filtering are surveyed and related by applying a duality association. Four efficient square root implementations are suggested, and compared with three common conventional implementations in terms of computational complexity and precision. It is shown that the square root computational burden should not exceed the conventional by more than 50% in most practical problems. An examination of numerical conditioning predicts that the square root approach can yield twice the effective precision of the conventional filter in ill-conditioned problems. This prediction is verified in two examples.

On the Denesting of Nested Square Roots

ERIC Educational Resources Information Center

Gkioulekas, Eleftherios

2017-01-01

We present the basic theory of denesting nested square roots, from an elementary point of view, suitable for lower level coursework. Necessary and sufficient conditions are given for direct denesting, where the nested expression is rewritten as a sum of square roots of rational numbers, and for indirect denesting, where the nested expression is…

Quantified Choice of Root-Mean-Square Errors of Approximation for Evaluation and Power Analysis of Small Differences between Structural Equation Models

ERIC Educational Resources Information Center

Li, Libo; Bentler, Peter M.

2011-01-01

MacCallum, Browne, and Cai (2006) proposed a new framework for evaluation and power analysis of small differences between nested structural equation models (SEMs). In their framework, the null and alternative hypotheses for testing a small difference in fit and its related power analyses were defined by some chosen root-mean-square error of…

Maximum correntropy square-root cubature Kalman filter with application to SINS/GPS integrated systems.

PubMed

Liu, Xi; Qu, Hua; Zhao, Jihong; Yue, Pengcheng

2018-05-31

For a nonlinear system, the cubature Kalman filter (CKF) and its square-root version are useful methods to solve the state estimation problems, and both can obtain good performance in Gaussian noises. However, their performances often degrade significantly in the face of non-Gaussian noises, particularly when the measurements are contaminated by some heavy-tailed impulsive noises. By utilizing the maximum correntropy criterion (MCC) to improve the robust performance instead of traditional minimum mean square error (MMSE) criterion, a new square-root nonlinear filter is proposed in this study, named as the maximum correntropy square-root cubature Kalman filter (MCSCKF). The new filter not only retains the advantage of square-root cubature Kalman filter (SCKF), but also exhibits robust performance against heavy-tailed non-Gaussian noises. A judgment condition that avoids numerical problem is also given. The results of two illustrative examples, especially the SINS/GPS integrated systems, demonstrate the desirable performance of the proposed filter. Copyright © 2018 ISA. Published by Elsevier Ltd. All rights reserved.

On the role of thermal backbone fluctuations in myoglobin ligand gate dynamics.

PubMed

Krokhotin, Andrey; Niemi, Antti J; Peng, Xubiao

2013-05-07

We construct an energy function that describes the crystallographic structure of sperm whale myoglobin backbone. As a model in our construction, we use the Protein Data Bank entry 1ABS that has been measured at liquid helium temperature. Consequently, the thermal B-factor fluctuations are very small, which is an advantage in our construction. The energy function that we utilize resembles that of the discrete nonlinear Schrödinger equation. Likewise, ours supports topological solitons as local minimum energy configurations. We describe the 1ABS backbone in terms of topological solitons with a precision that deviates from 1ABS by an average root-mean-square distance, which is less than the experimentally observed Debye-Waller B-factor fluctuation distance. We then subject the topological multi-soliton solution to extensive numerical heating and cooling experiments, over a very wide range of temperatures. We concentrate in particular to temperatures above 300 K and below the Θ-point unfolding temperature, which is around 348 K. We confirm that the behavior of the topological multi-soliton is fully consistent with Anfinsen's thermodynamic principle, up to very high temperatures. We observe that the structure responds to an increase of temperature consistently in a very similar manner. This enables us to characterize the onset of thermally induced conformational changes in terms of three distinct backbone ligand gates. One of the gates is made of the helix F and the helix E. The two other gates are chosen similarly, when open they provide a direct access route for a ligand to reach the heme. We find that out of the three gates we investigate, the one which is formed by helices B and G is the most sensitive to thermally induced conformational changes. Our approach provides a novel perspective to the important problem of ligand entry and exit.

On the role of thermal backbone fluctuations in myoglobin ligand gate dynamics

NASA Astrophysics Data System (ADS)

Krokhotin, Andrey; Niemi, Antti J.; Peng, Xubiao

2013-05-01

We construct an energy function that describes the crystallographic structure of sperm whale myoglobin backbone. As a model in our construction, we use the Protein Data Bank entry 1ABS that has been measured at liquid helium temperature. Consequently, the thermal B-factor fluctuations are very small, which is an advantage in our construction. The energy function that we utilize resembles that of the discrete nonlinear Schrödinger equation. Likewise, ours supports topological solitons as local minimum energy configurations. We describe the 1ABS backbone in terms of topological solitons with a precision that deviates from 1ABS by an average root-mean-square distance, which is less than the experimentally observed Debye-Waller B-factor fluctuation distance. We then subject the topological multi-soliton solution to extensive numerical heating and cooling experiments, over a very wide range of temperatures. We concentrate in particular to temperatures above 300 K and below the Θ-point unfolding temperature, which is around 348 K. We confirm that the behavior of the topological multi-soliton is fully consistent with Anfinsen's thermodynamic principle, up to very high temperatures. We observe that the structure responds to an increase of temperature consistently in a very similar manner. This enables us to characterize the onset of thermally induced conformational changes in terms of three distinct backbone ligand gates. One of the gates is made of the helix F and the helix E. The two other gates are chosen similarly, when open they provide a direct access route for a ligand to reach the heme. We find that out of the three gates we investigate, the one which is formed by helices B and G is the most sensitive to thermally induced conformational changes. Our approach provides a novel perspective to the important problem of ligand entry and exit.

Moments and Root-Mean-Square Error of the Bayesian MMSE Estimator of Classification Error in the Gaussian Model.

PubMed

Zollanvari, Amin; Dougherty, Edward R

2014-06-01

The most important aspect of any classifier is its error rate, because this quantifies its predictive capacity. Thus, the accuracy of error estimation is critical. Error estimation is problematic in small-sample classifier design because the error must be estimated using the same data from which the classifier has been designed. Use of prior knowledge, in the form of a prior distribution on an uncertainty class of feature-label distributions to which the true, but unknown, feature-distribution belongs, can facilitate accurate error estimation (in the mean-square sense) in circumstances where accurate completely model-free error estimation is impossible. This paper provides analytic asymptotically exact finite-sample approximations for various performance metrics of the resulting Bayesian Minimum Mean-Square-Error (MMSE) error estimator in the case of linear discriminant analysis (LDA) in the multivariate Gaussian model. These performance metrics include the first, second, and cross moments of the Bayesian MMSE error estimator with the true error of LDA, and therefore, the Root-Mean-Square (RMS) error of the estimator. We lay down the theoretical groundwork for Kolmogorov double-asymptotics in a Bayesian setting, which enables us to derive asymptotic expressions of the desired performance metrics. From these we produce analytic finite-sample approximations and demonstrate their accuracy via numerical examples. Various examples illustrate the behavior of these approximations and their use in determining the necessary sample size to achieve a desired RMS. The Supplementary Material contains derivations for some equations and added figures.

An algorithm for propagating the square-root covariance matrix in triangular form

NASA Technical Reports Server (NTRS)

Tapley, B. D.; Choe, C. Y.

1976-01-01

A method for propagating the square root of the state error covariance matrix in lower triangular form is described. The algorithm can be combined with any triangular square-root measurement update algorithm to obtain a triangular square-root sequential estimation algorithm. The triangular square-root algorithm compares favorably with the conventional sequential estimation algorithm with regard to computation time.

Determining a one-tailed upper limit for future sample relative reproducibility standard deviations.

PubMed

McClure, Foster D; Lee, Jung K

2006-01-01

A formula was developed to determine a one-tailed 100p% upper limit for future sample percent relative reproducibility standard deviations (RSD(R),%= 100s(R)/y), where S(R) is the sample reproducibility standard deviation, which is the square root of a linear combination of the sample repeatability variance (s(r)2) plus the sample laboratory-to-laboratory variance (s(L)2), i.e., S(R) = s(L)2, and y is the sample mean. The future RSD(R),% is expected to arise from a population of potential RSD(R),% values whose true mean is zeta(R),% = 100sigmaR, where sigmaR and mu are the population reproducibility standard deviation and mean, respectively.

Protein backbone and sidechain torsion angles predicted from NMR chemical shifts using artificial neural networks

PubMed Central

Shen, Yang; Bax, Ad

2013-01-01

A new program, TALOS-N, is introduced for predicting protein backbone torsion angles from NMR chemical shifts. The program relies far more extensively on the use of trained artificial neural networks than its predecessor, TALOS+. Validation on an independent set of proteins indicates that backbone torsion angles can be predicted for a larger, ≥ 90% fraction of the residues, with an error rate smaller than ca 3.5%, using an acceptance criterion that is nearly two-fold tighter than that used previously, and a root mean square difference between predicted and crystallographically observed (φ,ψ) torsion angles of ca 12°. TALOS-N also reports sidechain χ1 rotameric states for about 50% of the residues, and a consistency with reference structures of 89%. The program includes a neural network trained to identify secondary structure from residue sequence and chemical shifts. PMID:23728592

Deviations of Mesial Root Canals of Mandibular First Molar Teeth at the Apical Third: A Micro-computed Tomographic Study.

PubMed

Keles, Ali; Keskin, Cangül

2018-06-01

The present study aimed to quantitatively analyze apical foramen deviations of mesial root canals of mandibular first molar teeth by means of micro-computed tomographic (micro-CT) imaging. Micro-CT images of the mesial roots of 109 mandibular first molar teeth with independent mesiobuccal (MB) and mesiolingual (ML) root canals were analyzed. The deviations of the apical foramina of the MB, ML, and middle mesial root canals from the anatomic apex were measured. The vertical distance between the apical foramina of each mesial root canal in relation to each other was also calculated. The distances from the apical foramina of the MB, ML, and middle mesial root canals to the anatomic apex of the mesial root were up to 2.51 mm, 3.21 mm, and 5.67 mm, respectively. There was no significant difference between the deviations of MB and ML root canals from each other (P > .05). The middle mesial root canal showed the greatest deviation compared with the MB and ML canals (P < .05). The apical foramina of mesial root canals of mandibular first molar teeth showed greater variations from each other and anatomic apices than previously reported. Clinically, the use of electronic apex locators for the detection of minor apical foramen of each mesial root canal is of the utmost important. Copyright © 2018 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

Charge transport properties of poly(dA)-poly(dT) DNA in variation of backbone disorder and amplitude of base-pair twisting motion

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

Rahmi, Kinanti Aldilla, E-mail: kinanti.aldilla@ui.ac.id; Yudiarsah, Efta

By using tight binding Hamiltonian model, charge transport properties of poly(dA)-poly(dT) DNA in variation of backbone disorder and amplitude of base-pair twisting motion is studied. The DNA chain used is 32 base pairs long poly(dA)-poly(dT) molecule. The molecule is contacted to electrode at both ends. The influence of environment on charge transport in DNA is modeled as variation of backbone disorder. The twisting motion amplitude is taking into account by assuming that the twisting angle distributes following Gaussian distribution function with zero average and standard deviation proportional to square root of temperature and inversely proportional to the twisting motion frequency.more » The base-pair twisting motion influences both the onsite energy of the bases and electron hopping constant between bases. The charge transport properties are studied by calculating current using Landauer-Buttiker formula from transmission probabilities which is calculated by transfer matrix methods. The result shows that as the backbone disorder increases, the maximum current decreases. By decreasing the twisting motion frequency, the current increases rapidly at low voltage, but the current increases slower at higher voltage. The threshold voltage can increase or decrease with increasing backbone disorder and increasing twisting frequency.« less

Three-dimensional relationship between high-order root-mean-square wavefront error, pupil diameter, and aging

PubMed Central

Applegate, Raymond A.; Donnelly, William J.; Marsack, Jason D.; Koenig, Darren E.; Pesudovs, Konrad

2007-01-01

We report root-mean-square (RMS) wavefront error (WFE) for individual aberrations and cumulative high-order (HO) RMS WFE for the normal human eye as a function of age by decade and pupil diameter in 1 mm steps from 3 to 7 mm and determine the relationship among HO RMS WFE, mean age for each decade of life, and luminance for physiologic pupil diameters. Subjects included 146 healthy individuals from 20 to 80 years of age. Ocular aberration was measured on the preferred eye of each subject (for a total of 146 eyes through dilated pupils; computed for 3, 4, 5, 6, and 7 mm pupils; and described with a tenth-radial-order normalized Zernike expansion. We found that HO RMS WFE increases faster with increasing pupil diameter for any given age and pupil diameter than it does with increasing age alone. A planar function accounts for 99% of the variance in the 3-D space defined by mean log HO RMS WFE, mean age for each decade of life, and pupil diameter. When physiologic pupil diameters are used to estimate HO RMS WFE as a function of luminance and age, at low luminance (9 cd/m2) HO RMS WFE decreases with increasing age. This normative data set details (1) the 3-D relationship between HO RMS WFE and age for fixed pupil diameters and (2) the 3-D relationship among HO RMS WFE, age, and luminance for physiologic pupil diameters. PMID:17301847

Introducing the Mean Absolute Deviation "Effect" Size

ERIC Educational Resources Information Center

Gorard, Stephen

2015-01-01

This paper revisits the use of effect sizes in the analysis of experimental and similar results, and reminds readers of the relative advantages of the mean absolute deviation as a measure of variation, as opposed to the more complex standard deviation. The mean absolute deviation is easier to use and understand, and more tolerant of extreme…

Multistep modeling of protein structure: application towards refinement of tyr-tRNA synthetase

NASA Technical Reports Server (NTRS)

Srinivasan, S.; Shibata, M.; Roychoudhury, M.; Rein, R.

1987-01-01

The scope of multistep modeling (MSM) is expanding by adding a least-squares minimization step in the procedure to fit backbone reconstruction consistent with a set of C-alpha coordinates. The analytical solution of Phi and Psi angles, that fits a C-alpha x-ray coordinate is used for tyr-tRNA synthetase. Phi and Psi angles for the region where the above mentioned method fails, are obtained by minimizing the difference in C-alpha distances between the computed model and the crystal structure in a least-squares sense. We present a stepwise application of this part of MSM to the determination of the complete backbone geometry of the 321 N terminal residues of tyrosine tRNA synthetase to a root mean square deviation of 0.47 angstroms from the crystallographic C-alpha coordinates.

A Continuous Square Root in Formation Filter-Swoother with Discrete Data Update

NASA Technical Reports Server (NTRS)

Miller, J. K.

1994-01-01

A differential equation for the square root information matrix is derived and adapted to the problems of filtering and smoothing. The resulting continuous square root information filter (SRIF) performs the mapping of state and process noise by numerical integration of the SRIF matrix and admits data via a discrete least square update.

On Roots and Squares--Estimation, Intuition and Creativity

ERIC Educational Resources Information Center

Patkin, Dorit; Gazit, Avikam

2013-01-01

The paper presents findings of a small scale study of a few items related to problem solving with squares and roots, for different teacher groups (pre-service and in-service mathematics teachers: elementary and junior high school). The research participants were asked to explain what would be the units digit of a natural number to be squared in…

Estimate of standard deviation for a log-transformed variable using arithmetic means and standard deviations.

PubMed

Quan, Hui; Zhang, Ji

2003-09-15

Analyses of study variables are frequently based on log transformations. To calculate the power for detecting the between-treatment difference in the log scale, we need an estimate of the standard deviation of the log-transformed variable. However, in many situations a literature search only provides the arithmetic means and the corresponding standard deviations. Without individual log-transformed data to directly calculate the sample standard deviation, we need alternative methods to estimate it. This paper presents methods for estimating and constructing confidence intervals for the standard deviation of a log-transformed variable given the mean and standard deviation of the untransformed variable. It also presents methods for estimating the standard deviation of change from baseline in the log scale given the means and standard deviations of the untransformed baseline value, on-treatment value and change from baseline. Simulations and examples are provided to assess the performance of these estimates. Copyright 2003 John Wiley & Sons, Ltd.

Unusual square roots in the ghost-free theory of massive gravity

NASA Astrophysics Data System (ADS)

Golovnev, Alexey; Smirnov, Fedor

2017-06-01

A crucial building block of the ghost free massive gravity is the square root function of a matrix. This is a problematic entity from the viewpoint of existence and uniqueness properties. We accurately describe the freedom of choosing a square root of a (non-degenerate) matrix. It has discrete and (in special cases) continuous parts. When continuous freedom is present, the usual perturbation theory in terms of matrices can be critically ill defined for some choices of the square root. We consider the new formulation of massive and bimetric gravity which deals directly with eigenvalues (in disguise of elementary symmetric polynomials) instead of matrices. It allows for a meaningful discussion of perturbation theory in such cases, even though certain non-analytic features arise.

A decentralized square root information filter/smoother

NASA Technical Reports Server (NTRS)

Bierman, G. J.; Belzer, M. R.

1985-01-01

A number of developments has recently led to a considerable interest in the decentralization of linear least squares estimators. The developments are partly related to the impending emergence of VLSI technology, the realization of parallel processing, and the need for algorithmic ways to speed the solution of dynamically decoupled, high dimensional estimation problems. A new method is presented for combining Square Root Information Filters (SRIF) estimates obtained from independent data sets. The new method involves an orthogonal transformation, and an information matrix filter 'homework' problem discussed by Schweppe (1973) is generalized. The employed SRIF orthogonal transformation methodology has been described by Bierman (1977).

Quantified choice of root-mean-square errors of approximation for evaluation and power analysis of small differences between structural equation models.

PubMed

Li, Libo; Bentler, Peter M

2011-06-01

MacCallum, Browne, and Cai (2006) proposed a new framework for evaluation and power analysis of small differences between nested structural equation models (SEMs). In their framework, the null and alternative hypotheses for testing a small difference in fit and its related power analyses were defined by some chosen root-mean-square error of approximation (RMSEA) pairs. In this article, we develop a new method that quantifies those chosen RMSEA pairs and allows a quantitative comparison of them. Our method proposes the use of single RMSEA values to replace the choice of RMSEA pairs for model comparison and power analysis, thus avoiding the differential meaning of the chosen RMSEA pairs inherent in the approach of MacCallum et al. (2006). With this choice, the conventional cutoff values in model overall evaluation can directly be transferred and applied to the evaluation and power analysis of model differences. © 2011 American Psychological Association

Quantized kernel least mean square algorithm.

PubMed

Chen, Badong; Zhao, Songlin; Zhu, Pingping; Príncipe, José C

2012-01-01

In this paper, we propose a quantization approach, as an alternative of sparsification, to curb the growth of the radial basis function structure in kernel adaptive filtering. The basic idea behind this method is to quantize and hence compress the input (or feature) space. Different from sparsification, the new approach uses the "redundant" data to update the coefficient of the closest center. In particular, a quantized kernel least mean square (QKLMS) algorithm is developed, which is based on a simple online vector quantization method. The analytical study of the mean square convergence has been carried out. The energy conservation relation for QKLMS is established, and on this basis we arrive at a sufficient condition for mean square convergence, and a lower and upper bound on the theoretical value of the steady-state excess mean square error. Static function estimation and short-term chaotic time-series prediction examples are presented to demonstrate the excellent performance.

Mean-deviation analysis in the theory of choice.

PubMed

Grechuk, Bogdan; Molyboha, Anton; Zabarankin, Michael

2012-08-01

Mean-deviation analysis, along with the existing theories of coherent risk measures and dual utility, is examined in the context of the theory of choice under uncertainty, which studies rational preference relations for random outcomes based on different sets of axioms such as transitivity, monotonicity, continuity, etc. An axiomatic foundation of the theory of coherent risk measures is obtained as a relaxation of the axioms of the dual utility theory, and a further relaxation of the axioms are shown to lead to the mean-deviation analysis. Paradoxes arising from the sets of axioms corresponding to these theories and their possible resolutions are discussed, and application of the mean-deviation analysis to optimal risk sharing and portfolio selection in the context of rational choice is considered. © 2012 Society for Risk Analysis.

1.5% root-mean-square flat-intensity laser beam formed using a binary-amplitude spatial light modulator.

PubMed

Liang, Jinyang; Kohn, Rudolph N; Becker, Michael F; Heinzen, Daniel J

2009-04-01

We demonstrate a digital micromirror device (DMD)-based optical system that converts a spatially noisy quasi-Gaussian to an eighth-order super-Lorentzian flat-top beam. We use an error-diffusion algorithm to design the binary pattern for the Texas Instruments DLP device. Following the DMD, a telescope with a pinhole low-pass filters the beam and scales it to the desired sized image. Experimental measurements show a 1% root-mean-square (RMS) flatness over a diameter of 0.28 mm in the center of the flat-top beam and better than 1.5% RMS flatness over its entire 1.43 mm diameter. The power conversion efficiency is 37%. We develop an alignment technique to ensure that the DMD pattern is correctly positioned on the incident beam. An interferometric measurement of the DMD surface flatness shows that phase uniformity is maintained in the output beam. Our approach is highly flexible and is able to produce not only flat-top beams with different parameters, but also any slowly varying target beam shape. It can be used to generate the homogeneous optical lattice required for Bose-Einstein condensate cold atom experiments.

Comparison of estimators of standard deviation for hydrologic time series

USGS Publications Warehouse

Tasker, Gary D.; Gilroy, Edward J.

1982-01-01

Unbiasing factors as a function of serial correlation, ρ, and sample size, n for the sample standard deviation of a lag one autoregressive model were generated by random number simulation. Monte Carlo experiments were used to compare the performance of several alternative methods for estimating the standard deviation σ of a lag one autoregressive model in terms of bias, root mean square error, probability of underestimation, and expected opportunity design loss. Three methods provided estimates of σ which were much less biased but had greater mean square errors than the usual estimate of σ: s = (1/(n - 1) ∑ (xi −x¯)2)½. The three methods may be briefly characterized as (1) a method using a maximum likelihood estimate of the unbiasing factor, (2) a method using an empirical Bayes estimate of the unbiasing factor, and (3) a robust nonparametric estimate of σ suggested by Quenouille. Because s tends to underestimate σ, its use as an estimate of a model parameter results in a tendency to underdesign. If underdesign losses are considered more serious than overdesign losses, then the choice of one of the less biased methods may be wise.

Evaluation of data transformations used with the square root and schoolfield models for predicting bacterial growth rate.

PubMed Central

Alber, S A; Schaffner, D W

1992-01-01

A comparison was made between mathematical variations of the square root and Schoolfield models for predicting growth rate as a function of temperature. The statistical consequences of square root and natural logarithm transformations of growth rate use in several variations of the Schoolfield and square root models were examined. Growth rate variances of Yersinia enterocolitica in brain heart infusion broth increased as a function of temperature. The ability of the two data transformations to correct for the heterogeneity of variance was evaluated. A natural logarithm transformation of growth rate was more effective than a square root transformation at correcting for the heterogeneity of variance. The square root model was more accurate than the Schoolfield model when both models used natural logarithm transformation. PMID:1444367

An adaptive beamforming method for ultrasound imaging based on the mean-to-standard-deviation factor.

PubMed

Wang, Yuanguo; Zheng, Chichao; Peng, Hu; Chen, Qiang

2018-06-12

The beamforming performance has a large impact on image quality in ultrasound imaging. Previously, several adaptive weighting factors including coherence factor (CF) and generalized coherence factor (GCF) have been proposed to improved image resolution and contrast. In this paper, we propose a new adaptive weighting factor for ultrasound imaging, which is called signal mean-to-standard-deviation factor (SMSF). SMSF is defined as the mean-to-standard-deviation of the aperture data and is used to weight the output of delay-and-sum (DAS) beamformer before image formation. Moreover, we develop a robust SMSF (RSMSF) by extending the SMSF to the spatial frequency domain using an altered spectrum of the aperture data. In addition, a square neighborhood average is applied on the RSMSF to offer a more smoothed square neighborhood RSMSF (SN-RSMSF) value. We compared our methods with DAS, CF, and GCF using simulated and experimental synthetic aperture data sets. The quantitative results show that SMSF results in an 82% lower full width at half-maximum (FWHM) but a 12% lower contrast ratio (CR) compared with CF. Moreover, the SN-RSMSF leads to 15% and 10% improvement, on average, in FWHM and CR compared with GCF while maintaining the speckle quality. This demonstrates that the proposed methods can effectively improve the image resolution and contrast. Copyright © 2018 Elsevier B.V. All rights reserved.

Role of location-dependent transverse wind on root-mean-square bandwidth of temporal light-flux fluctuations in the turbulent atmosphere.

PubMed

Chen, Chunyi; Yang, Huamin

2017-11-01

The root-mean-square (RMS) bandwidth of temporal light-flux fluctuations is formulated for both plane and spherical waves propagating in the turbulent atmosphere with location-dependent transverse wind. Two path weighting functions characterizing the joint contributions of turbulent eddies and transverse winds at various locations toward the RMS bandwidth are derived. Based on the developed formulations, the roles of variations in both the direction and magnitude of transverse wind velocity with locations over a path on the RMS bandwidth are elucidated. For propagation paths between ground and space, comparisons of the RMS bandwidth computed based on the Bufton wind profile with that calculated by assuming a nominal constant transverse wind velocity are made to exemplify the effect that location dependence of transverse wind velocity has on the RMS bandwidth. Moreover, an expression for the weighted RMS transverse wind velocity has been derived, which can be used as a nominal constant transverse wind velocity over a path for accurately determining the RMS bandwidth.

Derivation of formulas for root-mean-square errors in location, orientation, and shape in triangulation solution of an elongated object in space

NASA Technical Reports Server (NTRS)

Long, S. A. T.

1974-01-01

Formulas are derived for the root-mean-square (rms) displacement, slope, and curvature errors in an azimuth-elevation image trace of an elongated object in space, as functions of the number and spacing of the input data points and the rms elevation error in the individual input data points from a single observation station. Also, formulas are derived for the total rms displacement, slope, and curvature error vectors in the triangulation solution of an elongated object in space due to the rms displacement, slope, and curvature errors, respectively, in the azimuth-elevation image traces from different observation stations. The total rms displacement, slope, and curvature error vectors provide useful measure numbers for determining the relative merits of two or more different triangulation procedures applicable to elongated objects in space.

New method for propagating the square root covariance matrix in triangular form. [using Kalman-Bucy filter

NASA Technical Reports Server (NTRS)

Choe, C. Y.; Tapley, B. D.

1975-01-01

A method proposed by Potter of applying the Kalman-Bucy filter to the problem of estimating the state of a dynamic system is described, in which the square root of the state error covariance matrix is used to process the observations. A new technique which propagates the covariance square root matrix in lower triangular form is given for the discrete observation case. The technique is faster than previously proposed algorithms and is well-adapted for use with the Carlson square root measurement algorithm.

Examining the Reliability of Interval Level Data Using Root Mean Square Differences and Concordance Correlation Coefficients

ERIC Educational Resources Information Center

Barchard, Kimberly A.

2012-01-01

This article introduces new statistics for evaluating score consistency. Psychologists usually use correlations to measure the degree of linear relationship between 2 sets of scores, ignoring differences in means and standard deviations. In medicine, biology, chemistry, and physics, a more stringent criterion is often used: the extent to which…

An Alternative to Cohen's Standardized Mean Difference Effect Size: A Robust Parameter and Confidence Interval in the Two Independent Groups Case

ERIC Educational Resources Information Center

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

2005-01-01

The authors argue that a robust version of Cohen's effect size constructed by replacing population means with 20% trimmed means and the population standard deviation with the square root of a 20% Winsorized variance is a better measure of population separation than is Cohen's effect size. The authors investigated coverage probability for…

Root mean square fluctuation of a weak magnetic field in an infinite medium of homogeneous stationary turbulence.

NASA Technical Reports Server (NTRS)

Low, B.-C.

1972-01-01

The generation of a magnetic field by statistically homogeneous, stationary velocity turbulence is considered. The generation of rms magnetic fluctuation is explicitly demonstrated in the limit of short turbulence correlation time. It is shown that the fluctuation associated with a growing or stationary mean field grows with time such that the ratio of the fluctuation and the square of the mean field tends to a steady value, which is a monotonically decreasing function of the growth rate of the mean field.

The Application of Root Mean Square Electrocardiography (RMS ECG) for the Detection of Acquired and Congenital Long QT Syndrome

PubMed Central

Lux, Robert L.; Sower, Christopher Todd; Allen, Nancy; Etheridge, Susan P.; Tristani-Firouzi, Martin; Saarel, Elizabeth V.

2014-01-01

Background Precise measurement of the QT interval is often hampered by difficulty determining the end of the low amplitude T wave. Root mean square electrocardiography (RMS ECG) provides a novel alternative measure of ventricular repolarization. Experimental data have shown that the interval between the RMS ECG QRS and T wave peaks (RTPK) closely reflects the mean ventricular action potential duration while the RMS T wave width (TW) tracks the dispersion of repolarization timing. Here, we tested the precision of RMS ECG to assess ventricular repolarization in humans in the setting of drug-induced and congenital Long QT Syndrome (LQTS). Methods RMS ECG signals were derived from high-resolution 24 hour Holter monitor recordings from 68 subjects after receiving placebo and moxifloxacin and from standard 12 lead ECGs obtained in 97 subjects with LQTS and 97 age- and sex-matched controls. RTPK, QTRMS and RMS TW intervals were automatically measured using custom software and compared to traditional QT measures using lead II. Results All measures of repolarization were prolonged during moxifloxacin administration and in LQTS subjects, but the variance of RMS intervals was significantly smaller than traditional lead II measurements. TW was prolonged during moxifloxacin and in subjects with LQT-2, but not LQT-1 or LQT-3. Conclusion These data validate the application of RMS ECG for the detection of drug-induced and congenital LQTS. RMS ECG measurements are more precise than the current standard of care lead II measurements. PMID:24454918

The application of root mean square electrocardiography (RMS ECG) for the detection of acquired and congenital long QT syndrome.

PubMed

Lux, Robert L; Sower, Christopher Todd; Allen, Nancy; Etheridge, Susan P; Tristani-Firouzi, Martin; Saarel, Elizabeth V

2014-01-01

Precise measurement of the QT interval is often hampered by difficulty determining the end of the low amplitude T wave. Root mean square electrocardiography (RMS ECG) provides a novel alternative measure of ventricular repolarization. Experimental data have shown that the interval between the RMS ECG QRS and T wave peaks (RTPK) closely reflects the mean ventricular action potential duration while the RMS T wave width (TW) tracks the dispersion of repolarization timing. Here, we tested the precision of RMS ECG to assess ventricular repolarization in humans in the setting of drug-induced and congenital Long QT Syndrome (LQTS). RMS ECG signals were derived from high-resolution 24 hour Holter monitor recordings from 68 subjects after receiving placebo and moxifloxacin and from standard 12 lead ECGs obtained in 97 subjects with LQTS and 97 age- and sex-matched controls. RTPK, QTRMS and RMS TW intervals were automatically measured using custom software and compared to traditional QT measures using lead II. All measures of repolarization were prolonged during moxifloxacin administration and in LQTS subjects, but the variance of RMS intervals was significantly smaller than traditional lead II measurements. TW was prolonged during moxifloxacin and in subjects with LQT-2, but not LQT-1 or LQT-3. These data validate the application of RMS ECG for the detection of drug-induced and congenital LQTS. RMS ECG measurements are more precise than the current standard of care lead II measurements.

Predicting backbone Cα angles and dihedrals from protein sequences by stacked sparse auto-encoder deep neural network.

PubMed

Lyons, James; Dehzangi, Abdollah; Heffernan, Rhys; Sharma, Alok; Paliwal, Kuldip; Sattar, Abdul; Zhou, Yaoqi; Yang, Yuedong

2014-10-30

Because a nearly constant distance between two neighbouring Cα atoms, local backbone structure of proteins can be represented accurately by the angle between C(αi-1)-C(αi)-C(αi+1) (θ) and a dihedral angle rotated about the C(αi)-C(αi+1) bond (τ). θ and τ angles, as the representative of structural properties of three to four amino-acid residues, offer a description of backbone conformations that is complementary to φ and ψ angles (single residue) and secondary structures (>3 residues). Here, we report the first machine-learning technique for sequence-based prediction of θ and τ angles. Predicted angles based on an independent test have a mean absolute error of 9° for θ and 34° for τ with a distribution on the θ-τ plane close to that of native values. The average root-mean-square distance of 10-residue fragment structures constructed from predicted θ and τ angles is only 1.9Å from their corresponding native structures. Predicted θ and τ angles are expected to be complementary to predicted ϕ and ψ angles and secondary structures for using in model validation and template-based as well as template-free structure prediction. The deep neural network learning technique is available as an on-line server called Structural Property prediction with Integrated DEep neuRal network (SPIDER) at http://sparks-lab.org. Copyright © 2014 Wiley Periodicals, Inc.

Using weighted power mean for equivalent square estimation.

PubMed

Zhou, Sumin; Wu, Qiuwen; Li, Xiaobo; Ma, Rongtao; Zheng, Dandan; Wang, Shuo; Zhang, Mutian; Li, Sicong; Lei, Yu; Fan, Qiyong; Hyun, Megan; Diener, Tyler; Enke, Charles

2017-11-01

Equivalent Square (ES) enables the calculation of many radiation quantities for rectangular treatment fields, based only on measurements from square fields. While it is widely applied in radiotherapy, its accuracy, especially for extremely elongated fields, still leaves room for improvement. In this study, we introduce a novel explicit ES formula based on Weighted Power Mean (WPM) function and compare its performance with the Sterling formula and Vadash/Bjärngard's formula. The proposed WPM formula is ESWPMa,b=waα+1-wbα1/α for a rectangular photon field with sides a and b. The formula performance was evaluated by three methods: standard deviation of model fitting residual error, maximum relative model prediction error, and model's Akaike Information Criterion (AIC). Testing datasets included the ES table from British Journal of Radiology (BJR), photon output factors (S cp ) from the Varian TrueBeam Representative Beam Data (Med Phys. 2012;39:6981-7018), and published S cp data for Varian TrueBeam Edge (J Appl Clin Med Phys. 2015;16:125-148). For the BJR dataset, the best-fit parameter value α = -1.25 achieved a 20% reduction in standard deviation in ES estimation residual error compared with the two established formulae. For the two Varian datasets, employing WPM reduced the maximum relative error from 3.5% (Sterling) or 2% (Vadash/Bjärngard) to 0.7% for open field sizes ranging from 3 cm to 40 cm, and the reduction was even more prominent for 1 cm field sizes on Edge (J Appl Clin Med Phys. 2015;16:125-148). The AIC value of the WPM formula was consistently lower than its counterparts from the traditional formulae on photon output factors, most prominent on very elongated small fields. The WPM formula outperformed the traditional formulae on three testing datasets. With increasing utilization of very elongated, small rectangular fields in modern radiotherapy, improved photon output factor estimation is expected by adopting the WPM formula in treatment

Comments on real tachyon vacuum solution without square roots

NASA Astrophysics Data System (ADS)

Arroyo, E. Aldo

2018-01-01

We analyze the consistency of a recently proposed real tachyon vacuum solution without square roots in open bosonic string field theory. We show that the equation of motion contracted with the solution itself is satisfied. Additionally, by expanding the solution in the basis of the curly ℒ0 and the traditional L 0 eigenstates, we evaluate numerically the vacuum energy and obtain a result in agreement with Sen's conjecture.

Centralized Multi-Sensor Square Root Cubature Joint Probabilistic Data Association

PubMed Central

Liu, Jun; Li, Gang; Qi, Lin; Li, Yaowen; He, You

2017-01-01

This paper focuses on the tracking problem of multiple targets with multiple sensors in a nonlinear cluttered environment. To avoid Jacobian matrix computation and scaling parameter adjustment, improve numerical stability, and acquire more accurate estimated results for centralized nonlinear tracking, a novel centralized multi-sensor square root cubature joint probabilistic data association algorithm (CMSCJPDA) is proposed. Firstly, the multi-sensor tracking problem is decomposed into several single-sensor multi-target tracking problems, which are sequentially processed during the estimation. Then, in each sensor, the assignment of its measurements to target tracks is accomplished on the basis of joint probabilistic data association (JPDA), and a weighted probability fusion method with square root version of a cubature Kalman filter (SRCKF) is utilized to estimate the targets’ state. With the measurements in all sensors processed CMSCJPDA is derived and the global estimated state is achieved. Experimental results show that CMSCJPDA is superior to the state-of-the-art algorithms in the aspects of tracking accuracy, numerical stability, and computational cost, which provides a new idea to solve multi-sensor tracking problems. PMID:29113085

Centralized Multi-Sensor Square Root Cubature Joint Probabilistic Data Association.

PubMed

Liu, Yu; Liu, Jun; Li, Gang; Qi, Lin; Li, Yaowen; He, You

2017-11-05

This paper focuses on the tracking problem of multiple targets with multiple sensors in a nonlinear cluttered environment. To avoid Jacobian matrix computation and scaling parameter adjustment, improve numerical stability, and acquire more accurate estimated results for centralized nonlinear tracking, a novel centralized multi-sensor square root cubature joint probabilistic data association algorithm (CMSCJPDA) is proposed. Firstly, the multi-sensor tracking problem is decomposed into several single-sensor multi-target tracking problems, which are sequentially processed during the estimation. Then, in each sensor, the assignment of its measurements to target tracks is accomplished on the basis of joint probabilistic data association (JPDA), and a weighted probability fusion method with square root version of a cubature Kalman filter (SRCKF) is utilized to estimate the targets' state. With the measurements in all sensors processed CMSCJPDA is derived and the global estimated state is achieved. Experimental results show that CMSCJPDA is superior to the state-of-the-art algorithms in the aspects of tracking accuracy, numerical stability, and computational cost, which provides a new idea to solve multi-sensor tracking problems.

Explicit Formulae for the Continued Fraction Convergents of "Square Root of D"

ERIC Educational Resources Information Center

Braza, Peter A.

2010-01-01

The formulae for the convergents of continued fractions are always given recursively rather than in explicit form. This article derives explicit formulae for the convergents of the continued fraction expansions for square roots.

Weibull Modulus Estimated by the Non-linear Least Squares Method: A Solution to Deviation Occurring in Traditional Weibull Estimation

NASA Astrophysics Data System (ADS)

Li, T.; Griffiths, W. D.; Chen, J.

2017-11-01

The Maximum Likelihood method and the Linear Least Squares (LLS) method have been widely used to estimate Weibull parameters for reliability of brittle and metal materials. In the last 30 years, many researchers focused on the bias of Weibull modulus estimation, and some improvements have been achieved, especially in the case of the LLS method. However, there is a shortcoming in these methods for a specific type of data, where the lower tail deviates dramatically from the well-known linear fit in a classic LLS Weibull analysis. This deviation can be commonly found from the measured properties of materials, and previous applications of the LLS method on this kind of dataset present an unreliable linear regression. This deviation was previously thought to be due to physical flaws ( i.e., defects) contained in materials. However, this paper demonstrates that this deviation can also be caused by the linear transformation of the Weibull function, occurring in the traditional LLS method. Accordingly, it may not be appropriate to carry out a Weibull analysis according to the linearized Weibull function, and the Non-linear Least Squares method (Non-LS) is instead recommended for the Weibull modulus estimation of casting properties.

Using Least Squares for Error Propagation

ERIC Educational Resources Information Center

Tellinghuisen, Joel

2015-01-01

The method of least-squares (LS) has a built-in procedure for estimating the standard errors (SEs) of the adjustable parameters in the fit model: They are the square roots of the diagonal elements of the covariance matrix. This means that one can use least-squares to obtain numerical values of propagated errors by defining the target quantities as…

Storage and computationally efficient permutations of factorized covariance and square-root information matrices

NASA Technical Reports Server (NTRS)

Muellerschoen, R. J.

1988-01-01

A unified method to permute vector-stored upper-triangular diagonal factorized covariance (UD) and vector stored upper-triangular square-root information filter (SRIF) arrays is presented. The method involves cyclical permutation of the rows and columns of the arrays and retriangularization with appropriate square-root-free fast Givens rotations or elementary slow Givens reflections. A minimal amount of computation is performed and only one scratch vector of size N is required, where N is the column dimension of the arrays. To make the method efficient for large SRIF arrays on a virtual memory machine, three additional scratch vectors each of size N are used to avoid expensive paging faults. The method discussed is compared with the methods and routines of Bierman's Estimation Subroutine Library (ESL).

Outcome analysis after helmet therapy using 3D photogrammetry in patients with deformational plagiocephaly: the role of root mean square.

PubMed

Moghaddam, Mahsa Bidgoli; Brown, Trevor M; Clausen, April; DaSilva, Trevor; Ho, Emily; Forrest, Christopher R

2014-02-01

Deformational plagiocephaly (DP) is a multifactorial non-synostotic cranial deformity with a reported incidence as high as 1 in 7 infants in North America. Treatment options have focused on non-operative interventions including head repositioning and the use of an orthotic helmet device. Previous studies have used linear and two dimensional outcome measures to assess changes in cranial symmetry after helmet therapy. Our objective was to demonstrate improvement in head shape after treatment with a cranial molding helmet by using Root Mean Square (RMS), a measure unique to 3D photogrammetry, which takes into account both changes in volume and shape over time. Three dimensional photographs were obtained before and after molding helmet treatment in 40 infants (4-10 months old) with deformational plagiocephaly. Anatomical reference planes and measurements were recorded using the 3dMD Vultus(®) analysis software. RMS was used to quantify symmetry by superimposing left and right quadrants and calculating the mean value of aggregate distances between surfaces. Over 95% of the patients demonstrated an improvement in symmetry with helmet therapy. Furthermore, when the sample of infants was divided into two treatment subgroups, a statistically significant correlation was found between the age at the beginning of treatment and the change in the RMS value. When helmet therapy was started before 7 months of age a greater improvement in symmetry was seen. This work represents application of the technique of RMS analysis to demonstrate the efficacy of treatment of deformational plagiocephaly with a cranial molding helmet. Copyright © 2014. Published by Elsevier Ltd.

Transverse-momentum and pseudorapidity distributions of charged hadrons in pp collisions at square root of s = 7 TeV.

PubMed

Khachatryan, V; Sirunyan, A M; Tumasyan, A; Adam, W; Bergauer, T; Dragicevic, M; Erö, J; Fabjan, C; Friedl, M; Frühwirth, R; Ghete, V M; Hammer, J; Hänsel, S; Hoch, M; Hörmann, N; Hrubec, J; Jeitler, M; Kasieczka, G; Kiesenhofer, W; Krammer, M; Liko, D; Mikulec, I; Pernicka, M; Rohringer, H; Schöfbeck, R; Strauss, J; Taurok, A; Teischinger, F; Waltenberger, W; Walzel, G; Widl, E; Wulz, C-E; Mossolov, V; Shumeiko, N; Suarez Gonzalez, J; Benucci, L; Ceard, L; De Wolf, E A; Hashemi, M; Janssen, X; Maes, T; Mucibello, L; Ochesanu, S; Roland, B; Rougny, R; Selvaggi, M; Van Haevermaet, H; Van Mechelen, P; Van Remortel, N; Adler, V; Beauceron, S; Blyweert, S; D'Hondt, J; Devroede, O; Kalogeropoulos, A; Maes, J; Maes, M; Tavernier, S; Van Doninck, W; Van Mulders, P; Villella, I; Chabert, E C; Charaf, O; Clerbaux, B; De Lentdecker, G; Dero, V; Gay, A P R; Hammad, G H; Marage, P E; Vander Velde, C; Vanlaer, P; Wickens, J; Costantini, S; Grunewald, M; Klein, B; Marinov, A; Ryckbosch, D; Thyssen, F; Tytgat, M; Vanelderen, L; Verwilligen, P; Walsh, S; Zaganidis, N; Basegmez, S; Bruno, G; Caudron, J; De Favereau De Jeneret, J; Delaere, C; Demin, P; Favart, D; Giammanco, A; Grégoire, G; Hollar, J; Lemaitre, V; Militaru, O; Ovyn, S; Pagano, D; Pin, A; Piotrzkowski, K; Quertenmont, L; Schul, N; Beliy, N; Caebergs, T; Daubie, E; Alves, G A; Pol, M E; Souza, M H G; Carvalho, W; Da Costa, E M; De Jesus Damiao, D; De Oliveira Martins, C; Fonseca De Souza, S; Mundim, L; Oguri, V; Santoro, A; Silva Do Amaral, S M; Sznajder, A; Torres Da Silva De Araujo, F; Dias, F A; Dias, M A F; Fernandez Perez Tomei, T R; Gregores, E M; Marinho, F; Novaes, S F; Padula, Sandra S; Darmenov, N; Dimitrov, L; Genchev, V; Iaydjiev, P; Piperov, S; Stoykova, S; Sultanov, G; Trayanov, R; Vankov, I; Dyulendarova, M; Hadjiiska, R; Kozhuharov, V; Litov, L; Marinova, E; Mateev, M; Pavlov, B; Petkov, P; Bian, J G; Chen, G M; Chen, H S; Jiang, C H; Liang, D; Liang, S; Wang, J; Wang, J; Wang, X; Wang, Z; Yang, M; Zang, J; Zhang, Z; Ban, Y; Guo, S; Hu, Z; Mao, Y; Qian, S J; Teng, H; Zhu, B; Cabrera, A; Carrillo Montoya, C A; Gomez Moreno, B; Ocampo Rios, A A; Osorio Oliveros, A F; Sanabria, J C; Godinovic, N; Lelas, D; Lelas, K; Plestina, R; Polic, D; Puljak, I; Antunovic, Z; Dzelalija, M; Brigljevic, V; Duric, S; Kadija, K; Morovic, S; Attikis, A; Fereos, R; Galanti, M; Mousa, J; Nicolaou, C; Papadakis, A; Ptochos, F; Razis, P A; Rykaczewski, H; Tsiakkouri, D; Zinonos, Z; Mahmoud, M; Hektor, A; Kadastik, M; Kannike, K; Müntel, M; Raidal, M; Rebane, L; Azzolini, V; Eerola, P; Czellar, S; Härkönen, J; Heikkinen, A; Karimäki, V; Kinnunen, R; Klem, J; Kortelainen, M J; Lampén, T; Lassila-Perini, K; Lehti, S; Lindén, T; Luukka, P; Mäenpää, T; Tuominen, E; Tuominiemi, J; Tuovinen, E; Ungaro, D; Wendland, L; Banzuzi, K; Korpela, A; Tuuva, T; Sillou, D; Besancon, M; Dejardin, M; Denegri, D; Descamps, J; Fabbro, B; Faure, J L; Ferri, F; Ganjour, S; Gentit, F X; Givernaud, A; Gras, P; Hamel de Monchenault, G; Jarry, P; Locci, E; Malcles, J; Marionneau, M; Millischer, L; Rander, J; Rosowsky, A; Rousseau, D; Titov, M; Verrecchia, P; Baffioni, S; Bianchini, L; Bluj, M; Broutin, C; Busson, P; Charlot, C; Dobrzynski, L; Elgammal, S; Granier de Cassagnac, R; Haguenauer, M; Kalinowski, A; Miné, P; Paganini, P; Sabes, D; Sirois, Y; Thiebaux, C; Zabi, A; Agram, J-L; Besson, A; Bloch, D; Bodin, D; Brom, J-M; Cardaci, M; Conte, E; Drouhin, F; Ferro, C; Fontaine, J-C; Gelé, D; Goerlach, U; Greder, S; Juillot, P; Karim, M; Le Bihan, A-C; Mikami, Y; Speck, J; Van Hove, P; Fassi, F; Mercier, D; Baty, C; Beaupere, N; Bedjidian, M; Bondu, O; Boudoul, G; Boumediene, D; Brun, H; Chanon, N; Chierici, R; Contardo, D; Depasse, P; El Mamouni, H; Fay, J; Gascon, S; Ille, B; Kurca, T; Le Grand, T; Lethuillier, M; Mirabito, L; Perries, S; Tosi, S; Tschudi, Y; Verdier, P; Xiao, H; Roinishvili, V; Anagnostou, G; Edelhoff, M; Feld, L; Heracleous, N; Hindrichs, O; Jussen, R; Klein, K; Merz, J; Mohr, N; Ostapchuk, A; Perieanu, A; Raupach, F; Sammet, J; Schael, S; Sprenger, D; Weber, H; Weber, M; Wittmer, B; Actis, O; Ata, M; Bender, W; Biallass, P; Erdmann, M; Frangenheim, J; Hebbeker, T; Hinzmann, A; Hoepfner, K; Hof, C; Kirsch, M; Klimkovich, T; Kreuzer, P; Lanske, D; Magass, C; Merschmeyer, M; Meyer, A; Papacz, P; Pieta, H; Reithler, H; Schmitz, S A; Sonnenschein, L; Sowa, M; Steggemann, J; Teyssier, D; Zeidler, C; Bontenackels, M; Davids, M; Duda, M; Flügge, G; Geenen, H; Giffels, M; Haj Ahmad, W; Heydhausen, D; Kress, T; Kuessel, Y; Linn, A; Nowack, A; Perchalla, L; Pooth, O; Sauerland, P; Stahl, A; Thomas, M; Tornier, D; Zoeller, M H; Aldaya Martin, M; Behrenhoff, W; Behrens, U; Bergholz, M; Borras, K; Campbell, A; Castro, E; Dammann, D; Eckerlin, G; Flossdorf, A; Flucke, G; Geiser, A; Hauk, J; Jung, H; Kasemann, M; Katkov, I; Kleinwort, C; Kluge, H; Knutsson, A; Kuznetsova, E; Lange, W; Lohmann, W; Mankel, R; Marienfeld, M; Melzer-Pellmann, I-A; Meyer, A B; Mnich, J; Mussgiller, A; Olzem, J; Parenti, A; Raspereza, A; Schmidt, R; Schoerner-Sadenius, T; Sen, N; Stein, M; Tomaszewska, J; Volyanskyy, D; Wissing, C; Autermann, C; Draeger, J; Eckstein, D; Enderle, H; Gebbert, U; Kaschube, K; Kaussen, G; Klanner, R; Mura, B; Naumann-Emme, S; Nowak, F; Sander, C; Schettler, H; Schleper, P; Schröder, M; Schum, T; Schwandt, J; Stadie, H; Steinbrück, G; Thomsen, J; Wolf, R; Bauer, J; Buege, V; Cakir, A; Chwalek, T; Daeuwel, D; De Boer, W; Dierlamm, A; Dirkes, G; Feindt, M; Gruschke, J; Hackstein, C; Hartmann, F; Heinrich, M; Held, H; Hoffmann, K H; Honc, S; Kuhr, T; Martschei, D; Mueller, S; Müller, Th; Niegel, M; Oberst, O; Oehler, A; Ott, J; Peiffer, T; Piparo, D; Quast, G; Rabbertz, K; Ratnikov, F; Renz, M; Sabellek, A; Saout, C; Scheurer, A; Schieferdecker, P; Schilling, F-P; Schott, G; Simonis, H J; Stober, F M; Troendle, D; Wagner-Kuhr, J; Zeise, M; Zhukov, V; Ziebarth, E B; Daskalakis, G; Geralis, T; Kyriakis, A; Loukas, D; Manolakos, I; Markou, A; Markou, C; Mavrommatis, C; Petrakou, E; Gouskos, L; Katsas, P; Panagiotou, A; Evangelou, I; Kokkas, P; Manthos, N; Papadopoulos, I; Patras, V; Triantis, F A; Aranyi, A; Bencze, G; Boldizsar, L; Debreczeni, G; Hajdu, C; Horvath, D; Kapusi, A; Krajczar, K; Laszlo, A; Sikler, F; Vesztergombi, G; Beni, N; Molnar, J; Palinkas, J; Szillasi, Z; Veszpremi, V; Raics, P; Trocsanyi, Z L; Ujvari, B; Bansal, S; Beri, S B; Bhatnagar, V; Jindal, M; Kaur, M; Kohli, J M; Mehta, M Z; Nishu, N; Saini, L K; Sharma, A; Sharma, R; Singh, A P; Singh, J B; Singh, S P; Ahuja, S; Bhattacharya, S; Chauhan, S; Choudhary, B C; Gupta, P; Jain, S; Jain, S; Kumar, A; Ranjan, K; Shivpuri, R K; Choudhury, R K; Dutta, D; Kailas, S; Kataria, S K; Mohanty, A K; Pant, L M; Shukla, P; Suggisetti, P; Aziz, T; Guchait, M; Gurtu, A; Maity, M; Majumder, D; Majumder, G; Mazumdar, K; Mohanty, G B; Saha, A; Sudhakar, K; Wickramage, N; Banerjee, S; Dugad, S; Mondal, N K; Arfaei, H; Bakhshiansohi, H; Fahim, A; Jafari, A; Mohammadi Najafabadi, M; Paktinat Mehdiabadi, S; Safarzadeh, B; Zeinali, M; Abbrescia, M; Barbone, L; Colaleo, A; Creanza, D; De Filippis, N; De Palma, M; Dimitrov, A; Fedele, F; Fiore, L; Iaselli, G; Lusito, L; Maggi, G; Maggi, M; Manna, N; Marangelli, B; My, S; Nuzzo, S; Pierro, G A; Pompili, A; Pugliese, G; Romano, F; Roselli, G; Selvaggi, G; Silvestris, L; Trentadue, R; Tupputi, S; Zito, G; Abbiendi, G; Benvenuti, A C; Bonacorsi, D; Braibant-Giacomelli, S; Castro, A; Cavallo, F R; Codispoti, G; Dallavalle, G M; Fabbri, F; Fanfani, A; Fasanella, D; Giacomelli, P; Giunta, M; Grandi, C; Marcellini, S; Masetti, G; Montanari, A; Navarria, F L; Odorici, F; Perrotta, A; Rossi, A M; Rovelli, T; Siroli, G; Travaglini, R; Albergo, S; Cappello, G; Chiorboli, M; Costa, S; Tricomi, A; Tuve, C; Barbagli, G; Broccolo, G; Ciulli, V; Civinini, C; D'Alessandro, R; Focardi, E; Frosali, S; Gallo, E; Genta, C; Lenzi, P; Meschini, M; Paoletti, S; Sguazzoni, G; Tropiano, A; Benussi, L; Bianco, S; Colafranceschi, S; Fabbri, F; Piccolo, D; Fabbricatore, P; Musenich, R; 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de Barbaro, P; Demina, R; Flacher, H; Garcia-Bellido, A; Gotra, Y; Han, J; Harel, A; Miner, D C; Orbaker, D; Petrillo, G; Vishnevskiy, D; Zielinski, M; Bhatti, A; Demortier, L; Goulianos, K; Hatakeyama, K; Lungu, G; Mesropian, C; Yan, M; Atramentov, O; Gershtein, Y; Gray, R; Halkiadakis, E; Hidas, D; Hits, D; Lath, A; Rose, K; Schnetzer, S; Somalwar, S; Stone, R; Thomas, S; Cerizza, G; Hollingsworth, M; Spanier, S; Yang, Z C; York, A; Asaadi, J; Eusebi, R; Gilmore, J; Gurrola, A; Kamon, T; Khotilovich, V; Montalvo, R; Nguyen, C N; Pivarski, J; Safonov, A; Sengupta, S; Toback, D; Weinberger, M; Akchurin, N; Bardak, C; Damgov, J; Jeong, C; Kovitanggoon, K; Lee, S W; Mane, P; Roh, Y; Sill, A; Volobouev, I; Wigmans, R; Yazgan, E; Appelt, E; Brownson, E; Engh, D; Florez, C; Gabella, W; Johns, W; Kurt, P; Maguire, C; Melo, A; Sheldon, P; Velkovska, J; Arenton, M W; Balazs, M; Buehler, M; Conetti, S; Cox, B; Hirosky, R; Ledovskoy, A; Neu, C; Yohay, R; Gollapinni, S; Gunthoti, K; Harr, R; Karchin, P E; Mattson, M; Milstène, C; Sakharov, A; Anderson, M; Bachtis, M; Bellinger, J N; Carlsmith, D; Dasu, S; Dutta, S; Efron, J; Gray, L; Grogg, K S; Grothe, M; Hall-Wilton, R; Herndon, M; Klabbers, P; Klukas, J; Lanaro, A; Lazaridis, C; Leonard, J; Lomidze, D; Loveless, R; Mohapatra, A; Polese, G; Reeder, D; Savin, A; Smith, W H; Swanson, J; Weinberg, M

2010-07-09

Charged-hadron transverse-momentum and pseudorapidity distributions in proton-proton collisions at square root of s = 7  TeV are measured with the inner tracking system of the CMS detector at the LHC. The charged-hadron yield is obtained by counting the number of reconstructed hits, hit pairs, and fully reconstructed charged-particle tracks. The combination of the three methods gives a charged-particle multiplicity per unit of pseudorapidity dN(ch)/dη|(|η|<0.5) = 5.78 ± 0.01(stat) ± 0.23(syst) for non-single-diffractive events, higher than predicted by commonly used models. The relative increase in charged-particle multiplicity from square root of s = 0.9 to 7 TeV is [66.1 ± 1.0(stat) ± 4.2(syst)]%. The mean transverse momentum is measured to be 0.545 ± 0.005(stat) ± 0.015(syst)  GeV/c. The results are compared with similar measurements at lower energies.

Downdating a time-varying square root information filter

NASA Technical Reports Server (NTRS)

Muellerschoen, Ronald J.

1990-01-01

A new method to efficiently downdate an estimate and covariance generated by a discrete time Square Root Information Filter (SRIF) is presented. The method combines the QR factor downdating algorithm of Gill and the decentralized SRIF algorithm of Bierman. Efficient removal of either measurements or a priori information is possible without loss of numerical integrity. Moreover, the method includes features for detecting potential numerical degradation. Performance on a 300 parameter system with 5800 data points shows that the method can be used in real time and hence is a promising tool for interactive data analysis. Additionally, updating a time-varying SRIF filter with either additional measurements or a priori information proceeds analogously.

Advances of the smooth variable structure filter: square-root and two-pass formulations

NASA Astrophysics Data System (ADS)

Gadsden, S. Andrew; Lee, Andrew S.

2017-01-01

The smooth variable structure filter (SVSF) has seen significant development and research activity in recent years. It is based on sliding mode concepts, which utilize a switching gain that brings an inherent amount of stability to the estimation process. In an effort to improve upon the numerical stability of the SVSF, a square-root formulation is derived. The square-root SVSF is based on Potter's algorithm. The proposed formulation is computationally more efficient and reduces the risks of failure due to numerical instability. The new strategy is applied on target tracking scenarios for the purposes of state estimation, and the results are compared with the popular Kalman filter. In addition, the SVSF is reformulated to present a two-pass smoother based on the SVSF gain. The proposed method is applied on an aerospace flight surface actuator, and the results are compared with the Kalman-based two-pass smoother.

Recognition of coarse-grained protein tertiary structure.

PubMed

Lezon, Timothy; Banavar, Jayanth R; Maritan, Amos

2004-05-15

A model of the protein backbone is considered in which each residue is characterized by the location of its C(alpha) atom and one of a discrete set of conformal (phi, psi) states. We investigate the key differences between a description that offers a locally precise fit to known backbone structures and one that provides a globally accurate fit to protein structures. Using a statistical scoring scheme and threading, a protein's local best-fit conformation is highly recognizable, but its global structure cannot be directly determined from an amino acid sequence. The incorporation of information about the conformal states of neighboring residues along the chain allows one to accurately translate the local structure into a global structure. We present a two-step algorithm, which recognizes up to 95% of the tested protein native-state structures to within a 2.5 A root mean square deviation. Copyright 2004 Wiley-Liss, Inc.

Ponce de Leon Inlet, FL: An Integrated Hydrodynamic and Morphologic Assessment of Design Alternatives using the U.S. Army Corps of Engineers’ Coastal Modeling System

DTIC Science & Technology

2009-07-01

produce a configuration parallel to, and longitudinally aligned with, the north jetty, but the rebuilt structure essentially cuts off the inner south...Normalized Root Mean Square Deviation PMAB Prototype Measurement and Analysis Branch RGB Red, Green, Blue RMSD Root Mean Square Deviation SHOALS...intended height of the rubble mound off the seafloor (submergent). The latter method is used for a variety of structural assignments besides a

A Visual Model for the Variance and Standard Deviation

ERIC Educational Resources Information Center

Orris, J. B.

2011-01-01

This paper shows how the variance and standard deviation can be represented graphically by looking at each squared deviation as a graphical object--in particular, as a square. A series of displays show how the standard deviation is the size of the average square.

Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters

PubMed Central

Zgarbová, Marie; Luque, F. Javier; Šponer, Jiří; Cheatham, Thomas E.; Otyepka, Michal; Jurečka, Petr

2013-01-01

We present a refinement of the backbone torsion parameters ε and ζ of the Cornell et al. AMBER force field for DNA simulations. The new parameters, denoted as εζOL1, were derived from quantum-mechanical calculations with inclusion of conformation-dependent solvation effects according to the recently reported methodology (J. Chem. Theory Comput. 2012, 7(9), 2886-2902). The performance of the refined parameters was analyzed by means of extended molecular dynamics (MD) simulations for several representative systems. The results showed that the εζOL1 refinement improves the backbone description of B-DNA double helices and G-DNA stem. In B-DNA simulations, we observed an average increase of the helical twist and narrowing of the major groove, thus achieving better agreement with X-ray and solution NMR data. The balance between populations of BI and BII backbone substates was shifted towards the BII state, in better agreement with ensemble-refined solution experimental results. Furthermore, the refined parameters decreased the backbone RMS deviations in B-DNA MD simulations. In the antiparallel guanine quadruplex (G-DNA) the εζOL1 modification improved the description of non-canonical α/γ backbone substates, which were shown to be coupled to the ε/ζ torsion potential. Thus, the refinement is suggested as a possible alternative to the current ε/ζ torsion potential, which may enable more accurate modeling of nucleic acids. However, long-term testing is recommended before its routine application in DNA simulations. PMID:24058302

An Algorithm for Computing Matrix Square Roots with Application to Riccati Equation Implementation,

DTIC Science & Technology

1977-01-01

pansion is compared to Euclid’s method. The apriori by Aerospace Medical Research Laboratory, Aero— upper and lower bounds are also calculated. The third ... space Medical Division , Air Force Systems Command , part of this paper extends the scalar square root al— Wright—Patterson Air Force Base, Ohio 45433

Independent Metrics for Protein Backbone and Side-Chain Flexibility: Time Scales and Effects of Ligand Binding.

PubMed

Fuchs, Julian E; Waldner, Birgit J; Huber, Roland G; von Grafenstein, Susanne; Kramer, Christian; Liedl, Klaus R

2015-03-10

Conformational dynamics are central for understanding biomolecular structure and function, since biological macromolecules are inherently flexible at room temperature and in solution. Computational methods are nowadays capable of providing valuable information on the conformational ensembles of biomolecules. However, analysis tools and intuitive metrics that capture dynamic information from in silico generated structural ensembles are limited. In standard work-flows, flexibility in a conformational ensemble is represented through residue-wise root-mean-square fluctuations or B-factors following a global alignment. Consequently, these approaches relying on global alignments discard valuable information on local dynamics. Results inherently depend on global flexibility, residue size, and connectivity. In this study we present a novel approach for capturing positional fluctuations based on multiple local alignments instead of one single global alignment. The method captures local dynamics within a structural ensemble independent of residue type by splitting individual local and global degrees of freedom of protein backbone and side-chains. Dependence on residue type and size in the side-chains is removed via normalization with the B-factors of the isolated residue. As a test case, we demonstrate its application to a molecular dynamics simulation of bovine pancreatic trypsin inhibitor (BPTI) on the millisecond time scale. This allows for illustrating different time scales of backbone and side-chain flexibility. Additionally, we demonstrate the effects of ligand binding on side-chain flexibility of three serine proteases. We expect our new methodology for quantifying local flexibility to be helpful in unraveling local changes in biomolecular dynamics.

Double closed-loop control of integrated optical resonance gyroscope with mean-square exponential stability.

PubMed

Li, Hui; Liu, Liying; Lin, Zhili; Wang, Qiwei; Wang, Xiao; Feng, Lishuang

2018-01-22

A new double closed-loop control system with mean-square exponential stability is firstly proposed to optimize the detection accuracy and dynamic response characteristic of the integrated optical resonance gyroscope (IORG). The influence mechanism of optical nonlinear effects on system detection sensitivity is investigated to optimize the demodulation gain, the maximum sensitivity and the linear work region of a gyro system. Especially, we analyze the effect of optical parameter fluctuation on the parameter uncertainty of system, and investigate the influence principle of laser locking-frequency noise on the closed-loop detection accuracy of angular velocity. The stochastic disturbance model of double closed-loop IORG is established that takes the unfavorable factors such as optical effect nonlinearity, disturbed disturbance, optical parameter fluctuation and unavoidable system noise into consideration. A robust control algorithm is also designed to guarantee the mean-square exponential stability of system with a prescribed H ∞ performance in order to improve the detection accuracy and dynamic performance of IORG. The conducted experiment results demonstrate that the IORG has a dynamic response time less than 76us, a long-term bias stability 7.04°/h with an integration time of 10s over one-hour test, and the corresponding bias stability 1.841°/h based on Allan deviation, which validate the effectiveness and usefulness of the proposed detection scheme.

Application of Least Mean Square Algorithms to Spacecraft Vibration Compensation

NASA Technical Reports Server (NTRS)

Woodard , Stanley E.; Nagchaudhuri, Abhijit

1998-01-01

This paper describes the application of the Least Mean Square (LMS) algorithm in tandem with the Filtered-X Least Mean Square algorithm for controlling a science instrument's line-of-sight pointing. Pointing error is caused by a periodic disturbance and spacecraft vibration. A least mean square algorithm is used on-orbit to produce the transfer function between the instrument's servo-mechanism and error sensor. The result is a set of adaptive transversal filter weights tuned to the transfer function. The Filtered-X LMS algorithm, which is an extension of the LMS, tunes a set of transversal filter weights to the transfer function between the disturbance source and the servo-mechanism's actuation signal. The servo-mechanism's resulting actuation counters the disturbance response and thus maintains accurate science instrumental pointing. A simulation model of the Upper Atmosphere Research Satellite is used to demonstrate the algorithms.

Application of square-root filtering for spacecraft attitude control

NASA Technical Reports Server (NTRS)

Sorensen, J. A.; Schmidt, S. F.; Goka, T.

1978-01-01

Suitable digital algorithms are developed and tested for providing on-board precision attitude estimation and pointing control for potential use in the Landsat-D spacecraft. These algorithms provide pointing accuracy of better than 0.01 deg. To obtain necessary precision with efficient software, a six state-variable square-root Kalman filter combines two star tracker measurements to update attitude estimates obtained from processing three gyro outputs. The validity of the estimation and control algorithms are established, and the sensitivity of their performance to various error sources and software parameters are investigated by detailed digital simulation. Spacecraft computer memory, cycle time, and accuracy requirements are estimated.

Normal Mode Analysis of Polytheonamide B

NASA Astrophysics Data System (ADS)

Mori, Takaharu; Kokubo, Hironori; Shimizu, Hirofumi; Iwamoto, Masayuki; Oiki, Shigetoshi; Okamoto, Yuko

2007-09-01

Polytheonamide B is a linear 48-residue peptide which forms a single β-helix structure with alternating d- and l-amino acids and contains methylated and hydroxy variants of proteinogenic amino acids. To investigate the dynamical properties of polytheonamide B we perform the normal mode analysis. Root-mean-square displacements of all backbone atoms, root-mean-square fluctuations of the backbone dihedral angles (φ,\\psi), and correlation factors for the Cα atom fluctuations and for the dihedral angle fluctuations are calculated. The normal mode analysis reveals that polytheonamide B shows the elastic rod behavior in the very low-frequency regions and that librational motions of backbone amide planes have the modes with relatively low frequencies, which is relevant to the function of polytheonamide B. In addition, these librational motions occur almost independently and weakly anticorrelate with those of the hydrogen-bonded neighboring amide planes. Calculations of the backbone fluctuations show that the flexibility of polytheonamide B is roughly uniform over the entire helix. We compare our results with those of gramicidin A, the analogue of polytheonamide B, to discuss the structures and functions, and obtain some common features in the flexibilities and dynamics of the backbone atoms. These results present important clues for clarifying the function of polytheonamide B at the atomic level.

Isotope pattern deconvolution for peptide mass spectrometry by non-negative least squares/least absolute deviation template matching

PubMed Central

2012-01-01

Background The robust identification of isotope patterns originating from peptides being analyzed through mass spectrometry (MS) is often significantly hampered by noise artifacts and the interference of overlapping patterns arising e.g. from post-translational modifications. As the classification of the recorded data points into either ‘noise’ or ‘signal’ lies at the very root of essentially every proteomic application, the quality of the automated processing of mass spectra can significantly influence the way the data might be interpreted within a given biological context. Results We propose non-negative least squares/non-negative least absolute deviation regression to fit a raw spectrum by templates imitating isotope patterns. In a carefully designed validation scheme, we show that the method exhibits excellent performance in pattern picking. It is demonstrated that the method is able to disentangle complicated overlaps of patterns. Conclusions We find that regularization is not necessary to prevent overfitting and that thresholding is an effective and user-friendly way to perform feature selection. The proposed method avoids problems inherent in regularization-based approaches, comes with a set of well-interpretable parameters whose default configuration is shown to generalize well without the need for fine-tuning, and is applicable to spectra of different platforms. The R package IPPD implements the method and is available from the Bioconductor platform (http://bioconductor.fhcrc.org/help/bioc-views/devel/bioc/html/IPPD.html). PMID:23137144

TMFF-A Two-Bead Multipole Force Field for Coarse-Grained Molecular Dynamics Simulation of Protein.

PubMed

Li, Min; Liu, Fengjiao; Zhang, John Z H

2016-12-13

Coarse-grained (CG) models are desirable for studying large and complex biological systems. In this paper, we propose a new two-bead multipole force field (TMFF) in which electric multipoles up to the quadrupole are included in the CG force field. The inclusion of electric multipoles in the proposed CG force field enables a more realistic description of the anisotropic electrostatic interactions in the protein system and, thus, provides an improvement over the standard isotropic two-bead CG models. In order to test the accuracy of the new CG force field model, extensive molecular dynamics simulations were carried out for a series of benchmark protein systems. These simulation studies showed that the TMFF model can realistically reproduce the structural and dynamical properties of proteins, as demonstrated by the close agreement of the CG results with those from the corresponding all-atom simulations in terms of root-mean-square deviations (RMSDs) and root-mean-square fluctuations (RMSFs) of the protein backbones. The current two-bead model is highly coarse-grained and is 50-fold more efficient than all-atom method in MD simulation of proteins in explicit water.

Standard deviation and standard error of the mean.

PubMed

Lee, Dong Kyu; In, Junyong; Lee, Sangseok

2015-06-01

In most clinical and experimental studies, the standard deviation (SD) and the estimated standard error of the mean (SEM) are used to present the characteristics of sample data and to explain statistical analysis results. However, some authors occasionally muddle the distinctive usage between the SD and SEM in medical literature. Because the process of calculating the SD and SEM includes different statistical inferences, each of them has its own meaning. SD is the dispersion of data in a normal distribution. In other words, SD indicates how accurately the mean represents sample data. However the meaning of SEM includes statistical inference based on the sampling distribution. SEM is the SD of the theoretical distribution of the sample means (the sampling distribution). While either SD or SEM can be applied to describe data and statistical results, one should be aware of reasonable methods with which to use SD and SEM. We aim to elucidate the distinctions between SD and SEM and to provide proper usage guidelines for both, which summarize data and describe statistical results.

Standard deviation and standard error of the mean

PubMed Central

In, Junyong; Lee, Sangseok

2015-01-01

In most clinical and experimental studies, the standard deviation (SD) and the estimated standard error of the mean (SEM) are used to present the characteristics of sample data and to explain statistical analysis results. However, some authors occasionally muddle the distinctive usage between the SD and SEM in medical literature. Because the process of calculating the SD and SEM includes different statistical inferences, each of them has its own meaning. SD is the dispersion of data in a normal distribution. In other words, SD indicates how accurately the mean represents sample data. However the meaning of SEM includes statistical inference based on the sampling distribution. SEM is the SD of the theoretical distribution of the sample means (the sampling distribution). While either SD or SEM can be applied to describe data and statistical results, one should be aware of reasonable methods with which to use SD and SEM. We aim to elucidate the distinctions between SD and SEM and to provide proper usage guidelines for both, which summarize data and describe statistical results. PMID:26045923

The structure and dynamics of rat apo-cellular retinol-binding protein II in solution: comparison with the X-ray structure.

PubMed

Lu, J; Lin, C L; Tang, C; Ponder, J W; Kao, J L; Cistola, D P; Li, E

1999-03-05

The structure and dynamics of rat apo-cellular retinol binding protein II (apo-CRBP II) in solution has been determined by multidimensional NMR analysis of uniformly enriched recombinant rat 13C, 15N-apo-CRBP II and 15N-apo-CRBP II. The final ensemble of 24 NMR structures has been calculated from 3274 conformational restraints or 24.4 restraints/residue. The average root-mean-square deviation of the backbone atoms for the final 24 structures relative to their mean structure is 1.06 A. Although the average solution structure is very similar to the crystal structure, it differs at the putative entrance to the binding cavity, which is formed by the helix-turn-helix motif, the betaC-betaD turn and the betaE-betaF turn. The mean coordinates of the main-chain atoms of amino acid residues 28-38 are displaced in the solution structure relative to the crystal structure. The side-chain of F58, located on the betaC-betaD turn, is reoriented such that it interacts with L37 and no longer blocks entry into the ligand-binding pocket. Residues 28-35, which form the second helix of the helix-turn-helix motif in the crystal structure, do not exhibit a helical conformation in the solution structure. The solution structure of apo-CRBP II exhibits discrete regions of backbone disorder which are most pronounced at residues 28-32, 37-38 and 73-76 in the betaE-betaF turn as evaluated by the consensus chemical shift index, the root-mean-square deviation, amide 1H exchange rates and 15N relaxation studies. These studies indicate that fluctuations in protein conformation occur on the microseconds to ms time-scale in these regions of the protein. Some of these exchange processes can be directly observed in the three-dimensional 15N-resolved NOESY spectrum. These results suggest that in solution, apo-CRBP II undergoes conformational changes on the microseconds to ms time-scale which result in increased access to the binding cavity. Copyright 1999 Academic Press.

External apical root resorption in maxillary root-filled incisors after orthodontic treatment: a split-mouth design study.

PubMed

Llamas-Carreras, José María; Amarilla, Almudena; Espinar-Escalona, Eduardo; Castellanos-Cosano, Lizett; Martín-González, Jenifer; Sánchez-Domínguez, Benito; López-Frías, Francisco Javier

2012-05-01

The purpose of this study was to compare, in a split mouth design, the external apical root resorption (EARR) associated with orthodontic treatment in root-filled maxillary incisors and their contralateral teeth with vital pulps. The study sample consisted of 38 patients (14 males and 24 females), who had one root-filled incisor before completion of multiband/bracket orthodontic therapy for at least 1 year. For each patient, digital panoramic radiographs taken before and after orthodontic treatment were used to determine the root resortion and the proportion of external root resorption (PRR), defined as the ratio between the root resorption in the endodontically treated incisor and that in its contralateral incisor with a vital pulp. The student's t-test, chi-square test and logistic regression analysis were used to determine statistical significance. There was no statistically significant difference (p > 0.05) between EARR in vital teeth (1.1 ± 1.0 mm) and endodontically treated incisors (1.1 ± 0.8 mm). Twenty-six patients (68.4%) showed greater resorption of the endodontically treated incisor than its homolog vital tooth (p > 0.05). The mean and standard deviation of PPR were 1.0 ± 0.2. Multivariate logistic regression suggested that PRR does not correlate with any of the variables analyzed. There was no significant difference in the amount or severity of external root resorption during orthodontic movement between root-filled incisors and their contralateral teeth with vital pulps.

Packing of sidechains in low-resolution models for proteins.

PubMed

Keskin, O; Bahar, I

1998-01-01

Atomic level rotamer libraries for sidechains in proteins have been proposed by several groups. Conformations of side groups in coarse-grained models, on the other hand, have not yet been analyzed, although low resolution approaches are the only efficient way to explore global structural features. A residue-specific backbone-dependent library for sidechain isomers, compatible with a coarse-grained model, is proposed. The isomeric states are utilized in packing sidechains of known backbone structures. Sidechain positions are predicted with a root-mean-square deviation (r.m.s.d.) of 2.40 A with respect to crystal structure for 50 test proteins. The rmsd for core residues is 1.60 A and decreases to 1.35 A when conformational correlations and directional effects in inter-residue couplings are considered. An automated method for assigning sidechain positions in coarse-grained model proteins is proposed and made available on the internet; the method accounts satisfactorily for sidechain packing, particularly in the core.

External apical root resorption in maxillary root-filled incisors after orthodontic treatment: A split-mouth design study

PubMed Central

Amarilla, Almudena; Espinar-Escalona, Eduardo; Castellanos-Cosano, Lizett; Martín-González, Jenifer; Sánchez-Domínguez, Benito; López-Frías, Francisco J.

2012-01-01

Introduction: The purpose of this study was to compare, in a split mouth design, the external apical root resorption (EARR) associated with orthodontic treatment in root-filled maxillary incisors and their contralateral teeth with vital pulps. Methodology: The study sample consisted of 38 patients (14 males and 24 females), who had one root-filled incisor before completion of multiband/bracket orthodontic therapy for at least 1 year. For each patient, digital panoramic radiographs taken before and after orthodontic treatment were used to determine the root resortion and the proportion of external root resorption (PRR), defined as the ratio between the root resorption in the endodontically treated incisor and that in its contralateral incisor with a vital pulp. The student’s t-test, chi-square test and logistic regression analysis were used to determine statistical significance. Results: There was no statistically significant difference (p > 0.05) between EARR in vital teeth (1.1 ± 1.0 mm) and endodontically treated incisors (1.1 ± 0.8 mm). Twenty-six patients (68.4%) showed greater resorption of the endodontically treated incisor than its homolog vital tooth (p > 0.05). The mean and standard deviation of PPR were 1.0 ± 0.2. Multivariate logistic regression suggested that PRR does not correlate with any of the variables analyzed. Conclusions: There was no significant difference in the amount or severity of external root resorption during orthodontic movement between root-filled incisors and their contralateral teeth with vital pulps. Key words:Endodontics, orthodontics, root canal treatment, root resorption. PMID:22143731

A Stochastic Total Least Squares Solution of Adaptive Filtering Problem

PubMed Central

Ahmad, Noor Atinah

2014-01-01

An efficient and computationally linear algorithm is derived for total least squares solution of adaptive filtering problem, when both input and output signals are contaminated by noise. The proposed total least mean squares (TLMS) algorithm is designed by recursively computing an optimal solution of adaptive TLS problem by minimizing instantaneous value of weighted cost function. Convergence analysis of the algorithm is given to show the global convergence of the proposed algorithm, provided that the stepsize parameter is appropriately chosen. The TLMS algorithm is computationally simpler than the other TLS algorithms and demonstrates a better performance as compared with the least mean square (LMS) and normalized least mean square (NLMS) algorithms. It provides minimum mean square deviation by exhibiting better convergence in misalignment for unknown system identification under noisy inputs. PMID:24688412

Fast and stable algorithms for computing the principal square root of a complex matrix

NASA Technical Reports Server (NTRS)

Shieh, Leang S.; Lian, Sui R.; Mcinnis, Bayliss C.

1987-01-01

This note presents recursive algorithms that are rapidly convergent and more stable for finding the principal square root of a complex matrix. Also, the developed algorithms are utilized to derive the fast and stable matrix sign algorithms which are useful in developing applications to control system problems.

Ratio of jet cross sections at square root of s = 630 GeV and 1800 GeV.

PubMed

Abbott, B; Abolins, M; Abramov, V; Acharya, B S; Adams, D L; Adams, M; Alves, G A; Amos, N; Anderson, E W; Baarmand, M M; Babintsev, V V; Babukhadia, L; Baden, A; Baldin, B; Balm, P W; Banerjee, S; Bantly, J; Barberis, E; Baringer, P; Bartlett, J F; Bassler, U; Bean, A; Begel, M; Belyaev, A; Beri, S B; Bernardi, G; Bertram, I; Besson, A; Bezzubov, V A; Bhat, P C; Bhatnagar, V; Bhattacharjee, M; Blazey, G; Blessing, S; Boehnlein, A; Bojko, N I; Borcherding, F; Brandt, A; Breedon, R; Briskin, G; Brock, R; Brooijmans, G; Bross, A; Buchholz, D; Buehler, M; Buescher, V; Burtovoi, V S; Butler, J M; Canelli, F; Carvalho, W; Casey, D; Casilum, Z; Castilla-Valdez, H; Chakraborty, D; Chan, K M; Chekulaev, S V; Cho, D K; Choi, S; Chopra, S; Christenson, J H; Chung, M; Claes, D; Clark, A R; Cochran, J; Coney, L; Connolly, B; Cooper, W E; Coppage, D; Cummings, M A; Cutts, D; Dahl, O I; Davis, G A; Davis, K; De, K; Del Signore, K; Demarteau, M; Demina, R; Demine, P; Denisov, D; Denisov, S P; Desai, S; Diehl, H T; Diesburg, M; Di Loreto, G; Doulas, S; Draper, P; Ducros, Y; Dudko, L V; Duensing, S; Dugad, S R; Dyshkant, A; Edmunds, D; Ellison, J; Elvira, V D; Engelmann, R; Eno, S; Eppley, G; Ermolov, P; Eroshin, O V; Estrada, J; Evans, H; Evdokimov, V N; Fahland, T; Feher, S; Fein, D; Ferbel, T; Fisk, H E; Fisyak, Y; Flattum, E; Fleuret, F; Fortner, M; Frame, K C; Fuess, S; Gallas, E; Galyaev, A N; Gartung, P; Gavrilov, V; Genik, R J; Genser, K; Gerber, C E; Gershtein, Y; Gibbard, B; Gilmartin, R; Ginther, G; Gómez, B; Gómez, G; Goncharov, P I; González Solís, J L; Gordon, H; Goss, L T; Gounder, K; Goussiou, A; Graf, N; Graham, G; Grannis, P D; Green, J A; Greenlee, H; Grinstein, S; Groer, L; Grudberg, P; Grünendahl, S; Gupta, A; Gurzhiev, S N; Gutierrez, G; Gutierrez, P; Hadley, N J; Haggerty, H; Hagopian, S; Hagopian, V; Hahn, K S; Hall, R E; Hanlet, P; Hansen, S; Hauptman, J M; Hays, C; Hebert, C; Hedin, D; Heinson, A P; Heintz, U; Heuring, T; Hirosky, R; Hobbs, J D; Hoeneisen, B; Hoftun, J S; Hou, S; Huang, Y; Ito, A S; Jerger, S A; Jesik, R; Johns, K; Johnson, M; Jonckheere, A; Jones, M; Jöstlein, H; Juste, A; Kahn, S; Kajfasz, E; Karmanov, D; Karmgard, D; Kehoe, R; Kim, S K; Klima, B; Klopfenstein, C; Knuteson, B; Ko, W; Kohli, J M; Kostritskiy, A V; Kotcher, J; Kotwal, A V; Kozelov, A V; Kozlovsky, E A; Krane, J; Krishnaswamy, M R; Krzywdzinski, S; Kubantsev, M; Kuleshov, S; Kulik, Y; Kunori, S; Kuznetsov, V E; Landsberg, G; Leflat, A; Lehner, F; Li, J; Li, Q Z; Lima, J G; Lincoln, D; Linn, S L; Linnemann, J; Lipton, R; Lucotte, A; Lueking, L; Lundstedt, C; Maciel, A K; Madaras, R J; Manankov, V; Mao, H S; Marshall, T; Martin, M I; Martin, R D; Mauritz, K M; May, B; Mayorov, A A; McCarthy, R; McDonald, J; McMahon, T; Melanson, H L; Meng, X C; Merkin, M; Merritt, K W; Miao, C; Miettinen, H; Mihalcea, D; Mincer, A; Mishra, C S; Mokhov, N; Mondal, N K; Montgomery, H E; Moore, R W; Mostafa, M; da Motta, H; Nagy, E; Nang, F; Narain, M; Narasimham, V S; Neal, H A; Negret, J P; Negroni, S; Norman, D; Oesch, L; Oguri, V; Olivier, B; Oshima, N; Padley, P; Pan, L J; Para, A; Parashar, N; Partridge, R; Parua, N; Paterno, M; Patwa, A; Pawlik, B; Perkins, J; Peters, M; Peters, O; Piegaia, R; Piekarz, H; Pope, B G; Popkov, E; Prosper, H B; Protopopescu, S; Qian, J; Quintas, P Z; Raja, R; Rajagopalan, S; Ramberg, E; Rapidis, P A; Reay, N W; Reucroft, S; Rha, J; Rijssenbeek, M; Rockwell, T; Roco, M; Rubinov, P; Ruchti, R; Rutherfoord, J; Santoro, A; Sawyer, L; Schamberger, R D; Schellman, H; Schwartzman, A; Sculli, J; Sen, N; Shabalina, E; Shankar, H C; Shivpuri, R K; Shpakov, D; Shupe, M; Sidwell, R A; Simak, V; Singh, H; Singh, J B; Sirotenko, V; Slattery, P; Smith, E; Smith, R P; Snihur, R; Snow, G R; Snow, J; Snyder, S; Solomon, J; Sorín, V; Sosebee, M; Sotnikova, N; Soustruznik, K; Souza, M; Stanton, N R; Steinbrück, G; Stephens, R W; Stevenson, M L; Stichelbaut, F; Stoker, D; Stolin, V; Stoyanova, D A; Strauss, M; Streets, K; Strovink, M; Stutte, L; Sznajder, A; Taylor, W; Tentindo-Repond, S; Thompson, J; Toback, D; Tripathi, S M; Trippe, T G; Turcot, A S; Tuts, P M; van Gemmeren, P; Vaniev, V; Van Kooten, R; Varelas, N; Volkov, A A; Vorobiev, A P; Wahl, H D; Wang, H; Wang, Z M; Warchol, J; Watts, G; Wayne, M; Weerts, H; White, A; White, J T; Whiteson, D; Wightman, J A; Wijngaarden, D A; Willis, S; Wimpenny, S J; Wirjawan, J V; Womersley, J; Wood, D R; Yamada, R; Yamin, P; Yasuda, T; Yip, K; Youssef, S; Yu, J; Yu, Z; Zanabria, M; Zheng, H; Zhou, Z; Zhu, Z H; Zielinski, M; Zieminska, D; Zieminski, A; Zutshi, V; Zverev, E G; Zylberstejn, A

2001-03-19

The D0 Collaboration has measured the inclusive jet cross section in barpp collisions at square root of s = 630 GeV. The results for pseudorapidities (eta)<0.5 are combined with our previous results at square root of s = 1800 GeV to form a ratio of cross sections with smaller uncertainties than either individual measurement. Next-to-leading-order QCD predictions show excellent agreement with the measurement at 630 GeV; agreement is also satisfactory for the ratio. Specifically, despite a 10% to 15% difference in the absolute magnitude, the dependence of the ratio on jet transverse momentum is very similar for data and theory.

Quality assessment of gasoline using comprehensive two-dimensional gas chromatography combined with unfolded partial least squares: A reliable approach for the detection of gasoline adulteration.

PubMed

Parastar, Hadi; Mostafapour, Sara; Azimi, Gholamhasan

2016-01-01

Comprehensive two-dimensional gas chromatography and flame ionization detection combined with unfolded-partial least squares is proposed as a simple, fast and reliable method to assess the quality of gasoline and to detect its potential adulterants. The data for the calibration set are first baseline corrected using a two-dimensional asymmetric least squares algorithm. The number of significant partial least squares components to build the model is determined using the minimum value of root-mean square error of leave-one out cross validation, which was 4. In this regard, blends of gasoline with kerosene, white spirit and paint thinner as frequently used adulterants are used to make calibration samples. Appropriate statistical parameters of regression coefficient of 0.996-0.998, root-mean square error of prediction of 0.005-0.010 and relative error of prediction of 1.54-3.82% for the calibration set show the reliability of the developed method. In addition, the developed method is externally validated with three samples in validation set (with a relative error of prediction below 10.0%). Finally, to test the applicability of the proposed strategy for the analysis of real samples, five real gasoline samples collected from gas stations are used for this purpose and the gasoline proportions were in range of 70-85%. Also, the relative standard deviations were below 8.5% for different samples in the prediction set. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Least-mean-square spatial filter for IR sensors.

PubMed

Takken, E H; Friedman, D; Milton, A F; Nitzberg, R

1979-12-15

A new least-mean-square filter is defined for signal-detection problems. The technique is proposed for scanning IR surveillance systems operating in poorly characterized but primarily low-frequency clutter interference. Near-optimal detection of point-source targets is predicted both for continuous-time and sampled-data systems.

Changes in the mean square charge radii and electromagnetic moments of neutron-deficient Bi isotopes

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

Barzakh, A. E., E-mail: barzakh@mail.ru; Batist, L. Kh.; Fedorov, D. V.

In-source laser spectroscopy experiments for neutron deficient bismuth isotopes at the 306.77 nm atomic transition were carried out at the IRIS (Investigation of Radioactive Isotopes on Synchrocyclotron) facility of Petersburg Nuclear Physics Institute (PNPI). New data on isotope shifts and hyperfine structure for {sup 189–198,} {sup 211}Bi isotopes and isomers were obtained. The changes in the mean-square charge radii and the magnetic moment values were deduced. Marked deviation from the nearly spherical behavior for ground states of bismuth isotopes at N < 109 is demonstrated, in contrast to the lead and thallium isotopic chains. The big isomer shift between Imore » = 1/2 (intruder) and I = 9/2 (normal) states for odd Bi isotopes (A = 193, 195, 197) was found.« less

Association of auricular pressing and heart rate variability in pre-exam anxiety students.

PubMed

Wu, Wocao; Chen, Junqi; Zhen, Erchuan; Huang, Huanlin; Zhang, Pei; Wang, Jiao; Ou, Yingyi; Huang, Yong

2013-03-25

A total of 30 students scoring between 12 and 20 on the Test Anxiety Scale who had been exhibiting an anxious state > 24 hours, and 30 normal control students were recruited. Indices of heart rate variability were recorded using an Actiheart electrocardiogram recorder at 10 minutes before auricular pressing, in the first half of stimulation and in the second half of stimulation. The results revealed that the standard deviation of all normal to normal intervals and the root mean square of standard deviation of normal to normal intervals were significantly increased after stimulation. The heart rate variability triangular index, very-low-frequency power, low-frequency power, and the ratio of low-frequency to high-frequency power were increased to different degrees after stimulation. Compared with normal controls, the root mean square of standard deviation of normal to normal intervals was significantly increased in anxious students following auricular pressing. These results indicated that auricular pressing can elevate heart rate variability, especially the root mean square of standard deviation of normal to normal intervals in students with pre-exam anxiety.

Association of auricular pressing and heart rate variability in pre-exam anxiety students

PubMed Central

Wu, Wocao; Chen, Junqi; Zhen, Erchuan; Huang, Huanlin; Zhang, Pei; Wang, Jiao; Ou, Yingyi; Huang, Yong

2013-01-01

A total of 30 students scoring between 12 and 20 on the Test Anxiety Scale who had been exhibiting an anxious state > 24 hours, and 30 normal control students were recruited. Indices of heart rate variability were recorded using an Actiheart electrocardiogram recorder at 10 minutes before auricular pressing, in the first half of stimulation and in the second half of stimulation. The results revealed that the standard deviation of all normal to normal intervals and the root mean square of standard deviation of normal to normal intervals were significantly increased after stimulation. The heart rate variability triangular index, very-low-frequency power, low-frequency power, and the ratio of low-frequency to high-frequency power were increased to different degrees after stimulation. Compared with normal controls, the root mean square of standard deviation of normal to normal intervals was significantly increased in anxious students following auricular pressing. These results indicated that auricular pressing can elevate heart rate variability, especially the root mean square of standard deviation of normal to normal intervals in students with pre-exam anxiety. PMID:25206734

Closed-form confidence intervals for functions of the normal mean and standard deviation.

PubMed

Donner, Allan; Zou, G Y

2012-08-01

Confidence interval methods for a normal mean and standard deviation are well known and simple to apply. However, the same cannot be said for important functions of these parameters. These functions include the normal distribution percentiles, the Bland-Altman limits of agreement, the coefficient of variation and Cohen's effect size. We present a simple approach to this problem by using variance estimates recovered from confidence limits computed for the mean and standard deviation separately. All resulting confidence intervals have closed forms. Simulation results demonstrate that this approach performs very well for limits of agreement, coefficients of variation and their differences.

Smoothness of In vivo Spectral Baseline Determined by Mean Squared Error

PubMed Central

Zhang, Yan; Shen, Jun

2013-01-01

Purpose A nonparametric smooth line is usually added to spectral model to account for background signals in vivo magnetic resonance spectroscopy (MRS). The assumed smoothness of the baseline significantly influences quantitative spectral fitting. In this paper, a method is proposed to minimize baseline influences on estimated spectral parameters. Methods In this paper, the non-parametric baseline function with a given smoothness was treated as a function of spectral parameters. Its uncertainty was measured by root-mean-squared error (RMSE). The proposed method was demonstrated with a simulated spectrum and in vivo spectra of both short echo time (TE) and averaged echo times. The estimated in vivo baselines were compared with the metabolite-nulled spectra, and the LCModel-estimated baselines. The accuracies of estimated baseline and metabolite concentrations were further verified by cross-validation. Results An optimal smoothness condition was found that led to the minimal baseline RMSE. In this condition, the best fit was balanced against minimal baseline influences on metabolite concentration estimates. Conclusion Baseline RMSE can be used to indicate estimated baseline uncertainties and serve as the criterion for determining the baseline smoothness of in vivo MRS. PMID:24259436

Detection of novel coupled mutations in the katG gene (His276Met, Gln295His and Ser315Thr) in a multidrug-resistant Mycobacterium tuberculosis strain from Chennai, India, and insight into the molecular mechanism of isoniazid resistance using structural bioinformatics approaches.

PubMed

Ramasubban, Gayathri; Therese, Kulandai Lily; Vetrivel, Umashankar; Sivashanmugam, Muthukumaran; Rajan, Parvathy; Sridhar, R; Madhavan, Hajib N; Meenakshi, N

2011-04-01

This study reports on the structural basis of drug resistance targeting the katG gene in a multidrug-resistant Mycobacterium tuberculosis (MDR-TB) strain with two novel mutations (His276Met and Gln295His) in addition to the most commonly reported mutation (Ser315Thr). A structural bioinformatics approach was used to predict the structure of the mutant KatG enzyme (MT). Subsequent molecular dynamics and docking studies were performed to explain the mechanism of isoniazid (INH) resistance. The results show significant conformational changes in the structure of MT leading to a change in INH binding residues at the active site, with a significant increase in the inhibition constant (Ki) of 5.67 μm in the mutant KatG-isoniazid complex (MT-INH) compared with the wild-type KatG-isoniazid complex (WT-INH). In the case of molecular dynamics studies, root mean square deviation (RMSD) analysis of the protein backbone in simulated biological conditions revealed an unstable trajectory with higher deviations in MT throughout the simulation process (1 ns). Moreover, root mean square fluctuation (RMSF) analysis revealed an overall increase in residual fluctuations in MT compared with the wild-type KatG enzyme (WT), whilst the INH binding residues of MT showed a decreased fluctuation that can be observed as peak deviations. Hence, the present study suggests that His276Met, Gln295His and Ser315Thr mutations targeting the katG gene result in decreased stability and flexibility of the protein at INH binding residues leading to impaired enzyme function. Copyright © 2010 Elsevier B.V. and the International Society of Chemotherapy. All rights reserved.

Ex Vivo Comparison of Mtwo and RaCe Rotary File Systems in Root Canal Deviation: One File Only versus the Conventional Method.

PubMed

Aminsobhani, Mohsen; Razmi, Hasan; Nozari, Solmaz

2015-07-01

Cleaning and shaping of the root canal system is an important step in endodontic therapy. New instruments incorporate new preparation techniques that can improve the efficacy of cleaning and shaping. The aim of this study was to compare the efficacy of Mtwo and RaCe rotary file systems in straightening the canal curvature using only one file or the conventional method. Sixty mesial roots of extracted human mandibular molars were prepared by RaCe and Mtwo nickel-titanium (NiTi) rotary files using the conventional and only one rotary file methods. The working length was 18 mm and the curvatures of the root canals were between 15-45°. By superimposing x-ray images before and after the instrumentation, deviation of the canals was assessed using Adobe Photoshop CS3 software. Preparation time was recorded. Data were analyzed using three-way ANOVA and Tukey's post hoc test. There were no significant differences between RaCe and Mtwo or between the two root canal preparation methods in root canal deviation in buccolingual and mesiodistal radiographs (P>0.05). Changes of root canal curvature in >35° subgroups were significantly more than in other subgroups with smaller canal curvatures. Preparation time was shorter in one file only technique. According to the results, the two rotary systems and the two root canal preparation methods had equal efficacy in straightening the canals; but the preparation time was shorter in one file only group.

Optimization of Protein Backbone Dihedral Angles by Means of Hamiltonian Reweighting

PubMed Central

2016-01-01

Molecular dynamics simulations depend critically on the accuracy of the underlying force fields in properly representing biomolecules. Hence, it is crucial to validate the force-field parameter sets in this respect. In the context of the GROMOS force field, this is usually achieved by comparing simulation data to experimental observables for small molecules. In this study, we develop new amino acid backbone dihedral angle potential energy parameters based on the widely used 54A7 parameter set by matching to experimental J values and secondary structure propensity scales. In order to find the most appropriate backbone parameters, close to 100 000 different combinations of parameters have been screened. However, since the sheer number of combinations considered prohibits actual molecular dynamics simulations for each of them, we instead predicted the values for every combination using Hamiltonian reweighting. While the original 54A7 parameter set fails to reproduce the experimental data, we are able to provide parameters that match significantly better. However, to ensure applicability in the context of larger peptides and full proteins, further studies have to be undertaken. PMID:27559757

Simulation-based estimation of mean and standard deviation for meta-analysis via Approximate Bayesian Computation (ABC).

PubMed

Kwon, Deukwoo; Reis, Isildinha M

2015-08-12

When conducting a meta-analysis of a continuous outcome, estimated means and standard deviations from the selected studies are required in order to obtain an overall estimate of the mean effect and its confidence interval. If these quantities are not directly reported in the publications, they must be estimated from other reported summary statistics, such as the median, the minimum, the maximum, and quartiles. We propose a simulation-based estimation approach using the Approximate Bayesian Computation (ABC) technique for estimating mean and standard deviation based on various sets of summary statistics found in published studies. We conduct a simulation study to compare the proposed ABC method with the existing methods of Hozo et al. (2005), Bland (2015), and Wan et al. (2014). In the estimation of the standard deviation, our ABC method performs better than the other methods when data are generated from skewed or heavy-tailed distributions. The corresponding average relative error (ARE) approaches zero as sample size increases. In data generated from the normal distribution, our ABC performs well. However, the Wan et al. method is best for estimating standard deviation under normal distribution. In the estimation of the mean, our ABC method is best regardless of assumed distribution. ABC is a flexible method for estimating the study-specific mean and standard deviation for meta-analysis, especially with underlying skewed or heavy-tailed distributions. The ABC method can be applied using other reported summary statistics such as the posterior mean and 95 % credible interval when Bayesian analysis has been employed.

Collinearity in Least-Squares Analysis

ERIC Educational Resources Information Center

de Levie, Robert

2012-01-01

How useful are the standard deviations per se, and how reliable are results derived from several least-squares coefficients and their associated standard deviations? When the output parameters obtained from a least-squares analysis are mutually independent, as is often assumed, they are reliable estimators of imprecision and so are the functions…

Mean square cordial labelling related to some acyclic graphs and its rough approximations

NASA Astrophysics Data System (ADS)

Dhanalakshmi, S.; Parvathi, N.

2018-04-01

In this paper we investigate that the path Pn, comb graph Pn⊙K1, n-centipede graph,centipede graph (n,2) and star Sn admits mean square cordial labeling. Also we proved that the induced sub graph obtained by the upper approximation of any sub graph H of the above acyclic graphs admits mean square cordial labeling.

Dictionary Learning on the Manifold of Square Root Densities and Application to Reconstruction of Diffusion Propagator Fields*

PubMed Central

Sun, Jiaqi; Xie, Yuchen; Ye, Wenxing; Ho, Jeffrey; Entezari, Alireza; Blackband, Stephen J.

2013-01-01

In this paper, we present a novel dictionary learning framework for data lying on the manifold of square root densities and apply it to the reconstruction of diffusion propagator (DP) fields given a multi-shell diffusion MRI data set. Unlike most of the existing dictionary learning algorithms which rely on the assumption that the data points are vectors in some Euclidean space, our dictionary learning algorithm is designed to incorporate the intrinsic geometric structure of manifolds and performs better than traditional dictionary learning approaches when applied to data lying on the manifold of square root densities. Non-negativity as well as smoothness across the whole field of the reconstructed DPs is guaranteed in our approach. We demonstrate the advantage of our approach by comparing it with an existing dictionary based reconstruction method on synthetic and real multi-shell MRI data. PMID:24684004

Impact of deglycosylation and thermal stress on conformational stability of a full length murine IgG2a monoclonal antibody: observations from molecular dynamics simulations.

PubMed

Wang, Xiaoling; Kumar, Sandeep; Buck, Patrick M; Singh, Satish K

2013-03-01

With the rise of antibody based therapeutics as successful medicines, there is an emerging need to understand the fundamental antibody conformational dynamics and its implications towards stability of these medicines. Both deglycosylation and thermal stress have been shown to cause conformational destabilization and aggregation in monoclonal antibodies. Here, we study instabilities caused by deglycosylation and by elevated temperature (400 K) by performing molecular dynamic simulations on a full length murine IgG2a mAb whose crystal structure is available in the Protein Data bank. C(α)-atom root mean square deviation and backbone root mean square fluctuation calculations show that deglycosylation perturbs quaternary and tertiary structures in the C(H) 2 domains. In contrast, thermal stress pervades throughout the antibody structure and both Fabs and Fc regions are destabilized. The thermal stress applied in this study was not sufficient to cause large scale unfolding within the simulation time and most amino acid residues showed similar average solvent accessible surface area and secondary structural conformations in all trajectories. C(H) 3 domains were the most successful at resisting the conformational destabilization. The simulations helped identify aggregation prone regions, which may initiate cross-β motif formation upon deglycosylation and upon applying thermal stress. Deglycosylation leads to increased backbone fluctuations and solvent exposure of a highly conserved APR located in the edge β-strand A of the C(H) 2 domains. Aggregation upon thermal stress is most likely initiated by two APRs that overlap with the complementarity determining regions. This study has important implications for rational design of antibody based therapeutics that are resistant towards aggregation. Copyright © 2012 Wiley Periodicals, Inc.

Ex Vivo Comparison of Mtwo and RaCe Rotary File Systems in Root Canal Deviation: One File Only versus the Conventional Method

PubMed Central

Aminsobhani, Mohsen; Nozari, Solmaz

2015-01-01

Objectives: Cleaning and shaping of the root canal system is an important step in endodontic therapy. New instruments incorporate new preparation techniques that can improve the efficacy of cleaning and shaping. The aim of this study was to compare the efficacy of Mtwo and RaCe rotary file systems in straightening the canal curvature using only one file or the conventional method. Materials and Methods: Sixty mesial roots of extracted human mandibular molars were prepared by RaCe and Mtwo nickel-titanium (NiTi) rotary files using the conventional and only one rotary file methods. The working length was 18 mm and the curvatures of the root canals were between 15–45°. By superimposing x-ray images before and after the instrumentation, deviation of the canals was assessed using Adobe Photoshop CS3 software. Preparation time was recorded. Data were analyzed using three-way ANOVA and Tukey’s post hoc test. Results: There were no significant differences between RaCe and Mtwo or between the two root canal preparation methods in root canal deviation in buccolingual and mesiodistal radiographs (P>0.05). Changes of root canal curvature in >35° subgroups were significantly more than in other subgroups with smaller canal curvatures. Preparation time was shorter in one file only technique. Conclusion: According to the results, the two rotary systems and the two root canal preparation methods had equal efficacy in straightening the canals; but the preparation time was shorter in one file only group. PMID:26877736

Mean-square state and parameter estimation for stochastic linear systems with Gaussian and Poisson noises

NASA Astrophysics Data System (ADS)

Basin, M.; Maldonado, J. J.; Zendejo, O.

2016-07-01

This paper proposes new mean-square filter and parameter estimator design for linear stochastic systems with unknown parameters over linear observations, where unknown parameters are considered as combinations of Gaussian and Poisson white noises. The problem is treated by reducing the original problem to a filtering problem for an extended state vector that includes parameters as additional states, modelled as combinations of independent Gaussian and Poisson processes. The solution to this filtering problem is based on the mean-square filtering equations for incompletely polynomial states confused with Gaussian and Poisson noises over linear observations. The resulting mean-square filter serves as an identifier for the unknown parameters. Finally, a simulation example shows effectiveness of the proposed mean-square filter and parameter estimator.

Estimating the sample mean and standard deviation from the sample size, median, range and/or interquartile range.

PubMed

Wan, Xiang; Wang, Wenqian; Liu, Jiming; Tong, Tiejun

2014-12-19

In systematic reviews and meta-analysis, researchers often pool the results of the sample mean and standard deviation from a set of similar clinical trials. A number of the trials, however, reported the study using the median, the minimum and maximum values, and/or the first and third quartiles. Hence, in order to combine results, one may have to estimate the sample mean and standard deviation for such trials. In this paper, we propose to improve the existing literature in several directions. First, we show that the sample standard deviation estimation in Hozo et al.'s method (BMC Med Res Methodol 5:13, 2005) has some serious limitations and is always less satisfactory in practice. Inspired by this, we propose a new estimation method by incorporating the sample size. Second, we systematically study the sample mean and standard deviation estimation problem under several other interesting settings where the interquartile range is also available for the trials. We demonstrate the performance of the proposed methods through simulation studies for the three frequently encountered scenarios, respectively. For the first two scenarios, our method greatly improves existing methods and provides a nearly unbiased estimate of the true sample standard deviation for normal data and a slightly biased estimate for skewed data. For the third scenario, our method still performs very well for both normal data and skewed data. Furthermore, we compare the estimators of the sample mean and standard deviation under all three scenarios and present some suggestions on which scenario is preferred in real-world applications. In this paper, we discuss different approximation methods in the estimation of the sample mean and standard deviation and propose some new estimation methods to improve the existing literature. We conclude our work with a summary table (an Excel spread sheet including all formulas) that serves as a comprehensive guidance for performing meta-analysis in different

Computing daily mean streamflow at ungaged locations in Iowa by using the Flow Anywhere and Flow Duration Curve Transfer statistical methods

USGS Publications Warehouse

Linhart, S. Mike; Nania, Jon F.; Sanders, Curtis L.; Archfield, Stacey A.

2012-01-01

error ranged from 13.0 to 5.3 percent. Root-mean-square-error observations standard-deviation-ratio values ranged from 0.80 to 0.40. Percent-bias values ranged from 25.4 to 4.0 percent. Untransformed streamflow Nash-Sutcliffe efficiency values ranged from 0.84 to 0.35. The logarithm (base 10) streamflow Nash-Sutcliffe efficiency values ranged from 0.86 to 0.56. For the streamgage with the best agreement between observed and estimated streamflow, higher streamflows appear to be underestimated. For the streamgage with the worst agreement between observed and estimated streamflow, low flows appear to be overestimated whereas higher flows seem to be underestimated. Estimated cumulative streamflows for the period October 1, 2004, to September 30, 2009, are underestimated by -25.8 and -7.4 percent for the closest and poorest comparisons, respectively. For the Flow Duration Curve Transfer method, results of the validation study conducted by using the same six streamgages show that differences between the root-mean-square error and the mean absolute error ranged from 437 to 93.9 ft3/s, with the larger value signifying a greater occurrence of outliers between observed and estimated streamflows. Root-mean-square-error values ranged from 906 to 169 ft3/s. Values of the percent root-mean-square-error ranged from 67.0 to 25.6 percent. The logarithm (base 10) streamflow percent root-mean-square error ranged from 12.5 to 4.4 percent. Root-mean-square-error observations standard-deviation-ratio values ranged from 0.79 to 0.40. Percent-bias values ranged from 22.7 to 0.94 percent. Untransformed streamflow Nash-Sutcliffe efficiency values ranged from 0.84 to 0.38. The logarithm (base 10) streamflow Nash-Sutcliffe efficiency values ranged from 0.89 to 0.48. For the streamgage with the closest agreement between observed and estimated streamflow, there is relatively good agreement between observed and estimated streamflows. For the streamgage with the poorest agreement between observed and

Variable forgetting factor mechanisms for diffusion recursive least squares algorithm in sensor networks

NASA Astrophysics Data System (ADS)

Zhang, Ling; Cai, Yunlong; Li, Chunguang; de Lamare, Rodrigo C.

2017-12-01

In this work, we present low-complexity variable forgetting factor (VFF) techniques for diffusion recursive least squares (DRLS) algorithms. Particularly, we propose low-complexity VFF-DRLS algorithms for distributed parameter and spectrum estimation in sensor networks. For the proposed algorithms, they can adjust the forgetting factor automatically according to the posteriori error signal. We develop detailed analyses in terms of mean and mean square performance for the proposed algorithms and derive mathematical expressions for the mean square deviation (MSD) and the excess mean square error (EMSE). The simulation results show that the proposed low-complexity VFF-DRLS algorithms achieve superior performance to the existing DRLS algorithm with fixed forgetting factor when applied to scenarios of distributed parameter and spectrum estimation. Besides, the simulation results also demonstrate a good match for our proposed analytical expressions.

Search for the production of scalar bottom quarks in pp collisions at square root(s) = 1.96 TeV.

PubMed

Aaltonen, T; Adelman, J; Alvarez González, B; Amerio, S; Amidei, D; Anastassov, A; Annovi, A; Antos, J; Apollinari, G; Apresyan, A; Arisawa, T; Artikov, A; Asaadi, J; Ashmanskas, W; Attal, A; Aurisano, A; Azfar, F; Badgett, W; Barbaro-Galtieri, A; Barnes, V E; Barnett, B A; Barria, P; Bartos, P; Bauer, G; Beauchemin, P-H; Bedeschi, F; Beecher, D; Behari, S; Bellettini, G; Bellinger, J; Benjamin, D; Beretvas, A; Bhatti, A; Binkley, M; Bisello, D; Bizjak, I; Blair, R E; Blocker, C; Blumenfeld, B; Bocci, A; Bodek, A; Boisvert, V; Bortoletto, D; Boudreau, J; Boveia, A; Brau, B; Bridgeman, A; Brigliadori, L; Bromberg, C; Brubaker, E; Budagov, J; Budd, H S; Budd, S; Burkett, K; Busetto, G; Bussey, P; Buzatu, A; Byrum, K L; Cabrera, S; Calancha, C; Camarda, S; Campanelli, M; Campbell, M; Canelli, F; Canepa, A; Carls, B; Carlsmith, D; Carosi, R; Carrillo, S; Carron, S; Casal, B; Casarsa, M; Castro, A; Catastini, P; Cauz, D; Cavaliere, V; Cavalli-Sforza, M; Cerri, A; Cerrito, L; Chang, S H; Chen, Y C; Chertok, M; Chiarelli, G; Chlachidze, G; Chlebana, F; Cho, K; Chokheli, D; Chou, J P; Chung, K; Chung, W H; Chung, Y S; Chwalek, T; Ciobanu, C I; Ciocci, M A; Clark, A; Clark, D; Compostella, G; Convery, M E; Conway, J; Corbo, M; Cordelli, M; Cox, C A; Cox, D J; Crescioli, F; Cuenca Almenar, C; Cuevas, J; Culbertson, R; Cully, J C; Dagenhart, D; Datta, M; Davies, T; de Barbaro, P; De Cecco, S; Deisher, A; De Lorenzo, G; Dell'Orso, M; Deluca, C; Demortier, L; Deng, J; Deninno, M; d'Errico, M; Di Canto, A; di Giovanni, G P; Di Ruzza, B; Dittmann, J R; D'Onofrio, M; Donati, S; Dong, P; Dorigo, T; Dube, S; Ebina, K; Elagin, A; Erbacher, R; Errede, D; Errede, S; Ershaidat, N; Eusebi, R; Fang, H C; Farrington, S; Fedorko, W T; Feild, R G; Feindt, M; Fernandez, J P; Ferrazza, C; Field, R; Flanagan, G; Forrest, R; Frank, M J; Franklin, M; Freeman, J C; Furic, I; Gallinaro, M; Galyardt, J; Garberson, F; Garcia, J E; Garfinkel, A F; Garosi, P; Gerberich, H; Gerdes, D; Gessler, A; Giagu, S; Giakoumopoulou, V; Giannetti, P; Gibson, K; Gimmell, J L; Ginsburg, C M; Giokaris, N; Giordani, M; Giromini, P; Giunta, M; Giurgiu, G; Glagolev, V; Glenzinski, D; Gold, M; Goldschmidt, N; Golossanov, A; Gomez, G; Gomez-Ceballos, G; Goncharov, M; González, O; Gorelov, I; Goshaw, A T; Goulianos, K; Gresele, A; Grinstein, S; Grosso-Pilcher, C; Group, R C; Grundler, U; Guimaraes da Costa, J; Gunay-Unalan, Z; Haber, C; Hahn, S R; Halkiadakis, E; Han, B-Y; Han, J Y; Happacher, F; Hara, K; Hare, D; Hare, M; Harr, R F; Hartz, M; Hatakeyama, K; Hays, C; Heck, M; Heinrich, J; Herndon, M; Heuser, J; Hewamanage, S; Hidas, D; Hill, C S; Hirschbuehl, D; Hocker, A; Hou, S; Houlden, M; Hsu, S-C; Hughes, R E; Hurwitz, M; Husemann, U; Hussein, M; Huston, J; Incandela, J; Introzzi, G; Iori, M; Ivanov, A; James, E; Jang, D; Jayatilaka, B; Jeon, E J; Jha, M K; Jindariani, S; Johnson, W; Jones, M; Joo, K K; Jun, S Y; Jung, J E; Junk, T R; Kamon, T; Kar, D; Karchin, P E; Kato, Y; Kephart, R; Ketchum, W; Keung, J; Khotilovich, V; Kilminster, B; Kim, D H; Kim, H S; Kim, H W; Kim, J E; Kim, M J; Kim, S B; Kim, S H; Kim, Y K; Kimura, N; Kirsch, L; Klimenko, S; Kondo, K; Kong, D J; Konigsberg, J; Korytov, A; Kotwal, A V; Kreps, M; Kroll, J; Krop, D; Krumnack, N; Kruse, M; Krutelyov, V; Kuhr, T; Kulkarni, N P; Kurata, M; Kwang, S; Laasanen, A T; Lami, S; Lammel, S; Lancaster, M; Lander, R L; Lannon, K; Lath, A; Latino, G; Lazzizzera, I; LeCompte, T; Lee, E; Lee, H S; Lee, J S; Lee, S W; Leone, S; Lewis, J D; Lin, C-J; Linacre, J; Lindgren, M; Lipeles, E; Lister, A; Litvintsev, D O; Liu, C; Liu, T; Lockyer, N S; Loginov, A; Lovas, L; Lucchesi, D; Lueck, J; Lujan, P; Lukens, P; Lungu, G; Lys, J; Lysak, R; MacQueen, D; Madrak, R; Maeshima, K; Makhoul, K; Maksimovic, P; Malde, S; Malik, S; Manca, G; Manousakis-Katsikakis, A; Margaroli, F; Marino, C; Marino, C P; Martin, A; Martin, V; Martínez, M; Martínez-Ballarín, R; Mastrandrea, P; Mathis, M; Mattson, M E; Mazzanti, P; McFarland, K S; McIntyre, P; McNulty, R; Mehta, A; Mehtala, P; Menzione, A; Mesropian, C; Miao, T; Mietlicki, D; Miladinovic, N; Miller, R; Mills, C; Milnik, M; Mitra, A; Mitselmakher, G; Miyake, H; Moed, S; Moggi, N; Mondragon, M N; Moon, C S; Moore, R; Morello, M J; Morlock, J; Movilla Fernandez, P; Mülmenstädt, J; Mukherjee, A; Muller, Th; Murat, P; Mussini, M; Nachtman, J; Nagai, Y; Naganoma, J; Nakamura, K; Nakano, I; Napier, A; Nett, J; Neu, C; Neubauer, M S; Neubauer, S; Nielsen, J; Nodulman, L; Norman, M; Norniella, O; Nurse, E; Oakes, L; Oh, S H; Oh, Y D; Oksuzian, I; Okusawa, T; Orava, R; Osterberg, K; Pagan Griso, S; Pagliarone, C; Palencia, E; Papadimitriou, V; Papaikonomou, A; Paramanov, A A; Parks, B; Pashapour, S; Patrick, J; Pauletta, G; Paulini, M; Paus, C; Peiffer, T; Pellett, D E; Penzo, A; Phillips, T J; Piacentino, G; Pianori, E; Pinera, L; Pitts, K; Plager, C; Pondrom, L; Potamianos, K; Poukhov, O; Prokoshin, F; Pronko, A; Ptohos, F; Pueschel, E; Punzi, G; Pursley, J; Rademacker, J; Rahaman, A; Ramakrishnan, V; Ranjan, N; Redondo, I; Renton, P; Renz, M; Rescigno, M; Richter, S; Rimondi, F; Ristori, L; Robson, A; Rodrigo, T; Rodriguez, T; Rogers, E; Rolli, S; Roser, R; Rossi, M; Rossin, R; Roy, P; Ruiz, A; Russ, J; Rusu, V; Rutherford, B; Saarikko, H; Safonov, A; Sakumoto, W K; Santi, L; Sartori, L; Sato, K; Savoy-Navarro, A; Schlabach, P; Schmidt, A; Schmidt, E E; Schmidt, M A; Schmidt, M P; Schmitt, M; Schwarz, T; Scodellaro, L; Scribano, A; Scuri, F; Sedov, A; Seidel, S; Seiya, Y; Semenov, A; Sexton-Kennedy, L; Sforza, F; Sfyrla, A; Shalhout, S Z; Shears, T; Shepard, P F; Shimojima, M; Shiraishi, S; Shochet, M; Shon, Y; Shreyber, I; Simonenko, A; Sinervo, P; Sisakyan, A; Slaughter, A J; Slaunwhite, J; Sliwa, K; Smith, J R; Snider, F D; Snihur, R; Soha, A; Somalwar, S; Sorin, V; Squillacioti, P; Stanitzki, M; St Denis, R; Stelzer, B; Stelzer-Chilton, O; Stentz, D; Strologas, J; Strycker, G L; Suh, J S; Sukhanov, A; Suslov, I; Taffard, A; Takashima, R; Takeuchi, Y; Tanaka, R; Tang, J; Tecchio, M; Teng, P K; Thom, J; Thome, J; Thompson, G A; Thomson, E; Tipton, P; Ttito-Guzmán, P; Tkaczyk, S; Toback, D; Tokar, S; Tollefson, K; Tomura, T; Tonelli, D; Torre, S; Torretta, D; Totaro, P; Tourneur, S; Trovato, M; Tsai, S-Y; Tu, Y; Turini, N; Ukegawa, F; Uozumi, S; van Remortel, N; Varganov, A; Vataga, E; Vázquez, F; Velev, G; Vellidis, C; Vidal, M; Vila, I; Vilar, R; Vogel, M; Volobouev, I; Volpi, G; Wagner, P; Wagner, R G; Wagner, R L; Wagner, W; Wagner-Kuhr, J; Wakisaka, T; Wallny, R; Wang, S M; Warburton, A; Waters, D; Weinberger, M; Weinelt, J; Wester, W C; Whitehouse, B; Whiteson, D; Wicklund, A B; Wicklund, E; Wilbur, S; Williams, G; Williams, H H; Wilson, P; Winer, B L; Wittich, P; Wolbers, S; Wolfe, C; Wolfe, H; Wright, T; Wu, X; Würthwein, F; Yagil, A; Yamamoto, K; Yamaoka, J; Yang, U K; Yang, Y C; Yao, W M; Yeh, G P; Yi, K; Yoh, J; Yorita, K; Yoshida, T; Yu, G B; Yu, I; Yu, S S; Yun, J C; Zanetti, A; Zeng, Y; Zhang, X; Zheng, Y; Zucchelli, S

2010-08-20

We report on a search for direct scalar bottom quark (sbottom) pair production in pp collisions at square root(s) = 1.96 TeV, in events with large missing transverse energy and two jets of hadrons in the final state, where at least one of the jets is required to be identified as originating from a b quark. The study uses a collider detector at Fermilab Run II data sample corresponding to 2.65 fb(-1) of integrated luminosity. The data are in agreement with the standard model. In an R-parity conserving minimal supersymmetric scenario, and assuming that the sbottom decays exclusively into a bottom quark and a neutralino, 95% confidence-level upper limits on the sbottom pair production cross section of 0.1 pb are obtained. For neutralino masses below 70 GeV/c2, sbottom masses up to 230 GeV/c2 are excluded at 95% confidence level.

Spectral combination of spherical gravitational curvature boundary-value problems

NASA Astrophysics Data System (ADS)

PitoÅák, Martin; Eshagh, Mehdi; Šprlák, Michal; Tenzer, Robert; Novák, Pavel

2018-04-01

Four solutions of the spherical gravitational curvature boundary-value problems can be exploited for the determination of the Earth's gravitational potential. In this article we discuss the combination of simulated satellite gravitational curvatures, i.e., components of the third-order gravitational tensor, by merging these solutions using the spectral combination method. For this purpose, integral estimators of biased- and unbiased-types are derived. In numerical studies, we investigate the performance of the developed mathematical models for the gravitational field modelling in the area of Central Europe based on simulated satellite measurements. Firstly, we verify the correctness of the integral estimators for the spectral downward continuation by a closed-loop test. Estimated errors of the combined solution are about eight orders smaller than those from the individual solutions. Secondly, we perform a numerical experiment by considering the Gaussian noise with the standard deviation of 6.5× 10-17 m-1s-2 in the input data at the satellite altitude of 250 km above the mean Earth sphere. This value of standard deviation is equivalent to a signal-to-noise ratio of 10. Superior results with respect to the global geopotential model TIM-r5 are obtained by the spectral downward continuation of the vertical-vertical-vertical component with the standard deviation of 2.104 m2s-2, but the root mean square error is the largest and reaches 9.734 m2s-2. Using the spectral combination of all gravitational curvatures the root mean square error is more than 400 times smaller but the standard deviation reaches 17.234 m2s-2. The combination of more components decreases the root mean square error of the corresponding solutions while the standard deviations of the combined solutions do not improve as compared to the solution from the vertical-vertical-vertical component. The presented method represents a weight mean in the spectral domain that minimizes the root mean square error

An on-line modified least-mean-square algorithm for training neurofuzzy controllers.

PubMed

Tan, Woei Wan

2007-04-01

The problem hindering the use of data-driven modelling methods for training controllers on-line is the lack of control over the amount by which the plant is excited. As the operating schedule determines the information available on-line, the knowledge of the process may degrade if the setpoint remains constant for an extended period. This paper proposes an identification algorithm that alleviates "learning interference" by incorporating fuzzy theory into the normalized least-mean-square update rule. The ability of the proposed methodology to achieve faster learning is examined by employing the algorithm to train a neurofuzzy feedforward controller for controlling a liquid level process. Since the proposed identification strategy has similarities with the normalized least-mean-square update rule and the recursive least-square estimator, the on-line learning rates of these algorithms are also compared.

Elastic Backbone Defines a New Transition in the Percolation Model

NASA Astrophysics Data System (ADS)

Sampaio Filho, Cesar I. N.; Andrade, José S.; Herrmann, Hans J.; Moreira, André A.

2018-04-01

The elastic backbone is the set of all shortest paths. We found a new phase transition at peb above the classical percolation threshold at which the elastic backbone becomes dense. At this transition in 2D, its fractal dimension is 1.750 ±0.003 , and one obtains a novel set of critical exponents βeb=0.50 ±0.02 , γeb=1.97 ±0.05 , and νeb=2.00 ±0.02 , fulfilling consistent critical scaling laws. Interestingly, however, the hyperscaling relation is violated. Using Binder's cumulant, we determine, with high precision, the critical probabilities peb for the triangular and tilted square lattice for site and bond percolation. This transition describes a sudden rigidification as a function of density when stretching a damaged tissue.

SU-G-BRC-17: Using Generalized Mean for Equivalent Square Estimation

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

Zhou, S; Fan, Q; Lei, Y

Purpose: Equivalent Square (ES) is a widely used concept in radiotherapy. It enables us to determine many important quantities for a rectangular treatment field, without measurement, based on the corresponding values from its ES field. In this study, we propose a Generalized Mean (GM) type ES formula and compare it with other established formulae using benchmark datasets. Methods: Our GM approach is expressed as ES=(w•fx^α+(1-w)•fy^α)^(1/α), where fx, fy, α, and w represent field sizes, power index, and a weighting factor, respectively. When α=−1 it reduces to well-known Sterling type ES formulae. In our study, α and w are determined throughmore » least-square-fitting. Akaike Information Criterion (AIC) was used to benchmark the performance of each formula. BJR (Supplement 17) ES field table for X-ray PDDs and open field output factor tables in Varian TrueBeam representative dataset were used for validation. Results: Switching from α=−1 to α=−1.25, a 20% reduction in standard deviation of residual error in ES estimation was achieved for the BJR dataset. The maximum relative residual error was reduced from ∼3% (in Sterling formula) or ∼2% (in Vadash/Bjarngard formula) down to ∼1% in GM formula for open fields of all energies and at rectangular field sizes from 3cm to 40cm in the Varian dataset. The improvement of the GM over the Sterling type ES formulae is particularly noticeable for very elongated rectangular fields with short width. AIC analysis confirmed the superior performance of the GM formula after taking into account the expanded parameter space. Conclusion: The GM significantly outperforms Sterling type formulae at slightly increased computational cost. The GM calculation may nullify the requirement of data measurement for many rectangular fields and hence shorten the Linac commissioning process. Improved dose calculation accuracy is also expected by adopting the GM formula into treatment planning and secondary MU check systems.« less

Reification in the Learning of Square Roots in a Ninth Grade Classroom: Combining Semiotic and Discursive Approaches

ERIC Educational Resources Information Center

Shinno, Yusuke

2018-01-01

This paper reports on combining semiotic and discursive approaches to reification in classroom interactions. It focuses on the discursive characteristics and semiotic processes involved in the teaching and learning of square roots in a ninth grade classroom in Japan. The purpose of this study is to characterize the development of mathematical…

SUPPLEMENTARY COMPARISON: EUROMET.L-S10 Comparison of squareness measurements

NASA Astrophysics Data System (ADS)

Mokros, Jiri

2005-01-01

from the weighted mean of data from participating laboratories, while some of them were excluded on the basis of statistical evaluation. Graphical interpretations of all deviations are contained in the Final Report. In order to compare the individual deviations mutually (25 profiles for the granite square and 44 profiles for the cylinder), graphical illustrations of 'standard deviations' and both extreme values (max. and min.) of deviations were created. This regional supplementary comparison has provided independent information about the metrological properties of the measuring equipment and method used by the participating NMIs. The Final Report does not contain the En values. Participants could not estimate some contributions in the uncertainty budget on the basis of previous comparisons, since no comparison of this kind had ever been organized. Therefore the En value cannot reflect the actual state of the given NMI. Instead of En, an analysis has been performed by means of the Grubbs test according to ISO 5725-2. This comparison provided information about the state of provision of metrological services in the field of big squares measurement. Main text. To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/. The final report has been peer-reviewed and approved for publication by EUROMET, according to the provisions of the Mutual Recognition Arrangement (MRA).

The Mean Life Squared Relationship for Abundances of Extinct Radioactivities

NASA Technical Reports Server (NTRS)

Lodders, K.; Cameron, A. G. W.

2004-01-01

We discovered that the abundances of now extinct radioactivities (relative to stable reference isotopes) in meteorites vary as a function of their mean lifetimes squared. This relationship applies to chondrites, achondrites, and irons but to calcium-aluminum inclusions (CAIs). Certain meteorites contain excesses in isotopic abundances from the decay of radioactive isotopes with half-lives much less than the age of the solar system. These short-lived radioactivities are now extinct, but they were alive when meteorites assembled in the early solar system. The origin of these radioactivities and the processes which control their abundances in the solar nebula are still not well understood. Some clues may come from our finding that the meteoritic abundances of now extinct radioactivities (relative to stable reference isotopes) vary as a function of their mean lifetimes squared. This relationship applies to chondrites, achondrites, and irons, but not to CAIs. This points to at least two different processes establishing the abundances of short-lived isotopes found in the meteoritic record.

Precision of intraoral digital dental impressions with iTero and extraoral digitization with the iTero and a model scanner.

PubMed

Flügge, Tabea V; Schlager, Stefan; Nelson, Katja; Nahles, Susanne; Metzger, Marc C

2013-09-01

Digital impression devices are used alternatively to conventional impression techniques and materials. The aims of this study were to evaluate the precision of digital intraoral scanning under clinical conditions (iTero; Align Technologies, San Jose, Calif) and to compare it with the precision of extraoral digitization. One patient received 10 full-arch intraoral scans with the iTero and conventional impressions with a polyether impression material (Impregum Penta; 3M ESPE, Seefeld, Germany). Stone cast models manufactured from the impressions were digitized 10 times with an extraoral scanner (D250; 3Shape, Copenhagen, Denmark) and 10 times with the iTero. Virtual models provided by each method were roughly aligned, and the model edges were trimmed with cutting planes to create common borders (Rapidform XOR; Inus Technologies, Seoul, Korea). A second model alignment was then performed along the closest distances of the surfaces (Artec Studio software; Artec Group, Luxembourg, Luxembourg). To assess precision, deviations between corresponding models were compared. Repeated intraoral scanning was evaluated in group 1, repeated extraoral model scanning with the iTero was assessed in group 2, and repeated model scanning with the D250 was assessed in group 3. Deviations between models were measured and expressed as maximums, means, medians, and root mean square errors for quantitative analysis. Color-coded displays of the deviations allowed qualitative visualization of the deviations. The greatest deviations and therefore the lowest precision were in group 1, with mean deviations of 50 μm, median deviations of 37 μm, and root mean square errors of 73 μm. Group 2 showed a higher precision, with mean deviations of 25 μm, median deviations of 18 μm, and root mean square errors of 51 μm. Scanning with the D250 had the highest precision, with mean deviations of 10 μm, median deviations of 5 μm, and root mean square errors of 20 μm. Intraoral and extraoral scanning

Sea surface mean square slope from Ku-band backscatter data

NASA Technical Reports Server (NTRS)

Jackson, F. C.; Walton, W. T.; Hines, D. E.; Walter, B. A.; Peng, C. Y.

1992-01-01

A surface mean-square-slope parameter analysis is conducted for 14-GHz airborne radar altimeter near-nadir, quasi-specular backscatter data, which in raw form obtained by least-squares fitting of an optical scattering model to the return waveform show an approximately linear dependence over the 7-15 m/sec wind speed range. Slope data are used to draw inferences on the structure of the high-wavenumber portion of the spectrum. A directionally-integrated model height spectrum that encompasses wind speed-dependent k exp -5/2 and classical Phillips k exp -3 power laws subranges in the range of gravity waves is supported by the data.

Anisotropic mean-square displacements in two-dimensional colloidal crystals of tilted dipoles

NASA Astrophysics Data System (ADS)

Froltsov, V. A.; Likos, C. N.; Löwen, H.; Eisenmann, C.; Gasser, U.; Keim, P.; Maret, G.

2005-03-01

Superparamagnetic colloidal particles confined to a flat horizontal air-water interface in an external magnetic field, which is tilted relative to the interface, form anisotropic two-dimensional crystals resulting from their mutual dipole-dipole interactions. Using real-space experiments and harmonic lattice theory we explore the mean-square displacements of the particles in the directions parallel and perpendicular to the in-plane component of the external magnetic field as a function of the tilt angle. We find that the anisotropy of the mean-square displacement behaves nonmonotonically as a function of the tilt angle and does not correlate with the structural anisotropy of the crystal.

Storage and computationally efficient permutations of factorized covariance and square-root information arrays

NASA Technical Reports Server (NTRS)

Muellerschoen, R. J.

1988-01-01

A unified method to permute vector stored Upper triangular Diagonal factorized covariance and vector stored upper triangular Square Root Information arrays is presented. The method involves cyclic permutation of the rows and columns of the arrays and retriangularization with fast (slow) Givens rotations (reflections). Minimal computation is performed, and a one dimensional scratch array is required. To make the method efficient for large arrays on a virtual memory machine, computations are arranged so as to avoid expensive paging faults. This method is potentially important for processing large volumes of radio metric data in the Deep Space Network.

Fast algorithm for computing a primitive /2 to power p + 1/p-th root of unity in GF/q squared/

NASA Technical Reports Server (NTRS)

Reed, I. S.; Truong, T. K.; Miller, R. L.

1978-01-01

A quick method is described for finding the primitive (2 to power p + 1)p-th root of unity in the Galois field GF(q squared), where q = (2 to power p) - 1 and is known as a Mersenne prime. Determination of this root is necessary to implement complex integer transforms of length (2 to power k) times p over the Galois field, with k varying between 3 and p + 1.

Input Forces Estimation for Nonlinear Systems by Applying a Square-Root Cubature Kalman Filter.

PubMed

Song, Xuegang; Zhang, Yuexin; Liang, Dakai

2017-10-10

This work presents a novel inverse algorithm to estimate time-varying input forces in nonlinear beam systems. With the system parameters determined, the input forces can be estimated in real-time from dynamic responses, which can be used for structural health monitoring. In the process of input forces estimation, the Runge-Kutta fourth-order algorithm was employed to discretize the state equations; a square-root cubature Kalman filter (SRCKF) was employed to suppress white noise; the residual innovation sequences, a priori state estimate, gain matrix, and innovation covariance generated by SRCKF were employed to estimate the magnitude and location of input forces by using a nonlinear estimator. The nonlinear estimator was based on the least squares method. Numerical simulations of a large deflection beam and an experiment of a linear beam constrained by a nonlinear spring were employed. The results demonstrated accuracy of the nonlinear algorithm.

Some Results on Mean Square Error for Factor Score Prediction

ERIC Educational Resources Information Center

Krijnen, Wim P.

2006-01-01

For the confirmatory factor model a series of inequalities is given with respect to the mean square error (MSE) of three main factor score predictors. The eigenvalues of these MSE matrices are a monotonic function of the eigenvalues of the matrix gamma[subscript rho] = theta[superscript 1/2] lambda[subscript rho] 'psi[subscript rho] [superscript…

Application of Partial Least Square (PLS) Analysis on Fluorescence Data of 8-Anilinonaphthalene-1-Sulfonic Acid, a Polarity Dye, for Monitoring Water Adulteration in Ethanol Fuel.

PubMed

Kumar, Keshav; Mishra, Ashok Kumar

2015-07-01

Fluorescence characteristic of 8-anilinonaphthalene-1-sulfonic acid (ANS) in ethanol-water mixture in combination with partial least square (PLS) analysis was used to propose a simple and sensitive analytical procedure for monitoring the adulteration of ethanol by water. The proposed analytical procedure was found to be capable of detecting even small adulteration level of ethanol by water. The robustness of the procedure is evident from the statistical parameters such as square of correlation coefficient (R(2)), root mean square of calibration (RMSEC) and root mean square of prediction (RMSEP) that were found to be well with in the acceptable limits.

Building alternate protein structures using the elastic network model.

PubMed

Yang, Qingyi; Sharp, Kim A

2009-02-15

We describe a method for efficiently generating ensembles of alternate, all-atom protein structures that (a) differ significantly from the starting structure, (b) have good stereochemistry (bonded geometry), and (c) have good steric properties (absence of atomic overlap). The method uses reconstruction from a series of backbone framework structures that are obtained from a modified elastic network model (ENM) by perturbation along low-frequency normal modes. To ensure good quality backbone frameworks, the single force parameter ENM is modified by introducing two more force parameters to characterize the interaction between the consecutive carbon alphas and those within the same secondary structure domain. The relative stiffness of the three parameters is parameterized to reproduce B-factors, while maintaining good bonded geometry. After parameterization, violations of experimental Calpha-Calpha distances and Calpha-Calpha-Calpha pseudo angles along the backbone are reduced to less than 1%. Simultaneously, the average B-factor correlation coefficient improves to R = 0.77. Two applications illustrate the potential of the approach. (1) 102,051 protein backbones spanning a conformational space of 15 A root mean square deviation were generated from 148 nonredundant proteins in the PDB database, and all-atom models with minimal bonded and nonbonded violations were produced from this ensemble of backbone structures using the SCWRL side chain building program. (2) Improved backbone templates for homology modeling. Fifteen query sequences were each modeled on two targets. For each of the 30 target frameworks, dozens of improved templates could be produced In all cases, improved full atom homology models resulted, of which 50% could be identified blind using the D-Fire statistical potential. (c) 2008 Wiley-Liss, Inc.

Robust Mean and Covariance Structure Analysis through Iteratively Reweighted Least Squares.

ERIC Educational Resources Information Center

Yuan, Ke-Hai; Bentler, Peter M.

2000-01-01

Adapts robust schemes to mean and covariance structures, providing an iteratively reweighted least squares approach to robust structural equation modeling. Each case is weighted according to its distance, based on first and second order moments. Test statistics and standard error estimators are given. (SLD)

Entropy-guided switching trimmed mean deviation-boosted anisotropic diffusion filter

NASA Astrophysics Data System (ADS)

Nnolim, Uche A.

2016-07-01

An effective anisotropic diffusion (AD) mean filter variant is proposed for filtering of salt-and-pepper impulse noise. The implemented filter is robust to impulse noise ranging from low to high density levels. The algorithm involves a switching scheme in addition to utilizing the unsymmetric trimmed mean/median deviation to filter image noise while greatly preserving image edges, regardless of impulse noise density (ND). It operates with threshold parameters selected manually or adaptively estimated from the image statistics. It is further combined with the partial differential equations (PDE)-based AD for edge preservation at high NDs to enhance the properties of the trimmed mean filter. Based on experimental results, the proposed filter easily and consistently outperforms the median filter and its other variants ranging from simple to complex filter structures, especially the known PDE-based variants. In addition, the switching scheme and threshold calculation enables the filter to avoid smoothing an uncorrupted image, and filtering is activated only when impulse noise is present. Ultimately, the particular properties of the filter make its combination with the AD algorithm a unique and powerful edge-preservation smoothing filter at high-impulse NDs.

Search for deviations from the inverse square law of gravity at nm range using a pulsed neutron beam

NASA Astrophysics Data System (ADS)

Haddock, Christopher C.; Oi, Noriko; Hirota, Katsuya; Ino, Takashi; Kitaguchi, Masaaki; Matsumoto, Satoru; Mishima, Kenji; Shima, Tatsushi; Shimizu, Hirohiko M.; Snow, W. Michael; Yoshioka, Tamaki

2018-03-01

We describe an experimental search for deviations from the inverse-square law of gravity at the nanometer length scale using neutron scattering from noble gases on a pulsed slow neutron beam line. By measuring the neutron momentum transfer (q ) dependence of the differential cross section for xenon and helium and comparing to their well-known analytical forms, we place an upper bound on the strength of a new interaction as a function of interaction length λ which improves upon previous results in the region λ <0.1 nm , and remains competitive in the larger-λ region. A pseudoexperimental simulation is developed for this experiment and its role in the data analysis is described. We conclude with plans for improving sensitivity in the larger-λ region.

On the relationship between NMR-derived amide order parameters and protein backbone entropy changes

PubMed Central

Sharp, Kim A.; O’Brien, Evan; Kasinath, Vignesh; Wand, A. Joshua

2015-01-01

Molecular dynamics simulations are used to analyze the relationship between NMR-derived squared generalized order parameters of amide NH groups and backbone entropy. Amide order parameters (O2NH) are largely determined by the secondary structure and average values appear unrelated to the overall flexibility of the protein. However, analysis of the more flexible subset (O2NH < 0.8) shows that these report both on the local flexibility of the protein and on a different component of the conformational entropy than that reported by the side chain methyl axis order parameters, O2axis. A calibration curve for backbone entropy vs. O2NH is developed which accounts for both correlations between amide group motions of different residues, and correlations between backbone and side chain motions. This calibration curve can be used with experimental values of O2NH changes obtained by NMR relaxation measurements to extract backbone entropy changes, e.g. upon ligand binding. In conjunction with our previous calibration for side chain entropy derived from measured O2axis values this provides a prescription for determination of the total protein conformational entropy changes from NMR relaxation measurements. PMID:25739366

On the relationship between NMR-derived amide order parameters and protein backbone entropy changes.

PubMed

Sharp, Kim A; O'Brien, Evan; Kasinath, Vignesh; Wand, A Joshua

2015-05-01

Molecular dynamics simulations are used to analyze the relationship between NMR-derived squared generalized order parameters of amide NH groups and backbone entropy. Amide order parameters (O(2) NH ) are largely determined by the secondary structure and average values appear unrelated to the overall flexibility of the protein. However, analysis of the more flexible subset (O(2) NH  < 0.8) shows that these report both on the local flexibility of the protein and on a different component of the conformational entropy than that reported by the side chain methyl axis order parameters, O(2) axis . A calibration curve for backbone entropy vs. O(2) NH is developed, which accounts for both correlations between amide group motions of different residues, and correlations between backbone and side chain motions. This calibration curve can be used with experimental values of O(2) NH changes obtained by NMR relaxation measurements to extract backbone entropy changes, for example, upon ligand binding. In conjunction with our previous calibration for side chain entropy derived from measured O(2) axis values this provides a prescription for determination of the total protein conformational entropy changes from NMR relaxation measurements. © 2015 Wiley Periodicals, Inc.

Study of the convergence behavior of the complex kernel least mean square algorithm.

PubMed

Paul, Thomas K; Ogunfunmi, Tokunbo

2013-09-01

The complex kernel least mean square (CKLMS) algorithm is recently derived and allows for online kernel adaptive learning for complex data. Kernel adaptive methods can be used in finding solutions for neural network and machine learning applications. The derivation of CKLMS involved the development of a modified Wirtinger calculus for Hilbert spaces to obtain the cost function gradient. We analyze the convergence of the CKLMS with different kernel forms for complex data. The expressions obtained enable us to generate theory-predicted mean-square error curves considering the circularity of the complex input signals and their effect on nonlinear learning. Simulations are used for verifying the analysis results.

Protein-Backbone Thermodynamics across the Membrane Interface.

PubMed

Bereau, Tristan; Kremer, Kurt

2016-07-07

The thermodynamics of insertion of a protein in a membrane depends on the fine interplay between backbone and side-chain contributions interacting with the lipid environment. Using computer simulations, we probe how different descriptions of the backbone glycyl unit affect the thermodynamics of insertion of individual residues, dipeptides, and entire transmembrane helices. Due to the lack of reference data, we first introduce an efficient methodology to estimate atomistic potential of mean force (PMF) curves from a series of representative and uncorrelated coarse-grained (CG) snapshots. We find strong discrepancies between two CG models, Martini and PLUM, against reference atomistic PMFs and experiments. Atomistic simulations suggest a weak free energy of insertion between water and a POPC membrane for the glycyl unit, in overall agreement with experimental results despite severe assumptions in our calculations. We show that refining the backbone contribution in PLUM significantly improves the PMF of insertion of the WALP16 transmembrane peptide. An improper balance between the glycyl backbone and the attached side chain will lead to energetic artifacts, rationalizing Martini's overstabilization of WALP's adsorbed interfacial state. It illustrates difficulties associated with free-energy-based parametrizations of single-residue models, as the relevant free energy of partitioning used for force-field parametrization does not arise from the entire residue but rather the solvent-accessible chemical groups.

Plant responses to heterogeneous salinity: growth of the halophyte Atriplex nummularia is determined by the root-weighted mean salinity of the root zone

PubMed Central

Bazihizina, Nadia

2012-01-01

Soil salinity is generally spatially heterogeneous, but our understanding of halophyte physiology under such conditions is limited. The growth and physiology of the dicotyledonous halophyte Atriplex nummularia was evaluated in split-root experiments to test whether growth is determined by: (i) the lowest; (ii) the highest; or (iii) the mean salinity of the root zone. In two experiments, plants were grown with uniform salinities or horizontally heterogeneous salinities (10–450mM NaCl in the low-salt side and 670mM in the high-salt side, or 10mM NaCl in the low-salt side and 500–1500mM in the high-salt side). The combined data showed that growth and gas exchange parameters responded most closely to the root-weighted mean salinity rather than to the lowest, mean, or highest salinity in the root zone. In contrast, midday shoot water potentials were determined by the lowest salinity in the root zone, consistent with most water being taken from the least negative water potential source. With uniform salinity, maximum shoot growth was at 120–230mM NaCl; ~90% of maximum growth occurred at 10mM and 450mM NaCl. Exposure of part of the roots to 1500mM NaCl resulted in an enhanced (+40%) root growth on the low-salt side, which lowered root-weighted mean salinity and enabled the maintenance of shoot growth. Atriplex nummularia grew even with extreme salinity in part of the roots, as long as the root-weighted mean salinity of the root zone was within the 10–450mM range. PMID:23125356

Plant responses to heterogeneous salinity: growth of the halophyte Atriplex nummularia is determined by the root-weighted mean salinity of the root zone.

PubMed

Bazihizina, Nadia; Barrett-Lennard, Edward G; Colmer, Timothy D

2012-11-01

Soil salinity is generally spatially heterogeneous, but our understanding of halophyte physiology under such conditions is limited. The growth and physiology of the dicotyledonous halophyte Atriplex nummularia was evaluated in split-root experiments to test whether growth is determined by: (i) the lowest; (ii) the highest; or (iii) the mean salinity of the root zone. In two experiments, plants were grown with uniform salinities or horizontally heterogeneous salinities (10-450 mM NaCl in the low-salt side and 670 mM in the high-salt side, or 10 mM NaCl in the low-salt side and 500-1500 mM in the high-salt side). The combined data showed that growth and gas exchange parameters responded most closely to the root-weighted mean salinity rather than to the lowest, mean, or highest salinity in the root zone. In contrast, midday shoot water potentials were determined by the lowest salinity in the root zone, consistent with most water being taken from the least negative water potential source. With uniform salinity, maximum shoot growth was at 120-230 mM NaCl; ~90% of maximum growth occurred at 10 mM and 450 mM NaCl. Exposure of part of the roots to 1500 mM NaCl resulted in an enhanced (+40%) root growth on the low-salt side, which lowered root-weighted mean salinity and enabled the maintenance of shoot growth. Atriplex nummularia grew even with extreme salinity in part of the roots, as long as the root-weighted mean salinity of the root zone was within the 10-450 mM range.

The Wording of a Proof: Hardy's Second "Elegant" Proof--The Pythagorean School's Irrationality of Square Root of 2

ERIC Educational Resources Information Center

Padula, Janice

2006-01-01

One of the most interesting and important proofs in the history of mathematics is the Pythagorean school's proof of the "irrationality" of the square root of 2. After a brief look at G. H. Hardy (1941) thoughts regarding it, two versions of the classic Pythagorean proof are examined and discussed in this article, one written by an American…

A compact and accurate semi-global potential energy surface for malonaldehyde from constrained least squares regression

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

Mizukami, Wataru, E-mail: wataru.mizukami@bristol.ac.uk; Tew, David P., E-mail: david.tew@bristol.ac.uk; Habershon, Scott, E-mail: S.Habershon@warwick.ac.uk

2014-10-14

We present a new approach to semi-global potential energy surface fitting that uses the least absolute shrinkage and selection operator (LASSO) constrained least squares procedure to exploit an extremely flexible form for the potential function, while at the same time controlling the risk of overfitting and avoiding the introduction of unphysical features such as divergences or high-frequency oscillations. Drawing from a massively redundant set of overlapping distributed multi-dimensional Gaussian functions of inter-atomic separations we build a compact full-dimensional surface for malonaldehyde, fit to explicitly correlated coupled cluster CCSD(T)(F12*) energies with a root mean square deviations accuracy of 0.3%–0.5% up tomore » 25 000 cm{sup −1} above equilibrium. Importance-sampled diffusion Monte Carlo calculations predict zero point energies for malonaldehyde and its deuterated isotopologue of 14 715.4(2) and 13 997.9(2) cm{sup −1} and hydrogen transfer tunnelling splittings of 21.0(4) and 3.2(4) cm{sup −1}, respectively, which are in excellent agreement with the experimental values of 21.583 and 2.915(4) cm{sup −1}.« less

Search for gluinos and scalar quarks in pp collisions at square root[s] = 1.8 TeV using the missing energy plus multijets signature.

PubMed

Affolder, T; Akimoto, H; Akopian, A; Albrow, M G; Amaral, P; Amidei, D; Anikeev, K; Antos, J; Apollinari, G; Arisawa, T; Artikov, A; Asakawa, T; Ashmanskas, W; Azfar, F; Azzi-Bacchetta, P; Bacchetta, N; Bachacou, H; Bailey, S; de Barbaro, P; Barbaro-Galtieri, A; Barnes, V E; Barnett, B A; Baroiant, S; Barone, M; Bauer, G; Bedeschi, F; Belforte, S; Bell, W H; Bellettini, G; Bellinger, J; Benjamin, D; Bensinger, J; Beretvas, A; Berge, J P; Berryhill, J; Bhatti, A; Binkley, M; Bisello, D; Bishai, M; Blair, R E; Blocker, C; Bloom, K; Blumenfeld, B; Blusk, S R; Bocci, A; Bodek, A; Bokhari, W; Bolla, G; Bonushkin, Y; Bortoletto, D; Boudreau, J; Brandl, A; van den Brink, S; Bromberg, C; Brozovic, M; Brubaker, E; Bruner, N; Buckley-Geer, E; Budagov, J; Budd, H S; Burkett, K; Busetto, G; Byon-Wagner, A; Byrum, K L; Cabrera, S; Calafiura, P; Campbell, M; Carithers, W; Carlson, J; Carlsmith, D; Caskey, W; Castro, A; Cauz, D; Cerri, A; Chan, A W; Chang, P S; Chang, P T; Chapman, J; Chen, C; Chen, Y C; Cheng, M-T; Chertok, M; Chiarelli, G; Chirikov-Zorin, I; Chlachidze, G; Chlebana, F; Christofek, L; Chu, M L; Chung, Y S; Ciobanu, C I; Clark, A G; Connolly, A; Conway, J; Cordelli, M; Cranshaw, J; Cropp, R; Culbertson, R; Dagenhart, D; D'Auria, S; DeJongh, F; Dell'Agnello, S; Dell'Orso, M; Demortier, L; Deninno, M; Derwent, P F; Devlin, T; Dittmann, J R; Dominguez, A; Donati, S; Done, J; D'Onofrio, M; Dorigo, T; Eddy, N; Einsweiler, K; Elias, J E; Engels, E; Erbacher, R; Errede, D; Errede, S; Fan, Q; Feild, R G; Fernandez, J P; Ferretti, C; Field, R D; Fiori, I; Flaugher, B; Foster, G W; Franklin, M; Freeman, J; Friedman, J; Frisch, H J; Fukui, Y; Furic, I; Galeotti, S; Gallas, A; Gallinaro, M; Gao, T; Garcia-Sciveres, M; Garfinkel, A F; Gatti, P; Gay, C; Gerdes, D W; Giannetti, P; Giromini, P; Glagolev, V; Glenzinski, D; Gold, M; Goldstein, J; Gorelov, I; Goshaw, A T; Gotra, Y; Goulianos, K; Green, C; Grim, G; Gris, P; Groer, L; Grosso-Pilcher, C; Guenther, M; Guillian, G; Guimaraes da Costa, J; Haas, R M; Haber, C; Hahn, S R; Hall, C; Handa, T; Handler, R; Hao, W; Happacher, F; Hara, K; Hardman, A D; Harris, R M; Hartmann, F; Hatakeyama, K; Hauser, J; Heinrich, J; Heiss, A; Herndon, M; Hill, C; Hoffman, K D; Holck, C; Hollebeek, R; Holloway, L; Hughes, R; Huston, J; Huth, J; Ikeda, H; Incandela, J; Introzzi, G; Iwai, J; Iwata, Y; James, E; Jones, M; Joshi, U; Kambara, H; Kamon, T; Kaneko, T; Karr, K; Kasha, H; Kato, Y; Keaffaber, T A; Kelley, K; Kelly, M; Kennedy, R D; Kephart, R; Khazins, D; Kikuchi, T; Kilminster, B; Kim, B J; Kim, D H; Kim, H S; Kim, M J; Kim, S B; Kim, S H; Kim, Y K; Kirby, M; Kirk, M; Kirsch, L; Klimenko, S; Koehn, P; Kondo, K; Konigsberg, J; Korn, A; Korytov, A; Kovacs, E; Kroll, J; Kruse, M; Kuhlmann, S E; Kurino, K; Kuwabara, T; Laasanen, A T; Lai, N; Lami, S; Lammel, S; Lancaster, J; Lancaster, M; Lander, R; Lath, A; Latino, G; LeCompte, T; Lee, A M; Lee, K; Leone, S; Lewis, J D; Lindgren, M; Liss, T M; Liu, J B; Liu, Y C; Litvintsev, D O; Lobban, O; Lockyer, N; Loken, J; Loreti, M; Lucchesi, D; Lukens, P; Lusin, S; Lyons, L; Lys, J; Madrak, R; Maeshima, K; Maksimovic, P; Malferrari, L; Mangano, M; Mariotti, M; Martignon, G; Martin, A; Matthews, J A J; Mayer, J; Mazzanti, P; McFarland, K S; McIntyre, P; McKigney, E; Menguzzato, M; Menzione, A; Mesropian, C; Meyer, A; Miao, T; Miller, R; Miller, J S; Minato, H; Miscetti, S; Mishina, M; Mitselmakher, G; Moggi, N; Moore, E; Moore, R; Morita, Y; Moulik, T; Mulhearn, M; Mukherjee, A; Muller, T; Munar, A; Murat, P; Murgia, S; Nachtman, J; Nagaslaev, V; Nahn, S; Nakada, H; Nakano, I; Nelson, C; Nelson, T; Neu, C; Neuberger, D; Newman-Holmes, C; Ngan, C-Y P; Niu, H; Nodulman, L; Nomerotski, A; Oh, S H; Oh, Y D; Ohmoto, T; Ohsugi, T; Oishi, R; Okusawa, T; Olsen, J; Orejudos, W; Pagliarone, C; Palmonari, F; Paoletti, R; Papadimitriou, V; Partos, D; Patrick, J; Pauletta, G; Paulini, M; Paus, C; Pescara, L; Phillips, T J; Piacentino, G; Pitts, K T; Pompos, A; Pondrom, L; Pope, G; Popovic, M; Prokoshin, F; Proudfoot, J; Ptohos, F; Pukhov, O; Punzi, G; Rakitine, A; Ratnikov, F; Reher, D; Reichold, A; Ribon, A; Riegler, W; Rimondi, F; Ristori, L; Riveline, M; Robertson, W J; Robinson, A; Rodrigo, T; Rolli, S; Rosenson, L; Roser, R; Rossin, R; Roy, A; Ruiz, A; Safonov, A; St Denis, R; Sakumoto, W K; Saltzberg, D; Sanchez, C; Sansoni, A; Santi, L; Sato, H; Savard, P; Schlabach, P; Schmidt, E E; Schmidt, M P; Schmitt, M; Scodellaro, L; Scott, A; Scribano, A; Segler, S; Seidel, S; Seiya, Y; Semenov, A; Semeria, F; Shah, T; Shapiro, M D; Shepard, P F; Shibayama, T; Shimojima, M; Shochet, M; Sidoti, A; Siegrist, J; Sill, A; Sinervo, P; Singh, P; Slaughter, A J; Sliwa, K; Smith, C; Snider, F D; Solodsky, A; Spalding, J; Speer, T; Sphicas, P; Spinella, F; Spiropulu, M; Spiegel, L; Steele, J; Stefanini, A; Strologas, J; Strumia, F; Stuart, D; Sumorok, K; Suzuki, T; Takano, T; Takashima, R; Takikawa, K; Tamburello, P; Tanaka, M; Tannenbaum, B; Tecchio, M; Tesarek, R; Teng, P K; Terashi, K; Tether, S; Thompson, A S; Thurman-Keup, R; Tipton, P; Tkaczyk, S; Toback, D; Tollefson, K; Tollestrup, A; Tonelli, D; Toyoda, H; Trischuk, W; de Troconiz, J F; Tseng, J; Turini, N; Ukegawa, F; Vaiciulis, T; Valls, J; Vejcik, S; Velev, G; Veramendi, G; Vidal, R; Vila, I; Vilar, R; Volobouev, I; von der Mey, M; Vucinic, D; Wagner, R G; Wagner, R L; Wallace, N B; Wan, Z; Wang, C; Wang, M J; Ward, B; Waschke, S; Watanabe, T; Waters, D; Watts, T; Webb, R; Wenzel, H; Wester, W C; Wicklund, A B; Wicklund, E; Wilkes, T; Williams, H H; Wilson, P; Winer, B L; Winn, D; Wolbers, S; Wolinski, D; Wolinski, J; Wolinski, S; Worm, S; Wu, X; Wyss, J; Yao, W; Yagil, A; Yeh, G P; Yoh, J; Yosef, C; Yoshida, T; Yu, I; Yu, S; Yu, Z; Zanetti, A; Zetti, F; Zucchelli, S

2002-01-28

We have performed a search for gluinos (g) and scalar quarks (q) in a data sample of 84 pb(-1) of pp collisions at square root[s] = 1.8 TeV, recorded by the Collider Detector at Fermilab. We investigate the final state of large missing transverse energy and three or more jets, a characteristic signature in R-parity-conserving supersymmetric models. The analysis has been performed "blind," in that the inspection of the signal region is made only after the predictions from standard model backgrounds have been calculated. Comparing the data with predictions of constrained supersymmetric models, we exclude gluino masses below 195 GeV/c2 (95% C.L.), independent of the squark mass. For the case m(q) approximately m(g), gluino masses below 300 GeV/c2 are excluded.

Tri-Squared Mean Cross Comparative Analysis: An Advanced Post Hoc Qualitative and Quantitative Metric for a More In-Depth Examination of the Initial Research Outcomes of the Tri-Square Test

ERIC Educational Resources Information Center

Osler, James Edward

2013-01-01

This monograph provides an epistemological rational for the design of an advanced novel analysis metric. The metric is designed to analyze the outcomes of the Tri-Squared Test. This methodology is referred to as: "Tri-Squared Mean Cross Comparative Analysis" (given the acronym TSMCCA). Tri-Squared Mean Cross Comparative Analysis involves…

Triazine-Based Sequence-Defined Polymers with Side-Chain Diversity and Backbone-Backbone Interaction Motifs.

PubMed

Grate, Jay W; Mo, Kai-For; Daily, Michael D

2016-03-14

Sequence control in polymers, well-known in nature, encodes structure and functionality. Here we introduce a new architecture, based on the nucleophilic aromatic substitution chemistry of cyanuric chloride, that creates a new class of sequence-defined polymers dubbed TZPs. Proof of concept is demonstrated with two synthesized hexamers, having neutral and ionizable side chains. Molecular dynamics simulations show backbone-backbone interactions, including H-bonding motifs and pi-pi interactions. This architecture is arguably biomimetic while differing from sequence-defined polymers having peptide bonds. The synthetic methodology supports the structural diversity of side chains known in peptides, as well as backbone-backbone hydrogen-bonding motifs, and will thus enable new macromolecules and materials with useful functions. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Search for Higgs boson production in dilepton and missing energy final states with 5.4 fb(-1) of pp collisions at square root(s) = 1.96 TeV.

PubMed

Abazov, V M; Abbott, B; Abolins, M; Acharya, B S; Adams, M; Adams, T; Aguilo, E; Alexeev, G D; Alkhazov, G; Alton, A; Alverson, G; Alves, G A; Ancu, L S; Aoki, M; Arnoud, Y; Arov, M; Askew, A; Asman, B; Atramentov, O; Avila, C; BackusMayes, J; Badaud, F; Bagby, L; Baldin, B; Bandurin, D V; Banerjee, S; Barberis, E; Barfuss, A-F; Baringer, P; Barreto, J; Bartlett, J F; Bassler, U; Bauer, D; Beale, S; Bean, A; Begalli, M; Begel, M; Belanger-Champagne, C; Bellantoni, L; Benitez, J A; Beri, S B; Bernardi, G; Bernhard, R; Bertram, I; Besançon, M; Beuselinck, R; Bezzubov, V A; Bhat, P C; Bhatnagar, V; Blazey, G; Blessing, S; Bloom, K; Boehnlein, A; Boline, D; Bolton, T A; Boos, E E; Borissov, G; Bose, T; Brandt, A; Brock, R; Brooijmans, G; Bross, A; Brown, D; Bu, X B; Buchholz, D; Buehler, M; Buescher, V; Bunichev, V; Burdin, S; Burnett, T H; Buszello, C P; Calfayan, P; Calpas, B; Calvet, S; Camacho-Pérez, E; Cammin, J; Carrasco-Lizarraga, M A; Carrera, E; Casey, B C K; Castilla-Valdez, H; Chakrabarti, S; Chakraborty, D; Chan, K M; Chandra, A; Cheu, E; Chevalier-Théry, S; Cho, D K; Cho, S W; Choi, S; Choudhary, B; Christoudias, T; Cihangir, S; Claes, D; Clutter, J; Cooke, M; Cooper, W E; Corcoran, M; Couderc, F; Cousinou, M-C; Cutts, D; Cwiok, M; Das, A; Davies, G; De, K; de Jong, S J; De la Cruz-Burelo, E; DeVaughan, K; Déliot, F; Demarteau, M; Demina, R; Denisov, D; Denisov, S P; Desai, S; Diehl, H T; Diesburg, M; Dominguez, A; Dorland, T; Dubey, A; Dudko, L V; Duflot, L; Duggan, D; Duperrin, A; Dutt, S; Dyshkant, A; Eads, M; Edmunds, D; Ellison, J; Elvira, V D; Enari, Y; Eno, S; Evans, H; Evdokimov, A; Evdokimov, V N; Facini, G; Ferapontov, A V; Ferbel, T; Fiedler, F; Filthaut, F; Fisher, W; Fisk, H E; Fortner, M; Fox, H; Fuess, S; Gadfort, T; Galea, C F; Garcia-Bellido, A; Gavrilov, V; Gay, P; Geist, W; Geng, W; Gerbaudo, D; Gerber, C E; Gershtein, Y; Gillberg, D; Ginther, G; Golovanov, G; Gómez, B; Goussiou, A; Grannis, P D; Greder, S; Greenlee, H; Greenwood, Z D; Gregores, E M; Grenier, G; Gris, Ph; Grivaz, J-F; Grohsjean, A; Grünendahl, S; Grünewald, M W; Guo, F; Guo, J; Gutierrez, G; Gutierrez, P; Haas, A; Haefner, P; Hagopian, S; Haley, J; Hall, I; Han, L; Harder, K; Harel, A; Hauptman, J M; Hays, J; Hebbeker, T; Hedin, D; Hegeman, J G; Heinson, A P; Heintz, U; Hensel, C; Heredia-De la Cruz, I; Herner, K; Hesketh, G; Hildreth, M D; Hirosky, R; Hoang, T; Hobbs, J D; Hoeneisen, B; Hohlfeld, M; Hossain, S; Houben, P; Hu, Y; Hubacek, Z; Huske, N; Hynek, V; Iashvili, I; Illingworth, R; Ito, A S; Jabeen, S; Jaffré, M; Jain, S; Jamin, D; Jesik, R; Johns, K; Johnson, C; Johnson, M; Johnston, D; Jonckheere, A; Jonsson, P; Juste, A; Kajfasz, E; Karmanov, D; Kasper, P A; Katsanos, I; Kaushik, V; Kehoe, R; Kermiche, S; Khalatyan, N; Khanov, A; Kharchilava, A; Kharzheev, Y N; Khatidze, D; Kirby, M H; Kirsch, M; Kohli, J M; Kozelov, A V; Kraus, J; Kumar, A; Kupco, A; Kurca, T; Kuzmin, V A; Kvita, J; Lam, D; Lammers, S; Landsberg, G; Lebrun, P; Lee, H S; Lee, W M; Leflat, A; Lellouch, J; Li, L; Li, Q Z; Lietti, S M; Lim, J K; Lincoln, D; Linnemann, J; Lipaev, V V; Lipton, R; Liu, Y; Liu, Z; Lobodenko, A; Lokajicek, M; Love, P; Lubatti, H J; Luna-Garcia, R; Lyon, A L; Maciel, A K A; Mackin, D; Mättig, P; Magaña-Villalba, R; Mal, P K; Malik, S; Malyshev, V L; Maravin, Y; Martínez-Ortega, J; McCarthy, R; McGivern, C L; Meijer, M M; Melnitchouk, A; Mendoza, L; Menezes, D; Mercadante, P G; Merkin, M; Meyer, A; Meyer, J; Mondal, N K; Moulik, T; Muanza, G S; Mulhearn, M; Mundal, O; Mundim, L; Nagy, E; Naimuddin, M; Narain, M; Nayyar, R; Neal, H A; Negret, J P; Neustroev, P; Nilsen, H; Nogima, H; Novaes, S F; Nunnemann, T; Obrant, G; Onoprienko, D; Orduna, J; Osman, N; Osta, J; Otec, R; Otero y Garzón, G J; Owen, M; Padilla, M; Padley, P; Pangilinan, M; Parashar, N; Parihar, V; Park, S-J; Park, S K; Parsons, J; Partridge, R; Parua, N; Patwa, A; Penning, B; Perfilov, M; Peters, K; Peters, Y; Pétroff, P; Piegaia, R; Piper, J; Pleier, M-A; Podesta-Lerma, P L M; Podstavkov, V M; Pol, M-E; Polozov, P; Popov, A V; Prewitt, M; Price, D; Protopopescu, S; Qian, J; Quadt, A; Quinn, B; Rangel, M S; Ranjan, K; Ratoff, P N; Razumov, I; Renkel, P; Rich, P; Rijssenbeek, M; Ripp-Baudot, I; Rizatdinova, F; Robinson, S; Rominsky, M; Royon, C; Rubinov, P; Ruchti, R; Safronov, G; Sajot, G; Sánchez-Hernández, A; Sanders, M P; Sanghi, B; Savage, G; Sawyer, L; Scanlon, T; Schaile, D; Schamberger, R D; Scheglov, Y; Schellman, H; Schliephake, T; Schlobohm, S; Schwanenberger, C; Schwienhorst, R; Sekaric, J; Severini, H; Shabalina, E; Shary, V; Shchukin, A A; Shivpuri, R K; Simak, V; Sirotenko, V; Skubic, P; Slattery, P; Smirnov, D; Snow, G R; Snow, J; Snyder, S; Söldner-Rembold, S; Sonnenschein, L; Sopczak, A; Sosebee, M; Soustruznik, K; Spurlock, B; Stark, J; Stolin, V; Stoyanova, D A; Strandberg, J; Strang, M A; Strauss, E; Strauss, M; Ströhmer, R; Strom, D; Stutte, L; Svoisky, P; Takahashi, M; Tanasijczuk, A; Taylor, W; Tiller, B; Titov, M; Tokmenin, V V; Tsybychev, D; Tuchming, B; Tully, C; Tuts, P M; Unalan, R; Uvarov, L; Uvarov, S; Uzunyan, S; van den Berg, P J; Van Kooten, R; van Leeuwen, W M; Varelas, N; Varnes, E W; Vasilyev, I A; Verdier, P; Vertogradov, L S; Verzocchi, M; Vesterinen, M; Vilanova, D; Vint, P; Vokac, P; Wahl, H D; Wang, M H L S; Warchol, J; Watts, G; Wayne, M; Weber, G; Weber, M; Wetstein, M; White, A; Wicke, D; Williams, M R J; Wilson, G W; Wimpenny, S J; Wobisch, M; Wood, D R; Wyatt, T R; Xie, Y; Xu, C; Yacoob, S; Yamada, R; Yang, W-C; Yasuda, T; Yatsunenko, Y A; Ye, Z; Yin, H; Yip, K; Yoo, H D; Youn, S W; Yu, J; Zeitnitz, C; Zelitch, S; Zhao, T; Zhou, B; Zhu, J; Zielinski, M; Zieminska, D; Zivkovic, L; Zutshi, V; Zverev, E G

2010-02-12

A search for the standard model Higgs boson is presented using events with two charged leptons and large missing transverse energy selected from 5.4 fb(-1) of integrated luminosity in pp collisions at square root(s) = 1.96 TeV collected with the D0 detector at the Fermilab Tevatron collider. No significant excess of events above background predictions is found, and observed (expected) upper limits at 95% confidence level on the rate of Higgs boson production are derived that are a factor of 1.55 (1.36) above the predicted standard model cross section at m(H) = 165 GeV.

On the linear relation between the mean and the standard deviation of a response time distribution.

PubMed

Wagenmakers, Eric-Jan; Brown, Scott

2007-07-01

Although it is generally accepted that the spread of a response time (RT) distribution increases with the mean, the precise nature of this relation remains relatively unexplored. The authors show that in several descriptive RT distributions, the standard deviation increases linearly with the mean. Results from a wide range of tasks from different experimental paradigms support a linear relation between RT mean and RT standard deviation. Both R. Ratcliff's (1978) diffusion model and G. D. Logan's (1988) instance theory of automatization provide explanations for this linear relation. The authors identify and discuss 3 specific boundary conditions for the linear law to hold. The law constrains RT models and supports the use of the coefficient of variation to (a) compare variability while controlling for differences in baseline speed of processing and (b) assess whether changes in performance with practice are due to quantitative speedup or qualitative reorganization. Copyright 2007 APA.

On the Linear Relation between the Mean and the Standard Deviation of a Response Time Distribution

ERIC Educational Resources Information Center

Wagenmakers, Eric-Jan; Brown, Scott

2007-01-01

Although it is generally accepted that the spread of a response time (RT) distribution increases with the mean, the precise nature of this relation remains relatively unexplored. The authors show that in several descriptive RT distributions, the standard deviation increases linearly with the mean. Results from a wide range of tasks from different…

A partial least squares based spectrum normalization method for uncertainty reduction for laser-induced breakdown spectroscopy measurements

NASA Astrophysics Data System (ADS)

Li, Xiongwei; Wang, Zhe; Lui, Siu-Lung; Fu, Yangting; Li, Zheng; Liu, Jianming; Ni, Weidou

2013-10-01

A bottleneck of the wide commercial application of laser-induced breakdown spectroscopy (LIBS) technology is its relatively high measurement uncertainty. A partial least squares (PLS) based normalization method was proposed to improve pulse-to-pulse measurement precision for LIBS based on our previous spectrum standardization method. The proposed model utilized multi-line spectral information of the measured element and characterized the signal fluctuations due to the variation of plasma characteristic parameters (plasma temperature, electron number density, and total number density) for signal uncertainty reduction. The model was validated by the application of copper concentration prediction in 29 brass alloy samples. The results demonstrated an improvement on both measurement precision and accuracy over the generally applied normalization as well as our previously proposed simplified spectrum standardization method. The average relative standard deviation (RSD), average of the standard error (error bar), the coefficient of determination (R2), the root-mean-square error of prediction (RMSEP), and average value of the maximum relative error (MRE) were 1.80%, 0.23%, 0.992, 1.30%, and 5.23%, respectively, while those for the generally applied spectral area normalization were 3.72%, 0.71%, 0.973, 1.98%, and 14.92%, respectively.

Signal averaging limitations in heterodyne- and direct-detection laser remote sensing measurements

NASA Technical Reports Server (NTRS)

Menyuk, N.; Killinger, D. K.; Menyuk, C. R.

1983-01-01

The improvement in measurement uncertainty brought about by the averaging of increasing numbers of pulse return signals in both heterodyne- and direct-detection lidar systems is investigated. A theoretical analysis is presented which shows the standard deviation of the mean measurement to decrease as the inverse square root of the number of measurements, except in the presence of temporal correlation. Experimental measurements based on a dual-hybrid-TEA CO2 laser differential absorption lidar system are reported which demonstrate that the actual reduction in the standard deviation of the mean in both heterodyne- and direct-detection systems is much slower than the inverse square-root dependence predicted for uncorrelated signals, but is in agreement with predictions in the event of temporal correlation. Results thus favor the use of direct detection at relatively short range where the lower limit of the standard deviation of the mean is about 2 percent, but advantages of heterodyne detection at longer ranges are noted.

An estimator for the standard deviation of a natural frequency. I.

NASA Technical Reports Server (NTRS)

Schiff, A. J.; Bogdanoff, J. L.

1971-01-01

A brief review of mean-square approximate systems is given. The case in which the masses are deterministic is considered first in the derivation of an estimator for the upper bound of the standard deviation of a natural frequency. Two examples presented include a two-degree-of-freedom system and a case in which the disorder in the springs is perfectly correlated. For purposes of comparison, a Monte Carlo simulation was done on a digital computer.

Mean-square angle-of-arrival difference between two counter-propagating spherical waves in the presence of atmospheric turbulence.

PubMed

Chen, Chunyi; Yang, Huamin; Tong, Shoufeng; Lou, Yan

2015-09-21

The mean-square angle-of-arrival (AOA) difference between two counter-propagating spherical waves in atmospheric turbulence is theoretically formulated. Closed-form expressions for the path weighting functions are obtained. It is found that the diffraction and refraction effects of turbulent cells make negative and positive contributions to the mean-square AOA difference, respectively, and the turbulent cells located at the midpoint of the propagation path have no contributions to the mean-square AOA difference. If the mean-square AOA difference is separated into the refraction and diffraction parts, the refraction part always dominates the diffraction one, and the ratio of the diffraction part to the refraction one is never larger than 0.5 for any turbulence spectrum. Based on the expressions for the mean-square AOA difference, formulae for the correlation coefficient between the angles of arrival of two counter-propagating spherical waves in atmospheric turbulence are derived. Numerical calculations are carried out by considering that the turbulence spectrum has no path dependence. It is shown that the mean-square AOA difference always approximates to the variance of AOA fluctuations. It is found that the correlation coefficient between the angles of arrival in the x or y direction of two counter-propagating spherical waves ranges from 0.46 to 0.5, implying that the instantaneous angles of arrival of two counter-propagating spherical waves in atmospheric turbulence are far from being perfectly correlated even when the turbulence spectrum does not vary along the path.

SU-F-T-408: On the Determination of Equivalent Squares for Rectangular Small MV Photon Fields

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

Sauer, OA; Wegener, S; Exner, F

Purpose: It is common practice to tabulate dosimetric data like output factors, scatter factors and detector signal correction factors for a set of square fields. In order to get the data for an arbitrary field, it is mapped to an equivalent square, having the same scatter as the field of interest. For rectangular fields both, tabulated data and empiric formula exist. We tested the applicability of such rules for very small fields. Methods: Using the Monte-Carlo method (EGSnrc-doseRZ), the dose to a point in 10cm depth in water was calculated for cylindrical impinging fluence distributions. Radii were from 0.5mm tomore » 11.5mm with 1mm thickness of the rings. Different photon energies were investigated. With these data a matrix was constructed assigning the amount of dose to the field center to each matrix element. By summing up the elements belonging to a certain field, the dose for an arbitrary point in 10cm depth could be determined. This was done for rectangles up to 21mm side length. Comparing the dose to square field results, equivalent squares could be assigned. The results were compared to using the geometrical mean and the 4Xperimeter/area rule. Results: For side length differences less than 2mm, the difference between all methods was in general less than 0.2mm. For more elongated fields, relevant differences of more than 1mm and up to 3mm for the fields investigated occurred. The mean square side length calculated from both empiric formulas fitted much better, deviating hardly more than 1mm and for the very elongated fields only. Conclusion: For small rectangular photon fields, deviating only moderately from square both investigated empiric methods are sufficiently accurate. As the deviations often differ regarding their sign, using the mean improves the accuracy and the useable elongation range. For ratios larger than 2, Monte-Carlo generated data are recommended. SW is funded by Deutsche Forschungsgemeinschaft (SA481/10-1)« less

Mean deviation coupling synchronous control for multiple motors via second-order adaptive sliding mode control.

PubMed

Li, Lebao; Sun, Lingling; Zhang, Shengzhou

2016-05-01

A new mean deviation coupling synchronization control strategy is developed for multiple motor control systems, which can guarantee the synchronization performance of multiple motor control systems and reduce complexity of the control structure with the increasing number of motors. The mean deviation coupling synchronization control architecture combining second-order adaptive sliding mode control (SOASMC) approach is proposed, which can improve synchronization control precision of multiple motor control systems and make speed tracking errors, mean speed errors of each motor and speed synchronization errors converge to zero rapidly. The proposed control scheme is robustness to parameter variations and random external disturbances and can alleviate the chattering phenomena. Moreover, an adaptive law is employed to estimate the unknown bound of uncertainty, which is obtained in the sense of Lyapunov stability theorem to minimize the control effort. Performance comparisons with master-slave control, relative coupling control, ring coupling control, conventional PI control and SMC are investigated on a four-motor synchronization control system. Extensive comparative results are given to shown the good performance of the proposed control scheme. Copyright © 2016 ISA. Published by Elsevier Ltd. All rights reserved.

An Approach for a Mathematical Description of Human Root Canals by Means of Elementary Parameters.

PubMed

Dannemann, Martin; Kucher, Michael; Kirsch, Jasmin; Binkowski, Alexander; Modler, Niels; Hannig, Christian; Weber, Marie-Theres

2017-04-01

Root canal geometry is an important factor for instrumentation and preparation of the canals. Curvature, length, shape, and ramifications need to be evaluated in advance to enhance the success of the treatment. Therefore, the present study aimed to design and realize a method for analyzing the geometric characteristics of human root canals. Two extracted human lower molars were radiographed in the occlusal direction using micro-computed tomographic imaging. The 3-dimensional geometry of the root canals, calculated by a self-implemented image evaluation algorithm, was described by 3 different mathematical models: the elliptical model, the 1-circle model, and the 3-circle model. The different applied mathematical models obtained similar geometric properties depending on the parametric model used. Considering more complex root canals, the differences of the results increase because of the different adaptability and the better approximation of the geometry. With the presented approach, it is possible to estimate and compare the geometry of natural root canals. Therefore, the deviation of the canal can be assessed, which is important for the choice of taper of root canal instruments. Root canals with a nearly elliptical cross section are reasonably approximated by the elliptical model, whereas the 3-circle model obtains a good agreement for curved shapes. Copyright © 2017 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

Static Scene Statistical Non-Uniformity Correction

DTIC Science & Technology

2015-03-01

Error NUC Non-Uniformity Correction RMSE Root Mean Squared Error RSD Relative Standard Deviation S3NUC Static Scene Statistical Non-Uniformity...Deviation ( RSD ) which normalizes the standard deviation, σ, to the mean estimated value, µ using the equation RS D = σ µ × 100. The RSD plot of the gain...estimates is shown in Figure 4.1(b). The RSD plot shows that after a sample size of approximately 10, the different photocount values and the inclusion

AnchorDock: Blind and Flexible Anchor-Driven Peptide Docking.

PubMed

Ben-Shimon, Avraham; Niv, Masha Y

2015-05-05

The huge conformational space stemming from the inherent flexibility of peptides is among the main obstacles to successful and efficient computational modeling of protein-peptide interactions. Current peptide docking methods typically overcome this challenge using prior knowledge from the structure of the complex. Here we introduce AnchorDock, a peptide docking approach, which automatically targets the docking search to the most relevant parts of the conformational space. This is done by precomputing the free peptide's structure and by computationally identifying anchoring spots on the protein surface. Next, a free peptide conformation undergoes anchor-driven simulated annealing molecular dynamics simulations around the predicted anchoring spots. In the challenging task of a completely blind docking test, AnchorDock produced exceptionally good results (backbone root-mean-square deviation ≤ 2.2Å, rank ≤15) for 10 of 13 unbound cases tested. The impressive performance of AnchorDock supports a molecular recognition pathway that is driven via pre-existing local structural elements. Copyright © 2015 Elsevier Ltd. All rights reserved.

Experimental Protein Structure Verification by Scoring with a Single, Unassigned NMR Spectrum

PubMed Central

Courtney, Joseph M.; Ye, Qing; Nesbitt, Anna E.; Tang, Ming; Tuttle, Marcus D.; Watt, Eric D.; Nuzzio, Kristin M.; Sperling, Lindsay J.; Comellas, Gemma; Peterson, Joseph R.; Morrissey, James H.; Rienstra, Chad M.

2016-01-01

Standard methods for de novo protein structure determination by nuclear magnetic resonance (NMR) require time-consuming data collection and interpretation efforts. Here we present a qualitatively distinct and novel approach, called Comparative, Objective Measurement of Protein Architectures by Scoring Shifts (COMPASS), which identifies the best structures from a set of structural models by numerical comparison with a single, unassigned 2D 13C-13C NMR spectrum containing backbone and side-chain aliphatic signals. COMPASS does not require resonance assignments. It is particularly well suited for interpretation of magic-angle spinning solid-state NMR spectra, but also applicable to solution NMR spectra. We demonstrate COMPASS with experimental data from four proteins—GB1, ubiquitin, DsbA, and the extracellular domain of human tissue factor—and with reconstructed spectra from 11 additional proteins. For all these proteins, with molecular mass up to 25 kDa, COMPASS distinguished the correct fold, most often within 1.5 Å root-mean-square deviation of the reference structure. PMID:26365800

Conformational landscape of the HIV-V3 hairpin loop from all-atom free-energy simulations

NASA Astrophysics Data System (ADS)

Verma, Abhinav; Wenzel, Wolfgang

2008-03-01

Small beta hairpins have many distinct biological functions, including their involvement in chemokine and viral receptor recognition. The relevance of structural similarities between different hairpin loops with near homologous sequences is not yet understood, calling for the development of methods for de novo hairpin structure prediction and simulation. De novo folding of beta strands is more difficult than that of helical proteins because of nonlocal hydrogen bonding patterns that connect amino acids that are distant in the amino acid sequence and there is a large variety of possible hydrogen bond patterns. Here we use a greedy version of the basin hopping technique with our free-energy forcefield PFF02 to reproducibly and predictively fold the hairpin structure of a HIV-V3 loop. We performed 20 independent basin hopping runs for 500cycles corresponding to 7.4×107 energy evaluations each. The lowest energy structure found in the simulation has a backbone root mean square deviation (bRMSD) of only 2.04Å to the native conformation. The lowest 9 out of the 20 simulations converged to conformations deviating less than 2.5Å bRMSD from native.

Conformational landscape of the HIV-V3 hairpin loop from all-atom free-energy simulations.

PubMed

Verma, Abhinav; Wenzel, Wolfgang

2008-03-14

Small beta hairpins have many distinct biological functions, including their involvement in chemokine and viral receptor recognition. The relevance of structural similarities between different hairpin loops with near homologous sequences is not yet understood, calling for the development of methods for de novo hairpin structure prediction and simulation. De novo folding of beta strands is more difficult than that of helical proteins because of nonlocal hydrogen bonding patterns that connect amino acids that are distant in the amino acid sequence and there is a large variety of possible hydrogen bond patterns. Here we use a greedy version of the basin hopping technique with our free-energy forcefield PFF02 to reproducibly and predictively fold the hairpin structure of a HIV-V3 loop. We performed 20 independent basin hopping runs for 500 cycles corresponding to 7.4 x 10(7) energy evaluations each. The lowest energy structure found in the simulation has a backbone root mean square deviation (bRMSD) of only 2.04 A to the native conformation. The lowest 9 out of the 20 simulations converged to conformations deviating less than 2.5 A bRMSD from native.

Theoretical and experimental studies of error in square-law detector circuits

NASA Technical Reports Server (NTRS)

Stanley, W. D.; Hearn, C. P.; Williams, J. B.

1984-01-01

Square law detector circuits to determine errors from the ideal input/output characteristic function were investigated. The nonlinear circuit response is analyzed by a power series expansion containing terms through the fourth degree, from which the significant deviation from square law can be predicted. Both fixed bias current and flexible bias current configurations are considered. The latter case corresponds with the situation where the mean current can change with the application of a signal. Experimental investigations of the circuit arrangements are described. Agreement between the analytical models and the experimental results are established. Factors which contribute to differences under certain conditions are outlined.

Mean square consensus of leader-following multi-agent systems with measurement noises and time delays.

PubMed

Ren, Hongwei; Deng, Feiqi

2017-11-01

This paper investigates the mean square consensus problem of dynamical networks of leader-following multi-agent systems with measurement noises and time-varying delays. We consider that the fixed undirected communication topologies are connected. A neighbor-based tracking algorithm together with distributed estimators are presented. Using tools of algebraic graph theory and the Gronwall-Bellman-Halanay type inequality, we establish sufficient conditions to reach consensus in mean square sense via the proposed consensus protocols. Finally, a numerical simulation is provided to demonstrate the effectiveness of the obtained theoretical result. Copyright © 2017 ISA. Published by Elsevier Ltd. All rights reserved.

First measurement of the ratio of central-electron to forward-electron W partial cross sections in pp[over] collisions at (square root)s =1.96 TeV.

PubMed

Abulencia, A; Adelman, J; Affolder, T; Akimoto, T; Albrow, M G; Amerio, S; Amidei, D; Anastassov, A; Anikeev, K; Annovi, A; Antos, J; Aoki, M; Apollinari, G; Arisawa, T; Artikov, A; Ashmanskas, W; Attal, A; Aurisano, A; Azfar, F; Azzi-Bacchetta, P; Azzurri, P; Bacchetta, N; Badgett, W; Barbaro-Galtieri, A; Barnes, V E; Barnett, B A; Baroiant, S; Bartsch, V; Bauer, G; Beauchemin, P-H; Bedeschi, F; Behari, S; Bellettini, G; Bellinger, J; Belloni, A; Benjamin, D; Beretvas, A; Beringer, J; Berry, T; Bhatti, A; Binkley, M; Bisello, D; Bizjak, I; Blair, R E; Blocker, C; Blumenfeld, B; Bocci, A; Bodek, A; Boisvert, V; Bolla, G; Bolshov, A; Bortoletto, D; Boudreau, J; Boveia, A; Brau, B; Brigliadori, L; Bromberg, C; Brubaker, E; Budagov, J; Budd, H S; Budd, S; Burkett, K; Busetto, G; Bussey, P; Buzatu, A; Byrum, K L; Cabrera, S; Campanelli, M; Campbell, M; Canelli, F; Canepa, A; Carillo, S; Carlsmith, D; Carosi, R; Carron, S; Casal, B; Casarsa, M; Castro, A; Catastini, P; Cauz, D; Cavalli-Sforza, M; Cerri, A; Cerrito, L; Chang, S H; Chen, Y C; Chertok, M; Chiarelli, G; Chlachidze, G; Chlebana, F; Cho, I; Cho, K; Chokheli, D; Chou, J P; Choudalakis, G; Chuang, S H; Chung, K; Chung, W H; Chung, Y S; Cilijak, M; Ciobanu, C I; Ciocci, M A; Clark, A; Clark, D; Coca, M; Compostella, G; Convery, M E; Conway, J; Cooper, B; Copic, K; Cordelli, M; Cortiana, G; Crescioli, F; Almenar, C Cuenca; Cuevas, J; Culbertson, R; Cully, J C; DaRonco, S; Datta, M; D'Auria, S; Davies, T; Dagenhart, D; de Barbaro, P; De Cecco, S; Deisher, A; De Lentdecker, G; De Lorenzo, G; Dell'Orso, M; Delli Paoli, F; Demortier, L; Deng, J; Deninno, M; De Pedis, D; Derwent, P F; Giovanni, G P Di; Dionisi, C; Di Ruzza, B; Dittmann, J R; D'Onofrio, M; Dörr, C; Donati, S; Dong, P; Donini, J; Dorigo, T; Dube, S; Efron, J; Erbacher, R; Errede, D; Errede, S; Eusebi, R; Fang, H C; Farrington, S; Fedorko, I; Fedorko, W T; Feild, R G; Feindt, M; Fernandez, J P; Field, R; Flanagan, G; Forrest, R; Forrester, S; Franklin, M; Freeman, J C; Furic, I; Gallinaro, M; Galyardt, J; Garcia, J E; Garberson, F; Garfinkel, A F; Gay, C; Gerberich, H; Gerdes, D; Giagu, S; Giannetti, P; Gibson, K; Gimmell, J L; Ginsburg, C; Giokaris, N; Giordani, M; Giromini, P; Giunta, M; Giurgiu, G; Glagolev, V; Glenzinski, D; Gold, M; Goldschmidt, N; Goldstein, J; Golossanov, A; Gomez, G; Gomez-Ceballos, G; Goncharov, M; González, O; Gorelov, I; Goshaw, A T; Goulianos, K; Gresele, A; Grinstein, S; Grosso-Pilcher, C; Grundler, U; Guimaraes da Costa, J; Gunay-Unalan, Z; Haber, C; Hahn, K; Hahn, S R; Halkiadakis, E; Hamilton, A; Han, B-Y; Han, J Y; Handler, R; Happacher, F; Hara, K; Hare, D; Hare, M; Harper, S; Harr, R F; Harris, R M; Hartz, M; Hatakeyama, K; Hauser, J; Hays, C; Heck, M; Heijboer, A; Heinemann, B; Heinrich, J; Henderson, C; Herndon, M; Heuser, J; Hidas, D; Hill, C S; Hirschbuehl, D; Hocker, A; Holloway, A; Hou, S; Houlden, M; Hsu, S-C; Huffman, B T; Hughes, R E; Husemann, U; Huston, J; Incandela, J; Introzzi, G; Iori, M; Ivanov, A; Iyutin, B; James, E; Jang, D; Jayatilaka, B; Jeans, D; Jeon, E J; Jindariani, S; Johnson, W; Jones, M; Joo, K K; Jun, S Y; Jung, J E; Junk, T R; Kamon, T; Karchin, P E; Kato, Y; Kemp, Y; Kephart, R; Kerzel, U; Khotilovich, V; Kilminster, B; Kim, D H; Kim, H S; Kim, J E; Kim, M J; Kim, S B; Kim, S H; Kim, Y K; Kimura, N; Kirsch, L; Klimenko, S; Klute, M; Knuteson, B; Ko, B R; Kondo, K; Kong, D J; Konigsberg, J; Korytov, A; Kotwal, A V; Kraan, A C; Kraus, J; Kreps, M; Kroll, J; Krumnack, N; Kruse, M; Krutelyov, V; Kubo, T; Kuhlmann, S E; Kuhr, T; Kulkarni, N P; Kusakabe, Y; Kwang, S; Laasanen, A T; Lai, S; Lami, S; Lammel, S; Lancaster, M; Lander, R L; Lannon, K; Lath, A; Latino, G; Lazzizzera, I; LeCompte, T; Lee, J; Lee, J; Lee, Y J; Lee, S W; Lefèvre, R; Leonardo, N; Leone, S; Levy, S; Lewis, J D; Lin, C; Lin, C S; Lindgren, M; Lipeles, E; Lister, A; Litvintsev, D O; Liu, T; Lockyer, N S; Loginov, A; Loreti, M; Lu, R-S; Lucchesi, D; Lujan, P; Lukens, P; Lungu, G; Lyons, L; Lys, J; Lysak, R; Lytken, E; Mack, P; MacQueen, D; Madrak, R; Maeshima, K; Makhoul, K; Maki, T; Maksimovic, P; Malde, S; Malik, S; Manca, G; Manousakis, A; Margaroli, F; Marginean, R; Marino, C; Marino, C P; Martin, A; Martin, M; Martin, V; Martínez, M; Martínez-Ballarín, R; Maruyama, T; Mastrandrea, P; Masubuchi, T; Matsunaga, H; Mattson, M E; Mazini, R; Mazzanti, P; McFarland, K S; McIntyre, P; McNulty, R; Mehta, A; Mehtala, P; Menzemer, S; Menzione, A; Merkel, P; Mesropian, C; Messina, A; Miao, T; Miladinovic, N; Miles, J; Miller, R; Mills, C; Milnik, M; Mitra, A; Mitselmakher, G; Miyamoto, A; Moed, S; Moggi, N; Mohr, B; Moon, C S; Moore, R; Morello, M; Fernandez, P Movilla; Mülmenstädt, J; Mukherjee, A; Muller, Th; Mumford, R; Murat, P; Mussini, M; Nachtman, J; Nagano, A; Naganoma, J; Nakamura, K; Nakano, I; Napier, A; Necula, V; Neu, C; Neubauer, M S; Nielsen, J; Nodulman, L; Norniella, O; Nurse, E; Oh, S H; Oh, Y D; Oksuzian, I; Okusawa, T; Oldeman, R; Orava, R; Osterberg, K; Pagliarone, C; Palencia, E; Papadimitriou, V; Papaikonomou, A; Paramonov, A A; Parks, B; Pashapour, S; Patrick, J; Pauletta, G; Paulini, M; Paus, C; Pellett, D E; Penzo, A; Phillips, T J; Piacentino, G; Piedra, J; Pinera, L; Pitts, K; Plager, C; Pondrom, L; Portell, X; Poukhov, O; Pounder, N; Prakoshyn, F; Pronko, A; Proudfoot, J; Ptohos, F; Punzi, G; Pursley, J; Rademacker, J; Rahaman, A; Ramakrishnan, V; Ranjan, N; Redondo, I; Reisert, B; Rekovic, V; Renton, P; Rescigno, M; Richter, S; Rimondi, F; Ristori, L; Robson, A; Rodrigo, T; Rogers, E; Rolli, S; Roser, R; Rossi, M; Rossin, R; Roy, P; Ruiz, A; Russ, J; Rusu, V; Saarikko, H; Safonov, A; Sakumoto, W K; Salamanna, G; Saltó, O; Santi, L; Sarkar, S; Sartori, L; Sato, K; Savard, P; Savoy-Navarro, A; Scheidle, T; Schlabach, P; Schmidt, E E; Schmidt, M P; Schmitt, M; Schwarz, T; Scodellaro, L; Scott, A L; Scribano, A; Scuri, F; Sedov, A; Seidel, S; Seiya, Y; Semenov, A; Sexton-Kennedy, L; Sfyrla, A; Shalhout, S Z; Shapiro, M D; Shears, T; Shepard, P F; Sherman, D; Shimojima, M; Shochet, M; Shon, Y; Shreyber, I; Sidoti, A; Sinervo, P; Sisakyan, A; Slaughter, A J; Slaunwhite, J; Sliwa, K; Smith, J R; Snider, F D; Snihur, R; Soderberg, M; Soha, A; Somalwar, S; Sorin, V; Spalding, J; Spinella, F; Spreitzer, T; Squillacioti, P; Stanitzki, M; Staveris-Polykalas, A; Denis, R St; Stelzer, B; Stelzer-Chilton, O; Stentz, D; Strologas, J; Stuart, D; Suh, J S; Sukhanov, A; Sun, H; Suslov, I; Suzuki, T; Taffard, A; Takashima, R; Takeuchi, Y; Tanaka, R; Tecchio, M; Teng, P K; Terashi, K; Thom, J; Thompson, A S; Thomson, E; Tipton, P; Tiwari, V; Tkaczyk, S; Toback, D; Tokar, S; Tollefson, K; Tomura, T; Tonelli, D; Torre, S; Torretta, D; Tourneur, S; Trischuk, W; Tsuno, S; Tu, Y; Turini, N; Ukegawa, F; Uozumi, S; Vallecorsa, S; van Remortel, N; Varganov, A; Vataga, E; Vazquez, F; Velev, G; Vellidis, C; Veramendi, G; Veszpremi, V; Vidal, M; Vidal, R; Vila, I; Vilar, R; Vine, T; Vollrath, I; Volobouev, I; Volpi, G; Würthwein, F; Wagner, P; Wagner, R G; Wagner, R L; Wagner, J; Wagner, W; Wallny, R; Wang, S M; Warburton, A; Waters, D; Weinberger, M; Wester, W C; Whitehouse, B; Whiteson, D; Wicklund, A B; Wicklund, E; Williams, G; Williams, H H; Wilson, P; Winer, B L; Wittich, P; Wolbers, S; Wolfe, C; Wright, T; Wu, X; Wynne, S M; Yagil, A; Yamamoto, K; Yamaoka, J; Yamashita, T; Yang, C; Yang, U K; Yang, Y C; Yao, W M; Yeh, G P; Yoh, J; Yorita, K; Yoshida, T; Yu, G B; Yu, I; Yu, S S; Yun, J C; Zanello, L; Zanetti, A; Zaw, I; Zhang, X; Zhou, J; Zucchelli, S

2007-06-22

We present a measurement of sigma(pp[over] --> W) x B(W --> e nu) at (square root)s = 1.96 TeV, using electrons identified in the forward region (1.2 < |eta| < 2.8) of the CDF II detector, in 223 pb(-1) of data. We measure sigma x B = 2796 +/- 13(stat)(-90)(+95)(syst) +/- 162(lum) pb. Combining this result with a previous CDF measurement obtained using electrons in the central region (|eta| approximately < 1), we present the first measurement of the ratio of central-electron to forward-electron W partial cross sections R(exp) = 0.925 +/- 0.006(stat) +/- 0.032(syst), consistent with theoretical predictions using Coordinated Theoretical-Experimental Project on QCD (CTEQ) and Martin-Roberts-Stirling-Thorne (MRST) parton distribution functions.

On the best mean-square approximations to a planet's gravitational potential

NASA Astrophysics Data System (ADS)

Lobkova, N. I.

1985-02-01

The continuous problem of approximating the gravitational potential of a planet in the form of polynomials of solid spherical functions is considered. The best mean-square polynomials, referred to different parts of space, are compared with each other. The harmonic coefficients corresponding to the surface of a planet are shown to be unstable with respect to the degree of the polynomial and to differ from the Stokes constants.

Self-healing of Hermite-Gauss and Ince-Gauss beams

NASA Astrophysics Data System (ADS)

Aguirre-Olivas, Dilia; Mellado-Villaseñor, Gabriel; Arrizón, Victor; Chávez-Cerda, Sabino

2015-08-01

We analyze and demonstrate, numerically and experimentally, the self-healing effect in scaled propagation invariant beams, subject to opaque obstructions. The effect is quantitatively evaluated employing the Root Mean Square deviation and the similarity function.

Temperature dependence of fast carbonyl backbone dynamics in chicken villin headpiece subdomain

PubMed Central

Vugmeyster, Liliya; Ostrovsky, Dmitry

2012-01-01

Temperature-dependence of protein dynamics can provide information on details of the free energy landscape by probing the characteristics of the potential responsible for the fluctuations. We have investigated the temperature-dependence of picosecond to nanosecond backbone dynamics at carbonyl carbon sites in chicken villin headpiece subdomain protein using a combination of three NMR relaxation rates: 13C′ longitudinal rate, and two cross-correlated rates involving dipolar and chemical shift anisotropy (CSA) relaxation mechanisms, 13C′/13C′−13Cα CSA/dipolar and 13C′/13C′−15N CSA/dipolar. Order parameters have been extracted using the Lipari-Szabo model-free approach assuming a separation of the time scales of internal and molecular motions in the 2–16°C temperature range. There is a gradual deviation from this assumption from lower to higher temperatures, such that above 16°C the separation of the time scales is inconsistent with the experimental data and, thus, the Lipari-Szabo formalism can not be applied. While there are variations among the residues, on the average the order parameters indicate a markedly steeper temperature dependence at backbone carbonyl carbons compared to that probed at amide nitrogens in an earlier study. This strongly advocates for probing sites other than amide nitrogen for accurate characterization of the potential and other thermodynamics characteristics of protein backbone. PMID:21416162

ROOTing Out Meaning: More Morphemic Analysis for Primary Pupils

ERIC Educational Resources Information Center

Mountain, Lee

2005-01-01

In an elementary-school professional development program, a group of primary teachers and a university consultant reviewed the research on morphemic analysis and then explored ways to give pupils in grades 1, 2, and 3 an early start on using prefixes, suffixes, and roots to construct word meaning. The teachers examined some middle-grade strategies…

Temperature sensitivity of soil microbial activity modeled by the square root equation as a unifying model to differentiate between direct temperature effects and microbial community adaptation.

PubMed

Bååth, Erland

2018-07-01

Numerous models have been used to express the temperature sensitivity of microbial growth and activity in soil making it difficult to compare results from different habitats. Q10 still is one of the most common ways to express temperature relationships. However, Q10 is not constant with temperature and will differ depending on the temperature interval used for the calculation. The use of the square root (Ratkowsky) relationship between microbial activity (A) and temperature below optimum temperature, √A = a × (T-T min ), is proposed as a simple and adequate model that allow for one descriptor, T min (a theoretical minimum temperature for growth and activity), to estimate correct Q10-values over the entire in situ temperature interval. The square root model can adequately describe both microbial growth and respiration, allowing for an easy determination of T min . Q10 for any temperature interval can then be calculated by Q10 = [(T + 10 - T min )/(T-T min )] 2 , where T is the lowest temperature in the Q10 comparison. T min also describes the temperature adaptation of the microbial community. An envelope of T min covering most natural soil habitats varying between -15°C (cold habitats like Antarctica/Arctic) to 0°C (tropical habitats like rain forests and deserts) is suggested, with an 0.3°C increase in T min per 1°C increase in mean annual temperature. It is shown that the main difference between common temperature relationships used in global models is differences in the assumed temperature adaptation of the soil microbial community. The use of the square root equation will allow for one descriptor, T min , determining the temperature response of soil microorganisms, and at the same time allow for comparing temperature sensitivity of microbial activity between habitats, including future projections. © 2018 John Wiley & Sons Ltd.

Accurate human limb angle measurement: sensor fusion through Kalman, least mean squares and recursive least-squares adaptive filtering

NASA Astrophysics Data System (ADS)

Olivares, A.; Górriz, J. M.; Ramírez, J.; Olivares, G.

2011-02-01

Inertial sensors are widely used in human body motion monitoring systems since they permit us to determine the position of the subject's limbs. Limb angle measurement is carried out through the integration of the angular velocity measured by a rate sensor and the decomposition of the components of static gravity acceleration measured by an accelerometer. Different factors derived from the sensors' nature, such as the angle random walk and dynamic bias, lead to erroneous measurements. Dynamic bias effects can be reduced through the use of adaptive filtering based on sensor fusion concepts. Most existing published works use a Kalman filtering sensor fusion approach. Our aim is to perform a comparative study among different adaptive filters. Several least mean squares (LMS), recursive least squares (RLS) and Kalman filtering variations are tested for the purpose of finding the best method leading to a more accurate and robust limb angle measurement. A new angle wander compensation sensor fusion approach based on LMS and RLS filters has been developed.

Identified particle distributions in pp and Au+Au collisions at square root of (sNN)=200 GeV.

PubMed

Adams, J; Adler, C; Aggarwal, M M; Ahammed, Z; Amonett, J; Anderson, B D; Anderson, M; Arkhipkin, D; Averichev, G S; Badyal, S K; Balewski, J; Barannikova, O; Barnby, L S; Baudot, J; Bekele, S; Belaga, V V; Bellwied, R; Berger, J; Bezverkhny, B I; Bhardwaj, S; Bhaskar, P; Bhati, A K; Bichsel, H; Billmeier, A; Bland, L C; Blyth, C O; Bonner, B E; Botje, M; Boucham, A; Brandin, A; Bravar, A; Cadman, R V; Cai, X Z; Caines, H; Calderón de la Barca Sánchez, M; Carroll, J; Castillo, J; Castro, M; Cebra, D; Chaloupka, P; Chattopadhyay, S; Chen, H F; Chen, Y; Chernenko, S P; Cherney, M; Chikanian, A; Choi, B; Christie, W; Coffin, J P; Cormier, T M; Cramer, J G; Crawford, H J; Das, D; Das, S; Derevschikov, A A; Didenko, L; Dietel, T; Dong, X; Draper, J E; Du, F; Dubey, A K; Dunin, V B; Dunlop, J C; Dutta Majumdar, M R; Eckardt, V; Efimov, L G; Emelianov, V; Engelage, J; Eppley, G; Erazmus, B; Estienne, M; Fachini, P; Faine, V; Faivre, J; Fatemi, R; Filimonov, K; Filip, P; Finch, E; Fisyak, Y; Flierl, D; Foley, K J; Fu, J; Gagliardi, C A; Ganti, M S; Gutierrez, T D; Gagunashvili, N; Gans, J; Gaudichet, L; Germain, M; Geurts, F; Ghazikhanian, V; Ghosh, P; Gonzalez, J E; Grachov, O; Grigoriev, V; Gronstal, S; Grosnick, D; Guedon, M; Guertin, S M; Gupta, A; Gushin, E; Hallman, T J; Hardtke, D; Harris, J W; Heinz, M; Henry, T W; Heppelmann, S; Herston, T; Hippolyte, B; Hirsch, A; Hjort, E; Hoffmann, G W; Horsley, M; Huang, H Z; Huang, S L; Humanic, T J; Igo, G; Ishihara, A; Jacobs, P; Jacobs, W W; Janik, M; Johnson, I; Jones, P G; Judd, E G; Kabana, S; Kaneta, M; Kaplan, M; Keane, D; Kiryluk, J; Kisiel, A; Klay, J; Klein, S R; Klyachko, A; Koetke, D D; Kollegger, T; Konstantinov, A S; Kopytine, M; Kotchenda, L; Kovalenko, A D; Kramer, M; Kravtsov, P; Krueger, K; Kuhn, C; Kulikov, A I; Kumar, A; Kunde, G J; Kunz, C L; Kutuev, R Kh; Kuznetsov, A A; Lamont, M A C; Landgraf, J M; Lange, S; Lansdell, C P; Lasiuk, B; Laue, F; Lauret, J; Lebedev, A; Lednický, R; Leontiev, V M; LeVine, M J; Li, C; Li, Q; Lindenbaum, S J; Lisa, M A; Liu, F; Liu, L; Liu, Z; Liu, Q J; Ljubicic, T; Llope, W J; Long, H; Longacre, R S; Lopez-Noriega, M; Love, W A; Ludlam, T; Lynn, D; Ma, J; Ma, Y G; Magestro, D; Mahajan, S; Mangotra, L K; Mahapatra, D P; Majka, R; Manweiler, R; Margetis, S; Markert, C; Martin, L; Marx, J; Matis, H S; Matulenko, Yu A; McShane, T S; Meissner, F; Melnick, Yu; Meschanin, A; Messer, M; Miller, M L; Milosevich, Z; Minaev, N G; Mironov, C; Mishra, D; Mitchell, J; Mohanty, B; Molnar, L; Moore, C F; Mora-Corral, M J; Morozov, V; de Moura, M M; Munhoz, M G; Nandi, B K; Nayak, S K; Nayak, T K; Nelson, J M; Nevski, P; Nikitin, V A; Nogach, L V; Norman, B; Nurushev, S B; Odyniec, G; Ogawa, A; Okorokov, V; Oldenburg, M; Olson, D; Paic, G; Pandey, S U; Pal, S K; Panebratsev, Y; Panitkin, S Y; Pavlinov, A I; Pawlak, T; Perevoztchikov, V; Peryt, W; Petrov, V A; Phatak, S C; Picha, R; Planinic, M; Pluta, J; Porile, N; Porter, J; Poskanzer, A M; Potekhin, M; Potrebenikova, E; Potukuchi, B V K S; Prindle, D; Pruneau, C; Putschke, J; Rai, G; Rakness, G; Raniwala, R; Raniwala, S; Ravel, O; Ray, R L; Razin, S V; Reichhold, D; Reid, J G; Renault, G; Retiere, F; Ridiger, A; Ritter, H G; Roberts, J B; Rogachevski, O V; Romero, J L; Rose, A; Roy, C; Ruan, L J; Sahoo, R; Sakrejda, I; Salur, S; Sandweiss, J; Savin, I; Schambach, J; Scharenberg, R P; Schmitz, N; Schroeder, L S; Schweda, K; Seger, J; Seliverstov, D; Seyboth, P; Shahaliev, E; Shao, M; Sharma, M; Shestermanov, K E; Shimanskii, S S; Singaraju, R N; Simon, F; Skoro, G; Smirnov, N; Snellings, R; Sood, G; Sorensen, P; Sowinski, J; Spinka, H M; Srivastava, B; Stanislaus, S; Stock, R; Stolpovsky, A; Strikhanov, M; Stringfellow, B; Struck, C; Suaide, A A P; Sugarbaker, E; Suire, C; Sumbera, M; Surrow, B; Symons, T J M; de Toledo, A Szanto; Szarwas, P; Tai, A; Takahashi, J; Tang, A H; Thein, D; Thomas, J H; Tikhomirov, V; Tokarev, M; Tonjes, M B; Trainor, T A; Trentalange, S; Tribble, R E; Trivedi, M D; Trofimov, V; Tsai, O; Ullrich, T; Underwood, D G; Van Buren, G; VanderMolen, A M; Vasiliev, A N; Vasiliev, M; Vigdor, S E; Viyogi, Y P; Voloshin, S A; Waggoner, W; Wang, F; Wang, G; Wang, X L; Wang, Z M; Ward, H; Watson, J W; Wells, R; Westfall, G D; Whitten, C; Wieman, H; Willson, R; Wissink, S W; Witt, R; Wood, J; Wu, J; Xu, N; Xu, Z; Xu, Z Z; Yakutin, A E; Yamamoto, E; Yang, J; Yepes, P; Yurevich, V I; Zanevski, Y V; Zborovský, I; Zhang, H; Zhang, H Y; Zhang, W M; Zhang, Z P; Zołnierczuk, P A; Zoulkarneev, R; Zoulkarneeva, J; Zubarev, A N

2004-03-19

Transverse mass and rapidity distributions for charged pions, charged kaons, protons, and antiprotons are reported for square root of [sNN]=200 GeV pp and Au+Au collisions at Relativistic Heary Ion Collider (RHIC). Chemical and kinetic equilibrium model fits to our data reveal strong radial flow and long duration from chemical to kinetic freeze-out in central Au+Au collisions. The chemical freeze-out temperature appears to be independent of initial conditions at RHIC energies.

Mean-Square Amplitudes of Vibration and Anisotropic Motion of Metal Atoms in Iron Organometallics

NASA Astrophysics Data System (ADS)

Herber, Rolfe H.; Nowik, Israel

2002-12-01

Mössbauer recoil-free fraction (f) data for ferrocene [(η5-(C5H5)2Fe] over the temperature range 90≤T≤370 K have been used to calculate the mean-square-amplitude-of-vibration (msav) of the iron atom, and these data have been compared to the thermal factors (U ij ) extracted from X-ray diffraction data reported in the literature. The agreement between these two independent data sets is taken as a validation of the interpretation of the Mössbauer data in terms of the mean-square-amplitude-of-vibration of the metal atom in iron organometallic solids. The contribution of three low-frequency IR active modes of ferrocene (ω11, ω21, and ω22) to the f(T) parameter is discussed in detail.

Deviations from Newton's law in supersymmetric large extra dimensions

NASA Astrophysics Data System (ADS)

Callin, P.; Burgess, C. P.

2006-09-01

Deviations from Newton's inverse-squared law at the micron length scale are smoking-gun signals for models containing supersymmetric large extra dimensions (SLEDs), which have been proposed as approaches for resolving the cosmological constant problem. Just like their non-supersymmetric counterparts, SLED models predict gravity to deviate from the inverse-square law because of the advent of new dimensions at sub-millimeter scales. However SLED models differ from their non-supersymmetric counterparts in three important ways: (i) the size of the extra dimensions is fixed by the observed value of the dark energy density, making it impossible to shorten the range over which new deviations from Newton's law must be seen; (ii) supersymmetry predicts there to be more fields in the extra dimensions than just gravity, implying different types of couplings to matter and the possibility of repulsive as well as attractive interactions; and (iii) the same mechanism which is purported to keep the cosmological constant naturally small also keeps the extra-dimensional moduli effectively massless, leading to deviations from general relativity in the far infrared of the scalar-tensor form. We here explore the deviations from Newton's law which are predicted over micron distances, and show the ways in which they differ and resemble those in the non-supersymmetric case.

[A method for rapid extracting three-dimensional root model of vivo tooth from cone beam computed tomography data based on the anatomical characteristics of periodontal ligament].

PubMed

Zhao, Y J; Wang, S W; Liu, Y; Wang, Y

2017-02-18

To explore a new method for rapid extracting and rebuilding three-dimensional (3D) digital root model of vivo tooth from cone beam computed tomography (CBCT) data based on the anatomical characteristics of periodontal ligament, and to evaluate the extraction accuracy of the method. In the study, 15 extracted teeth (11 with single root, 4 with double roots) were collected from oral clinic and 3D digital root models of each tooth were obtained by 3D dental scanner with a high accuracy 0.02 mm in STL format. CBCT data for each patient were acquired before tooth extraction, DICOM data with a voxel size 0.3 mm were input to Mimics 18.0 software. Segmentation, Morphology operations, Boolean operations and Smart expanded function in Mimics software were used to edit teeth, bone and periodontal ligament threshold mask, and root threshold mask were automatically acquired after a series of mask operations. 3D digital root models were extracted in STL format finally. 3D morphology deviation between the extracted root models and corresponding vivo root models were compared in Geomagic Studio 2012 software. The 3D size errors in long axis, bucco-lingual direction and mesio-distal direction were also calculated. The average value of the 3D morphology deviation for 15 roots by calculating Root Mean Square (RMS) value was 0.22 mm, the average size errors in the mesio-distal direction, the bucco-lingual direction and the long axis were 0.46 mm, 0.36 mm and -0.68 mm separately. The average time of this new method for extracting single root was about 2-3 min. It could meet the accuracy requirement of the root 3D reconstruction fororal clinical use. This study established a new method for rapid extracting 3D root model of vivo tooth from CBCT data. It could simplify the traditional manual operation and improve the efficiency and automation of single root extraction. The strategy of this method for complete dentition extraction needs further research.

Design of glucagon-like Peptide-1 receptor agonist for diabetes mellitus from traditional chinese medicine.

PubMed

Tang, Hsin-Chieh; Chen, Calvin Yu-Chian

2014-01-01

Glucagon-like peptide-1 (GLP-1) is a promising target for diabetes mellitus (DM) therapy and reduces the occurrence of diabetes due to obesity. However, GLP-1 will be hydrolyzed soon by the enzyme dipeptidyl peptidase-4 (DPP-4). We tried to design small molecular drugs for GLP-1 receptor agonist from the world's largest traditional Chinese medicine (TCM) Database@Taiwan. According to docking results of virtual screening, we selected 2 TCM compounds, wenyujinoside and 28-deglucosylchikusetsusaponin IV, for further molecular dynamics (MD) simulation. GLP-1 was assigned as the control compound. Based on the results of root mean square deviation (RMSD), solvent accessible surface (SAS), mean square deviation (MSD), Gyrate, total energy, root mean square fluctuation (RMSF), matrices of smallest distance of residues, database of secondary structure assignment (DSSP), cluster analysis, and distance of H-bond, we concluded that all the 3 compounds could bind and activate GLP-1 receptor by computational simulation. Wenyujinoside and 28-deglucosylchikusetsusaponin IV were the TCM compounds that could be GLP-1 receptor agonists.

Design of Glucagon-Like Peptide-1 Receptor Agonist for Diabetes Mellitus from Traditional Chinese Medicine

PubMed Central

Tang, Hsin-Chieh; Chen, Calvin Yu-Chian

2014-01-01

Glucagon-like peptide-1 (GLP-1) is a promising target for diabetes mellitus (DM) therapy and reduces the occurrence of diabetes due to obesity. However, GLP-1 will be hydrolyzed soon by the enzyme dipeptidyl peptidase-4 (DPP-4). We tried to design small molecular drugs for GLP-1 receptor agonist from the world's largest traditional Chinese medicine (TCM) Database@Taiwan. According to docking results of virtual screening, we selected 2 TCM compounds, wenyujinoside and 28-deglucosylchikusetsusaponin IV, for further molecular dynamics (MD) simulation. GLP-1 was assigned as the control compound. Based on the results of root mean square deviation (RMSD), solvent accessible surface (SAS), mean square deviation (MSD), Gyrate, total energy, root mean square fluctuation (RMSF), matrices of smallest distance of residues, database of secondary structure assignment (DSSP), cluster analysis, and distance of H-bond, we concluded that all the 3 compounds could bind and activate GLP-1 receptor by computational simulation. Wenyujinoside and 28-deglucosylchikusetsusaponin IV were the TCM compounds that could be GLP-1 receptor agonists. PMID:24891870

MD simulations of ligand-bound and ligand-free aptamer: molecular level insights into the binding and switching mechanism of the add A-riboswitch.

PubMed

Sharma, Monika; Bulusu, Gopalakrishnan; Mitra, Abhijit

2009-09-01

Riboswitches are structural cis-acting genetic regulatory elements in 5' UTRs of mRNAs, consisting of an aptamer domain that regulates the behavior of an expression platform in response to its recognition of, and binding to, specific ligands. While our understanding of the ligand-bound structure of the aptamer domain of the adenine riboswitches is based on crystal structure data and is well characterized, understanding of the structure and dynamics of the ligand-free aptamer is limited to indirect inferences from physicochemical probing experiments. Here we report the results of 15-nsec-long explicit-solvent molecular dynamics simulations of the add A-riboswitch crystal structure (1Y26), both in the adenine-bound (CLOSED) state and in the adenine-free (OPEN) state. Root-mean-square deviation, root-mean-square fluctuation, dynamic cross-correlation, and backbone torsion angle analyses are carried out on the two trajectories. These, along with solvent accessible surface area analysis of the two average structures, are benchmarked against available experimental data and are shown to constitute the basis for obtaining reliable insights into the molecular level details of the binding and switching mechanism. Our analysis reveals the interaction network responsible for, and conformational changes associated with, the communication between the binding pocket and the expression platform. It further highlights the significance of a, hitherto unreported, noncanonical W:H trans base pairing between A73 and A24, in the OPEN state, and also helps us to propose a possibly crucial role of U51 in the context of ligand binding and ligand discrimination.

Structural flexibility and protein adaptation to temperature: Molecular dynamics analysis of malate dehydrogenases of marine molluscs.

PubMed

Dong, Yun-Wei; Liao, Ming-Ling; Meng, Xian-Liang; Somero, George N

2018-02-06

Orthologous proteins of species adapted to different temperatures exhibit differences in stability and function that are interpreted to reflect adaptive variation in structural "flexibility." However, quantifying flexibility and comparing flexibility across proteins has remained a challenge. To address this issue, we examined temperature effects on cytosolic malate dehydrogenase (cMDH) orthologs from differently thermally adapted congeners of five genera of marine molluscs whose field body temperatures span a range of ∼60 °C. We describe consistent patterns of convergent evolution in adaptation of function [temperature effects on K M of cofactor (NADH)] and structural stability (rate of heat denaturation of activity). To determine how these differences depend on flexibilities of overall structure and of regions known to be important in binding and catalysis, we performed molecular dynamics simulation (MDS) analyses. MDS analyses revealed a significant negative correlation between adaptation temperature and heat-induced increase of backbone atom movements [root mean square deviation (rmsd) of main-chain atoms]. Root mean square fluctuations (RMSFs) of movement by individual amino acid residues varied across the sequence in a qualitatively similar pattern among orthologs. Regions of sequence involved in ligand binding and catalysis-termed mobile regions 1 and 2 (MR1 and MR2), respectively-showed the largest values for RMSF. Heat-induced changes in RMSF values across the sequence and, importantly, in MR1 and MR2 were greatest in cold-adapted species. MDS methods are shown to provide powerful tools for examining adaptation of enzymes by providing a quantitative index of protein flexibility and identifying sequence regions where adaptive change in flexibility occurs.

Two ways to solve, using Lie group analysis, the fundamental valuation equation in the double-square-root model of the term structure

NASA Astrophysics Data System (ADS)

Sinkala, W.

2011-01-01

Two approaches based on Lie group analysis are employed to obtain the closed-form solution of a partial differential equation derived by Francis A. Longstaff [J Financial Econom 1989;23:195-224] for the price of a discount bond in the double-square-root model of the term structure.

Prediction of Soil pH Hyperspectral Spectrum in Guanzhong Area of Shaanxi Province Based on PLS

NASA Astrophysics Data System (ADS)

Liu, Jinbao; Zhang, Yang; Wang, Huanyuan; Cheng, Jie; Tong, Wei; Wei, Jing

2017-12-01

The soil pH of Fufeng County, Yangling County and Wugong County in Shaanxi Province was studied. The spectral reflectance was measured by ASD Field Spec HR portable terrain spectrum, and its spectral characteristics were analyzed. The first deviation of the original spectral reflectance of the soil, the second deviation, the logarithm of the reciprocal logarithm, the first order differential of the reciprocal logarithm and the second order differential of the reciprocal logarithm were used to establish the soil pH Spectral prediction model. The results showed that the correlation between the reflectance spectra after SNV pre-treatment and the soil pH was significantly improved. The optimal prediction model of soil pH established by partial least squares method was a prediction model based on the first order differential of the reciprocal logarithm of spectral reflectance. The principal component factor was 10, the decision coefficient Rc2 = 0.9959, the model root means square error RMSEC = 0.0076, the correction deviation SEC = 0.0077; the verification decision coefficient Rv2 = 0.9893, the predicted root mean square error RMSEP = 0.0157, The deviation of SEP = 0.0160, the model was stable, the fitting ability and the prediction ability were high, and the soil pH can be measured quickly.

Removing Shape-Preserving Transformations in Square-Root Elastic (SRE) Framework for Shape Analysis of Curves

PubMed Central

Joshi, Shantanu H.; Klassen, Eric; Srivastava, Anuj; Jermyn, Ian

2011-01-01

This paper illustrates and extends an efficient framework, called the square-root-elastic (SRE) framework, for studying shapes of closed curves, that was first introduced in [2]. This framework combines the strengths of two important ideas - elastic shape metric and path-straightening methods - for finding geodesics in shape spaces of curves. The elastic metric allows for optimal matching of features between curves while path-straightening ensures that the algorithm results in geodesic paths. This paper extends this framework by removing two important shape preserving transformations: rotations and re-parameterizations, by forming quotient spaces and constructing geodesics on these quotient spaces. These ideas are demonstrated using experiments involving 2D and 3D curves. PMID:21738385

Community- Weighted Mean Plant Traits Predict Small Scale Distribution of Insect Root Herbivore Abundance

PubMed Central

Jeltsch, Florian; Wurst, Susanne

2015-01-01

Small scale distribution of insect root herbivores may promote plant species diversity by creating patches of different herbivore pressure. However, determinants of small scale distribution of insect root herbivores, and impact of land use intensity on their small scale distribution are largely unknown. We sampled insect root herbivores and measured vegetation parameters and soil water content along transects in grasslands of different management intensity in three regions in Germany. We calculated community-weighted mean plant traits to test whether the functional plant community composition determines the small scale distribution of insect root herbivores. To analyze spatial patterns in plant species and trait composition and insect root herbivore abundance we computed Mantel correlograms. Insect root herbivores mainly comprised click beetle (Coleoptera, Elateridae) larvae (43%) in the investigated grasslands. Total insect root herbivore numbers were positively related to community-weighted mean traits indicating high plant growth rates and biomass (specific leaf area, reproductive- and vegetative plant height), and negatively related to plant traits indicating poor tissue quality (leaf C/N ratio). Generalist Elaterid larvae, when analyzed independently, were also positively related to high plant growth rates and furthermore to root dry mass, but were not related to tissue quality. Insect root herbivore numbers were not related to plant cover, plant species richness and soil water content. Plant species composition and to a lesser extent plant trait composition displayed spatial autocorrelation, which was not influenced by land use intensity. Insect root herbivore abundance was not spatially autocorrelated. We conclude that in semi-natural grasslands with a high share of generalist insect root herbivores, insect root herbivores affiliate with large, fast growing plants, presumably because of availability of high quantities of food. Affiliation of insect root

Simulation of Ames Backbone Network

NASA Technical Reports Server (NTRS)

Shahnasser, Hamid

1998-01-01

The networking demands of Ames Research Center are dramatically increasing. More and more workstations are requested to run video and audio applications on the network. These applications require a much greater bandwidth than data applications. The existing ARCLAN 2000 network bandwidth is insufficient, due to the use of FDDI as its backbone, for accommodating video applications. Operating at a maximum of 100 Mbps, FDDI can handle only a few workstations running multimedia applications. The ideal solution is to replace the current ARCLAN 2000 FDDI backbone with an ATM backbone. ATM has the capability to handle the increasing traffic loads on the ARCLAN 2000 that results from these new applications. As it can be seen from Figure 1, ARCLAN 2000 have a total of 32 routers (5 being core routers) each connected to the FDDI backbone via a 100 Mbps link. This network serves 34 different locations by using 34 hubs that are connected to secondary routers. End users are connected to the secondary routers with 10 Mbps links.

Stock price estimation using ensemble Kalman Filter square root method

NASA Astrophysics Data System (ADS)

Karya, D. F.; Katias, P.; Herlambang, T.

2018-04-01

Shares are securities as the possession or equity evidence of an individual or corporation over an enterprise, especially public companies whose activity is stock trading. Investment in stocks trading is most likely to be the option of investors as stocks trading offers attractive profits. In determining a choice of safe investment in the stocks, the investors require a way of assessing the stock prices to buy so as to help optimize their profits. An effective method of analysis which will reduce the risk the investors may bear is by predicting or estimating the stock price. Estimation is carried out as a problem sometimes can be solved by using previous information or data related or relevant to the problem. The contribution of this paper is that the estimates of stock prices in high, low, and close categorycan be utilized as investors’ consideration for decision making in investment. In this paper, stock price estimation was made by using the Ensemble Kalman Filter Square Root method (EnKF-SR) and Ensemble Kalman Filter method (EnKF). The simulation results showed that the resulted estimation by applying EnKF method was more accurate than that by the EnKF-SR, with an estimation error of about 0.2 % by EnKF and an estimation error of 2.6 % by EnKF-SR.

Attacks exploiting deviation of mean photon number in quantum key distribution and coin tossing

NASA Astrophysics Data System (ADS)

Sajeed, Shihan; Radchenko, Igor; Kaiser, Sarah; Bourgoin, Jean-Philippe; Pappa, Anna; Monat, Laurent; Legré, Matthieu; Makarov, Vadim

2015-03-01

The security of quantum communication using a weak coherent source requires an accurate knowledge of the source's mean photon number. Finite calibration precision or an active manipulation by an attacker may cause the actual emitted photon number to deviate from the known value. We model effects of this deviation on the security of three quantum communication protocols: the Bennett-Brassard 1984 (BB84) quantum key distribution (QKD) protocol without decoy states, Scarani-Acín-Ribordy-Gisin 2004 (SARG04) QKD protocol, and a coin-tossing protocol. For QKD we model both a strong attack using technology possible in principle and a realistic attack bounded by today's technology. To maintain the mean photon number in two-way systems, such as plug-and-play and relativistic quantum cryptography schemes, bright pulse energy incoming from the communication channel must be monitored. Implementation of a monitoring detector has largely been ignored so far, except for ID Quantique's commercial QKD system Clavis2. We scrutinize this implementation for security problems and show that designing a hack-proof pulse-energy-measuring detector is far from trivial. Indeed, the first implementation has three serious flaws confirmed experimentally, each of which may be exploited in a cleverly constructed Trojan-horse attack. We discuss requirements for a loophole-free implementation of the monitoring detector.

Structure of the Bacillus subtilis phage SPO1-encoded type II DNA-binding protein TF1 in solution.

PubMed

Jia, X; Grove, A; Ivancic, M; Hsu, V L; Geiduscheck, E P; Kearns, D R

1996-10-25

The solution structure of a type II DNA-binding protein, the bacteriophage SPO1-encoded transcription factor 1 (TF1), was determined using NMR spectroscopy. Selective 2H-labeling, 13C-labeling and isotopic heterodimers were used to distinguish contacts between and within monomers of the dimeric protein. A total of 1914 distance and dihedral angle constraints derived from NMR experiments were used in structure calculations using restrained molecular dynamics and simulated annealing protocols. The ensemble of 30 calculated structures has a root-mean-square deviation (r.m.s.d.) of 0.9 A, about the average structure for the backbone atoms, and 1.2 A for all heavy-atoms of the dimeric core (helices 1 and 2) and the beta-sheets. A severe helix distortion at residues 92-93 in the middle of helix 3 is associated with r.m.s.d. of approximately 1.5 A for the helix 3 backbone. Deviations of approximately 5 A or larger are noted for the very flexible beta-ribbon arms that constitute part of a proposed DNA-binding region. A structural model of TF1 has been calculated based on the previously reported crystal structure of the homologous HU protein and this model was used as the starting structure for calculations. A comparison between the calculated average solution structure of TF1 and a solution structure of HU indicates a similarity in the dimeric core (excluding the nine amino acid residue tail) with pairwise deviations of 2 to 3 A. The largest deviations between the average structure and the HU solution structure were found in the beta-ribbon arms, as expected. A 4 A deviation is found at residue 15 of TF1 which is in a loop connecting two helical segments; it has been reported that substitution of Glu15 by Gly increases the thermostability of TF1. The homology between TF1 and other proteins of this family leads us to anticipate similar tertiary structures.

U.S. Navy Marine Climatic Atlas of the World. Volume IX. World-Wide Means and Standard Deviations

DTIC Science & Technology

1981-10-01

TITLE (..d SobtII,) S. TYPE OF REPORT & PERIOD COVERED U. S. Navy Marine Climatic Atlas of the World Volume IX World-wide Means and Standard Reference...Ives the best estimate of the population standard deviations. The means, , are com~nuted from: EX IIN I 90 80 70 60" 50’ 40, 30 20 10 0 1070 T- VErr ...or 10%, whichever is greater Since the mean ice limit approximates the minus two de l temperature isopleth, this analyzed lower limit was Wave Heights

Search for Randall-Sundrum gravitons in the dielectron and diphoton final states with 5.4  fb(-1) of data from pp collisions at square root(s) = 1.96  TeV.

PubMed

Abazov, V M; Abbott, B; Abolins, M; Acharya, B S; Adams, M; Adams, T; Aguilo, E; Alexeev, G D; Alkhazov, G; Alton, A; Alverson, G; Alves, G A; Ancu, L S; Aoki, M; Arnoud, Y; Arov, M; Askew, A; Asman, B; Atramentov, O; Avila, C; Backus Mayes, J; Badaud, F; Bagby, L; Baldin, B; Bandurin, D V; Banerjee, S; Barberis, E; Barfuss, A-F; Baringer, P; Barreto, J; Bartlett, J F; Bassler, U; Beale, S; Bean, A; Begalli, M; Begel, M; Belanger-Champagne, C; Bellantoni, L; Benitez, J A; Beri, S B; Bernardi, G; Bernhard, R; Bertram, I; Besançon, M; Beuselinck, R; Bezzubov, V A; Bhat, P C; Bhatnagar, V; Blazey, G; Blessing, S; Bloom, K; Boehnlein, A; Boline, D; Bolton, T A; Boos, E E; Borissov, G; Bose, T; Brandt, A; Brock, R; Brooijmans, G; Bross, A; Brown, D; Bu, X B; Buchholz, D; Buehler, M; Buescher, V; Bunichev, V; Burdin, S; Burnett, T H; Buszello, C P; Calfayan, P; Calpas, B; Calvet, S; Camacho-Pérez, E; Cammin, J; Carrasco-Lizarraga, M A; Carrera, E; Casey, B C K; Castilla-Valdez, H; Chakrabarti, S; Chakraborty, D; Chan, K M; Chandra, A; Chen, G; Chevalier-Théry, S; Cho, D K; Cho, S W; Choi, S; Choudhary, B; Christoudias, T; Cihangir, S; Claes, D; Clutter, J; Cooke, M S; Cooke, M; Cooper, W E; Corcoran, M; Couderc, F; Cousinou, M-C; Croc, A; Cutts, D; Cwiok, M; Das, A; Davies, G; De, K; de Jong, S J; De la Cruz-Burelo, E; DeVaughan, K; Déliot, F; Demarteau, M; Demina, R; Denisov, D; Denisov, S P; Desai, S; Diehl, H T; Diesburg, M; Dominguez, A; Dorland, T; Dubey, A; Dudko, L V; Duggan, D; Duperrin, A; Dutt, S; Dyshkant, A; Eads, M; Edmunds, D; Ellison, J; Elvira, V D; Enari, Y; Eno, S; Evans, H; Evdokimov, A; Evdokimov, V N; Facini, G; Ferapontov, A V; Ferbel, T; Fiedler, F; Filthaut, F; Fisher, W; Fisk, H E; Fortner, M; Fox, H; Fuess, S; Gadfort, T; Garcia-Bellido, A; Gavrilov, V; Gay, P; Geist, W; Geng, W; Gerbaudo, D; Gerber, C E; Gershtein, Y; Gillberg, D; Ginther, G; Golovanov, G; Goussiou, A; Grannis, P D; Greder, S; Greenlee, H; Greenwood, Z D; Gregores, E M; Grenier, G; Gris, Ph; Grivaz, J-F; Grohsjean, A; Grünendahl, S; Grünewald, M W; Guo, F; Guo, J; Gutierrez, G; Gutierrez, P; Haas, A; Haefner, P; Hagopian, S; Haley, J; Hall, I; Han, L; Harder, K; Harel, A; Hauptman, J M; Hays, J; Hebbeker, T; Hedin, D; Heinson, A P; Heintz, U; Hensel, C; Heredia-De la Cruz, I; Herner, K; Hesketh, G; Hildreth, M D; Hirosky, R; Hoang, T; Hobbs, J D; Hoeneisen, B; Hohlfeld, M; Hossain, S; Houben, P; Hu, Y; Hubacek, Z; Huske, N; Hynek, V; Iashvili, I; Illingworth, R; Ito, A S; Jabeen, S; Jaffré, M; Jain, S; Jamin, D; Jesik, R; Johns, K; Johnson, C; Johnson, M; Johnston, D; Jonckheere, A; Jonsson, P; Juste, A; Kaadze, K; Kajfasz, E; Karmanov, D; Kasper, P A; Katsanos, I; Kehoe, R; Kermiche, S; Khalatyan, N; Khanov, A; Kharchilava, A; Kharzheev, Y N; Khatidze, D; Kirby, M H; Kirsch, M; Kohli, J M; Kozelov, A V; Kraus, J; Kumar, A; Kupco, A; Kurca, T; Kuzmin, V A; Kvita, J; Lammers, S; Landsberg, G; Lebrun, P; Lee, H S; Lee, W M; Lellouch, J; Li, L; Li, Q Z; Lietti, S M; Lim, J K; Lincoln, D; Linnemann, J; Lipaev, V V; Lipton, R; Liu, Y; Liu, Z; Lobodenko, A; Lokajicek, M; Love, P; Lubatti, H J; Luna-Garcia, R; Lyon, A L; Maciel, A K A; Mackin, D; Madar, R; Magaña-Villalba, R; Mal, P K; Malik, S; Malyshev, V L; Maravin, Y; Martínez-Ortega, J; McCarthy, R; McGivern, C L; Meijer, M M; Melnitchouk, A; Menezes, D; Mercadante, P G; Merkin, M; Meyer, A; Meyer, J; Mondal, N K; Moulik, T; Muanza, G S; Mulhearn, M; Nagy, E; Naimuddin, M; Narain, M; Nayyar, R; Neal, H A; Negret, J P; Neustroev, P; Nilsen, H; Novaes, S F; Nunnemann, T; Obrant, G; Onoprienko, D; Orduna, J; Osman, N; Osta, J; Otero y Garzón, G J; Owen, M; Padilla, M; Pangilinan, M; Parashar, N; Parihar, V; Park, S-J; Park, S K; Parsons, J; Partridge, R; Parua, N; Patwa, A; Penning, B; Perfilov, M; Peters, K; Peters, Y; Petrillo, G; Pétroff, P; Piegaia, R; Piper, J; Pleier, M-A; Podesta-Lerma, P L M; Podstavkov, V M; Pol, M-E; Polozov, P; Popov, A V; Prewitt, M; Price, D; Protopopescu, S; Qian, J; Quadt, A; Quinn, B; Rangel, M S; Ranjan, K; Ratoff, P N; Razumov, I; Renkel, P; Rich, P; Rijssenbeek, M; Ripp-Baudot, I; Rizatdinova, F; Rominsky, M; Royon, C; Rubinov, P; Ruchti, R; Safronov, G; Sajot, G; Sánchez-Hernández, A; Sanders, M P; Sanghi, B; Savage, G; Sawyer, L; Scanlon, T; Schaile, D; Schamberger, R D; Scheglov, Y; Schellman, H; Schliephake, T; Schlobohm, S; Schwanenberger, C; Schwienhorst, R; Sekaric, J; Severini, H; Shabalina, E; Shary, V; Shchukin, A A; Shivpuri, R K; Simak, V; Sirotenko, V; Skubic, P; Slattery, P; Smirnov, D; Snow, G R; Snow, J; Snyder, S; Söldner-Rembold, S; Sonnenschein, L; Sopczak, A; Sosebee, M; Soustruznik, K; Spurlock, B; Stark, J; Stolin, V; Stoyanova, D A; Strang, M A; Strauss, E; Strauss, M; Ströhmer, R; Strom, D; Stutte, L; Svoisky, P; Takahashi, M; Tanasijczuk, A; Taylor, W; Tiller, B; Titov, M; Tokmenin, V V; Tsybychev, D; Tuchming, B; Tully, C; Tuts, P M; Unalan, R; Uvarov, L; Uvarov, S; Uzunyan, S; Van Kooten, R; van Leeuwen, W M; Varelas, N; Varnes, E W; Vasilyev, I A; Verdier, P; Vertogradov, L S; Verzocchi, M; Vesterinen, M; Vilanova, D; Vint, P; Vokac, P; Wahl, H D; Wang, M H L S; Warchol, J; Watts, G; Wayne, M; Weber, G; Weber, M; Wetstein, M; White, A; Wicke, D; Williams, M R J; Wilson, G W; Wimpenny, S J; Wobisch, M; Wood, D R; Wyatt, T R; Xie, Y; Xu, C; Yacoob, S; Yamada, R; Yang, W-C; Yasuda, T; Yatsunenko, Y A; Ye, Z; Yin, H; Yip, K; Yoo, H D; Youn, S W; Yu, J; Zelitch, S; Zhao, T; Zhou, B; Zhou, N; Zhu, J; Zielinski, M; Zieminska, D; Zivkovic, L

2010-06-18

Using 5.4  fb(-1) of integrated luminosity from pp collisions at square root(s)=1.96  TeV collected by the D0 detector at the Fermilab Tevatron Collider, we search for decays of the lightest Kaluza-Klein mode of the graviton in the Randall-Sundrum model to ee and γγ. We set 95% C.L. lower limits on the mass of the lightest graviton between 560 and 1050 GeV for values of the coupling k/M(Pl) between 0.01 and 0.1.

Optical pattern recognition architecture implementing the mean-square error correlation algorithm

DOEpatents

Molley, Perry A.

1991-01-01

An optical architecture implementing the mean-square error correlation algorithm, MSE=.SIGMA.[I-R].sup.2 for discriminating the presence of a reference image R in an input image scene I by computing the mean-square-error between a time-varying reference image signal s.sub.1 (t) and a time-varying input image signal s.sub.2 (t) includes a laser diode light source which is temporally modulated by a double-sideband suppressed-carrier source modulation signal I.sub.1 (t) having the form I.sub.1 (t)=A.sub.1 [1+.sqroot.2m.sub.1 s.sub.1 (t)cos (2.pi.f.sub.o t)] and the modulated light output from the laser diode source is diffracted by an acousto-optic deflector. The resultant intensity of the +1 diffracted order from the acousto-optic device is given by: I.sub.2 (t)=A.sub.2 [+2m.sub.2.sup.2 s.sub.2.sup.2 (t)-2.sqroot.2m.sub.2 (t) cos (2.pi.f.sub.o t] The time integration of the two signals I.sub.1 (t) and I.sub.2 (t) on the CCD deflector plane produces the result R(.tau.) of the mean-square error having the form: R(.tau.)=A.sub.1 A.sub.2 {[T]+[2m.sub.2.sup.2.multidot..intg.s.sub.2.sup.2 (t-.tau.)dt]-[2m.sub.1 m.sub.2 cos (2.tau.f.sub.o .tau.).multidot..intg.s.sub.1 (t)s.sub.2 (t-.tau.)dt]} where: s.sub.1 (t) is the signal input to the diode modulation source: s.sub.2 (t) is the signal input to the AOD modulation source; A.sub.1 is the light intensity; A.sub.2 is the diffraction efficiency; m.sub.1 and m.sub.2 are constants that determine the signal-to-bias ratio; f.sub.o is the frequency offset between the oscillator at f.sub.c and the modulation at f.sub.c +f.sub.o ; and a.sub.o and a.sub.1 are constant chosen to bias the diode source and the acousto-optic deflector into their respective linear operating regions so that the diode source exhibits a linear intensity characteristic and the AOD exhibits a linear amplitude characteristic.

A square root ensemble Kalman filter application to a motor-imagery brain-computer interface.

PubMed

Kamrunnahar, M; Schiff, S J

2011-01-01

We here investigated a non-linear ensemble Kalman filter (SPKF) application to a motor imagery brain computer interface (BCI). A square root central difference Kalman filter (SR-CDKF) was used as an approach for brain state estimation in motor imagery task performance, using scalp electroencephalography (EEG) signals. Healthy human subjects imagined left vs. right hand movements and tongue vs. bilateral toe movements while scalp EEG signals were recorded. Offline data analysis was conducted for training the model as well as for decoding the imagery movements. Preliminary results indicate the feasibility of this approach with a decoding accuracy of 78%-90% for the hand movements and 70%-90% for the tongue-toes movements. Ongoing research includes online BCI applications of this approach as well as combined state and parameter estimation using this algorithm with different system dynamic models.

A square root ensemble Kalman filter application to a motor-imagery brain-computer interface

PubMed Central

Kamrunnahar, M.; Schiff, S. J.

2017-01-01

We here investigated a non-linear ensemble Kalman filter (SPKF) application to a motor imagery brain computer interface (BCI). A square root central difference Kalman filter (SR-CDKF) was used as an approach for brain state estimation in motor imagery task performance, using scalp electroencephalography (EEG) signals. Healthy human subjects imagined left vs. right hand movements and tongue vs. bilateral toe movements while scalp EEG signals were recorded. Offline data analysis was conducted for training the model as well as for decoding the imagery movements. Preliminary results indicate the feasibility of this approach with a decoding accuracy of 78%–90% for the hand movements and 70%–90% for the tongue-toes movements. Ongoing research includes online BCI applications of this approach as well as combined state and parameter estimation using this algorithm with different system dynamic models. PMID:22255799

Estimation of water level and steam temperature using ensemble Kalman filter square root (EnKF-SR)

NASA Astrophysics Data System (ADS)

Herlambang, T.; Mufarrikoh, Z.; Karya, D. F.; Rahmalia, D.

2018-04-01

The equipment unit which has the most vital role in the steam-powered electric power plant is boiler. Steam drum boiler is a tank functioning to separate fluida into has phase and liquid phase. The existence in boiler system has a vital role. The controlled variables in the steam drum boiler are water level and the steam temperature. If the water level is higher than the determined level, then the gas phase resulted will contain steam endangering the following process and making the resulted steam going to turbine get less, and the by causing damages to pipes in the boiler. On the contrary, if less than the height of determined water level, the resulted height will result in dry steam likely to endanger steam drum. Thus an error was observed between the determined. This paper studied the implementation of the Ensemble Kalman Filter Square Root (EnKF-SR) method in nonlinear model of the steam drum boiler equation. The computation to estimate the height of water level and the temperature of steam was by simulation using Matlab software. Thus an error was observed between the determined water level and the steam temperature, and that of estimated water level and steam temperature. The result of simulation by Ensemble Kalman Filter Square Root (EnKF-SR) on the nonlinear model of steam drum boiler showed that the error was less than 2%. The implementation of EnKF-SR on the steam drum boiler r model comprises of three simulations, each of which generates 200, 300 and 400 ensembles. The best simulation exhibited the error between the real condition and the estimated result, by generating 400 ensemble. The simulation in water level in order of 0.00002145 m, whereas in the steam temperature was some 0.00002121 kelvin.

Predisposing factors to severe external root resorption associated to orthodontic treatment.

PubMed

Picanço, Gracemia Vasconcelos; de Freitas, Karina Maria Salvatore; Cançado, Rodrigo Hermont; Valarelli, Fabricio Pinelli; Picanço, Paulo Roberto Barroso; Feijão, Camila Pontes

2013-01-01

The aim of this study was to evaluate predisposing factors among patients who developed moderate or severe external root resorption (Malmgren's grades 3 and 4), on the maxillary incisors, during fixed orthodontic treatment in the permanent dentition. Ninety-nine patients who underwent orthodontic treatment with fixed edgewise appliances were selected. Patients were divided into two groups: G1 - 50 patients with no root resorption or presenting only apical irregularities (Malmgren's grades 0 and 1) at the end of the treatment, with mean initial age of 16.79 years and mean treatment time of 3.21 years; G2 - 49 patients presenting moderate or severe root resorption (Malmgren's grades 3 and 4) at the end of treatment on the maxillary incisors, with mean initial age of 19.92 years and mean treatment time of 3.98 years. Periapical radiographs and lateral cephalograms were evaluated. Factors that could influence the occurrence of severe root resorption were also recorded. Statistical analysis included chi-square tests, Fisher's exact test and independent t tests. The results demonstrated significant difference between the groups for the variables: Extractions, initial degree of root resorption, root length and crown/root ratio at the beginning, and cortical thickness of the alveolar bone. It can be concluded that: Presence of root resorption before the beginning of treatment, extractions, reduced root length, decreased crown/root ratio and thin alveolar bone represent risk factors for severe root resorption in maxillary incisors during orthodontic treatment.

Which similarity measure is better for analyzing protein structures in a molecular dynamics trajectory?

PubMed

Cossio, Pilar; Laio, Alessandro; Pietrucci, Fabio

2011-06-14

An important step in the computer simulation of the dynamics of biomolecules is the comparison of structures in a trajectory by exploiting a measure of distance. This allows distinguishing structures which are geometrically similar from those which are different. By analyzing microseconds-long all-atom molecular dynamics simulations of a polypeptide, we find that a distance based on backbone dihedral angles performs very well in distinguishing structures that are kinetically correlated from those that are not, while the widely used C(α) root mean square distance performs more poorly. The root mean square difference between contact matrices turns out instead to be the metric providing the highest clustering coefficient, namely, according to this similarity measure, the neighbors of a structure are also, on average, neighbors among themselves. We also propose a combined distance measure which, for the system considered here, performs well both for distinguishing structures which are distant in time and for giving a consistent cluster analysis. This journal is © the Owner Societies 2011

Crossover behavior of stock returns and mean square displacements of particles governed by the Langevin equation

NASA Astrophysics Data System (ADS)

Ma, Wen-Jong; Wang, Shih-Chieh; Chen, Chi-Ning; Hu, Chin-Kun

2013-06-01

It is found that the mean square log-returns calculated from the high-frequency one-day moving average of US and Taiwan stocks with the time internal τ show ballistic behavior \\theta \\tau^{\\alpha_1} with the exponent \\alpha_1 \\approx 2 for small τ and show diffusion-like behavior D \\tau^{\\alpha_2} with the exponent \\alpha_2 \\approx 1 for large τ. Such a crossover behavior can be well described by the mean square displacements of particles governed by the Langevin equation of motion. Thus, θ and D can be considered, respectively, as the temperature-like and diffusivity-like kinetic parameters of the market, and they can be used to characterize the behavior of the market.

Cost-effectiveness analysis of dolutegravir plus backbone compared with raltegravir plus backbone, darunavir+ritonavir plus backbone and efavirenz/tenofovir/emtricitabine in treatment naïve and experienced HIV-positive patients.

PubMed

Restelli, Umberto; Rizzardini, Giuliano; Antinori, Andrea; Lazzarin, Adriano; Bonfanti, Marzia; Bonfanti, Paolo; Croce, Davide

2017-01-01

In January 2014, the European Medicines Agency issued a marketing authorization for dolutegravir (DTG), a second-generation integrase strand transfer inhibitor for HIV treatment. The study aimed at determining the incremental cost-effectiveness ratio (ICER) of the use of DTG+backbone compared with raltegravir (RAL)+backbone, darunavir (DRV)+ritonavir(r)+backbone and efavirenz/tenofovir/emtricitabine (EFV/TDF/FTC) in HIV-positive treatment-naïve patients and compared with RAL+backbone in treatment-experienced patients, from the Italian National Health Service's point of view. A published Monte Carlo Individual Simulation Model (ARAMIS-DTG model) was used to perform the analysis. Patients pass through mutually exclusive health states (defined in terms of diagnosis of HIV with or without opportunistic infections [OIs] and cardiovascular disease [CVD]) and successive lines of therapy. The model considers costs (2014) and quality of life per monthly cycle in a lifetime horizon. Costs and quality-adjusted life years (QALYs) are dependent on OI, CVD, AIDS events, adverse events and antiretroviral therapies. In treatment-naïve patients, DTG dominates RAL; compared with DRV/r, the ICER obtained is of 38,586 €/QALY (6,170 €/QALY in patients with high viral load) and over EFV/TDF/FTC, DTG generates an ICER of 33,664 €/QALY. In treatment-experienced patients, DTG compared to RAL leads to an ICER of 12,074 €/QALY. The use of DTG+backbone may be cost effective in treatment-naïve and treatment-experienced patients compared with RAL+backbone and in treatment-naïve patients compared with DRV/r+backbone and EFV/TDF/FTC considering a threshold of 40,000 €/QALY.

A Simple Formula to Calculate Shallow-Water Transmission Loss by Means of a Least-Squares Surface Fit Technique.

DTIC Science & Technology

1980-09-01

HASTRUP , T REAL UNCLASSIFIED SACLAATCEN- SM-139 N SACLANTCEN Memorandum SM -139 -LEFW SACLANT ASW RESEARCH CENTRE ~ MEMORANDUM A SIMPLE FORMULA TO...CALCULATE SHALLOW-WATER TRANSMISSION LOSS BY MEANS OF A LEAST- SQUARES SURFACE FIT TECHNIQUE 7-sallby OLE F. HASTRUP and TUNCAY AKAL I SEPTEMBER 1980 NORTH...JRANSi4ISSION LOSS/ BY MEANS OF A LEAST-SQUARES SURFACE fIT TECHNIQUE, C T ~e F./ Hastrup .0TnaAa ()1 Sep 8 This memorandum has been prepared within the

Guided endodontics: accuracy of a novel method for guided access cavity preparation and root canal location.

PubMed

Zehnder, M S; Connert, T; Weiger, R; Krastl, G; Kühl, S

2016-10-01

To present a novel method utilizing 3D printed templates to gain guided access to root canals and to evaluate its accuracy in vitro. Sixty extracted human teeth were placed into six maxillary jaw models. Preoperative CBCT scans were matched with intra-oral scans using the coDiagnostix(™) software. Access cavities, sleeves and templates for guidance were virtually planned. Templates were produced by a 3D printer. After access cavity preparation by two operators, a postoperative CBCT scan was superimposed on the virtual planning. Accuracy was measured by calculating the deviation of planned and prepared cavities in three dimensions and angle. Ninety-five per cent confidence intervals were calculated for both operators. All root canals were accessible after cavity preparation with 'Guided Endodontics'. Deviations of planned and prepared access cavities were low with means ranging from 0.16 to 0.21 mm for different aspects at the base of the bur and 0.17-0.47 mm at the tip of the bur. Mean of angle deviation was 1.81°. Overlapping 95% confidence intervals revealed no significant difference between operators. 'Guided Endodontics' allowed an accurate access cavity preparation up to the apical third of the root utilizing printed templates for guidance. All root canals were accessible after preparation. © 2015 International Endodontic Journal. Published by John Wiley & Sons Ltd.

Force field-dependent structural divergence revealed during long time simulations of Calbindin d9k.

PubMed

Project, Elad; Nachliel, Esther; Gutman, Menachem

2010-07-15

The structural and the dynamic features of the Calbindin (CaB) protein in its holo and apo states are compared using molecular dynamics simulations under nine different force fields (FFs) (G43a1, G53a6, Opls-AA, Amber94, Amber99, Amber99p, AmberGS, AmberGSs, and Amber99sb). The results show that most FFs reproduce reasonably well the majority of the experimentally derived features of the CaB protein. However, in several cases, there are significant differences in secondary structure properties, root mean square deviations (RMSDs), root mean square fluctuations (RMSFs), and S(2) order parameters among the various FFs. What is more, in certain cases, these parameters differed from the experimentally derived values. Some of these deviations became noticeable only after 50 ns. A comparison with experimental data indicates that, for CaB, the Amber94 shows overall best agreement with the measured values, whereas several others seem to deviate from both crystal and nuclear magnetic resonance data. Copyright 2009 Wiley Periodicals, Inc.

What to use to express the variability of data: Standard deviation or standard error of mean?

PubMed

Barde, Mohini P; Barde, Prajakt J

2012-07-01

Statistics plays a vital role in biomedical research. It helps present data precisely and draws the meaningful conclusions. While presenting data, one should be aware of using adequate statistical measures. In biomedical journals, Standard Error of Mean (SEM) and Standard Deviation (SD) are used interchangeably to express the variability; though they measure different parameters. SEM quantifies uncertainty in estimate of the mean whereas SD indicates dispersion of the data from mean. As readers are generally interested in knowing the variability within sample, descriptive data should be precisely summarized with SD. Use of SEM should be limited to compute CI which measures the precision of population estimate. Journals can avoid such errors by requiring authors to adhere to their guidelines.

Effect of Deviated Nasal Septum on Mean Platelet Volume: A Prospective Study.

PubMed

Poorey, Vijay Kumar; Thakur, Pooja

2014-12-01

In E.N.T clinical practice, patients with nasal obstruction due to deviated nasal septum is a common presentation. Nasal airway obstruction is a common cause of upper airway obstruction further leading to obstructive and hypoxic manifestations. Mean platelet volume (MPV) levels increase in hypoxic conditions. MPV is one of the platelet activation index which reflects the platelet production rate. Present prospective study conducted in the department of Otorhinolaryngology and Head and Neck surgery, Gandhi Medical College and Hamidia Hospital, Bhopal, on 63 patients with the clinical evidence of DNS and 63 healthy age matched subjects as control group, aimed to evaluate the relationship between MPV levels and nasal obstruction due to deviated nasal septum (DNS). The diagnosis of patients with DNS was based on anterior rhinoscopy and endoscopic nasal examination. Blood samples were collected before surgical correction. In present study, the authors found that there is preponderance of DNS in the age group of 25-45 years being the most active age group, males having the higher incidence. Majority of cases of DNS being left sided and of obstructed type. MPV were significantly higher in patients with DNS than the control group. Among the cases MPV being higher in females and in the impacted type of DNS. Present study reemphasized the concept that MPV is increased in chronic nasal obstruction due to DNS and this increase is in accordance with the severity of DNS.

New theories of root growth modelling

NASA Astrophysics Data System (ADS)

Landl, Magdalena; Schnepf, Andrea; Vanderborght, Jan; Huber, Katrin; Javaux, Mathieu; Bengough, A. Glyn; Vereecken, Harry

2016-04-01

In dynamic root architecture models, root growth is represented by moving root tips whose line trajectory results in the creation of new root segments. Typically, the direction of root growth is calculated as the vector sum of various direction-affecting components. However, in our simulations this did not reproduce experimental observations of root growth in structured soil. We therefore developed a new approach to predict the root growth direction. In this approach we distinguish between, firstly, driving forces for root growth, i.e. the force exerted by the root which points in the direction of the previous root segment and gravitropism, and, secondly, the soil mechanical resistance to root growth or penetration resistance. The latter can be anisotropic, i.e. depending on the direction of growth, which leads to a difference between the direction of the driving force and the direction of the root tip movement. Anisotropy of penetration resistance can be caused either by microscale differences in soil structure or by macroscale features, including macropores. Anisotropy at the microscale is neglected in our model. To allow for this, we include a normally distributed random deflection angle α to the force which points in the direction of the previous root segment with zero mean and a standard deviation σ. The standard deviation σ is scaled, so that the deflection from the original root tip location does not depend on the spatial resolution of the root system model. Similarly to the water flow equation, the direction of the root tip movement corresponds to the water flux vector while the driving forces are related to the water potential gradient. The analogue of the hydraulic conductivity tensor is the root penetrability tensor. It is determined by the inverse of soil penetration resistance and describes the ease with which a root can penetrate the soil. By adapting the three dimensional soil and root water uptake model R-SWMS (Javaux et al., 2008) in this way

Search for the Higgs boson in events with missing transverse energy and b quark jets produced in pp collisions at square root(s)=1.96 TeV.

PubMed

Aaltonen, T; Adelman, J; Akimoto, T; Albrow, M G; Alvarez González, B; Amerio, S; Amidei, D; Anastassov, A; Annovi, A; Antos, J; Aoki, M; Apollinari, G; Apresyan, A; Arisawa, T; Artikov, A; Ashmanskas, W; Attal, A; Aurisano, A; Azfar, F; Azzi-Bacchetta, P; Azzurri, P; Bacchetta, N; Badgett, W; Barbaro-Galtieri, A; Barnes, V E; Barnett, B A; Baroiant, S; Bartsch, V; Bauer, G; Beauchemin, P-H; Bedeschi, F; Bednar, P; Behari, S; Bellettini, G; Bellinger, J; Belloni, A; Benjamin, D; Beretvas, A; Beringer, J; Berry, T; Bhatti, A; Binkley, M; Bisello, D; Bizjak, I; Blair, R E; Blocker, C; Blumenfeld, B; Bocci, A; Bodek, A; Boisvert, V; Bolla, G; Bolshov, A; Bortoletto, D; Boudreau, J; Boveia, A; Brau, B; Bridgeman, A; Brigliadori, L; Bromberg, C; Brubaker, E; Budagov, J; Budd, H S; Budd, S; Burkett, K; Busetto, G; Bussey, P; Buzatu, A; Byrum, K L; Cabrera, S; Campanelli, M; Campbell, M; Canelli, F; Canepa, A; Carlsmith, D; Carosi, R; Carrillo, S; Carron, S; Casal, B; Casarsa, M; Castro, A; Catastini, P; Cauz, D; Cavalli-Sforza, M; Cerri, A; Cerrito, L; Chang, S H; Chen, Y C; Chertok, M; Chiarelli, G; Chlachidze, G; Chlebana, F; Cho, K; Chokheli, D; Chou, J P; Choudalakis, G; Chuang, S H; Chung, K; Chung, W H; Chung, Y S; Ciobanu, C I; Ciocci, M A; Clark, A; Clark, D; Compostella, G; Convery, M E; Conway, J; Cooper, B; Copic, K; Cordelli, M; Cortiana, G; Crescioli, F; Cuenca Almenar, C; Cuevas, J; Culbertson, R; Cully, J C; Dagenhart, D; Datta, M; Davies, T; de Barbaro, P; De Cecco, S; Deisher, A; De Lentdecker, G; De Lorenzo, G; Dell'Orso, M; Demortier, L; Deng, J; Deninno, M; De Pedis, D; Derwent, P F; Di Giovanni, G P; Dionisi, C; Di Ruzza, B; Dittmann, J R; D'Onofrio, M; Donati, S; Dong, P; Donini, J; Dorigo, T; Dube, S; Efron, J; Erbacher, R; Errede, D; Errede, S; Eusebi, R; Fang, H C; Farrington, S; Fedorko, W T; Feild, R G; Feindt, M; Fernandez, J P; Ferrazza, C; Field, R; Flanagan, G; Forrest, R; Forrester, S; Franklin, M; Freeman, J C; Furic, I; Gallinaro, M; Galyardt, J; Garberson, F; Garcia, J E; Garfinkel, A F; Genser, K; Gerberich, H; Gerdes, D; Giagu, S; Giakoumopolou, V; Giannetti, P; Gibson, K; Gimmell, J L; Ginsburg, C M; Giokaris, N; Giordani, M; Giromini, P; Giunta, M; Glagolev, V; Glenzinski, D; Gold, M; Goldschmidt, N; Golossanov, A; Gomez, G; Gomez-Ceballos, G; Goncharov, M; González, O; Gorelov, I; Goshaw, A T; Goulianos, K; Gresele, A; Grinstein, S; Grosso-Pilcher, C; Grundler, U; Guimaraes da Costa, J; Gunay-Unalan, Z; Haber, C; Hahn, K; Hahn, S R; Halkiadakis, E; Hamilton, A; Han, B-Y; Han, J Y; Handler, R; Happacher, F; Hara, K; Hare, D; Hare, M; Harper, S; Harr, R F; Harris, R M; Hartz, M; Hatakeyama, K; Hauser, J; Hays, C; Heck, M; Heijboer, A; Heinemann, B; Heinrich, J; Henderson, C; Herndon, M; Heuser, J; Hewamanage, S; Hidas, D; Hill, C S; Hirschbuehl, D; Hocker, A; Hou, S; Houlden, M; Hsu, S-C; Huffman, B T; Hughes, R E; Husemann, U; Huston, J; Incandela, J; Introzzi, G; Iori, M; Ivanov, A; Iyutin, B; James, E; Jayatilaka, B; Jeans, D; Jeon, E J; Jindariani, S; Johnson, W; Jones, M; Joo, K K; Jun, S Y; Jung, J E; Junk, T R; Kamon, T; Kar, D; Karchin, P E; Kato, Y; Kephart, R; Kerzel, U; Khotilovich, V; Kilminster, B; Kim, D H; Kim, H S; Kim, J E; Kim, M J; Kim, S B; Kim, S H; Kim, Y K; Kimura, N; Kirsch, L; Klimenko, S; Klute, M; Knuteson, B; Ko, B R; Koay, S A; Kondo, K; Kong, D J; Konigsberg, J; Korytov, A; Kotwal, A V; Kraus, J; Kreps, M; Kroll, J; Krumnack, N; Kruse, M; Krutelyov, V; Kubo, T; Kuhlmann, S E; Kuhr, T; Kulkarni, N P; Kusakabe, Y; Kwang, S; Laasanen, A T; Lai, S; Lami, S; Lammel, S; Lancaster, M; Lander, R L; Lannon, K; Lath, A; Latino, G; Lazzizzera, I; LeCompte, T; Lee, J; Lee, J; Lee, Y J; Lee, S W; Lefèvre, R; Leonardo, N; Leone, S; Levy, S; Lewis, J D; Lin, C; Lin, C S; Linacre, J; Lindgren, M; Lipeles, E; Lister, A; Litvintsev, D O; Liu, T; Lockyer, N S; Loginov, A; Loreti, M; Lovas, L; Lu, R-S; Lucchesi, D; Lueck, J; Luci, C; Lujan, P; Lukens, P; Lungu, G; Lyons, L; Lys, J; Lysak, R; Lytken, E; Mack, P; Macqueen, D; Madrak, R; Maeshima, K; Makhoul, K; Maki, T; Maksimovic, P; Malde, S; Malik, S; Manca, G; Manousakis, A; Margaroli, F; Marino, C; Marino, C P; Martin, A; Martin, M; Martin, V; Martínez, M; Martínez-Ballarín, R; Maruyama, T; Mastrandrea, P; Masubuchi, T; Mattson, M E; Mazzanti, P; McFarland, K S; McIntyre, P; McNulty, R; Mehta, A; Mehtala, P; Menzemer, S; Menzione, A; Merkel, P; Mesropian, C; Messina, A; Miao, T; Miladinovic, N; Miles, J; Miller, R; Mills, C; Milnik, M; Mitra, A; Mitselmakher, G; Miyake, H; Moed, S; Moggi, N; Moon, C S; Moore, R; Morello, M; Movilla Fernandez, P; Mülmenstädt, J; Mukherjee, A; Muller, Th; Mumford, R; Murat, P; Mussini, M; Nachtman, J; Nagai, Y; Nagano, A; Naganoma, J; Nakamura, K; Nakano, I; Napier, A; Necula, V; Neu, C; Neubauer, M S; Nielsen, J; Nodulman, L; Norman, M; Norniella, O; Nurse, E; Oh, S H; Oh, Y D; Oksuzian, I; Okusawa, T; Oldeman, R; Orava, R; Osterberg, K; Pagan Griso, S; Pagliarone, C; Palencia, E; Papadimitriou, V; Papaikonomou, A; Paramonov, A A; Parks, B; Pashapour, S; Patrick, J; Pauletta, G; Paulini, M; Paus, C; Pellett, D E; Penzo, A; Phillips, T J; Piacentino, G; Piedra, J; Pinera, L; Pitts, K; Plager, C; Pondrom, L; Portell, X; Poukhov, O; Pounder, N; Prakoshyn, F; Pronko, A; Proudfoot, J; Ptohos, F; Punzi, G; Pursley, J; Rademacker, J; Rahaman, A; Ramakrishnan, V; Ranjan, N; Redondo, I; Reisert, B; Rekovic, V; Renton, P; Rescigno, M; Richter, S; Rimondi, F; Ristori, L; Robson, A; Rodrigo, T; Rogers, E; Rolli, S; Roser, R; Rossi, M; Rossin, R; Rott, C; Roy, P; Ruiz, A; Russ, J; Rusu, V; Saarikko, H; Safonov, A; Sakumoto, W K; Salamanna, G; Saltó, O; Santi, L; Sarkar, S; Sartori, L; Sato, K; Savoy-Navarro, A; Scheidle, T; Schlabach, P; Schmidt, E E; Schmidt, M A; Schmidt, M P; Schmitt, M; Schwarz, T; Scodellaro, L; Scott, A L; Scribano, A; Scuri, F; Sedov, A; Seidel, S; Seiya, Y; Semenov, A; Sexton-Kennedy, L; Sfyrla, A; Shalhout, S Z; Shapiro, M D; Shears, T; Shepard, P F; Sherman, D; Shimojima, M; Shochet, M; Shon, Y; Shreyber, I; Sidoti, A; Sinervo, P; Sisakyan, A; Slaughter, A J; Slaunwhite, J; Sliwa, K; Smith, J R; Snider, F D; Snihur, R; Soderberg, M; Soha, A; Somalwar, S; Sorin, V; Spalding, J; Spinella, F; Spreitzer, T; Squillacioti, P; Stanitzki, M; St Denis, R; Stelzer, B; Stelzer-Chilton, O; Stentz, D; Strologas, J; Stuart, D; Suh, J S; Sukhanov, A; Sun, H; Suslov, I; Suzuki, T; Taffard, A; Takashima, R; Takeuchi, Y; Tanaka, R; Tecchio, M; Teng, P K; Terashi, K; Thom, J; Thompson, A S; Thompson, G A; Thomson, E; Tipton, P; Tiwari, V; Tkaczyk, S; Toback, D; Tokar, S; Tollefson, K; Tomura, T; Tonelli, D; Torre, S; Torretta, D; Tourneur, S; Trischuk, W; Tu, Y; Turini, N; Ukegawa, F; Uozumi, S; Vallecorsa, S; van Remortel, N; Varganov, A; Vataga, E; Vázquez, F; Velev, G; Vellidis, C; Veszpremi, V; Vidal, M; Vidal, R; Vila, I; Vilar, R; Vine, T; Vogel, M; Volobouev, I; Volpi, G; Würthwein, F; Wagner, P; Wagner, R G; Wagner, R L; Wagner-Kuhr, J; Wagner, W; Wakisaka, T; Wallny, R; Wang, S M; Warburton, A; Waters, D; Weinberger, M; Wester, W C; Whitehouse, B; Whiteson, D; Wicklund, A B; Wicklund, E; Williams, G; Williams, H H; Wilson, P; Winer, B L; Wittich, P; Wolbers, S; Wolfe, C; Wright, T; Wu, X; Wynne, S M; Yagil, A; Yamamoto, K; Yamaoka, J; Yamashita, T; Yang, C; Yang, U K; Yang, Y C; Yao, W M; Yeh, G P; Yoh, J; Yorita, K; Yoshida, T; Yu, G B; Yu, I; Yu, S S; Yun, J C; Zanello, L; Zanetti, A; Zaw, I; Zhang, X; Zheng, Y; Zucchelli, S

2008-05-30

We search for the standard model Higgs boson produced in association with an electroweak vector boson in events with no identified charged leptons, large imbalance in transverse momentum, and two jets where at least one contains a secondary vertex consistent with the decay of b hadrons. We use approximately 1 fb(-1) integrated luminosity of pp collisions at square root(s)=1.96 TeV recorded by the Collider Detector at Fermilab II experiment at the Tevatron. We find 268 (16) single (double) b-tagged candidate events, where 248+/-43 (14.4+/-2.7) are expected from standard model background processes. We observe no significant excess over the expected background and thus set 95% confidence level upper limits on the Higgs boson production cross section for several Higgs boson masses ranging from 110 to 140 GeV/c(2). For a mass of 115 GeV/c(2), the observed (expected) limit is 20.4 (14.2) times the standard model prediction.

Cost-effectiveness analysis of dolutegravir plus backbone compared with raltegravir plus backbone, darunavir+ritonavir plus backbone and efavirenz/tenofovir/emtricitabine in treatment naïve and experienced HIV-positive patients

PubMed Central

Restelli, Umberto; Rizzardini, Giuliano; Antinori, Andrea; Lazzarin, Adriano; Bonfanti, Marzia; Bonfanti, Paolo; Croce, Davide

2017-01-01

Background In January 2014, the European Medicines Agency issued a marketing authorization for dolutegravir (DTG), a second-generation integrase strand transfer inhibitor for HIV treatment. The study aimed at determining the incremental cost-effectiveness ratio (ICER) of the use of DTG+backbone compared with raltegravir (RAL)+backbone, darunavir (DRV)+ritonavir(r)+backbone and efavirenz/tenofovir/emtricitabine (EFV/TDF/FTC) in HIV-positive treatment-naïve patients and compared with RAL+backbone in treatment-experienced patients, from the Italian National Health Service’s point of view. Materials and methods A published Monte Carlo Individual Simulation Model (ARAMIS-DTG model) was used to perform the analysis. Patients pass through mutually exclusive health states (defined in terms of diagnosis of HIV with or without opportunistic infections [OIs] and cardiovascular disease [CVD]) and successive lines of therapy. The model considers costs (2014) and quality of life per monthly cycle in a lifetime horizon. Costs and quality-adjusted life years (QALYs) are dependent on OI, CVD, AIDS events, adverse events and antiretroviral therapies. Results In treatment-naïve patients, DTG dominates RAL; compared with DRV/r, the ICER obtained is of 38,586 €/QALY (6,170 €/QALY in patients with high viral load) and over EFV/TDF/FTC, DTG generates an ICER of 33,664 €/QALY. In treatment-experienced patients, DTG compared to RAL leads to an ICER of 12,074 €/QALY. Conclusion The use of DTG+backbone may be cost effective in treatment-naïve and treatment-experienced patients compared with RAL+backbone and in treatment-naïve patients compared with DRV/r+backbone and EFV/TDF/FTC considering a threshold of 40,000 €/QALY. PMID:28721059

Large deviations in the random sieve

NASA Astrophysics Data System (ADS)

Grimmett, Geoffrey

1997-05-01

The proportion [rho]k of gaps with length k between square-free numbers is shown to satisfy log[rho]k=[minus sign](1+o(1))(6/[pi]2) klogk as k[rightward arrow][infty infinity]. Such asymptotics are consistent with Erdos's challenge to prove that the gap following the square-free number t is smaller than clogt/log logt, for all t and some constant c satisfying c>[pi]2/12. The results of this paper are achieved by studying the probabilities of large deviations in a certain ‘random sieve’, for which the proportions [rho]k have representations as probabilities. The asymptotic form of [rho]k may be obtained in situations of greater generality, when the squared primes are replaced by an arbitrary sequence (sr) of relatively prime integers satisfying [sum L: summation operator]r1/sr<[infty infinity], subject to two further conditions of regularity on this sequence.

Search for the Higgs boson using neural networks in events with missing energy and b-quark jets in pp collisions at square root(s) = 1.96 TeV.

PubMed

Aaltonen, T; Adelman, J; Alvarez González, B; Amerio, S; Amidei, D; Anastassov, A; Annovi, A; Antos, J; Apollinari, G; Apresyan, A; Arisawa, T; Artikov, A; Asaadi, J; Ashmanskas, W; Attal, A; Aurisano, A; Azfar, F; Badgett, W; Barbaro-Galtieri, A; Barnes, V E; Barnett, B A; Barria, P; Bartos, P; Bauer, G; Beauchemin, P-H; Bedeschi, F; Beecher, D; Behari, S; Bellettini, G; Bellinger, J; Benjamin, D; Beretvas, A; Bhatti, A; Binkley, M; Bisello, D; Bizjak, I; Blair, R E; Blocker, C; Blumenfeld, B; Bocci, A; Bodek, A; Boisvert, V; Bortoletto, D; Boudreau, J; Boveia, A; Brau, B; Bridgeman, A; Brigliadori, L; Bromberg, C; Brubaker, E; Budagov, J; Budd, H S; Budd, S; Burkett, K; Busetto, G; Bussey, P; Buzatu, A; Byrum, K L; Cabrera, S; Calancha, C; Camarda, S; Campanelli, M; Campbell, M; Canelli, F; Canepa, A; Carls, B; Carlsmith, D; Carosi, R; Carrillo, S; Carron, S; Casal, B; Casarsa, M; Castro, A; Catastini, P; Cauz, D; Cavaliere, V; Cavalli-Sforza, M; Cerri, A; Cerrito, L; Chang, S H; Chen, Y C; Chertok, M; Chiarelli, G; Chlachidze, G; Chlebana, F; Cho, K; Chokheli, D; Chou, J P; Chung, K; Chung, W H; Chung, Y S; Chwalek, T; Ciobanu, C I; Ciocci, M A; Clark, A; Clark, D; Compostella, G; Convery, M E; Conway, J; Corbo, M; Cordelli, M; Cox, C A; Cox, D J; Crescioli, F; Cuenca Almenar, C; Cuevas, J; Culbertson, R; Cully, J C; Dagenhart, D; Datta, M; Davies, T; de Barbaro, P; De Cecco, S; Deisher, A; De Lorenzo, G; Dell'Orso, M; Deluca, C; Demortier, L; Deng, J; Deninno, M; d'Errico, M; Di Canto, A; di Giovanni, G P; Di Ruzza, B; Dittmann, J R; D'Onofrio, M; Donati, S; Dong, P; Dorigo, T; Dube, S; Ebina, K; Elagin, A; Erbacher, R; Errede, D; Errede, S; Ershaidat, N; Eusebi, R; Fang, H C; Farrington, S; Fedorko, W T; Feild, R G; Feindt, M; Fernandez, J P; Ferrazza, C; Field, R; Flanagan, G; Forrest, R; Frank, M J; Franklin, M; Freeman, J C; Furic, I; Gallinaro, M; Galyardt, J; Garberson, F; Garcia, J E; Garfinkel, A F; Garosi, P; Gerberich, H; Gerdes, D; Gessler, A; Giagu, S; Giakoumopoulou, V; Giannetti, P; Gibson, K; Gimmell, J L; Ginsburg, C M; Giokaris, N; Giordani, M; Giromini, P; Giunta, M; Giurgiu, G; Glagolev, V; Glenzinski, D; Gold, M; Goldschmidt, N; Golossanov, A; Gomez, G; Gomez-Ceballos, G; Goncharov, M; González, O; Gorelov, I; Goshaw, A T; Goulianos, K; Gresele, A; Grinstein, S; Grosso-Pilcher, C; Group, R C; Grundler, U; Guimaraes da Costa, J; Gunay-Unalan, Z; Haber, C; Hahn, S R; Halkiadakis, E; Han, B-Y; Han, J Y; Happacher, F; Hara, K; Hare, D; Hare, M; Harr, R F; Hartz, M; Hatakeyama, K; Hays, C; Heck, M; Heinrich, J; Herndon, M; Heuser, J; Hewamanage, S; Hidas, D; Hill, C S; Hirschbuehl, D; Hocker, A; Hou, S; Houlden, M; Hsu, S-C; Hughes, R E; Hurwitz, M; Husemann, U; Hussein, M; Huston, J; Incandela, J; Introzzi, G; Iori, M; Ivanov, A; James, E; Jang, D; Jayatilaka, B; Jeon, E J; Jha, M K; Jindariani, S; Johnson, W; Jones, M; Joo, K K; Jun, S Y; Jung, J E; Junk, T R; Kamon, T; Kar, D; Karchin, P E; Kato, Y; Kephart, R; Ketchum, W; Keung, J; Khotilovich, V; Kilminster, B; Kim, D H; Kim, H S; Kim, H W; Kim, J E; Kim, M J; Kim, S B; Kim, S H; Kim, Y K; Kimura, N; Kirsch, L; Klimenko, S; Kondo, K; Kong, D J; Konigsberg, J; Korytov, A; Kotwal, A V; Kreps, M; Kroll, J; Krop, D; Krumnack, N; Kruse, M; Krutelyov, V; Kuhr, T; Kulkarni, N P; Kurata, M; Kwang, S; Laasanen, A T; Lami, S; Lammel, S; Lancaster, M; Lander, R L; Lannon, K; Lath, A; Latino, G; Lazzizzera, I; LeCompte, T; Lee, E; Lee, H S; Lee, J S; Lee, S W; Leone, S; Lewis, J D; Lin, C-J; Linacre, J; Lindgren, M; Lipeles, E; Lister, A; Litvintsev, D O; Liu, C; Liu, T; Lockyer, N S; Loginov, A; Lovas, L; Lucchesi, D; Lueck, J; Lujan, P; Lukens, P; Lungu, G; Lys, J; Lysak, R; MacQueen, D; Madrak, R; Maeshima, K; Makhoul, K; Maksimovic, P; Malde, S; Malik, S; Manca, G; Manousakis-Katsikakis, A; Margaroli, F; Marino, C; Marino, C P; Martin, A; Martin, V; Martínez, M; Martínez-Ballarín, R; Mastrandrea, P; Mathis, M; Mattson, M E; Mazzanti, P; McFarland, K S; McIntyre, P; McNulty, R; Mehta, A; Mehtala, P; Menzione, A; Mesropian, C; Miao, T; Mietlicki, D; Miladinovic, N; Miller, R; Mills, C; Milnik, M; Mitra, A; Mitselmakher, G; Miyake, H; Moed, S; Moggi, N; Mondragon, M N; Moon, C S; Moore, R; Morello, M J; Morlock, J; Movilla Fernandez, P; Mülmenstädt, J; Mukherjee, A; Muller, Th; Murat, P; Mussini, M; Nachtman, J; Nagai, Y; Naganoma, J; Nakamura, K; Nakano, I; Napier, A; Nett, J; Neu, C; Neubauer, M S; Neubauer, S; Nielsen, J; Nodulman, L; Norman, M; Norniella, O; Nurse, E; Oakes, L; Oh, S H; Oh, Y D; Oksuzian, I; Okusawa, T; Orava, R; Osterberg, K; Pagan Griso, S; Pagliarone, C; Palencia, E; Papadimitriou, V; Papaikonomou, A; Paramanov, A A; Parks, B; Pashapour, S; Patrick, J; Pauletta, G; Paulini, M; Paus, C; Peiffer, T; Pellett, D E; Penzo, A; Phillips, T J; Piacentino, G; Pianori, E; Pinera, L; Pitts, K; Plager, C; Pondrom, L; Potamianos, K; Poukhov, O; Prokoshin, F; Pronko, A; Ptohos, F; Pueschel, E; Punzi, G; Pursley, J; Rademacker, J; Rahaman, A; Ramakrishnan, V; Ranjan, N; Redondo, I; Renton, P; Renz, M; Rescigno, M; Richter, S; Rimondi, F; Ristori, L; Robson, A; Rodrigo, T; Rodriguez, T; Rogers, E; Rolli, S; Roser, R; Rossi, M; Rossin, R; Roy, P; Ruiz, A; Russ, J; Rusu, V; Rutherford, B; Saarikko, H; Safonov, A; Sakumoto, W K; Santi, L; Sartori, L; Sato, K; Savoy-Navarro, A; Schlabach, P; Schmidt, A; Schmidt, E E; Schmidt, M A; Schmidt, M P; Schmitt, M; Schwarz, T; Scodellaro, L; Scribano, A; Scuri, F; Sedov, A; Seidel, S; Seiya, Y; Semenov, A; Sexton-Kennedy, L; Sforza, F; Sfyrla, A; Shalhout, S Z; Shears, T; Shepard, P F; Shimojima, M; Shiraishi, S; Shochet, M; Shon, Y; Shreyber, I; Simonenko, A; Sinervo, P; Sisakyan, A; Slaughter, A J; Slaunwhite, J; Sliwa, K; Smith, J R; Snider, F D; Snihur, R; Soha, A; Somalwar, S; Sorin, V; Squillacioti, P; Stanitzki, M; St Denis, R; Stelzer, B; Stelzer-Chilton, O; Stentz, D; Strologas, J; Strycker, G L; Suh, J S; Sukhanov, A; Suslov, I; Taffard, A; Takashima, R; Takeuchi, Y; Tanaka, R; Tang, J; Tecchio, M; Teng, P K; Thom, J; Thome, J; Thompson, G A; Thomson, E; Tipton, P; Ttito-Guzmán, P; Tkaczyk, S; Toback, D; Tokar, S; Tollefson, K; Tomura, T; Tonelli, D; Torre, S; Torretta, D; Totaro, P; Tourneur, S; Trovato, M; Tsai, S-Y; Tu, Y; Turini, N; Ukegawa, F; Uozumi, S; van Remortel, N; Varganov, A; Vataga, E; Vázquez, F; Velev, G; Vellidis, C; Vidal, M; Vila, I; Vilar, R; Vogel, M; Volobouev, I; Volpi, G; Wagner, P; Wagner, R G; Wagner, R L; Wagner, W; Wagner-Kuhr, J; Wakisaka, T; Wallny, R; Wang, S M; Warburton, A; Waters, D; Weinberger, M; Weinelt, J; Wester, W C; Whitehouse, B; Whiteson, D; Wicklund, A B; Wicklund, E; Wilbur, S; Williams, G; Williams, H H; Wilson, P; Winer, B L; Wittich, P; Wolbers, S; Wolfe, C; Wolfe, H; Wright, T; Wu, X; Würthwein, F; Yagil, A; Yamamoto, K; Yamaoka, J; Yang, U K; Yang, Y C; Yao, W M; Yeh, G P; Yi, K; Yoh, J; Yorita, K; Yoshida, T; Yu, G B; Yu, I; Yu, S S; Yun, J C; Zanetti, A; Zeng, Y; Zhang, X; Zheng, Y; Zucchelli, S

2010-04-09

We report on a search for the standard model Higgs boson produced in association with a W or Z boson in pp collisions at square root(s)=1.96 TeV recorded by the CDF II experiment at the Tevatron in a data sample corresponding to an integrated luminosity of 2.1 fb(-1). We consider events which have no identified charged leptons, an imbalance in transverse momentum, and two or three jets where at least one jet is consistent with originating from the decay of a b hadron. We find good agreement between data and background predictions. We place 95% confidence level upper limits on the production cross section for several Higgs boson masses ranging from 110 GeV/c(2) to 150 GeV/c(2). For a mass of 115 GeV/c(2) the observed (expected) limit is 6.9 (5.6) times the standard model prediction.

The retest distribution of the visual field summary index mean deviation is close to normal.

PubMed

Anderson, Andrew J; Cheng, Allan C Y; Lau, Samantha; Le-Pham, Anne; Liu, Victor; Rahman, Farahnaz

2016-09-01

When modelling optimum strategies for how best to determine visual field progression in glaucoma, it is commonly assumed that the summary index mean deviation (MD) is normally distributed on repeated testing. Here we tested whether this assumption is correct. We obtained 42 reliable 24-2 Humphrey Field Analyzer SITA standard visual fields from one eye of each of five healthy young observers, with the first two fields excluded from analysis. Previous work has shown that although MD variability is higher in glaucoma, the shape of the MD distribution is similar to that found in normal visual fields. A Shapiro-Wilks test determined any deviation from normality. Kurtosis values for the distributions were also calculated. Data from each observer passed the Shapiro-Wilks normality test. Bootstrapped 95% confidence intervals for kurtosis encompassed the value for a normal distribution in four of five observers. When examined with quantile-quantile plots, distributions were close to normal and showed no consistent deviations across observers. The retest distribution of MD is not significantly different from normal in healthy observers, and so is likely also normally distributed - or nearly so - in those with glaucoma. Our results increase our confidence in the results of influential modelling studies where a normal distribution for MD was assumed. © 2016 The Authors Ophthalmic & Physiological Optics © 2016 The College of Optometrists.

Development of variable pathlength UV-vis spectroscopy combined with partial-least-squares regression for wastewater chemical oxygen demand (COD) monitoring.

PubMed

Chen, Baisheng; Wu, Huanan; Li, Sam Fong Yau

2014-03-01

To overcome the challenging task to select an appropriate pathlength for wastewater chemical oxygen demand (COD) monitoring with high accuracy by UV-vis spectroscopy in wastewater treatment process, a variable pathlength approach combined with partial-least squares regression (PLSR) was developed in this study. Two new strategies were proposed to extract relevant information of UV-vis spectral data from variable pathlength measurements. The first strategy was by data fusion with two data fusion levels: low-level data fusion (LLDF) and mid-level data fusion (MLDF). Predictive accuracy was found to improve, indicated by the lower root-mean-square errors of prediction (RMSEP) compared with those obtained for single pathlength measurements. Both fusion levels were found to deliver very robust PLSR models with residual predictive deviations (RPD) greater than 3 (i.e. 3.22 and 3.29, respectively). The second strategy involved calculating the slopes of absorbance against pathlength at each wavelength to generate slope-derived spectra. Without the requirement to select the optimal pathlength, the predictive accuracy (RMSEP) was improved by 20-43% as compared to single pathlength spectroscopy. Comparing to nine-factor models from fusion strategy, the PLSR model from slope-derived spectroscopy was found to be more parsimonious with only five factors and more robust with residual predictive deviation (RPD) of 3.72. It also offered excellent correlation of predicted and measured COD values with R(2) of 0.936. In sum, variable pathlength spectroscopy with the two proposed data analysis strategies proved to be successful in enhancing prediction performance of COD in wastewater and showed high potential to be applied in on-line water quality monitoring. Copyright © 2013 Elsevier B.V. All rights reserved.

Molecular dynamics simulation and binding free energy studies of novel leads belonging to the benzofuran class inhibitors of Mycobacterium tuberculosis Polyketide Synthase 13.

PubMed

Cruz, Jorddy N; Costa, José F S; Khayat, André S; Kuca, Kamil; Barros, Carlos A L; Neto, A M J C

2018-05-04

In this work, the binding mechanism of new Polyketide Synthase 13 (Pks13) inhibitors has been studied through molecular dynamics simulation and free energy calculations. The drug Tam1 and its analogs, belonging to the benzofuran class, were submitted to 100 ns simulations, and according to the results obtained for root mean square deviation, all the simulations converged from approximately 30 ns. For the analysis of backbone flotation, the root mean square fluctuations were plotted for the Cα atoms; analysis revealed that the greatest fluctuation occurred in the residues that are part of the protein lid domain. The binding free energy value (ΔG bind ) obtained for the Tam16 lead molecule was of -51.43 kcal/mol. When comparing this result with the ΔG bind values for the remaining analogs, the drug Tam16 was found to be the highest ranked: this result is in agreement with the experimental results obtained by Aggarwal and collaborators, where it was verified that the IC 50 for Tam16 is the smallest necessary to inhibit the Pks13 (IC 50  = 0.19 μM). The energy decomposition analysis suggested that the residues which most interact with inhibitors are: Ser1636, Tyr1637, Asn1640, Ala1667, Phe1670, and Tyr1674, from which the greatest energy contribution to Phe1670 was particularly notable. For the lead molecule Tam16, a hydrogen bond with the hydroxyl of the phenol not observed in the other analogs induced a more stable molecular structure. Aggarwal and colleagues reported this hydrogen bonding as being responsible for the stability of the molecule, optimizing its physic-chemical, toxicological, and pharmacokinetic properties.

Estimating the probability that the sample mean is within a desired fraction of the standard deviation of the true mean.

PubMed

Schillaci, Michael A; Schillaci, Mario E

2009-02-01

The use of small sample sizes in human and primate evolutionary research is commonplace. Estimating how well small samples represent the underlying population, however, is not commonplace. Because the accuracy of determinations of taxonomy, phylogeny, and evolutionary process are dependant upon how well the study sample represents the population of interest, characterizing the uncertainty, or potential error, associated with analyses of small sample sizes is essential. We present a method for estimating the probability that the sample mean is within a desired fraction of the standard deviation of the true mean using small (n<10) or very small (n < or = 5) sample sizes. This method can be used by researchers to determine post hoc the probability that their sample is a meaningful approximation of the population parameter. We tested the method using a large craniometric data set commonly used by researchers in the field. Given our results, we suggest that sample estimates of the population mean can be reasonable and meaningful even when based on small, and perhaps even very small, sample sizes.

High-resolution protein design with backbone freedom.

PubMed

Harbury, P B; Plecs, J J; Tidor, B; Alber, T; Kim, P S

1998-11-20

Recent advances in computational techniques have allowed the design of precise side-chain packing in proteins with predetermined, naturally occurring backbone structures. Because these methods do not model protein main-chain flexibility, they lack the breadth to explore novel backbone conformations. Here the de novo design of a family of alpha-helical bundle proteins with a right-handed superhelical twist is described. In the design, the overall protein fold was specified by hydrophobic-polar residue patterning, whereas the bundle oligomerization state, detailed main-chain conformation, and interior side-chain rotamers were engineered by computational enumerations of packing in alternate backbone structures. Main-chain flexibility was incorporated through an algebraic parameterization of the backbone. The designed peptides form alpha-helical dimers, trimers, and tetramers in accord with the design goals. The crystal structure of the tetramer matches the designed structure in atomic detail.

Middle School Learners' Use of Latin Roots to Infer the Meaning of Unfamiliar Words

ERIC Educational Resources Information Center

Crosson, Amy C.; McKeown, Margaret G.

2016-01-01

This study investigated how middle school students leverage information about bound Latin roots (e.g., "voc" in "advocate" and "vociferous") to infer meanings of unfamiliar words, and how instruction may facilitate morphological analysis using roots. A dynamic assessment of morphological analysis was administered to…

Optical burst switching based satellite backbone network

NASA Astrophysics Data System (ADS)

Li, Tingting; Guo, Hongxiang; Wang, Cen; Wu, Jian

2018-02-01

We propose a novel time slot based optical burst switching (OBS) architecture for GEO/LEO based satellite backbone network. This architecture can provide high speed data transmission rate and high switching capacity . Furthermore, we design the control plane of this optical satellite backbone network. The software defined network (SDN) and network slice (NS) technologies are introduced. Under the properly designed control mechanism, this backbone network is flexible to support various services with diverse transmission requirements. Additionally, the LEO access and handoff management in this network is also discussed.

Experimental Protein Structure Verification by Scoring with a Single, Unassigned NMR Spectrum.

PubMed

Courtney, Joseph M; Ye, Qing; Nesbitt, Anna E; Tang, Ming; Tuttle, Marcus D; Watt, Eric D; Nuzzio, Kristin M; Sperling, Lindsay J; Comellas, Gemma; Peterson, Joseph R; Morrissey, James H; Rienstra, Chad M

2015-10-06

Standard methods for de novo protein structure determination by nuclear magnetic resonance (NMR) require time-consuming data collection and interpretation efforts. Here we present a qualitatively distinct and novel approach, called Comparative, Objective Measurement of Protein Architectures by Scoring Shifts (COMPASS), which identifies the best structures from a set of structural models by numerical comparison with a single, unassigned 2D (13)C-(13)C NMR spectrum containing backbone and side-chain aliphatic signals. COMPASS does not require resonance assignments. It is particularly well suited for interpretation of magic-angle spinning solid-state NMR spectra, but also applicable to solution NMR spectra. We demonstrate COMPASS with experimental data from four proteins--GB1, ubiquitin, DsbA, and the extracellular domain of human tissue factor--and with reconstructed spectra from 11 additional proteins. For all these proteins, with molecular mass up to 25 kDa, COMPASS distinguished the correct fold, most often within 1.5 Å root-mean-square deviation of the reference structure. Copyright © 2015 Elsevier Ltd. All rights reserved.

Survey of Anatomy and Root Canal Morphology of Maxillary First Molars Regarding Age and Gender in an Iranian Population Using Cone-Beam Computed Tomography

PubMed Central

Naseri, Mandana; Safi, Yaser; Akbarzadeh Baghban, Alireza; Khayat, Akbar; Eftekhar, Leila

2016-01-01

Introduction: The purpose of this study was to investigate the root and canal morphology of maxillary first molars with regards to patients’ age and gender with cone-beam computed tomography (CBCT). Methods and Materials: A total of 149 CBCT scans from 92 (67.1%) female and 57 (31.3%) male patients with mean age of 40.5 years were evaluated. Tooth length, presence of root fusion, number of the roots and canals, canal types based on Vertucci’s classification, deviation of root and apical foramen in coronal and sagittal planes and the correlation of all items with gender and age were recorded. The Mann Whitney U, Kruskal Wallis and Fisher’s exact tests were used to analyze these items. Results: The rate of root fusion was 1.3%. Multiple canals were present in the following frequencies: four canals 78.5%, five canals 11.4% and three canals 10.1%. Additional canal was detected in 86.6% of mesiobuccal roots in which Vertucci’s type VI configuration was the most prevalent followed by type II and I. Type I was the most common one in distobuccal and palatal roots. There was no statistically significant difference in the canal configurations in relation to gender and age as well as the incidence root or canal numbers (P>0.05). The mean tooth length was 19.3 and 20.3 mm in female and male patients, respectively which was statistically significant (P<0.05). Evaluation of root deviation showed that most commonly, a general pattern of straight-distal in the mesiobuccal and straight-straight for distobuccal and palatal roots occurred. In mesiobuccal roots, straight and distal deviations were more dominant in male and female, respectively (P<0.05). The prevalence of apical foramen deviation in mesiobuccal and palatal roots statistically differed with gender. Conclusion: The root and canal configuration of Iranian population showed different features from those of other populations. PMID:27790259

A new validation technique for estimations of body segment inertia tensors: Principal axes of inertia do matter.

PubMed

Rossi, Marcel M; Alderson, Jacqueline; El-Sallam, Amar; Dowling, James; Reinbolt, Jeffrey; Donnelly, Cyril J

2016-12-08

The aims of this study were to: (i) establish a new criterion method to validate inertia tensor estimates by setting the experimental angular velocity data of an airborne objects as ground truth against simulations run with the estimated tensors, and (ii) test the sensitivity of the simulations to changes in the inertia tensor components. A rigid steel cylinder was covered with reflective kinematic markers and projected through a calibrated motion capture volume. Simulations of the airborne motion were run with two models, using inertia tensor estimated with geometric formula or the compound pendulum technique. The deviation angles between experimental (ground truth) and simulated angular velocity vectors and the root mean squared deviation angle were computed for every simulation. Monte Carlo analyses were performed to assess the sensitivity of simulations to changes in magnitude of principal moments of inertia within ±10% and to changes in orientation of principal axes of inertia within ±10° (of the geometric-based inertia tensor). Root mean squared deviation angles ranged between 2.9° and 4.3° for the inertia tensor estimated geometrically, and between 11.7° and 15.2° for the compound pendulum values. Errors up to 10% in magnitude of principal moments of inertia yielded root mean squared deviation angles ranging between 3.2° and 6.6°, and between 5.5° and 7.9° when lumped with errors of 10° in principal axes of inertia orientation. The proposed technique can effectively validate inertia tensors from novel estimation methods of body segment inertial parameter. Principal axes of inertia orientation should not be neglected when modelling human/animal mechanics. Copyright © 2016 Elsevier Ltd. All rights reserved.

Performance characteristics of an adaptive controller based on least-mean-square filters

NASA Technical Reports Server (NTRS)

Mehta, Rajiv S.; Merhav, Shmuel J.

1986-01-01

A closed loop, adaptive control scheme that uses a least mean square filter as the controller model is presented, along with simulation results that demonstrate the excellent robustness of this scheme. It is shown that the scheme adapts very well to unknown plants, even those that are marginally stable, responds appropriately to changes in plant parameters, and is not unduly affected by additive noise. A heuristic argument for the conditions necessary for convergence is presented. Potential applications and extensions of the scheme are also discussed.

Middle School Learners' Use of Latin Roots to Infer the Meaning of Unfamiliar Words

ERIC Educational Resources Information Center

Crosson, Amy C.; McKeown, Margaret G.

2016-01-01

This study investigated how middle school students leverage information about bound Latin roots (e.g., voc in "advocate" and "vociferous") to infer meanings of unfamiliar words, and how instruction may facilitate morphological analysis using roots. A dynamic assessment of morphological analysis was administered to 29 sixth…

Computational protein design with backbone plasticity

PubMed Central

MacDonald, James T.; Freemont, Paul S.

2016-01-01

The computational algorithms used in the design of artificial proteins have become increasingly sophisticated in recent years, producing a series of remarkable successes. The most dramatic of these is the de novo design of artificial enzymes. The majority of these designs have reused naturally occurring protein structures as ‘scaffolds’ onto which novel functionality can be grafted without having to redesign the backbone structure. The incorporation of backbone flexibility into protein design is a much more computationally challenging problem due to the greatly increased search space, but promises to remove the limitations of reusing natural protein scaffolds. In this review, we outline the principles of computational protein design methods and discuss recent efforts to consider backbone plasticity in the design process. PMID:27911735

Reduction in mean deviation values in automated perimetry in eyes with multifocal compared to monofocal intraocular lens implants.

PubMed

Farid, Marjan; Chak, Garrick; Garg, Sumit; Steinert, Roger F

2014-08-01

To evaluate differences in mean deviation values in automated perimetry in healthy eyes with multifocal compared to monofocal intraocular lens (IOL) implants. Prospective, age-matched, comparative analysis. Single-center, tertiary referral academic practice. A total of 37 healthy eyes in 37 patients with bilateral multifocal (n=22) or monofocal (n=15) IOL implants were studied. INTERVENTION/OBSERVATION PROCEDURE: Humphrey Visual Field 10-2 testing was performed on all patients. Mean deviation (MD) and pattern standard deviation (PSD) numerical values were evaluated and compared between groups. The average MD was -2.84 dB (SD 2.32) for the multifocal IOL group and -0.97 dB (SD 1.58) for the monofocal IOL group (P=.006). There was no significant difference in PSD between the 2 groups (P=.99). Eyes that had the visual field 10-2 testing≥6 months from time of IOL placement showed no improvement in MD when compared to eyes that were tested within 6 months from IOL placement. Multifocal IOL implants cause significant nonspecific reduction in MD values on Humphrey Visual Field 10-2 testing that does not improve with time or neuroadaptation. Multifocal IOL implants may be inadvisable in patients where central visual field reduction may not be tolerated, such as macular degeneration, retinal pigment epithelium changes, and glaucoma. Copyright © 2014 Elsevier Inc. All rights reserved.

Direct measurement of the W Boson width in ppover collisions at square roots = 1.96 TeV.

PubMed

Aaltonen, T; Adelman, J; Akimoto, T; Albrow, M G; González, B Alvarez; Amerio, S; Amidei, D; Anastassov, A; Annovi, A; Antos, J; Aoki, M; Apollinari, G; Apresyan, A; Arisawa, T; Artikov, A; Ashmanskas, W; Attal, A; Aurisano, A; Azfar, F; Azzi-Bacchetta, P; Azzurri, P; Bacchetta, N; Badgett, W; Barbaro-Galtieri, A; Barnes, V E; Barnett, B A; Baroiant, S; Bartsch, V; Bauer, G; Beauchemin, P-H; Bedeschi, F; Bednar, P; Beecher, D; Behari, S; Bellettini, G; Bellinger, J; Belloni, A; Benjamin, D; Beretvas, A; Beringer, J; Berry, T; Bhatti, A; Binkley, M; Bisello, D; Bizjak, I; Blair, R E; Blocker, C; Blumenfeld, B; Bocci, A; Bodek, A; Boisvert, V; Bolla, G; Bolshov, A; Bortoletto, D; Boudreau, J; Boveia, A; Brau, B; Bridgeman, A; Brigliadori, L; Bromberg, C; Brubaker, E; Budagov, J; Budd, H S; Budd, S; Burkett, K; Busetto, G; Bussey, P; Buzatu, A; Byrum, K L; Cabrera, S; Campanelli, M; Campbell, M; Canelli, F; Canepa, A; Carlsmith, D; Carosi, R; Carrillo, S; Carron, S; Casal, B; Casarsa, M; Castro, A; Catastini, P; Cauz, D; Cavalli-Sforza, M; Cerri, A; Cerrito, L; Chang, S H; Chen, Y C; Chertok, M; Chiarelli, G; Chlachidze, G; Chlebana, F; Cho, K; Chokheli, D; Chou, J P; Choudalakis, G; Chuang, S H; Chung, K; Chung, W H; Chung, Y S; Ciobanu, C I; Ciocci, M A; Clark, A; Clark, D; Compostella, G; Convery, M E; Conway, J; Cooper, B; Copic, K; Cordelli, M; Cortiana, G; Crescioli, F; Almenar, C Cuenca; Cuevas, J; Culbertson, R; Cully, J C; Dagenhart, D; Datta, M; Davies, T; de Barbaro, P; De Cecco, S; Deisher, A; De Lentdecker, G; De Lorenzo, G; Dell'orso, M; Demortier, L; Deng, J; Deninno, M; De Pedis, D; Derwent, P F; Giovanni, G P Di; Dionisi, C; Di Ruzza, B; Dittmann, J R; D'Onofrio, M; Donati, S; Dong, P; Donini, J; Dorigo, T; Dube, S; Efron, J; Erbacher, R; Errede, D; Errede, S; Eusebi, R; Fang, H C; Farrington, S; Fedorko, W T; Feild, R G; Feindt, M; Fernandez, J P; Ferrazza, C; Field, R; Flanagan, G; Forrest, R; Forrester, S; Franklin, M; Freeman, J C; Furic, I; Gallinaro, M; Galyardt, J; Garberson, F; Garcia, J E; Garfinkel, A F; Gerberich, H; Gerdes, D; Giagu, S; Giakoumopolou, V; Giannetti, P; Gibson, K; Gimmell, J L; Ginsburg, C M; Giokaris, N; Giordani, M; Giromini, P; Giunta, M; Glagolev, V; Glenzinski, D; Gold, M; Goldschmidt, N; Golossanov, A; Gomez, G; Gomez-Ceballos, G; Goncharov, M; González, O; Gorelov, I; Goshaw, A T; Goulianos, K; Gresele, A; Grinstein, S; Grosso-Pilcher, C; Grundler, U; da Costa, J Guimaraes; Gunay-Unalan, Z; Haber, C; Hahn, K; Hahn, S R; Halkiadakis, E; Hamilton, A; Han, B-Y; Han, J Y; Handler, R; Happacher, F; Hara, K; Hare, D; Hare, M; Harper, S; Harr, R F; Harris, R M; Hartz, M; Hatakeyama, K; Hauser, J; Hays, C; Heck, M; Heijboer, A; Heinemann, B; Heinrich, J; Henderson, C; Herndon, M; Heuser, J; Hewamanage, S; Hidas, D; Hill, C S; Hirschbuehl, D; Hocker, A; Hou, S; Houlden, M; Hsu, S-C; Huffman, B T; Hughes, R E; Husemann, U; Huston, J; Incandela, J; Introzzi, G; Iori, M; Ivanov, A; Iyutin, B; James, E; Jayatilaka, B; Jeans, D; Jeon, E J; Jindariani, S; Johnson, W; Jones, M; Joo, K K; Jun, S Y; Jung, J E; Junk, T R; Kamon, T; Kar, D; Karchin, P E; Kato, Y; Kephart, R; Kerzel, U; Khotilovich, V; Kilminster, B; Kim, D H; Kim, H S; Kim, J E; Kim, M J; Kim, S B; Kim, S H; Kim, Y K; Kimura, N; Kirsch, L; Klimenko, S; Klute, M; Knuteson, B; Ko, B R; Koay, S A; Kondo, K; Kong, D J; Konigsberg, J; Korytov, A; Kotwal, A V; Kraus, J; Kreps, M; Kroll, J; Krumnack, N; Kruse, M; Krutelyov, V; Kubo, T; Kuhlmann, S E; Kuhr, T; Kulkarni, N P; Kusakabe, Y; Kwang, S; Laasanen, A T; Lai, S; Lami, S; Lammel, S; Lancaster, M; Lander, R L; Lannon, K; Lath, A; Latino, G; Lazzizzera, I; Lecompte, T; Lee, J; Lee, J; Lee, Y J; Lee, S W; Lefèvre, R; Leonardo, N; Leone, S; Levy, S; Lewis, J D; Lin, C; Lin, C S; Linacre, J; Lindgren, M; Lipeles, E; Lister, A; Litvintsev, D O; Liu, T; Lockyer, N S; Loginov, A; Loreti, M; Lovas, L; Lu, R-S; Lucchesi, D; Lueck, J; Luci, C; Lujan, P; Lukens, P; Lungu, G; Lyons, L; Lys, J; Lysak, R; Lytken, E; Mack, P; Macqueen, D; Madrak, R; Maeshima, K; Makhoul, K; Maki, T; Maksimovic, P; Malde, S; Malik, S; Manca, G; Manousakis, A; Margaroli, F; Marino, C; Marino, C P; Martin, A; Martin, M; Martin, V; Martínez, M; Martínez-Ballarín, R; Maruyama, T; Mastrandrea, P; Masubuchi, T; Mattson, M E; Mazzanti, P; McFarland, K S; McIntyre, P; McNulty, R; Mehta, A; Mehtala, P; Menzemer, S; Menzione, A; Merkel, P; Mesropian, C; Messina, A; Miao, T; Miladinovic, N; Miles, J; Miller, R; Mills, C; Milnik, M; Mitra, A; Mitselmakher, G; Miyake, H; Moed, S; Moggi, N; Moon, C S; Moore, R; Morello, M; Fernandez, P Movilla; Mülmenstädt, J; Mukherjee, A; Muller, Th; Mumford, R; Murat, P; Mussini, M; Nachtman, J; Nagai, Y; Nagano, A; Naganoma, J; Nakamura, K; Nakano, I; Napier, A; Necula, V; Neu, C; Neubauer, M S; Nielsen, J; Nodulman, L; Norman, M; Norniella, O; Nurse, E; Oh, S H; Oh, Y D; Oksuzian, I; Okusawa, T; Oldeman, R; Orava, R; Osterberg, K; Griso, S Pagan; Pagliarone, C; Palencia, E; Papadimitriou, V; Papaikonomou, A; Paramonov, A A; Parks, B; Pashapour, S; Patrick, J; Pauletta, G; Paulini, M; Paus, C; Pellett, D E; Penzo, A; Phillips, T J; Piacentino, G; Piedra, J; Pinera, L; Pitts, K; Plager, C; Pondrom, L; Portell, X; Poukhov, O; Pounder, N; Prakoshyn, F; Pronko, A; Proudfoot, J; Ptohos, F; Punzi, G; Pursley, J; Rademacker, J; Rahaman, A; Ramakrishnan, V; Ranjan, N; Redondo, I; Reisert, B; Rekovic, V; Renton, P; Rescigno, M; Richter, S; Rimondi, F; Ristori, L; Robson, A; Rodrigo, T; Rogers, E; Rolli, S; Roser, R; Rossi, M; Rossin, R; Roy, P; Ruiz, A; Russ, J; Rusu, V; Saarikko, H; Safonov, A; Sakumoto, W K; Salamanna, G; Saltó, O; Santi, L; Sarkar, S; Sartori, L; Sato, K; Savoy-Navarro, A; Scheidle, T; Schlabach, P; Schmidt, E E; Schmidt, M A; Schmidt, M P; Schmitt, M; Schwarz, T; Scodellaro, L; Scott, A L; Scribano, A; Scuri, F; Sedov, A; Seidel, S; Seiya, Y; Semenov, A; Sexton-Kennedy, L; Sfyria, A; Shalhout, S Z; Shapiro, M D; Shears, T; Shepard, P F; Sherman, D; Shimojima, M; Shochet, M; Shon, Y; Shreyber, I; Sidoti, A; Sinervo, P; Sisakyan, A; Slaughter, A J; Slaunwhite, J; Sliwa, K; Smith, J R; Snider, F D; Snihur, R; Soderberg, M; Soha, A; Somalwar, S; Sorin, V; Spalding, J; Spinella, F; Spreitzer, T; Squillacioti, P; Stanitzki, M; Denis, R St; Stelzer, B; Stelzer-Chilton, O; Stentz, D; Strologas, J; Stuart, D; Suh, J S; Sukhanov, A; Sun, H; Suslov, I; Suzuki, T; Taffard, A; Takashima, R; Takeuchi, Y; Tanaka, R; Tecchio, M; Teng, P K; Terashi, K; Thom, J; Thompson, A S; Thompson, G A; Thomson, E; Tipton, P; Tiwari, V; Tkaczyk, S; Toback, D; Tokar, S; Tollefson, K; Tomura, T; Tonelli, D; Torre, S; Torretta, D; Tourneur, S; Trischuk, W; Tu, Y; Turini, N; Ukegawa, F; Uozumi, S; Vallecorsa, S; van Remortel, N; Varganov, A; Vataga, E; Vázquez, F; Velev, G; Vellidis, C; Veszpremi, V; Vidal, M; Vidal, R; Vila, I; Vilar, R; Vine, T; Vogel, M; Volobouev, I; Volpi, G; Würthwein, F; Wagner, P; Wagner, R G; Wagner, R L; Wagner-Kuhr, J; Wagner, W; Wakisaka, T; Wallny, R; Wang, S M; Warburton, A; Waters, D; Weinberger, M; Wester, W C; Whitehouse, B; Whiteson, D; Wicklund, A B; Wicklund, E; Williams, G; Williams, H H; Wilson, P; Winer, B L; Wittich, P; Wolbers, S; Wolfe, C; Wright, T; Wu, X; Wynne, S M; Yagil, A; Yamamoto, K; Yamaoka, J; Yamashita, T; Yang, C; Yang, U K; Yang, Y C; Yao, W M; Yeh, G P; Yoh, J; Yorita, K; Yoshida, T; Yu, G B; Yu, I; Yu, S S; Yun, J C; Zanello, L; Zanetti, A; Zaw, I; Zhang, X; Zheng, Y; Zucchelli, S

2008-02-22

A direct measurement of the total decay width of the W boson Gamma(W) is presented using 350 pb(-1) of data from pp[over ] collisions at square root s = 1.96 TeV collected with the CDF II detector at the Fermilab Tevatron. The width is determined by normalizing predicted signal and background distributions to 230 185 W candidates decaying to enu and micronu in the transverse-mass region 50

Molecular Dynamics Approach in Designing Thermostable Aspergillus niger Xylanase

NASA Astrophysics Data System (ADS)

Malau, N. D.; Sianturi, M.

2017-03-01

Molecular dynamics methods we have applied as a tool in designing thermostable Aspergillus niger Xylanase, by examining Root Mean Square Deviation (RMSD) and The Stability of the Secondary Structure of enzymes structure at its optimum temperature and compare with its high temperature behavior. As RMSD represents structural fluctuation at a particular temperature, a better understanding of this factor will suggest approaches to bioengineer these enzymes to enhance their thermostability. In this work molecular dynamic simulations of Aspergillus niger xylanase (ANX) have been carried at 400K (optimum catalytic temperature) for 2.5 ns and 500K (ANX reported inactive temperature) for 2.5 ns. Analysis have shown that the Root Mean Square Deviation (RMSD) significant increase at higher temperatures compared at optimum temperature and some of the secondary structures of ANX that have been damaged at high temperature. Structural analysis revealed that the fluctuations of the α-helix and β-sheet regions are larger at higher temperatures compared to the fluctuations at optimum temperature.

An efficient implementation of Forward-Backward Least-Mean-Square Adaptive Line Enhancers

NASA Technical Reports Server (NTRS)

Yeh, H.-G.; Nguyen, T. M.

1995-01-01

An efficient implementation of the forward-backward least-mean-square (FBLMS) adaptive line enhancer is presented in this article. Without changing the characteristics of the FBLMS adaptive line enhancer, the proposed implementation technique reduces multiplications by 25% and additions by 12.5% in two successive time samples in comparison with those operations of direct implementation in both prediction and weight control. The proposed FBLMS architecture and algorithm can be applied to digital receivers for enhancing signal-to-noise ratio to allow fast carrier acquisition and tracking in both stationary and nonstationary environments.

The failures of root canal preparation with hand ProTaper.

PubMed

Bătăiosu, Marilena; Diaconu, Oana; Moraru, Iren; Dăguci, C; Tuculină, Mihaela; Dăguci, Luminiţa; Gheorghiţă, Lelia

2012-07-01

The failures of root canal preparation are due to some anatomical deviation (canal in "C" or "S") and some technique errors. The technique errors are usually present in canal root cleansing and shaping stage and are the result of endodontic treatment objectives deviation. Our study was made on technique errors while preparing the canal roots with hand ProTaper. Our study was made "in vitro" on 84 extracted teeth (molars, premolars, incisors and canines). The canal root of these teeth were cleansed and shaped with hand ProTaper by crown-down technique and canal irrigation with NaOCl(2,5%). The dental preparation control was made by X-ray. During canal root preparation some failures were observed like: canal root overinstrumentation, zipping and stripping phenomenon, discarded and/or fractured instruments. Hand ProTaper represents a revolutionary progress of endodontic treatment, but a deviation from accepted rules of canal root instrumentation can lead to failures of endodontic treatment.

The failures of root canal preparation with hand ProTaper

PubMed Central

Bătăiosu, Marilena; Diaconu, Oana; Moraru, Iren; Dăguci, C.; Ţuculină, Mihaela; Dăguci, Luminiţa; Gheorghiţă, Lelia

2012-01-01

The failures of root canal preparation are due to some anatomical deviation (canal in “C” or “S”) and some technique errors. The technique errors are usually present in canal root cleansing and shaping stage and are the result of endodontic treatment objectives deviation. Objectives: Our study was made on technique errors while preparing the canal roots with hand ProTaper. Methodology: Our study was made “in vitro” on 84 extracted teeth (molars, premolars, incisors and canines). The canal root of these teeth were cleansed and shaped with hand ProTaper by crown-down technique and canal irrigation with NaOCl(2,5%). The dental preparation control was made by X-ray. Results: During canal root preparation some failures were observed like: canal root overinstrumentation, zipping and stripping phenomenon, discarded and/or fractured instruments. Conclusions: Hand ProTaper represents a revolutionary progress of endodontic treatment, but a deviation from accepted rules of canal root instrumentation can lead to failures of endodontic treatment. PMID:24778848

Effect of root planing on surface topography: an in-vivo randomized experimental trial.

PubMed

Rosales-Leal, J I; Flores, A B; Contreras, T; Bravo, M; Cabrerizo-Vílchez, M A; Mesa, F

2015-04-01

The root surface topography exerts a major influence on clinical attachment and bacterial recolonization after root planing. In-vitro topographic studies have yielded variable results, and clinical studies are necessary to compare root surface topography after planing with current ultrasonic devices and with traditional manual instrumentation. The aim of this study was to compare the topography of untreated single-rooted teeth planed in vivo with a curette, a piezoelectric ultrasonic (PU) scraper or a vertically oscillating ultrasonic (VOU) scraper. In a randomized experimental trial of 19 patients, 44 single-rooted teeth were randomly assigned to one of four groups for: no treatment; manual root planing with a curette; root planing with a PU scraper; or root planing with a VOU scraper. Post-treatment, the teeth were extracted and their topography was analyzed in 124 observations with white-light confocal microscopy, measuring the roughness parameters arithmetic average height, root-mean-square roughness, maximum height of peaks, maximum depth of valleys, absolute height, skewness and kurtosis. The roughness values arithmetic average height and root-mean-square roughness were similar after each treatment and lower than after no treatment ( p < 0.05). Absolute height was lower in the VOU group than in the untreated ( p = 0.0026) and PU (p = 0.045) groups. Surface morphology was similar after the three treatments and was less irregular than in the untreated group. Values for the remaining roughness parameters were similar among all treatment groups ( p > 0.05). Both ultrasonic devices reduce the roughness, producing a similar topography to that observed after manual instrumentation with a curette, to which they appear to represent a valid alternative. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

VARIABLE TIME DELAY MEANS

DOEpatents

Clemensen, R.E.

1959-11-01

An electrically variable time delay line is described which may be readily controlled simuitaneously with variable impedance matching means coupied thereto such that reflections are prevented. Broadly, the delay line includes a signal winding about a magnetic core whose permeability is electrically variable. Inasmuch as the inductance of the line varies directly with the permeability, the time delay and characteristic impedance of the line both vary as the square root of the permeability. Consequently, impedance matching means may be varied similariy and simultaneously w:th the electrically variable permeability to match the line impedance over the entire range of time delay whereby reflections are prevented.

Glucose control of root growth direction in Arabidopsis thaliana.

PubMed

Singh, Manjul; Gupta, Aditi; Laxmi, Ashverya

2014-07-01

Directional growth of roots is a complex process that is modulated by various environmental signals. This work shows that presence of glucose (Glc) in the medium also extensively modulated seedling root growth direction. Glc modulation of root growth direction was dramatically enhanced by simultaneous brassinosteroid (BR) application. Glc enhanced BR receptor BRASSINOSTEROID INSENSITIVE1 (BRI1) endocytosis from plasma membrane to early endosomes. Glc-induced root deviation was highly enhanced in a PP2A-defective mutant, roots curl in naphthyl phthalamic acid 1-1 (rcn1-1) suggesting that there is a role of phosphatase in Glc-induced root-growth deviation. RCN1, therefore, acted as a link between Glc and the BR-signalling pathway. Polar auxin transport worked further downstream to BR in controlling Glc-induced root deviation response. Glc also affected other root directional responses such as root waving and coiling leading to altered root architecture. High light intensity mimicked the Glc-induced changes in root architecture that were highly reduced in Glc-signalling mutants. Thus, under natural environmental conditions, changing light flux in the environment may lead to enhanced Glc production/response and is a way to manipulate root architecture for optimized development via integrating several extrinsic and intrinsic signalling cues. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Combined quantum-mechanics/molecular-mechanics dynamics simulation of A-DNA double strands irradiated by ultra-low-energy carbon ions

NASA Astrophysics Data System (ADS)

Ngaojampa, C.; Nimmanpipug, P.; Yu, L. D.; Anuntalabhochai, S.; Lee, V. S.

2011-02-01

In order to promote understanding of the fundamentals of ultra-low-energy ion interaction with DNA, molecular dynamics simulations using combined quantum-mechanics/molecular-mechanics of poly-AT and poly-GC A-DNA double strands irradiated by <200 eV carbon ions were performed to investigate the molecular implications of mutation bias. The simulations were focused on the responses of the DNA backbones and nitrogenous bases to irradiation. Analyses of the root mean square displacements of the backbones and non-hydrogen atoms of base rings of the simulated DNA structure after irradiation revealed a potential preference of DNA double strand separation, dependent on the irradiating energy. The results show that for the backbones, the large difference in the displacement between poly-GC and poly-AT in the initial time period could be the reason for the backbone breakage; for the nitrogenous base pairs, A-T is 30% more sensitive or vulnerable to ion irradiation than G-C, demonstrating a preferential, instead of random, effect of irradiation-induced mutation.

Protecting Patients from an Unsafe System: The Etiology & Recovery of Intra-Operative Deviations in Care

PubMed Central

Hu, Yue-Yung; Arriaga, Alexander F.; Roth, Emilie M.; Peyre, Sarah E.; Corso, Katherine A.; Swanson, Richard S.; Osteen, Robert T.; Schmitt, Pamela; Bader, Angela M.; Zinner, Michael J.; Greenberg, Caprice C.

2012-01-01

Objective To understand the etiology and resolution of unanticipated events in the operating room (OR). Background The majority of surgical adverse events occur intra-operatively. The OR represents a complex, high-risk system. The influence of different human, team, and organizational/environmental factors on safety and performance is unknown. Methods We video-recorded and transcribed 10 high-acuity operations, representing 43.7 hours of patient care. Deviations, defined as delays and/or episodes of decreased patient safety, were identified by majority consensus of a multidisciplinary team. Factors that contributed to each event and/or mitigated its impact were determined and attributed to the patient, providers, or environment/organization. Results Thirty-three deviations (10 delays, 17 safety compromises, 6 both) occurred – with a mean of one every 79.4 minutes. These deviations were multifactorial (mean 3.1 factors). Problems with communication and organizational structure appeared repeatedly at the root of both types of deviations. Delays tended to be resolved with vigilance, communication, coordination, and cooperation, while mediation of safety compromises was most frequently accomplished with vigilance, leadership, communication, and/or coordination. The organization/environment was not found to play a direct role in compensation. Conclusions Unanticipated events are common in the OR. Deviations result from poor organizational/environmental design and suboptimal team dynamics, with caregivers compensating to avoid patient harm. While recognized in other high risk domains, such human resilience has not yet been described in surgery and has major implications for the design of safety interventions. PMID:22750753

Minimization of deviations of gear real tooth surfaces determined by coordinate measurements

NASA Technical Reports Server (NTRS)

Litvin, F. L.; Kuan, C.; Wang, J.-C.; Handschuh, R. F.; Masseth, J.; Maruyama, N.

1992-01-01

The deviations of a gear's real tooth surface from the theoretical surface are determined by coordinate measurements at the grid of the surface. A method was developed to transform the deviations from Cartesian coordinates to those along the normal at the measurement locations. Equations are derived that relate the first order deviations with the adjustment to the manufacturing machine-tool settings. The deviations of the entire surface are minimized. The minimization is achieved by application of the least-square method for an overdetermined system of linear equations. The proposed method is illustrated with a numerical example for hypoid gear and pinion.

The relationship between purely stochastic sampling error and the number of technical replicates used to estimate concentration at an extreme dilution

USDA-ARS?s Scientific Manuscript database

For any analytical system the population mean (mu) number of entities (e.g., cells or molecules) per tested volume, surface area, or mass also defines the population standard deviation (sigma = square root of mu ). For a preponderance of analytical methods, sigma is very small relative to mu due to...

SQUARE WAVE AMPLIFIER

DOEpatents

Leavitt, M.A.; Lutz, I.C.

1958-08-01

An amplifier circuit is described for amplifying sigmals having an alternating current component superimposed upon a direct current component, without loss of any segnnent of the alternating current component. The general circuit arrangement includes a vibrator, two square wave amplifiers, and recombination means. The amplifier input is connected to the vibrating element of the vibrator and is thereby alternately applied to the input of each square wave amplifier. The detailed circuitry of the recombination means constitutes the novelty of the annplifier and consists of a separate, dual triode amplifier coupled to the output of each square wave amplifier with a recombination connection from the plate of one amplifier section to a grid of one section of the other amplifier. The recombination circuit has provisions for correcting distortion caused by overlapping of the two square wave voltages from the square wave amplifiers.

Understanding traffic dynamics at a backbone POP

NASA Astrophysics Data System (ADS)

Taft, Nina; Bhattacharyya, Supratik; Jetcheva, Jorjeta; Diot, Christophe

2001-07-01

Spatial and temporal information about traffic dynamics is central to the design of effective traffic engineering practices for IP backbones. In this paper we study backbone traffic dynamics using data collected at a major POP on a tier-1 IP backbone. We develop a methodology that combines packet-level traces from access links in the POP and BGP routing information to build components of POP-to-POP traffic matrices. Our results show that there is wide disparity in the volume of traffic headed towards different egress POPs. At the same time, we find that current routing practices in the backbone tend to constrain traffic between ingress-egress POP pairs to a small number of paths. As a result, there is a wide variation in the utilization level of links in the backbone. Frequent capacity upgrades of the heavily used links are expensive; the need for such upgrades can be reduced by designing load balancing policies that will route more traffic over less utilized links. We identify traffic aggregates based on destination address prefixes and find that this set of criteria isolates a few aggregates that account for an overwhelmingly large portion of inter-POP traffic. We also demonstrate that these aggregates exhibit stability throughout the day on per-hour time scales, and thus they form a natural basis for splitting traffic over multiple paths in order to improve load balancing.

J/Psi production in pp collisions at square root = 200 GeV at the BNL relativistic heavy ion collider.

PubMed

Cooper, Fred; Liu, Ming X; Nayak, Gouranga C

2004-10-22

We study J/psi production in pp collisions at BNL Relativistic Heavy Ion Collider (RHIC) within the PHENIX detector acceptance range using the color singlet and color octet mechanism which are based on perturbative QCD and nonrelativistic QCD. Here we show that the color octet mechanism reproduces the RHIC data for J/psi production in pp collisions with respect to the p(T) distribution, the rapidity distribution, and the total cross section at square root = 200 GeV. The color singlet mechanism leads to a relatively small contribution to the total cross section when compared to the octet contribution.

Simultaneous polarimeter retrievals of microphysical aerosol and ocean color parameters from the "MAPP" algorithm with comparison to high-spectral-resolution lidar aerosol and ocean products.

PubMed

Stamnes, S; Hostetler, C; Ferrare, R; Burton, S; Liu, X; Hair, J; Hu, Y; Wasilewski, A; Martin, W; van Diedenhoven, B; Chowdhary, J; Cetinić, I; Berg, L K; Stamnes, K; Cairns, B

2018-04-01

We present an optimal-estimation-based retrieval framework, the microphysical aerosol properties from polarimetry (MAPP) algorithm, designed for simultaneous retrieval of aerosol microphysical properties and ocean color bio-optical parameters using multi-angular total and polarized radiances. Polarimetric measurements from the airborne NASA Research Scanning Polarimeter (RSP) were inverted by MAPP to produce atmosphere and ocean products. The RSP MAPP results are compared with co-incident lidar measurements made by the NASA High-Spectral-Resolution Lidar HSRL-1 and HSRL-2 instruments. Comparisons are made of the aerosol optical depth (AOD) at 355 and 532 nm, lidar column-averaged measurements of the aerosol lidar ratio and Ångstrøm exponent, and lidar ocean measurements of the particulate hemispherical backscatter coefficient and the diffuse attenuation coefficient. The measurements were collected during the 2012 Two-Column Aerosol Project (TCAP) campaign and the 2014 Ship-Aircraft Bio-Optical Research (SABOR) campaign. For the SABOR campaign, 73% RSP MAPP retrievals fall within ±0.04 AOD at 532 nm as measured by HSRL-1, with an R value of 0.933 and root-mean-square deviation of 0.0372. For the TCAP campaign, 53% of RSP MAPP retrievals are within 0.04 AOD as measured by HSRL-2, with an R value of 0.927 and root-mean-square deviation of 0.0673. Comparisons with HSRL-2 AOD at 355 nm during TCAP result in an R value of 0.959 and a root-mean-square deviation of 0.0694. The RSP retrievals using the MAPP optimal estimation framework represent a key milestone on the path to a combined lidar + polarimeter retrieval using both HSRL and RSP measurements.

Interlaboratory comparison measurements of aspheres

NASA Astrophysics Data System (ADS)

Schachtschneider, R.; Fortmeier, I.; Stavridis, M.; Asfour, J.; Berger, G.; Bergmann, R. B.; Beutler, A.; Blümel, T.; Klawitter, H.; Kubo, K.; Liebl, J.; Löffler, F.; Meeß, R.; Pruss, C.; Ramm, D.; Sandner, M.; Schneider, G.; Wendel, M.; Widdershoven, I.; Schulz, M.; Elster, C.

2018-05-01

The need for high-quality aspheres is rapidly growing, necessitating increased accuracy in their measurement. A reliable uncertainty assessment of asphere form measurement techniques is difficult due to their complexity. In order to explore the accuracy of current asphere form measurement techniques, an interlaboratory comparison was carried out in which four aspheres were measured by eight laboratories using tactile measurements, optical point measurements, and optical areal measurements. Altogether, 12 different devices were employed. The measurement results were analysed after subtracting the design topography and subsequently a best-fit sphere from the measurements. The surface reduced in this way was compared to a reference topography that was obtained by taking the pointwise median across the ensemble of reduced topographies on a 1000 × 1000 Cartesian grid. The deviations of the reduced topographies from the reference topography were analysed in terms of several characteristics including peak-to-valley and root-mean-square deviations. Root-mean-square deviations of the reduced topographies from the reference topographies were found to be on the order of some tens of nanometres up to 89 nm, with most of the deviations being smaller than 20 nm. Our results give an indication of the accuracy that can currently be expected in form measurements of aspheres.

Multi-analyte quantification in bioprocesses by Fourier-transform-infrared spectroscopy by partial least squares regression and multivariate curve resolution.

PubMed

Koch, Cosima; Posch, Andreas E; Goicoechea, Héctor C; Herwig, Christoph; Lendl, Bernhard

2014-01-07

This paper presents the quantification of Penicillin V and phenoxyacetic acid, a precursor, inline during Pencillium chrysogenum fermentations by FTIR spectroscopy and partial least squares (PLS) regression and multivariate curve resolution - alternating least squares (MCR-ALS). First, the applicability of an attenuated total reflection FTIR fiber optic probe was assessed offline by measuring standards of the analytes of interest and investigating matrix effects of the fermentation broth. Then measurements were performed inline during four fed-batch fermentations with online HPLC for the determination of Penicillin V and phenoxyacetic acid as reference analysis. PLS and MCR-ALS models were built using these data and validated by comparison of single analyte spectra with the selectivity ratio of the PLS models and the extracted spectral traces of the MCR-ALS models, respectively. The achieved root mean square errors of cross-validation for the PLS regressions were 0.22 g L(-1) for Penicillin V and 0.32 g L(-1) for phenoxyacetic acid and the root mean square errors of prediction for MCR-ALS were 0.23 g L(-1) for Penicillin V and 0.15 g L(-1) for phenoxyacetic acid. A general work-flow for building and assessing chemometric regression models for the quantification of multiple analytes in bioprocesses by FTIR spectroscopy is given. Copyright © 2013 The Authors. Published by Elsevier B.V. All rights reserved.

Narrowing of the balance function with centrality in Au+Au collisions at the square root of SNN = 130 GeV.

PubMed

Adams, J; Adler, C; Ahammed, Z; Allgower, C; Amonett, J; Anderson, B D; Anderson, M; Averichev, G S; Balewski, J; Barannikova, O; Barnby, L S; Baudot, J; Bekele, S; Belaga, V V; Bellwied, R; Berger, J; Bichsel, H; Billmeier, A; Bland, L C; Blyth, C O; Bonner, B E; Boucham, A; Brandin, A; Bravar, A; Cadman, R V; Caines, H; Calderónde la Barca Sánchez, M; Cardenas, A; Carroll, J; Castillo, J; Castro, M; Cebra, D; Chaloupka, P; Chattopadhyay, S; Chen, Y; Chernenko, S P; Cherney, M; Chikanian, A; Choi, B; Christie, W; Coffin, J P; Cormier, T M; Corral, M M; Cramer, J G; Crawford, H J; Derevschikov, A A; Didenko, L; Dietel, T; Draper, J E; Dunin, V B; Dunlop, J C; Eckardt, V; Efimov, L G; Emelianov, V; Engelage, J; Eppley, G; Erazmus, B; Fachini, P; Faine, V; Faivre, J; Fatemi, R; Filimonov, K; Finch, E; Fisyak, Y; Flierl, D; Foley, K J; Fu, J; Gagliardi, C A; Gagunashvili, N; Gans, J; Gaudichet, L; Germain, M; Geurts, F; Ghazikhanian, V; Grachov, O; Grigoriev, V; Guedon, M; Guertin, S M; Gushin, E; Hallman, T J; Hardtke, D; Harris, J W; Heinz, M; Henry, T W; Heppelmann, S; Herston, T; Hippolyte, B; Hirsch, A; Hjort, E; Hoffmann, G W; Horsley, M; Huang, H Z; Humanic, T J; Igo, G; Ishihara, A; Ivanshin, Yu I; Jacobs, P; Jacobs, W W; Janik, M; Johnson, I; Jones, P G; Judd, E G; Kaneta, M; Kaplan, M; Keane, D; Kiryluk, J; Kisiel, A; Klay, J; Klein, S R; Klyachko, A; Kollegger, T; Konstantinov, A S; Kopytine, M; Kotchenda, L; Kovalenko, A D; Kramer, M; Kravtsov, P; Krueger, K; Kuhn, C; Kulikov, A I; Kunde, G J; Kunz, C L; Kutuev, R Kh; Kuznetsov, A A; Lamont, M A C; Landgraf, J M; Lange, S; Lansdell, C P; Lasiuk, B; Laue, F; Lauret, J; Lebedev, A; Lednický, R; Leontiev, V M; LeVine, M J; Li, Q; Lindenbaum, S J; Lisa, M A; Liu, F; Liu, L; Liu, Z; Liu, Q J; Ljubicic, T; Llope, W J; Long, H; Longacre, R S; Lopez-Noriega, M; Love, W A; Ludlam, T; Lynn, D; Ma, J; Magestro, D; Majka, R; Margetis, S; Markert, C; Martin, L; Marx, J; Matis, H S; Matulenko, Yu A; McShane, T S; Meissner, F; Melnick, Yu; Meschanin, A; Messer, M; Miller, M L; Milosevich, Z; Minaev, N G; Mitchell, J; Moore, C F; Morozov, V; de Moura, M M; Munhoz, M G; Nelson, J M; Nevski, P; Nikitin, V A; Nogach, L V; Norman, B; Nurushev, S B; Odyniec, G; Ogawa, A; Okorokov, V; Oldenburg, M; Olson, D; Paic, G; Pandey, S U; Panebratsev, Y; Panitkin, S Y; Pavlinov, A I; Pawlak, T; Perevoztchikov, V; Peryt, W; Petrov, V A; Planinic, M; Pluta, J; Porile, N; Porter, J; Poskanzer, A M; Potrebenikova, E; Prindle, D; Pruneau, C; Putschke, J; Rai, G; Rakness, G; Ravel, O; Ray, R L; Razin, S V; Reichhold, D; Reid, J G; Renault, G; Retiere, F; Ridiger, A; Ritter, H G; Roberts, J B; Rogachevski, O V; Romero, J L; Rose, A; Roy, C; Rykov, V; Sakrejda, I; Salur, S; Sandweiss, J; Savin, I; Schambach, J; Scharenberg, R P; Schmitz, N; Schroeder, L S; Schüttauf, A; Schweda, K; Seger, J; Seliverstov, D; Seyboth, P; Shahaliev, E; Shestermanov, K E; Shimanskii, S S; Simon, F; Skoro, G; Smirnov, N; Snellings, R; Sorensen, P; Sowinski, J; Spinka, H M; Srivastava, B; Stephenson, E J; Stock, R; Stolpovsky, A; Strikhanov, M; Stringfellow, B; Struck, C; Suaide, A A P; Sugarbaker, E; Suire, C; Sumbera, M; Surrow, B; Symons, T J M; de Toledo, A Szanto; Szarwas, P; Tai, A; Takahashi, J; Tang, A H; Thein, D; Thomas, J H; Thompson, M; Tikhomirov, V; Tokarev, M; Tonjes, M B; Trainor, T A; Trentalange, S; Tribble, R E; Trofimov, V; Tsai, O; Ullrich, T; Underwood, D G; Van Buren, G; Vander Molen, A M; Vasilevski, I M; Vasiliev, A N; Vigdor, S E; Voloshin, S A; Wang, F; Ward, H; Watson, J W; Wells, R; Westfall, G D; Whitten, C; Wieman, H; Willson, R; Wissink, S W; Witt, R; Wood, J; Xu, N; Xu, Z; Yakutin, A E; Yamamoto, E; Yang, J; Yepes, P; Yurevich, V I; Zanevski, Y V; Zborovský, I; Zhang, H; Zhang, W M; Zoulkarneev, R; Zubarev, A N

2003-05-02

The balance function is a new observable based on the principle that charge is locally conserved when particles are pair produced. Balance functions have been measured for charged particle pairs and identified charged pion pairs in Au+Au collisions at the square root of SNN = 130 GeV at the Relativistic Heavy Ion Collider using STAR. Balance functions for peripheral collisions have widths consistent with model predictions based on a superposition of nucleon-nucleon scattering. Widths in central collisions are smaller, consistent with trends predicted by models incorporating late hadronization.

Simulated Stochastic Approximation Annealing for Global Optimization with a Square-Root Cooling Schedule

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

Liang, Faming; Cheng, Yichen; Lin, Guang

2014-06-13

Simulated annealing has been widely used in the solution of optimization problems. As known by many researchers, the global optima cannot be guaranteed to be located by simulated annealing unless a logarithmic cooling schedule is used. However, the logarithmic cooling schedule is so slow that no one can afford to have such a long CPU time. This paper proposes a new stochastic optimization algorithm, the so-called simulated stochastic approximation annealing algorithm, which is a combination of simulated annealing and the stochastic approximation Monte Carlo algorithm. Under the framework of stochastic approximation Markov chain Monte Carlo, it is shown that themore » new algorithm can work with a cooling schedule in which the temperature can decrease much faster than in the logarithmic cooling schedule, e.g., a square-root cooling schedule, while guaranteeing the global optima to be reached when the temperature tends to zero. The new algorithm has been tested on a few benchmark optimization problems, including feed-forward neural network training and protein-folding. The numerical results indicate that the new algorithm can significantly outperform simulated annealing and other competitors.« less

Modes of Diffusion of Cholera Toxin Bound to GM1 on Live Cell Membrane by Image Mean Square Displacement Analysis

PubMed Central

Moens, Pierre D.J.; Digman, Michelle A.; Gratton, Enrico

2015-01-01

The image-mean square displacement technique applies the calculation of the mean square displacement commonly used in single-molecule tracking to images without resolving single particles. The image-mean square displacement plot obtained is similar to the mean square displacement plot obtained using the single-particle tracking technique. This plot is then used to reconstruct the protein diffusion law and to identify whether the labeled molecules are undergoing pure isotropic, restricted, corralled, transiently confined, or directed diffusion. In our study total internal reflection fluorescence microscopy images were taken of Cholera toxin subunit B (CtxB) membrane-labeled NIH 3T3 mouse fibroblasts and MDA 231 MB cells. We found a population of CTxB undergoing purely isotropic diffusion and one displaying restricted diffusion with corral sizes ranging from 150 to ∼1800 nm. We show that the diffusion rate of CTxB bound to GM1 is independent of the size of the confinement, suggesting that the mechanism of confinement is different from the mechanism controlling the diffusion rate of CtxB. We highlight the potential effect of continuous illumination on the diffusion mode of CTxB. We also show that aggregation of CTxB/GM1 in large complexes occurs and that these aggregates tend to have slower diffusion rates. PMID:25809257

Modes of diffusion of cholera toxin bound to GM1 on live cell membrane by image mean square displacement analysis.

PubMed

Moens, Pierre D J; Digman, Michelle A; Gratton, Enrico

2015-03-24

The image-mean square displacement technique applies the calculation of the mean square displacement commonly used in single-molecule tracking to images without resolving single particles. The image-mean square displacement plot obtained is similar to the mean square displacement plot obtained using the single-particle tracking technique. This plot is then used to reconstruct the protein diffusion law and to identify whether the labeled molecules are undergoing pure isotropic, restricted, corralled, transiently confined, or directed diffusion. In our study total internal reflection fluorescence microscopy images were taken of Cholera toxin subunit B (CtxB) membrane-labeled NIH 3T3 mouse fibroblasts and MDA 231 MB cells. We found a population of CTxB undergoing purely isotropic diffusion and one displaying restricted diffusion with corral sizes ranging from 150 to ∼1800 nm. We show that the diffusion rate of CTxB bound to GM1 is independent of the size of the confinement, suggesting that the mechanism of confinement is different from the mechanism controlling the diffusion rate of CtxB. We highlight the potential effect of continuous illumination on the diffusion mode of CTxB. We also show that aggregation of CTxB/GM1 in large complexes occurs and that these aggregates tend to have slower diffusion rates. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Large-scale measurement and modeling of backbone Internet traffic

NASA Astrophysics Data System (ADS)

Roughan, Matthew; Gottlieb, Joel

2002-07-01

There is a brewing controversy in the traffic modeling community concerning how to model backbone traffic. The fundamental work on self-similarity in data traffic appears to be contradicted by recent findings that suggest that backbone traffic is smooth. The traffic analysis work to date has focused on high-quality but limited-scope packet trace measurements; this limits its applicability to high-speed backbone traffic. This paper uses more than one year's worth of SNMP traffic data covering an entire Tier 1 ISP backbone to address the question of how backbone network traffic should be modeled. Although the limitations of SNMP measurements do not permit us to comment on the fine timescale behavior of the traffic, careful analysis of the data suggests that irrespective of the variation at fine timescales, we can construct a simple traffic model that captures key features of the observed traffic. Furthermore, the model's parameters are measurable using existing network infrastructure, making this model practical in a present-day operational network. In addition to its practicality, the model verifies basic statistical multiplexing results, and thus sheds deep insight into how smooth backbone traffic really is.

Sample Size and Item Parameter Estimation Precision When Utilizing the One-Parameter "Rasch" Model

ERIC Educational Resources Information Center

Custer, Michael

2015-01-01

This study examines the relationship between sample size and item parameter estimation precision when utilizing the one-parameter model. Item parameter estimates are examined relative to "true" values by evaluating the decline in root mean squared deviation (RMSD) and the number of outliers as sample size increases. This occurs across…

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

PubMed

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

2011-02-01

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

Square Root Graphical Models: Multivariate Generalizations of Univariate Exponential Families that Permit Positive Dependencies

PubMed Central

Inouye, David I.; Ravikumar, Pradeep; Dhillon, Inderjit S.

2016-01-01

We develop Square Root Graphical Models (SQR), a novel class of parametric graphical models that provides multivariate generalizations of univariate exponential family distributions. Previous multivariate graphical models (Yang et al., 2015) did not allow positive dependencies for the exponential and Poisson generalizations. However, in many real-world datasets, variables clearly have positive dependencies. For example, the airport delay time in New York—modeled as an exponential distribution—is positively related to the delay time in Boston. With this motivation, we give an example of our model class derived from the univariate exponential distribution that allows for almost arbitrary positive and negative dependencies with only a mild condition on the parameter matrix—a condition akin to the positive definiteness of the Gaussian covariance matrix. Our Poisson generalization allows for both positive and negative dependencies without any constraints on the parameter values. We also develop parameter estimation methods using node-wise regressions with ℓ1 regularization and likelihood approximation methods using sampling. Finally, we demonstrate our exponential generalization on a synthetic dataset and a real-world dataset of airport delay times. PMID:27563373

A Conditionally Integrable Bi-confluent Heun Potential Involving Inverse Square Root and Centrifugal Barrier Terms

NASA Astrophysics Data System (ADS)

Ishkhanyan, Tigran A.; Krainov, Vladimir P.; Ishkhanyan, Artur M.

2018-05-01

We present a conditionally integrable potential, belonging to the bi-confluent Heun class, for which the Schrödinger equation is solved in terms of the confluent hypergeometric functions. The potential involves an attractive inverse square root term x-1/2 with arbitrary strength and a repulsive centrifugal barrier core x-2 with the strength fixed to a constant. This is a potential well defined on the half-axis. Each of the fundamental solutions composing the general solution of the Schrödinger equation is written as an irreducible linear combination, with non-constant coefficients, of two confluent hypergeometric functions. We present the explicit solution in terms of the non-integer order Hermite functions of scaled and shifted argument and discuss the bound states supported by the potential. We derive the exact equation for the energy spectrum and approximate that by a highly accurate transcendental equation involving trigonometric functions. Finally, we construct an accurate approximation for the bound-state energy levels.

The Relationship between Mean Square Differences and Standard Error of Measurement: Comment on Barchard (2012)

ERIC Educational Resources Information Center

Pan, Tianshu; Yin, Yue

2012-01-01

In the discussion of mean square difference (MSD) and standard error of measurement (SEM), Barchard (2012) concluded that the MSD between 2 sets of test scores is greater than 2(SEM)[superscript 2] and SEM underestimates the score difference between 2 tests when the 2 tests are not parallel. This conclusion has limitations for 2 reasons. First,…

Characterizing the urban temperature trend using seasonal unit root analysis: Hong Kong from 1970 to 2015

NASA Astrophysics Data System (ADS)

To, Wai-Ming; Yu, Tat-Wai

2016-12-01

This paper explores urban temperature in Hong Kong using long-term time series. In particular, the characterization of the urban temperature trend was investigated using the seasonal unit root analysis of monthly mean air temperature data over the period January 1970 to December 2013. The seasonal unit root test makes it possible to determine the stochastic trend of monthly temperatures using an autoregressive model. The test results showed that mean air temperature has increased by 0.169°C (10 yr)-1 over the past four decades. The model of monthly temperature obtained from the seasonal unit root analysis was able to explain 95.9% of the variance in the measured monthly data — much higher than the variance explained by the ordinary least-squares model using annual mean air temperature data and other studies alike. The model accurately predicted monthly mean air temperatures between January 2014 and December 2015 with a root-mean-square percentage error of 4.2%. The correlation between the predicted and the measured monthly mean air temperatures was 0.989. By analyzing the monthly air temperatures recorded at an urban site and a rural site, it was found that the urban heat island effect led to the urban site being on average 0.865°C warmer than the rural site over the past two decades. Besides, the results of correlation analysis showed that the increase in annual mean air temperature was significantly associated with the increase in population, gross domestic product, urban land use, and energy use, with the R2 values ranging from 0.37 to 0.43.

Prediction of forced expiratory volume in pulmonary function test using radial basis neural networks and k-means clustering.

PubMed

Manoharan, Sujatha C; Ramakrishnan, Swaminathan

2009-10-01

In this work, prediction of forced expiratory volume in pulmonary function test, carried out using spirometry and neural networks is presented. The pulmonary function data were recorded from volunteers using commercial available flow volume spirometer in standard acquisition protocol. The Radial Basis Function neural networks were used to predict forced expiratory volume in 1 s (FEV1) from the recorded flow volume curves. The optimal centres of the hidden layer of radial basis function were determined by k-means clustering algorithm. The performance of the neural network model was evaluated by computing their prediction error statistics of average value, standard deviation, root mean square and their correlation with the true data for normal, restrictive and obstructive cases. Results show that the adopted neural networks are capable of predicting FEV1 in both normal and abnormal cases. Prediction accuracy was more in obstructive abnormality when compared to restrictive cases. It appears that this method of assessment is useful in diagnosing the pulmonary abnormalities with incomplete data and data with poor recording.

Dem Generation with WORLDVIEW-2 Images

NASA Astrophysics Data System (ADS)

Büyüksalih, G.; Baz, I.; Alkan, M.; Jacobsen, K.

2012-07-01

For planning purposes 42 km coast line of the Black Sea, starting at the Bosporus going in West direction, with a width of approximately 5 km, was imaged by WorldView-2. Three stereo scenes have been oriented at first by 3D-affine transformation and later by bias corrected RPC solution. The result is nearly the same, but it is limited by identification of the control points in the images. Nevertheless after blunder elimination by data snooping root mean square discrepancies below 1 pixel have been reached. The root mean square discrepancy at control point height reached 0.5 m up to 1.3 m with a base to height relation between 1:1.26 and 1:1.80. Digital Surface models (DSM) with 4 m spacing have been generated by least squares matching with region growing, supported by image pyramids. A higher percentage of the mountainous area is covered by forest, requiring the approximation based on image pyramids. In the forest area the approximation just by region growing leads to larger gaps in the DSM. Caused by the good image quality of WorldView-2 the correlation coefficients reached by least squares matching are high and even in most forest areas a satisfying density of accepted points was reached. Two stereo models have an overlapping area of 1.6 km times 6.7 km allowing an accuracy evaluation. Small, but nevertheless significant differences in scene orientation have been eliminated by least squares shift of both overlapping height models to each other. The root mean square differences of both independent DSM are 1.06m or as a function of terrain inclination 0.74 m + 0.55 m  tangent (slope). The terrain inclination in the average is 7° with 12% exceeding 17°. The frequency distribution of height discrepancies is not far away from normal distribution, but as usual, larger discrepancies are more often available as corresponding to normal distribution. This also can be seen by the normalized medium absolute deviation (NMAS) related to 68% probability level of 0.83m

Accuracy of a pulse-coherent acoustic Doppler profiler in a wave-dominated flow

USGS Publications Warehouse

Lacy, J.R.; Sherwood, C.R.

2004-01-01

The accuracy of velocities measured by a pulse-coherent acoustic Doppler profiler (PCADP) in the bottom boundary layer of a wave-dominated inner-shelf environment is evaluated. The downward-looking PCADP measured velocities in eight 10-cm cells at 1 Hz. Velocities measured by the PCADP are compared to those measured by an acoustic Doppler velocimeter for wave orbital velocities up to 95 cm s-1 and currents up to 40 cm s-1. An algorithm for correcting ambiguity errors using the resolution velocities was developed. Instrument bias, measured as the average error in burst mean speed, is -0.4 cm s-1 (standard deviation = 0.8). The accuracy (root-mean-square error) of instantaneous velocities has a mean of 8.6 cm s-1 (standard deviation = 6.5) for eastward velocities (the predominant direction of waves), 6.5 cm s-1 (standard deviation = 4.4) for northward velocities, and 2.4 cm s-1 (standard deviation = 1.6) for vertical velocities. Both burst mean and root-mean-square errors are greater for bursts with ub ??? 50 cm s-1. Profiles of burst mean speeds from the bottom five cells were fit to logarithmic curves: 92% of bursts with mean speed ??? 5 cm s-1 have a correlation coefficient R2 > 0.96. In cells close to the transducer, instantaneous velocities are noisy, burst mean velocities are biased low, and bottom orbital velocities are biased high. With adequate blanking distances for both the profile and resolution velocities, the PCADP provides sufficient accuracy to measure velocities in the bottom boundary layer under moderately energetic inner-shelf conditions.

Electrostatic and Small-Signal Analysis of CMUTs With Circular and Square Anisotropic Plates.

PubMed

Funding la Cour, Mette; Christiansen, Thomas Lehrmann; Jensen, Jørgen Arendt; Thomsen, Erik Vilain

2015-08-01

Traditionally, capacitive micromachined ultrasonic transducers (CMUTs) are modeled using the isotropic plate equation, and this leads to deviations between analytical calculations and finite element modeling (FEM). In this paper, the deflection is calculated for both circular and square plates using the full anisotropic plate equation. It is shown that the anisotropic calculations match excellently with FEM, whereas an isotropic approach causes up to 10% deviations in deflection. For circular plates, an exact solution can be found. For square plates using the Galerkin method, and utilizing the symmetry of the silicon crystal, a compact and accurate expression for the deflection can be obtained. The deviation from FEM in center deflection is <0.1%. The theory of multilayer plates is also applied to the CMUT. The deflection of a square plate was measured on fabricated CMUTs using a white light interferometer. Fitting the plate parameter for the anisotropic calculated deflection to the measurement, a deviation of 0.07% is seen. Electrostatic and small-signal dynamic analysis are performed using energy considerations including anisotropy. The stable position, effective spring constant, pullin distance, and pull-in voltage are found for both circular and square anisotropic plates, and the pressure dependence is included by comparison with the corresponding analysis for a parallel plate. Measurements on fabricated devices with both circular and square plates subjected to increasing bias voltage are performed, and it is observed that the models including anisotropic effects are within the uncertainty interval of the measurements. Finally, a lumped element small-signal model for both circular and square anisotropic plates is derived to describe the dynamics of the CMUT.

Triazine-based sequence-defined polymers with side-chain diversity and backbone-backbone interaction motifs

DOE PAGES

Grate, Jay W.; Mo, Kai -For; Daily, Michael D.

2016-02-10

Sequence control in polymers, well-known in nature, encodes structure and functionality. Here we introduce a new architecture, based on the nucleophilic aromatic substitution chemistry of cyanuric chloride, that creates a new class of sequence-defined polymers dubbed TZPs. Proof of concept is demonstrated with two synthesized hexamers, having neutral and ionizable side chains. Molecular dynamics simulations show backbone–backbone interactions, including H-bonding motifs and pi–pi interactions. This architecture is arguably biomimetic while differing from sequence-defined polymers having peptide bonds. In conclusion, the synthetic methodology supports the structural diversity of side chains known in peptides, as well as backbone–backbone hydrogen-bonding motifs, and willmore » thus enable new macromolecules and materials with useful functions.« less

Triazine-based sequence-defined polymers with side-chain diversity and backbone-backbone interaction motifs

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

Grate, Jay W.; Mo, Kai -For; Daily, Michael D.

Sequence control in polymers, well-known in nature, encodes structure and functionality. Here we introduce a new architecture, based on the nucleophilic aromatic substitution chemistry of cyanuric chloride, that creates a new class of sequence-defined polymers dubbed TZPs. Proof of concept is demonstrated with two synthesized hexamers, having neutral and ionizable side chains. Molecular dynamics simulations show backbone–backbone interactions, including H-bonding motifs and pi–pi interactions. This architecture is arguably biomimetic while differing from sequence-defined polymers having peptide bonds. In conclusion, the synthetic methodology supports the structural diversity of side chains known in peptides, as well as backbone–backbone hydrogen-bonding motifs, and willmore » thus enable new macromolecules and materials with useful functions.« less

Multistrange Baryon elliptic flow in Au+Au collisions at square root of sNN=200 GeV.

PubMed

Adams, J; Aggarwal, M M; Ahammed, Z; Amonett, J; Anderson, B D; Arkhipkin, D; Averichev, G S; Badyal, S K; Bai, Y; Balewski, J; Barannikova, O; Barnby, L S; Baudot, J; Bekele, S; Belaga, V V; Bellingeri-Laurikainen, A; Bellwied, R; Berger, J; Bezverkhny, B I; Bharadwaj, S; Bhasin, A; Bhati, A K; Bhatia, V S; Bichsel, H; Bielcik, J; Bielcikova, J; Billmeier, A; Bland, L C; Blyth, C O; Blyth, S L; Bonner, B E; Botje, M; Boucham, A; Bouchet, J; Brandin, A V; Bravar, A; Bystersky, M; Cadman, R V; Cai, X Z; Caines, H; Calderón de la Barca Sánchez, M; Castillo, J; Catu, O; Cebra, D; Chajecki, Z; Chaloupka, P; Chattopadhyay, S; Chen, H F; Chen, J H; Chen, Y; Cheng, J; Cherney, M; Chikanian, A; Christie, W; Coffin, J P; Cormier, T M; Cosentino, M R; Cramer, J G; Crawford, H J; Das, D; Das, S; Daugherity, M; de Moura, M M; Dedovich, T G; DePhillips, M; Derevschikov, A A; Didenko, L; Dietel, T; Dogra, S M; Dong, W J; Dong, X; Draper, J E; Du, F; Dubey, A K; Dunin, V B; Dunlop, J C; Dutta Mazumdar, M R; Eckardt, V; Edwards, W R; Efimov, L G; Emelianov, V; Engelage, J; Eppley, G; Erazmus, B; Estienne, M; Fachini, P; Faivre, J; Fatemi, R; Fedorisin, J; Filimonov, K; Filip, P; Finch, E; Fine, V; Fisyak, Y; Fornazier, K S F; Fu, J; Gagliardi, C A; Gaillard, L; Gans, J; Ganti, M S; Geurts, F; Ghazikhanian, V; Ghosh, P; Gonzalez, J E; Gos, H; Grachov, O; Grebenyuk, O; Grosnick, D; Guertin, S M; Guo, Y; Gupta, A; Gupta, N; Gutierrez, T D; Hallman, T J; Hamed, A; Hardtke, D; Harris, J W; Heinz, M; Henry, T W; Hepplemann, S; Hippolyte, B; Hirsch, A; Hjort, E; Hoffmann, G W; Horner, M J; Huang, H Z; Huang, S L; Hughes, E W; Humanic, T J; Igo, G; Ishihara, A; Jacobs, P; Jacobs, W W; Jedynak, M; Jiang, H; Jones, P G; Judd, E G; Kabana, S; Kang, K; Kaplan, M; Keane, D; Kechechyan, A; Khodyrev, V Yu; Kiryluk, J; Kisiel, A; Kislov, E M; Klay, J; Klein, S R; Koetke, D D; Kollegger, T; Kopytine, M; Kotchenda, L; Kowalik, K L; Kramer, M; Kravtsov, P; Kravtsov, V I; Krueger, K; Kuhn, C; Kulikov, A I; Kumar, A; Kutuev, R Kh; Kuznetsov, A A; Lamont, M A C; Landgraf, J M; Lange, S; Laue, F; Lauret, J; Lebedev, A; Lednicky, R; Lehocka, S; LeVine, M J; Li, C; Li, Q; Li, Y; Lin, G; Lindenbaum, S J; Lisa, M A; Liu, F; Liu, H; Liu, J; Liu, L; Liu, Q J; Liu, Z; Ljubicic, T; Llope, W J; Long, H; Longacre, R S; Lopez-Noriega, M; Love, W A; Lu, Y; Ludlam, T; Lynn, D; Ma, G L; Ma, J G; Ma, Y G; Magestro, D; Mahajan, S; Mahapatra, D P; Majka, R; Mangotra, L K; Manweiler, R; Margetis, S; Markert, C; Martin, L; Marx, J N; Matis, H S; Matulenko, Yu A; McClain, C J; McShane, T S; Meissner, F; Melnick, Yu; Meschanin, A; Miller, M L; Minaev, N G; Mironov, C; Mischke, A; Mishra, D K; Mitchell, J; Mohanty, B; Molnar, L; Moore, C F; Morozov, D A; Munhoz, M G; Nandi, B K; Nayak, S K; Nayak, T K; Nelson, J M; Netrakanti, P K; Nikitin, V A; Nogach, L V; Nurushev, S B; Odyniec, G; Ogawa, A; Okorokov, V; Oldenburg, M; Olson, D; Pal, S K; Panebratsev, Y; Panitkin, S Y; Pavlinov, A I; Pawlak, T; Peitzmann, T; Perevoztchikov, V; Perkins, C; Peryt, W; Petrov, V A; Phatak, S C; Picha, R; Planinic, M; Pluta, J; Porile, N; Porter, J; Poskanzer, A M; Potekhin, M; Potrebenikova, E; Potukuchi, B V K S; Prindle, D; Pruneau, C; Putschke, J; Rakness, G; Raniwala, R; Raniwala, S; Ravel, O; Ray, R L; Razin, S V; Reichhold, D; Reid, J G; Reinnarth, J; Renault, G; Retiere, F; Ridiger, A; Ritter, H G; Roberts, J B; Rogachevskiy, O V; Romero, J L; Rose, A; Roy, C; Ruan, L; Russcher, M; Sahoo, R; Sakrejda, I; Salur, S; Sandweiss, J; Sarsour, M; Savin, I; Sazhin, P S; Schambach, J; Scharenberg, R P; Schmitz, N; Schweda, K; Seger, J; Seyboth, P; Shahaliev, E; Shao, M; Shao, W; Sharma, M; Shen, W Q; Shestermanov, K E; Shimanskiy, S S; Sichtermann, E; Simon, F; Singaraju, R N; Smirnov, N; Snellings, R; Sood, G; Sorensen, P; Sowinski, J; Speltz, J; Spinka, H M; Srivastava, B; Stadnik, A; Stanislaus, T D S; Stock, R; Stolpovsky, A; Strikhanov, M; Stringfellow, B; Suaide, A A P; Sugarbaker, E; Suire, C; Sumbera, M; Surrow, B; Swanger, M; Symons, T J M; Szanto de Toledo, A; Tai, A; Takahashi, J; Tang, A H; Tarnowsky, T; Thein, D; Thomas, J H; Timmins, A R; Timoshenko, S; Tokarev, M; Trentalange, S; Tribble, R E; Tsai, O D; Ulery, J; Ullrich, T; Underwood, D G; Van Buren, G; van der Kolk, N; van Leeuwen, M; Vander Molen, A M; Varma, R; Vasilevski, I M; Vasiliev, A N; Vernet, R; Vigdor, S E; Viyogi, Y P; Vokal, S; Voloshin, S A; Waggoner, W T; Wang, F; Wang, G; Wang, G; Wang, X L; Wang, Y; Wang, Y; Wang, Z M; Ward, H; Watson, J W; Webb, J C; Westfall, G D; Wetzler, A; Whitten, C; Wieman, H; Wissink, S W; Witt, R; Wood, J; Wu, J; Xu, N; Xu, Z; Xu, Z Z; Yamamoto, E; Yepes, P; Yurevich, V I; Zborovsky, I; Zhang, H; Zhang, W M; Zhang, Y; Zhang, Z P; Zhong, C; Zoulkarneev, R; Zoulkarneeva, Y; Zubarev, A N; Zuo, J X

2005-09-16

We report on the first measurement of elliptic flow v2(pT) of multistrange baryons Xi- +Xi+ and Omega- + Omega+ in heavy-ion collisions. In minimum-bias Au+Au collisions at square root of s(NN)=200 GeV, a significant amount of elliptic flow, comparable to other nonstrange baryons, is observed for multistrange baryons which are expected to be particularly sensitive to the dynamics of the partonic stage of heavy-ion collisions. The pT dependence of v2 of the multistrange baryons confirms the number of constituent quark scaling previously observed for lighter hadrons. These results support the idea that a substantial fraction of the observed collective motion is developed at the early partonic stage in ultrarelativistic nuclear collisions at the Relativistic Heavy Ion Collider.

Electronic polarization stabilizes tertiary structure prediction of HP-36.

PubMed

Duan, Li L; Zhu, Tong; Zhang, Qing G; Tang, Bo; Zhang, John Z H

2014-04-01

Molecular dynamic (MD) simulations with both implicit and explicit solvent models have been carried out to study the folding dynamics of HP-36 protein. Starting from the extended conformation, the secondary structure of all three helices in HP-36 was formed in about 50 ns and remained stable in the remaining simulation. However, the formation of the tertiary structure was difficult. Although some intermediates were close to the native structure, the overall conformation was not stable. Further analysis revealed that the large structure fluctuation of loop and hydrophobic core regions was devoted mostly to the instability of the structure during MD simulation. The backbone root-mean-square deviation (RMSD) of the loop and hydrophobic core regions showed strong correlation with the backbone RMSD of the whole protein. The free energy landscape indicated that the distribution of main chain torsions in loop and turn regions was far away from the native state. Starting from an intermediate structure extracted from the initial AMBER simulation, HP-36 was found to generally fold to the native state under the dynamically adjusted polarized protein-specific charge (DPPC) simulation, while the peptide did not fold into the native structure when AMBER force filed was used. The two best folded structures were extracted and taken into further simulations in water employing AMBER03 charge and DPPC for 25 ns. Result showed that introducing polarization effect into interacting potential could stabilize the near-native protein structure.

How to Define the Mean Square Amplitude of Solar Wind Fluctuations With Respect to the Local Mean Magnetic Field

NASA Astrophysics Data System (ADS)

Podesta, John J.

2017-12-01

Over the last decade it has become popular to analyze turbulent solar wind fluctuations with respect to a coordinate system aligned with the local mean magnetic field. This useful analysis technique has provided new information and new insights about the nature of solar wind fluctuations and provided some support for phenomenological theories of MHD turbulence based on the ideas of Goldreich and Sridhar. At the same time it has drawn criticism suggesting that the use of a scale-dependent local mean field is somehow inconsistent or irreconcilable with traditional analysis techniques based on second-order structure functions and power spectra that, for stationary time series, are defined with respect to the constant (scale-independent) ensemble average magnetic field. Here it is shown that for fluctuations with power law spectra, such as those observed in solar wind turbulence, it is possible to define the local mean magnetic field in a special way such that the total mean square amplitude (trace amplitude) of turbulent fluctuations is approximately the same, scale by scale, as that obtained using traditional second-order structure functions or power spectra. This fact should dispel criticism concerning the physical validity or practical usefulness of the local mean magnetic field in these applications.

[Clinical evaluation on the operation of the deviated nose and the deviated nasal septum with the plastic operation--report of 268 cases].

PubMed

Wang, Gang; Liu, Liu; Li, Fang

2011-04-01

To explore the feasibility of combination plastic operation on the deviation nose and the deviation nasal septum. Design the butterfly cut from the root of the columella nasi to the middle part of each alae nasi. So that the nasal septum, the cartilage septodorsalis and the nose bones could be exposed well. It was key to separate and fix the arch keystone area in the plastic operation of the deviation nose. It was key to separate septal cartilage of nose from the perpendicular plate of ethmoid bone and maxilla nose pun in plastic operation of the deviation nasal septum. Pack the vaseline oil gauze or chitosan reshaping PVA into two side of nasal cavity in order to internal fixation of nasal cavity and prevent the hematoma of nasal septum. The vaseline oil gauze can be pull out on the morning and on the afternoon 24 hours after which can reduce the pain. The external fixation of nasal cavity is not important to which can be omitted. Two hundred and sixty-eight cases after 6 to 24 months follow-up. Two hundred and twenty-eight cases were satisfied. None was unsatisfied. The combination plastic operation on the deviation nose and the deviation nasal septum, could cope with both the beauty problem and reconstruct the nose function.

SMAP Level 4 Surface and Root Zone Soil Moisture

NASA Technical Reports Server (NTRS)

Reichle, R.; De Lannoy, G.; Liu, Q.; Ardizzone, J.; Kimball, J.; Koster, R.

2017-01-01

The SMAP Level 4 soil moisture (L4_SM) product provides global estimates of surface and root zone soil moisture, along with other land surface variables and their error estimates. These estimates are obtained through assimilation of SMAP brightness temperature observations into the Goddard Earth Observing System (GEOS-5) land surface model. The L4_SM product is provided at 9 km spatial and 3-hourly temporal resolution and with about 2.5 day latency. The soil moisture and temperature estimates in the L4_SM product are validated against in situ observations. The L4_SM product meets the required target uncertainty of 0.04 m(exp. 3)m(exp. -3), measured in terms of unbiased root-mean-square-error, for both surface and root zone soil moisture.

An improved partial least-squares regression method for Raman spectroscopy

NASA Astrophysics Data System (ADS)

Momenpour Tehran Monfared, Ali; Anis, Hanan

2017-10-01

It is known that the performance of partial least-squares (PLS) regression analysis can be improved using the backward variable selection method (BVSPLS). In this paper, we further improve the BVSPLS based on a novel selection mechanism. The proposed method is based on sorting the weighted regression coefficients, and then the importance of each variable of the sorted list is evaluated using root mean square errors of prediction (RMSEP) criterion in each iteration step. Our Improved BVSPLS (IBVSPLS) method has been applied to leukemia and heparin data sets and led to an improvement in limit of detection of Raman biosensing ranged from 10% to 43% compared to PLS. Our IBVSPLS was also compared to the jack-knifing (simpler) and Genetic Algorithm (more complex) methods. Our method was consistently better than the jack-knifing method and showed either a similar or a better performance compared to the genetic algorithm.

Odontometric evaluation of mandibular premolars with tooth shape deviation: a case-control study.

PubMed

Chate, Robert Anthony Clive

2012-09-01

To evaluate the mean dimensions and morphologic characteristics of mandibular premolars that had mesiodistally elongated and faciolingually squeezed tooth shape deviations (MnP-TSD) and determine the population prevalence of this anomaly. Clinical photographs and study models were made for all new patients with MnP-TSD teeth who were seen over 20 years. The mesiodistal (MD) and faciolingual (FL) dimensions of the anomalous premolars were measured. MD/FL indices and MD × FL mm(2) occlusal crown areas were calculated and means and standard deviations were derived. Male and female means from the mandibular first and second anomalous premolars (MnP1/MnP2-TSD) were statistically compared against gender-specific means derived from published normative data using Student's t-tests and chi-square tests. Fifty-six individuals (33 male and 23 female) with MnP-TSD were identified, giving a male to female ratio of 1.4:1, while the prevalence rate in the indigenous British population was estimated to be 0.6%. The MD widths of the MnP1-TSD and MnP2-TSD teeth were approximately 1 mm wider than normal, while the FL diameters were about 0.5 mm and 1.5 mm narrower respectively, for the first and second premolar teeth. The MD/FL indices, instead of being under 90 as usual were above 100, while the mean MD/FL mm(2) crown surface areas were normal. This study supplies odontometric dimensional and morphologic data on MnP-TSD teeth that provide a reference source for future comparisons.

Simultaneous polarimeter retrievals of microphysical aerosol and ocean color parameters from the “MAPP” algorithm with comparison to high-spectral-resolution lidar aerosol and ocean products

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

Stamnes, S.; Hostetler, C.; Ferrare, R.

We present an optimal estimation based retrieval framework, the Microphysical Aerosol Properties from Polarimetry (MAPP) algorithm, designed for simultaneous retrieval of aerosol microphysical properties and ocean color bio-optical parameters using multi-angular polarized radiances. Polarimetric measurements from the airborne NASA Research Scanning Polarimeter (RSP) were inverted by MAPP to produce atmosphere and ocean products. The RSP MAPP results are compared with co-incident lidar measurements made by the NASA High Spectral Resolution Lidar HSRL-1 and HSRL-2 instruments. Comparisons are made of the aerosol optical depth (AOD) at 355, 532, and 1064 nm, lidar column-averaged measurements of the aerosol lidar ratio and Ã…ngstrømmore » exponent, and lidar ocean measurements of the particulate hemispherical backscatter coefficient and the diffuse attenuation coefficient. The measurements were collected during the 2012 Two-Column Aerosol Project (TCAP) campaign and the 2014 Ship-Aircraft Bio- Optical Research (SABOR) campaign. For the SABOR campaign, 71% RSP MAPP retrievals fall within 0.04 AOD at 532 nm as measured by HSRL-1, with an R value of 0.925 and root-mean-square deviation of 0.04. For the TCAP campaign, 55% of RSP MAPP retrievals are within 0.04 AOD as measured by HSRL-2, with an R value of 0.925 and root-mean-square deviation of 0.07. Comparisons with HSRL-2 AOD at 355 nm during TCAP result in an R value of 0.96 and a root-mean-square deviation of also 0.07. The RSP retrievals using the MAPP optimal estimation framework represent a key milestone on the path to a combined lidar+polarimeter retrieval using both HSRL and RSP measurements.« less

Similarity Measures for Protein Ensembles

PubMed Central

Lindorff-Larsen, Kresten; Ferkinghoff-Borg, Jesper

2009-01-01

Analyses of similarities and changes in protein conformation can provide important information regarding protein function and evolution. Many scores, including the commonly used root mean square deviation, have therefore been developed to quantify the similarities of different protein conformations. However, instead of examining individual conformations it is in many cases more relevant to analyse ensembles of conformations that have been obtained either through experiments or from methods such as molecular dynamics simulations. We here present three approaches that can be used to compare conformational ensembles in the same way as the root mean square deviation is used to compare individual pairs of structures. The methods are based on the estimation of the probability distributions underlying the ensembles and subsequent comparison of these distributions. We first validate the methods using a synthetic example from molecular dynamics simulations. We then apply the algorithms to revisit the problem of ensemble averaging during structure determination of proteins, and find that an ensemble refinement method is able to recover the correct distribution of conformations better than standard single-molecule refinement. PMID:19145244

Assessment of Root Resorption and Root Shape by Periapical and Panoramic Radiographs: A Comparative Study.

PubMed

Ahuja, Puneeta D; Mhaske, Sheetal P; Mishra, Gaurav; Bhardwaj, Atul; Dwivedi, Ruby; Mangalekar, Sachin B

2017-06-01

One of the common findings encountered by the clinician at the end of orthodontic treatment is the apical root resorption. Root resorption occurs to various degrees. A severe form of root resorption is characterized by shortening of root for more than 4 mm or more than one-third of the total tooth length. A low incidence rate of resorption is observed based on radiographic findings for the diagnosis of root resorption, panoramic radiography, and periapical radiography. Hence, we evaluated the accuracy of panoramic radiographic films for assessing the root resorption in comparison with the periapical films. This study included the assessment of all the cases in which pre- and post-treatment radiographs were available for analysis of the assessment of the amount of root resorption. Complete records of 80 patients were analyzed. Examination of a total of 900 teeth was done. Mean age of the patients in this study was 21 years ranging from 11 to 38 years. The majority of the patients in the present study were females. All the treatments were carried out by registered experienced orthodontists having minimum experience of more than 10 years. All the cases were divided into two study groups. Group I comprised panoramic radiographic findings, while group II consisted of periapical radiographic findings. For the measurement of crown portion, root portion, and the complete root length, magnification loops of over 100 powers with parallax correction with inbuilt grids were used. Assessment of the tooth length and the crown length was done by the same observers. All the results were analyzed by Statistical Package for the Social Sciences software version 6.0. Maximum amount of root resorption was observed in case of maxillary central incisors and canines among group I and II cases respectively. However, nonsignificant difference was obtained while comparing the mean root resorption in relation to maxillary incisors and canines among the two study groups. While comparing the

Direct and simultaneous quantification of tannin mean degree of polymerization and percentage of galloylation in grape seeds using diffuse reflectance fourier transform-infrared spectroscopy.

PubMed

Pappas, Christos; Kyraleou, Maria; Voskidi, Eleni; Kotseridis, Yorgos; Taranilis, Petros A; Kallithraka, Stamatina

2015-02-01

The direct and simultaneous quantitative determination of the mean degree of polymerization (mDP) and the degree of galloylation (%G) in grape seeds were quantified using diffuse reflectance infrared Fourier transform spectroscopy and partial least squares (PLS). The results were compared with those obtained using the conventional analysis employing phloroglucinolysis as pretreatment followed by high performance liquid chromatography-UV and mass spectrometry detection. Infrared spectra were recorded in solid state samples after freeze drying. The 2nd derivative of the 1832 to 1416 and 918 to 739 cm(-1) spectral regions for the quantification of mDP, the 2nd derivative of the 1813 to 607 cm(-1) spectral region for the degree of %G determination and PLS regression were used. The determination coefficients (R(2) ) of mDP and %G were 0.99 and 0.98, respectively. The corresponding values of the root-mean-square error of calibration were found 0.506 and 0.692, the root-mean-square error of cross validation 0.811 and 0.921, and the root-mean-square error of prediction 0.612 and 0.801. The proposed method in comparison with the conventional method is simpler, less time consuming, more economical, and requires reduced quantities of chemical reagents and fewer sample pretreatment steps. It could be a starting point for the design of more specific models according to the requirements of the wineries. © 2015 Institute of Food Technologists®

Jatropha curcas L. Root Structure and Growth in Diverse Soils

PubMed Central

Valdés-Rodríguez, Ofelia Andrea; Sánchez-Sánchez, Odilón; Pérez-Vázquez, Arturo; Caplan, Joshua S.; Danjon, Frédéric

2013-01-01

Unlike most biofuel species, Jatropha curcas has promise for use in marginal lands, but it may serve an additional role by stabilizing soils. We evaluated the growth and structural responsiveness of young J. curcas plants to diverse soil conditions. Soils included a sand, a sandy-loam, and a clay-loam from eastern Mexico. Growth and structural parameters were analyzed for shoots and roots, although the focus was the plasticity of the primary root system architecture (the taproot and four lateral roots). The sandy soil reduced the growth of both shoot and root systems significantly more than sandy-loam or clay-loam soils; there was particularly high plasticity in root and shoot thickness, as well as shoot length. However, the architecture of the primary root system did not vary with soil type; the departure of the primary root system from an index of perfect symmetry was 14 ± 5% (mean ± standard deviation). Although J. curcas developed more extensively in the sandy-loam and clay-loam soils than in sandy soil, it maintained a consistent root to shoot ratio and root system architecture across all types of soil. This strong genetic determination would make the species useful for soil stabilization purposes, even while being cultivated primarily for seed oil. PMID:23844412

Jatropha curcas L. root structure and growth in diverse soils.

PubMed

Valdés-Rodríguez, Ofelia Andrea; Sánchez-Sánchez, Odilón; Pérez-Vázquez, Arturo; Caplan, Joshua S; Danjon, Frédéric

2013-01-01

Unlike most biofuel species, Jatropha curcas has promise for use in marginal lands, but it may serve an additional role by stabilizing soils. We evaluated the growth and structural responsiveness of young J. curcas plants to diverse soil conditions. Soils included a sand, a sandy-loam, and a clay-loam from eastern Mexico. Growth and structural parameters were analyzed for shoots and roots, although the focus was the plasticity of the primary root system architecture (the taproot and four lateral roots). The sandy soil reduced the growth of both shoot and root systems significantly more than sandy-loam or clay-loam soils; there was particularly high plasticity in root and shoot thickness, as well as shoot length. However, the architecture of the primary root system did not vary with soil type; the departure of the primary root system from an index of perfect symmetry was 14 ± 5% (mean ± standard deviation). Although J. curcas developed more extensively in the sandy-loam and clay-loam soils than in sandy soil, it maintained a consistent root to shoot ratio and root system architecture across all types of soil. This strong genetic determination would make the species useful for soil stabilization purposes, even while being cultivated primarily for seed oil.

Analysis of secondary motions in square duct flow

NASA Astrophysics Data System (ADS)

Modesti, Davide; Pirozzoli, Sergio; Orlandi, Paolo; Grasso, Francesco

2018-04-01

We carry out direct numerical simulations (DNS) of square duct flow spanning the friction Reynolds number range {Re}τ * =150-1055, to study the nature and the role of secondary motions. We preliminarily find that secondary motions are not the mere result of the time averaging procedure, but rather they are present in the instantaneous flow realizations, corresponding to large eddies persistent in both space and time. Numerical experiments have also been carried out whereby the secondary motions are suppressed, hence allowing to quantifying their effect on the mean flow field. At sufficiently high Reynolds number, secondary motions are found to increase the friction coefficient by about 3%, hence proportionally to their relative strength with respect to the bulk flow. Simulations without secondary motions are found to yield larger deviations on the mean velocity profiles from the standard law-of-the-wall, revealing that secondary motions act as a self-regulating mechanism of turbulence whereby the effect of the corners is mitigated.

Multiplicity and pseudorapidity distributions of photons in Au+Au collisions at square root of (S(NN)) = 62.4 GeV.

PubMed

Adams, J; Aggarwal, M M; Ahammed, Z; Amonett, J; Anderson, B D; Arkhipkin, D; Averichev, G S; Badyal, S K; Bai, Y; Balewski, J; Barannikova, O; Barnby, L S; Baudot, J; Bekele, S; Belaga, V V; Bellingeri-Laurikainen, A; Bellwied, R; Berger, J; Bezverkhny, B I; Bhardwaj, S; Bhasin, A; Bhati, A K; Bichsel, H; Bielcik, J; Bielcikova, J; Billmeier, A; Bland, L C; Blyth, C O; Blyth, S; Bonner, B E; Botje, M; Boucham, A; Bouchet, J; Brandin, A V; Bravar, A; Bystersky, M; Cadman, R V; Cai, X Z; Caines, H; de la Barca Sánchez, M Calderón; Castillo, J; Catu, O; Cebra, D; Chajecki, Z; Chaloupka, P; Chattopadhyay, S; Chen, H F; Chen, Y; Cheng, J; Cherney, M; Chikanian, A; Christie, W; Coffin, J P; Cormier, T M; Cosentino, M R; Cramer, J G; Crawford, H J; Das, D; Das, S; de Moura, M M; Dedovich, T G; Derevschikov, A A; Didenko, L; Dietel, T; Dogra, S M; Dong, W J; Dong, X; Draper, J E; Du, F; Dubey, A K; Dunin, V B; Dunlop, J C; Mazumdar, M R Dutta; Eckardt, V; Edwards, W R; Efimov, L G; Emelianov, V; Engelage, J; Eppley, G; Erazmus, B; Estienne, M; Fachini, P; Faivre, J; Fatemi, R; Fedorisin, J; Filimonov, K; Filip, P; Finch, E; Fine, V; Fisyak, Y; Fornazier, K S F; Fu, J; Gagliardi, C A; Gaillard, L; Gans, J; Ganti, M S; Geurts, F; Ghazikhanian, V; Ghosh, P; Gonzalez, J E; Gos, H; Grachov, O; Grebenyuk, O; Grosnick, D; Guertin, S M; Guo, Y; Gupta, A; Gutierrez, T D; Hallman, T J; Hamed, A; Hardtke, D; Harris, J W; Heinz, M; Henry, T W; Hepplemann, S; Hippolyte, B; Hirsch, A; Hjort, E; Hoffmann, G W; Horner, M; Huang, H Z; Huang, S L; Hughes, E W; Humanic, T J; Igo, G; Ishihara, A; Jacobs, P; Jacobs, W W; Jedynak, M; Jiang, H; Jones, P G; Judd, E G; Kabana, S; Kang, K; Kaplan, M; Keane, D; Kechechyan, A; Khodyrev, V Yu; Kiryluk, J; Kisiel, A; Kislov, E M; Klay, J; Klein, S R; Koetke, D D; Kollegger, T; Kopytine, M; Kotchenda, L; Kowalik, K L; Kramer, M; Kravtsov, P; Kravtsov, V I; Krueger, K; Kuhn, C; Kulikov, A I; Kumar, A; Kutuev, R Kh; Kuznetsov, A A; Lamont, M A C; Landgraf, J M; Lange, S; Laue, F; Lauret, J; Lebedev, A; Lednicky, R; Lehocka, S; Levine, M J; Li, C; Li, Q; Li, Y; Lin, G; Lindenbaum, S J; Lisa, M A; Liu, F; Liu, H; Liu, J; Liu, L; Liu, Q J; Liu, Z; Ljubicic, T; Llope, W J; Long, H; Longacre, R S; Lopez-Noriega, M; Love, W A; Lu, Y; Ludlam, T; Lynn, D; Ma, G L; Ma, J G; Ma, Y G; Magestro, D; Mahajan, S; Mahapatra, D P; Majka, R; Mangotra, L K; Manweiler, R; Margetis, S; Markert, C; Martin, L; Marx, J N; Matis, H S; Matulenko, Yu A; McClain, C J; McShane, T S; Meissner, F; Melnick, Yu; Meschanin, A; Miller, M L; Minaev, N G; Mironov, C; Mischke, A; Mishra, D K; Mitchell, J; Mohanty, B; Molnar, L; Moore, C F; Morozov, D A; Munhoz, M G; Nandi, B K; Nayak, S K; Nayak, T K; Nelson, J M; Netrakanti, P K; Nikitin, V A; Nogach, L V; Nurushev, S B; Odyniec, G; Ogawa, A; Okorokov, V; Oldenburg, M; Olson, D; Pal, S K; Panebratsev, Y; Panitkin, S Y; Pavlinov, A I; Pawlak, T; Peitzmann, T; Perevoztchikov, V; Perkins, C; Peryt, W; Petrov, V A; Phatak, S C; Picha, R; Planinic, M; Pluta, J; Porile, N; Porter, J; Poskanzer, A M; Potekhin, M; Potrebenikova, E; Potukuchi, B V K S; Prindle, D; Pruneau, C; Putschke, J; Rakness, G; Raniwala, R; Raniwala, S; Ravel, O; Ray, R L; Razin, S V; Reichhold, D; Reid, J G; Reinnarth, J; Renault, G; Retiere, F; Ridiger, A; Ritter, H G; Roberts, J B; Rogachevskiy, O V; Romero, J L; Rose, A; Roy, C; Ruan, L; Russcher, M J; Sahoo, R; Sakrejda, I; Salur, S; Sandweiss, J; Sarsour, M; Savin, I; Sazhin, P S; Schambach, J; Scharenberg, R P; Schmitz, N; Schweda, K; Seger, J; Seyboth, P; Shahaliev, E; Shao, M; Shao, W; Sharma, M; Shen, W Q; Shestermanov, K E; Shimanskiy, S S; Sichtermann, E; Simon, F; Singaraju, R N; Smirnov, N; Snellings, R; Sood, G; Sorensen, P; Sowinski, J; Speltz, J; Spinka, H M; Srivastava, B; Stadnik, A; Stanislaus, T D S; Stock, R; Stolpovsky, A; Strikhanov, M; Stringfellow, B; Suaide, A A P; Sugarbaker, E; Suire, C; Sumbera, M; Surrow, B; Swanger, M; Symons, T J M; de Toledo, A Szanto; Tai, A; Takahashi, J; Tang, A H; Tarnowsky, T; Thein, D; Thomas, J H; Timoshenko, S; Tokarev, M; Trainor, T A; Trentalange, S; Tribble, R E; Tsai, O D; Ulery, J; Ullrich, T; Underwood, D G; Buren, G Van; van Leeuwen, M; Molen, A M Vander; Varma, R; Vasilevski, I M; Vasiliev, A N; Vernet, R; Vigdor, S E; Viyogi, Y P; Vokal, S; Voloshin, S A; Waggoner, W T; Wang, F; Wang, G; Wang, G; Wang, X L; Wang, Y; Wang, Y; Wang, Z M; Ward, H; Watson, J W; Webb, J C; Westfall, G D; Wetzler, A; Whitten, C; Wieman, H; Wissink, S W; Witt, R; Wood, J; Wu, J; Xu, N; Xu, Z; Xu, Z Z; Yamamoto, E; Yepes, P; Yurevich, V I; Zborovsky, I; Zhang, H; Zhang, W M; Zhang, Y; Zhang, Z P; Zoulkarneev, R; Zoulkarneeva, Y; Zubarev, A N

2005-08-05

We present the first measurement of pseudorapidity distribution of photons in the region 2.3 < or = eta < or = 3.7 for different centralities in Au+Au collisions at square root of (S(NN)) = 62.4 GeV. We find that the photon yield scales with the number of participating nucleons at all collision centralities studied. The pseudorapidity distribution of photons, dominated by pi0 decays, has been compared to those of charged pions, photons, and inclusive charged particles from heavy-ion and nucleon-nucleon collisions at various energies. The photon production has been shown to be consistent with the energy and centrality independent limiting fragmentation scenario.

Search for pair production of scalar bottom quarks in pp collisions at square root of s = 1.96 TeV.

PubMed

Abazov, V M; Abbott, B; Abolins, M; Acharya, B S; Adams, M; Adams, T; Agelou, M; Ahn, S H; Ahsan, M; Alexeev, G D; Alkhazov, G; Alton, A; Alverson, G; Alves, G A; Anastasoaie, M; Andeen, T; Anderson, S; Andrieu, B; Anzelc, M S; Arnoud, Y; Arov, M; Askew, A; Asman, B; Jesus, A C S Assis; Atramentov, O; Autermann, C; Avila, C; Ay, C; Badaud, F; Baden, A; Bagby, L; Baldin, B; Bandurin, D V; Banerjee, P; Banerjee, S; Barberis, E; Bargassa, P; Baringer, P; Barnes, C; Barreto, J; Bartlett, J F; Bassler, U; Bauer, D; Bean, A; Begalli, M; Begel, M; Belanger-Champagne, C; Bellantoni, L; Bellavance, A; Benitez, J A; Beri, S B; Bernardi, G; Bernhard, R; Berntzon, L; Bertram, I; Besançon, M; Beuselinck, R; Bezzubov, V A; Bhat, P C; Bhatnagar, V; Binder, M; Biscarat, C; Black, K M; Blackler, I; Blazey, G; Blekman, F; Blessing, S; Bloch, D; Bloom, K; Blumenschein, U; Boehnlein, A; Boeriu, O; Bolton, T A; Borissov, G; Bos, K; Bose, T; Brandt, A; Brock, R; Brooijmans, G; Bross, A; Brown, D; Buchanan, N J; Buchholz, D; Buehler, M; Buescher, V; Burdin, S; Burke, S; Burnett, T H; Busato, E; Buszello, C P; Butler, J M; Calfayan, P; Calvet, S; Cammin, J; Caron, S; Carvalho, W; Casey, B C K; Cason, N M; Castilla-Valdez, H; Chakraborty, D; Chan, K M; Chandra, A; Charles, F; Cheu, E; Chevallier, F; Cho, D K; Choi, S; Choudhary, B; Christofek, L; Claes, D; Clément, B; Clément, C; Coadou, Y; Cooke, M; Cooper, W E; Coppage, D; Corcoran, M; Cousinou, M-C; Cox, B; Crépé-Renaudin, S; Cutts, D; Cwiok, M; da Motta, H; Das, A; Das, M; Davies, B; Davies, G; Davis, G A; De, K; de Jong, P; de Jong, S J; De La Cruz-Burelo, E; De Oliveira Martins, C; Degenhardt, J D; Déliot, F; Demarteau, M; Demina, R; Demine, P; Denisov, D; Denisov, S P; Desai, S; Diehl, H T; Diesburg, M; Doidge, M; Dominguez, A; Dong, H; Dudko, L V; Duflot, L; Dugad, S R; Duggan, D; Duperrin, A; Dyer, J; Dyshkant, A; Eads, M; Edmunds, D; Edwards, T; Ellison, J; Elmsheuser, J; Elvira, V D; Eno, S; Ermolov, P; Evans, H; Evdokimov, A; Evdokimov, V N; Fatakia, S N; Feligioni, L; Ferapontov, A V; Ferbel, T; Fiedler, F; Filthaut, F; Fisher, W; Fisk, H E; Fleck, I; Ford, M; Fortner, M; Fox, H; Fu, S; Fuess, S; Gadfort, T; Galea, C F; Gallas, E; Galyaev, E; Garcia, C; Garcia-Bellido, A; Gardner, J; Gavrilov, V; Gay, A; Gay, P; Gelé, D; Gelhaus, R; Gerber, C E; Gershtein, Y; Gillberg, D; Ginther, G; Gollub, N; Gómez, B; Goussiou, A; Grannis, P D; Greenlee, H; Greenwood, Z D; Gregores, E M; Grenier, G; Gris, Ph; Grivaz, J-F; Grünendahl, S; Grünewald, M W; Guo, F; Guo, J; Gutierrez, G; Gutierrez, P; Haas, A; Hadley, N J; Haefner, P; Hagopian, S; Haley, J; Hall, I; Hall, R E; Han, L; Hanagaki, K; Harder, K; Harel, A; Harrington, R; Hauptman, J M; Hauser, R; Hays, J; Hebbeker, T; Hedin, D; Hegeman, J G; Heinmiller, J M; Heinson, A P; Heintz, U; Hensel, C; Herner, K; Hesketh, G; Hildreth, M D; Hirosky, R; Hobbs, J D; Hoeneisen, B; Hoeth, H; Hohlfeld, M; Hong, S J; Hooper, R; Houben, P; Hu, Y; Hubacek, Z; Hynek, V; Iashvili, I; Illingworth, R; Ito, A S; Jabeen, S; Jaffré, M; Jain, S; Jakobs, K; Jarvis, C; Jenkins, A; Jesik, R; Johns, K; Johnson, C; Johnson, M; Jonckheere, A; Jonsson, P; Juste, A; Käfer, D; Kahn, S; Kajfasz, E; Kalinin, A M; Kalk, J M; Kalk, J R; Kappler, S; Karmanov, D; Kasper, J; Kasper, P; Katsanos, I; Kau, D; Kaur, R; Kehoe, R; Kermiche, S; Khalatyan, N; Khanov, A; Kharchilava, A; Kharzheev, Y M; Khatidze, D; Kim, H; Kim, T J; Kirby, M H; Klima, B; Kohli, J M; Konrath, J-P; Kopal, M; Korablev, V M; Kotcher, J; Kothari, B; Koubarovsky, A; Kozelov, A V; Kozminski, J; Krop, D; Kryemadhi, A; Kuhl, T; Kumar, A; Kunori, S; Kupco, A; Kurca, T; Kvita, J; Lammers, S; Landsberg, G; Lazoflores, J; Le Bihan, A-C; Lebrun, P; Lee, W M; Leflat, A; Lehner, F; Lesne, V; Leveque, J; Lewis, P; Li, J; Li, Q Z; Lima, J G R; Lincoln, D; Linnemann, J; Lipaev, V V; Lipton, R; Liu, Z; Lobo, L; Lobodenko, A; Lokajicek, M; Lounis, A; Love, P; Lubatti, H J; Lynker, M; Lyon, A L; Maciel, A K A; Madaras, R J; Mättig, P; Magass, C; Magerkurth, A; Magnan, A-M; Makovec, N; Mal, P K; Malbouisson, H B; Malik, S; Malyshev, V L; Mao, H S; Maravin, Y; Martens, M; McCarthy, R; Meder, D; Melnitchouk, A; Mendes, A; Mendoza, L; Merkin, M; Merritt, K W; Meyer, A; Meyer, J; Michaut, M; Miettinen, H; Millet, T; Mitrevski, J; Molina, J; Mondal, N K; Monk, J; Moore, R W; Moulik, T; Muanza, G S; Mulders, M; Mulhearn, M; Mundim, L; Mutaf, Y D; Nagy, E; Naimuddin, M; Narain, M; Naumann, N A; Neal, H A; Negret, J P; Neustroev, P; Noeding, C; Nomerotski, A; Novaes, S F; Nunnemann, T; O'Dell, V; O'Neil, D C; Obrant, G; Oguri, V; Oliveira, N; Oshima, N; Otec, R; Y Garzón, G J Otero; Owen, M; Padley, P; Parashar, N; Park, S-J; Park, S K; Parsons, J; Partridge, R; Parua, N; Patwa, A; Pawloski, G; Perea, P M; Perez, E; Peters, K; Pétroff, P; Petteni, M; Piegaia, R; Piper, J; Pleier, M-A; Podesta-Lerma, P L M; Podstavkov, V M; Pogorelov, Y; Pol, M-E; Pompos, A; Pope, B G; Popov, A V; Potter, C; Prado da Silva, W L; Prosper, H B; Protopopescu, S; Qian, J; Quadt, A; Quinn, B; Rangel, M S; Rani, K J; Ranjan, K; Ratoff, P N; Renkel, P; Reucroft, S; Rijssenbeek, M; Ripp-Baudot, I; Rizatdinova, F; Robinson, S; Rodrigues, R F; Royon, C; Rubinov, P; Ruchti, R; Rud, V I; Sajot, G; Sánchez-Hernández, A; Sanders, M P; Santoro, A; Savage, G; Sawyer, L; Scanlon, T; Schaile, D; Schamberger, R D; Scheglov, Y; Schellman, H; Schieferdecker, P; Schmitt, C; Schwanenberger, C; Schwartzman, A; Schwienhorst, R; Sekaric, J; Sengupta, S; Severini, H; Shabalina, E; Shamim, M; Shary, V; Shchukin, A A; Shephard, W D; Shivpuri, R K; Shpakov, D; Siccardi, V; Sidwell, R A; Simak, V; Sirotenko, V; Skubic, P; Slattery, P; Smith, R P; Snow, G R; Snow, J; Snyder, S; Söldner-Rembold, S; Song, X; Sonnenschein, L; Sopczak, A; Sosebee, M; Soustruznik, K; Souza, M; Spurlock, B; Stark, J; Steele, J; Stolin, V; Stone, A; Stoyanova, D A; Strandberg, J; Strandberg, S; Strang, M A; Strauss, M; Ströhmer, R; Strom, D; Strovink, M; Stutte, L; Sumowidagdo, S; Sznajder, A; Talby, M; Tamburello, P; Taylor, W; Telford, P; Temple, J; Tiller, B; Titov, M; Tokmenin, V V; Tomoto, M; Toole, T; Torchiani, I; Towers, S; Trefzger, T; Trincaz-Duvoid, S; Tsybychev, D; Tuchming, B; Tully, C; Turcot, A S; Tuts, P M; Unalan, R; Uvarov, L; Uvarov, S; Uzunyan, S; Vachon, B; van den Berg, P J; Van Kooten, R; van Leeuwen, W M; Varelas, N; Varnes, E W; Vartapetian, A; Vasilyev, I A; Vaupel, M; Verdier, P; Vertogradov, L S; Verzocchi, M; Villeneuve-Seguier, F; Vint, P; Vlimant, J-R; Von Toerne, E; Voutilainen, M; Vreeswijk, M; Wahl, H D; Wang, L; Wang, M H L S; Warchol, J; Watts, G; Wayne, M; Weber, M; Weerts, H; Wermes, N; Wetstein, M; White, A; Wicke, D; Wilson, G W; Wimpenny, S J; Wobisch, M; Womersley, J; Wood, D R; Wyatt, T R; Xie, Y; Xuan, N; Yacoob, S; Yamada, R; Yan, M; Yasuda, T; Yatsunenko, Y A; Yip, K; Yoo, H D; Youn, S W; Yu, C; Yu, J; Yurkewicz, A; Zatserklyaniy, A; Zeitnitz, C; Zhang, D; Zhao, T; Zhou, B; Zhu, J; Zielinski, M; Zieminska, D; Zieminski, A; Zutshi, V; Zverev, E G

2006-10-27

A search for direct production of scalar bottom quarks (b) is performed with 310 pb(-1) of data collected by the D0 experiment in pp collisions at square root s = 1.96 TeV at the Fermilab Tevatron Collider. The topology analyzed consists of two b jets and an imbalance in transverse momentum due to undetected neutralinos (chi(1)0), with chi(1)0 assumed to be the lightest supersymmetric particle. We find the data consistent with standard model expectations, and set a 95% C.L. exclusion domain in the (m(b), m(chi(1)0)) mass plane, improving significantly upon the results from run I of the Tevatron.

[Integral assessment of learning subjects difficulties].

PubMed

Grebniak, N P; Shchudro, S A

2010-01-01

The integral criterion for subject difficulties in senior classes is substantiated in terms of progress in studies, variation coefficient, and subjective and expert appraisals of the difficulty of subjects. The compiled regression models adequately determine the difficulty of academic subjects. According to the root-mean-square deviation, all subjects were found to have 3 degrees of difficulty.

Biomass estimators for thinned second-growth ponderosa pine trees.

Treesearch

P.H. Cochran; J.W. Jennings; C.T. Youngberg

1984-01-01

Usable estimates of the mass of live foliage and limbs of sapling and pole-sized ponderosa pine in managed stands in central Oregon can be obtained with equations using the logarithm of diameter as the only independent variable. These equations produce only slightly higher root mean square deviations than equations that include additional independent variables. A...

Adaptive resolution simulation of an atomistic protein in MARTINI water

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

Zavadlav, Julija; Melo, Manuel Nuno; Marrink, Siewert J., E-mail: s.j.marrink@rug.nl

2014-02-07

We present an adaptive resolution simulation of protein G in multiscale water. We couple atomistic water around the protein with mesoscopic water, where four water molecules are represented with one coarse-grained bead, farther away. We circumvent the difficulties that arise from coupling to the coarse-grained model via a 4-to-1 molecule coarse-grain mapping by using bundled water models, i.e., we restrict the relative movement of water molecules that are mapped to the same coarse-grained bead employing harmonic springs. The water molecules change their resolution from four molecules to one coarse-grained particle and vice versa adaptively on-the-fly. Having performed 15 ns long molecularmore » dynamics simulations, we observe within our error bars no differences between structural (e.g., root-mean-squared deviation and fluctuations of backbone atoms, radius of gyration, the stability of native contacts and secondary structure, and the solvent accessible surface area) and dynamical properties of the protein in the adaptive resolution approach compared to the fully atomistically solvated model. Our multiscale model is compatible with the widely used MARTINI force field and will therefore significantly enhance the scope of biomolecular simulations.« less

Adaptive resolution simulation of an atomistic protein in MARTINI water.

PubMed

Zavadlav, Julija; Melo, Manuel Nuno; Marrink, Siewert J; Praprotnik, Matej

2014-02-07

We present an adaptive resolution simulation of protein G in multiscale water. We couple atomistic water around the protein with mesoscopic water, where four water molecules are represented with one coarse-grained bead, farther away. We circumvent the difficulties that arise from coupling to the coarse-grained model via a 4-to-1 molecule coarse-grain mapping by using bundled water models, i.e., we restrict the relative movement of water molecules that are mapped to the same coarse-grained bead employing harmonic springs. The water molecules change their resolution from four molecules to one coarse-grained particle and vice versa adaptively on-the-fly. Having performed 15 ns long molecular dynamics simulations, we observe within our error bars no differences between structural (e.g., root-mean-squared deviation and fluctuations of backbone atoms, radius of gyration, the stability of native contacts and secondary structure, and the solvent accessible surface area) and dynamical properties of the protein in the adaptive resolution approach compared to the fully atomistically solvated model. Our multiscale model is compatible with the widely used MARTINI force field and will therefore significantly enhance the scope of biomolecular simulations.

Clustering biomolecular complexes by residue contacts similarity.

PubMed

Rodrigues, João P G L M; Trellet, Mikaël; Schmitz, Christophe; Kastritis, Panagiotis; Karaca, Ezgi; Melquiond, Adrien S J; Bonvin, Alexandre M J J

2012-07-01

Inaccuracies in computational molecular modeling methods are often counterweighed by brute-force generation of a plethora of putative solutions. These are then typically sieved via structural clustering based on similarity measures such as the root mean square deviation (RMSD) of atomic positions. Albeit widely used, these measures suffer from several theoretical and technical limitations (e.g., choice of regions for fitting) that impair their application in multicomponent systems (N > 2), large-scale studies (e.g., interactomes), and other time-critical scenarios. We present here a simple similarity measure for structural clustering based on atomic contacts--the fraction of common contacts--and compare it with the most used similarity measure of the protein docking community--interface backbone RMSD. We show that this method produces very compact clusters in remarkably short time when applied to a collection of binary and multicomponent protein-protein and protein-DNA complexes. Furthermore, it allows easy clustering of similar conformations of multicomponent symmetrical assemblies in which chain permutations can occur. Simple contact-based metrics should be applicable to other structural biology clustering problems, in particular for time-critical or large-scale endeavors. Copyright © 2012 Wiley Periodicals, Inc.

Root Canal Morphology and Configuration of 118 Mandibular First Molars by Means of Micro-Computed Tomography: An Ex Vivo Study.

PubMed

Wolf, Thomas Gerhard; Paqué, Frank; Zeller, Maximilian; Willershausen, Brita; Briseño-Marroquín, Benjamín

2016-04-01

The aim of this study was to investigate the root canal system morphology of the mandibular first molar by means of micro-computed tomography. The root canal configuration, foramina, and accessory canals frequency of 118 mandibular first molars were investigated by means of micro-computed tomography and 3-dimensional software imaging. A 4-digit system describes the root canal configuration from the coronal to apical thirds and the main foramina number. The most frequent root canal configurations in mesial root were 2-2-2/2 (31.4%), 2-2-1/1 (15.3%), and 2-2-2/3 (11.9%); another 24 different root canal configurations were observed in this root. A 1-1-1/1 (58.5%), 1-1-1/2 (10.2%), and 16 other root canal configurations were observed in the distal root. The mesiobuccal root canal showed 1-4 foramina in 24.6%, and the mesiolingual showed 1-3 foramina in 28.0%. One connecting canal between the mesial root canals was observed in 30.5% and 2 in 3.4%. The distolingual root canal showed 1-4 foramina in 23.7%, whereas a foramen in the distobuccal root canal was rarely detected (3.4%). The mesiobuccal, mesiolingual, and distolingual root canals showed at least 1 accessory canal (14.3, 10.2, and 4.2%, respectively), but the distobuccal had none. The root canal configuration of mandibular first molars varies strongly. According to our expectations, both the mesial and distal roots showed a high number of morphologic diversifications. The root canal system of the mesial root showed more root canal configuration variations, connecting and accessory canals than the distal root. Copyright © 2016 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

[Main Components of Xinjiang Lavender Essential Oil Determined by Partial Least Squares and Near Infrared Spectroscopy].

PubMed

Liao, Xiang; Wang, Qing; Fu, Ji-hong; Tang, Jun

2015-09-01

This work was undertaken to establish a quantitative analysis model which can rapid determinate the content of linalool, linalyl acetate of Xinjiang lavender essential oil. Totally 165 lavender essential oil samples were measured by using near infrared absorption spectrum (NIR), after analyzing the near infrared spectral absorption peaks of all samples, lavender essential oil have abundant chemical information and the interference of random noise may be relatively low on the spectral intervals of 7100~4500 cm(-1). Thus, the PLS models was constructed by using this interval for further analysis. 8 abnormal samples were eliminated. Through the clustering method, 157 lavender essential oil samples were divided into 105 calibration set samples and 52 validation set samples. Gas chromatography mass spectrometry (GC-MS) was used as a tool to determine the content of linalool and linalyl acetate in lavender essential oil. Then the matrix was established with the GC-MS raw data of two compounds in combination with the original NIR data. In order to optimize the model, different pretreatment methods were used to preprocess the raw NIR spectral to contrast the spectral filtering effect, after analysizing the quantitative model results of linalool and linalyl acetate, the root mean square error prediction (RMSEP) of orthogonal signal transformation (OSC) was 0.226, 0.558, spectrally, it was the optimum pretreatment method. In addition, forward interval partial least squares (FiPLS) method was used to exclude the wavelength points which has nothing to do with determination composition or present nonlinear correlation, finally 8 spectral intervals totally 160 wavelength points were obtained as the dataset. Combining the data sets which have optimized by OSC-FiPLS with partial least squares (PLS) to establish a rapid quantitative analysis model for determining the content of linalool and linalyl acetate in Xinjiang lavender essential oil, numbers of hidden variables of two

Search for a standard model Higgs boson in WH --> lvbb in pp collisions at square root s = 1.96 TeV.

PubMed

Aaltonen, T; Adelman, J; Akimoto, T; Alvarez González, B; Amerio, S; Amidei, D; Anastassov, A; Annovi, A; Antos, J; Apollinari, G; Apresyan, A; Arisawa, T; Artikov, A; Ashmanskas, W; Attal, A; Aurisano, A; Azfar, F; Azzurri, P; Badgett, W; Barbaro-Galtieri, A; Barnes, V E; Barnett, B A; Bartsch, V; Bauer, G; Beauchemin, P-H; Bedeschi, F; Beecher, D; Behari, S; Bellettini, G; Bellinger, J; Benjamin, D; Beretvas, A; Beringer, J; Bhatti, A; Binkley, M; Bisello, D; Bizjak, I; Blair, R E; Blocker, C; Blumenfeld, B; Bocci, A; Bodek, A; Boisvert, V; Bolla, G; Bortoletto, D; Boudreau, J; Boveia, A; Brau, B; Bridgeman, A; Brigliadori, L; Bromberg, C; Brubaker, E; Budagov, J; Budd, H S; Budd, S; Burke, S; Burkett, K; Busetto, G; Bussey, P; Buzatu, A; Byrum, K L; Cabrera, S; Calancha, C; Campanelli, M; Campbell, M; Canelli, F; Canepa, A; Carls, B; Carlsmith, D; Carosi, R; Carrillo, S; Carron, S; Casal, B; Casarsa, M; Castro, A; Catastini, P; Cauz, D; Cavaliere, V; Cavalli-Sforza, M; Cerri, A; Cerrito, L; Chang, S H; Chen, Y C; Chertok, M; Chiarelli, G; Chlachidze, G; Chlebana, F; Cho, K; Chokheli, D; Chou, J P; Choudalakis, G; Chuang, S H; Chung, K; Chung, W H; Chung, Y S; Chwalek, T; Ciobanu, C I; Ciocci, M A; Clark, A; Clark, D; Compostella, G; Convery, M E; Conway, J; Cordelli, M; Cortiana, G; Cox, C A; Cox, D J; Crescioli, F; Cuenca Almenar, C; Cuevas, J; Culbertson, R; Cully, J C; Dagenhart, D; Datta, M; Davies, T; de Barbaro, P; De Cecco, S; Deisher, A; De Lorenzo, G; Dell'orso, M; Deluca, C; Demortier, L; Deng, J; Deninno, M; Derwent, P F; di Giovanni, G P; Dionisi, C; Di Ruzza, B; Dittmann, J R; D'Onofrio, M; Donati, S; Dong, P; Donini, J; Dorigo, T; Dube, S; Efron, J; Elagin, A; Erbacher, R; Errede, D; Errede, S; Eusebi, R; Fang, H C; Farrington, S; Fedorko, W T; Feild, R G; Feindt, M; Fernandez, J P; Ferrazza, C; Field, R; Flanagan, G; Forrest, R; Frank, M J; Franklin, M; Freeman, J C; Furic, I; Gallinaro, M; Galyardt, J; Garberson, F; Garcia, J E; Garfinkel, A F; Genser, K; Gerberich, H; Gerdes, D; Gessler, A; Giagu, S; Giakoumopoulou, V; Giannetti, P; Gibson, K; Gimmell, J L; Ginsburg, C M; Giokaris, N; Giordani, M; Giromini, P; Giunta, M; Giurgiu, G; Glagolev, V; Glenzinski, D; Gold, M; Goldschmidt, N; Golossanov, A; Gomez, G; Gomez-Ceballos, G; Goncharov, M; González, O; Gorelov, I; Goshaw, A T; Goulianos, K; Gresele, A; Grinstein, S; Grosso-Pilcher, C; Grundler, U; Guimaraes da Costa, J; Gunay-Unalan, Z; Haber, C; Hahn, K; Hahn, S R; Halkiadakis, E; Han, B-Y; Han, J Y; Happacher, F; Hara, K; Hare, D; Hare, M; Harper, S; Harr, R F; Harris, R M; Hartz, M; Hatakeyama, K; Hays, C; Heck, M; Heijboer, A; Heinrich, J; Henderson, C; Herndon, M; Heuser, J; Hewamanage, S; Hidas, D; Hill, C S; Hirschbuehl, D; Hocker, A; Hou, S; Houlden, M; Hsu, S-C; Huffman, B T; Hughes, R E; Husemann, U; Hussein, M; Husemann, U; Huston, J; Incandela, J; Introzzi, G; Iori, M; Ivanov, A; James, E; Jayatilaka, B; Jeon, E J; Jha, M K; Jindariani, S; Johnson, W; Jones, M; Joo, K K; Jun, S Y; Jung, J E; Junk, T R; Kamon, T; Kar, D; Karchin, P E; Kato, Y; Kephart, R; Keung, J; Khotilovich, V; Kilminster, B; Kim, D H; Kim, H S; Kim, H W; Kim, J E; Kim, M J; Kim, S B; Kim, S H; Kim, Y K; Kimura, N; Kirsch, L; Klimenko, S; Knuteson, B; Ko, B R; Kondo, K; Kong, D J; Konigsberg, J; Korytov, A; Kotwal, A V; Kreps, M; Kroll, J; Krop, D; Krumnack, N; Kruse, M; Krutelyov, V; Kubo, T; Kuhr, T; Kulkarni, N P; Kurata, M; Kwang, S; Laasanen, A T; Lami, S; Lammel, S; Lancaster, M; Lander, R L; Lannon, K; Lath, A; Latino, G; Lazzizzera, I; Lecompte, T; Lee, E; Lee, H S; Lee, S W; Leone, S; Lewis, J D; Lin, C-S; Linacre, J; Lindgren, M; Lipeles, E; Lister, A; Litvintsev, D O; Liu, C; Liu, T; Lockyer, N S; Loginov, A; Loreti, M; Lovas, L; Lucchesi, D; Luci, C; Lueck, J; Lujan, P; Lukens, P; Lungu, G; Lyons, L; Lys, J; Lysak, R; Macqueen, D; Madrak, R; Maeshima, K; Makhoul, K; Maki, T; Maksimovic, P; Malde, S; Malik, S; Manca, G; Manousakis-Katsikakis, A; Margaroli, F; Marino, C; Marino, C P; Martin, A; Martin, V; Martínez, M; Martínez-Ballarín, R; Maruyama, T; Mastrandrea, P; Masubuchi, T; Mathis, M; Mattson, M E; Mazzanti, P; McFarland, K S; McIntyre, P; McNulty, R; Mehta, A; Mehtala, P; Menzione, A; Merkel, P; Mesropian, C; Miao, T; Miladinovic, N; Miller, R; Mills, C; Milnik, M; Mitra, A; Mitselmakher, G; Miyake, H; Moggi, N; Moon, C S; Moore, R; Morello, M J; Morlock, J; Movilla Fernandez, P; Mülmenstädt, J; Mukherjee, A; Muller, Th; Mumford, R; Murat, P; Mussini, M; Nachtman, J; Nagai, Y; Nagano, A; Naganoma, J; Nakamura, K; Nakano, I; Napier, A; Necula, V; Nett, J; Neu, C; Neubauer, M S; Neubauer, S; Nielsen, J; Nodulman, L; Norman, M; Norniella, O; Nurse, E; Oakes, L; Oh, S H; Oh, Y D; Oksuzian, I; Okusawa, T; Orava, R; Osterberg, K; Pagan Griso, S; Palencia, E; Papadimitriou, V; Papaikonomou, A; Paramonov, A A; Parks, B; Pashapour, S; Patrick, J; Pauletta, G; Paulini, M; Paus, C; Peiffer, T; Pellett, D E; Penzo, A; Phillips, T J; Piacentino, G; Pianori, E; Pinera, L; Pitts, K; Plager, C; Pondrom, L; Poukhov, O; Pounder, N; Prakoshyn, F; Pronko, A; Proudfoot, J; Ptohos, F; Pueschel, E; Punzi, G; Pursley, J; Rademacker, J; Rahaman, A; Ramakrishnan, V; Ranjan, N; Redondo, I; Renton, P; Renz, M; Rescigno, M; Richter, S; Rimondi, F; Ristori, L; Robson, A; Rodrigo, T; Rodriguez, T; Rogers, E; Rolli, S; Roser, R; Rossi, M; Rossin, R; Roy, P; Ruiz, A; Russ, J; Rusu, V; Saarikko, H; Safonov, A; Sakumoto, W K; Saltó, O; Santi, L; Sarkar, S; Sartori, L; Sato, K; Savoy-Navarro, A; Schlabach, P; Schmidt, A; Schmidt, E E; Schmidt, M A; Schmidt, M P; Schmitt, M; Schwarz, T; Scodellaro, L; Scribano, A; Scuri, F; Sedov, A; Seidel, S; Seiya, Y; Semenov, A; Sexton-Kennedy, L; Sforza, F; Sfyrla, A; Shalhout, S Z; Shears, T; Shepard, P F; Shimojima, M; Shiraishi, S; Shochet, M; Shon, Y; Shreyber, I; Sidoti, A; Sinervo, P; Sisakyan, A; Slaughter, A J; Slaunwhite, J; Sliwa, K; Smith, J R; Snider, F D; Snihur, R; Soha, A; Somalwar, S; Sorin, V; Spalding, J; Spreitzer, T; Squillacioti, P; Stanitzki, M; St Denis, R; Stelzer, B; Stelzer-Chilton, O; Stentz, D; Strologas, J; Strycker, G L; Stuart, D; Suh, J S; Sukhanov, A; Suslov, I; Suzuki, T; Taffard, A; Takashima, R; Takeuchi, Y; Tanaka, R; Tecchio, M; Teng, P K; Terashi, K; Thom, J; Thompson, A S; Thompson, G A; Thomson, E; Tipton, P; Ttito-Guzmán, P; Tkaczyk, S; Toback, D; Tokar, S; Tollefson, K; Tomura, T; Tonelli, D; Torre, S; Torretta, D; Totaro, P; Tourneur, S; Trovato, M; Tsai, S-Y; Tu, Y; Turini, N; Ukegawa, F; Vallecorsa, S; van Remortel, N; Varganov, A; Vataga, E; Vázquez, F; Velev, G; Vellidis, C; Vidal, M; Vidal, R; Vila, I; Vilar, R; Vine, T; Vogel, M; Volobouev, I; Volpi, G; Wagner, P; Wagner, R G; Wagner, R L; Wagner, W; Wagner-Kuhr, J; Wakisaka, T; Wallny, R; Wang, S M; Warburton, A; Waters, D; Weinberger, M; Weinelt, J; Wester, W C; Whitehouse, B; Whiteson, D; Wicklund, A B; Wicklund, E; Wilbur, S; Williams, G; Williams, H H; Wilson, P; Winer, B L; Wittich, P; Wolbers, S; Wolfe, C; Wright, T; Wu, X; Würthwein, F; Xie, S; Yagil, A; Yamamoto, K; Yamaoka, J; Yang, U K; Yang, Y C; Yao, W M; Yeh, G P; Yoh, J; Yorita, K; Yoshida, T; Yu, G B; Yu, I; Yu, S S; Yun, J C; Zanello, L; Zanetti, A; Zhang, X; Zheng, Y; Zucchelli, S

2009-09-04

We present a search for a standard model Higgs boson produced in association with a W boson using 2.7 fb(-1) of integrated luminosity of pp collision data taken at square root s = 1.96 TeV. Limits on the Higgs boson production rate are obtained for masses between 100 and 150 GeV/c(2). Through the use of multivariate techniques, the analysis achieves an observed (expected) 95% confidence level upper limit of 5.6 (4.8) times the theoretically expected production cross section for a standard model Higgs boson with a mass of 115 GeV/c(2).

Scatter-Reducing Sounding Filtration Using a Genetic Algorithm and Mean Monthly Standard Deviation

NASA Technical Reports Server (NTRS)

Mandrake, Lukas

2013-01-01

Retrieval algorithms like that used by the Orbiting Carbon Observatory (OCO)-2 mission generate massive quantities of data of varying quality and reliability. A computationally efficient, simple method of labeling problematic datapoints or predicting soundings that will fail is required for basic operation, given that only 6% of the retrieved data may be operationally processed. This method automatically obtains a filter designed to reduce scatter based on a small number of input features. Most machine-learning filter construction algorithms attempt to predict error in the CO2 value. By using a surrogate goal of Mean Monthly STDEV, the goal is to reduce the retrieved CO2 scatter rather than solving the harder problem of reducing CO2 error. This lends itself to improved interpretability and performance. This software reduces the scatter of retrieved CO2 values globally based on a minimum number of input features. It can be used as a prefilter to reduce the number of soundings requested, or as a post-filter to label data quality. The use of the MMS (Mean Monthly Standard deviation) provides a much cleaner, clearer filter than the standard ABS(CO2-truth) metrics previously employed by competitor methods. The software's main strength lies in a clearer (i.e., fewer features required) filter that more efficiently reduces scatter in retrieved CO2 rather than focusing on the more complex (and easily removed) bias issues.

Band head spin assignment of superdeformed bands in 133Pr using two-parameter formulae

NASA Astrophysics Data System (ADS)

Sharma, Honey; Mittal, H. M.

2018-03-01

The two-parameter formulae viz. the power index formula, the nuclear softness formula and the VMI model are adopted to accredit the band head spin (I0) of four superdeformed rotational bands in 133Pr. The technique of least square fitting is used to accredit the band head spin for four superdeformed rotational bands in 133Pr. The root mean deviation among the computed transition energies and well-known experimental transition energies are attained by extracting the model parameters from the two-parameter formulae. The determined transition energies are in excellent agreement with the experimental transition energies, whenever exact spins are accredited. The power index formula coincides well with the experimental data and provides minimum root mean deviation. So, the power index formula is more efficient tool than the nuclear softness formula and the VMI model. The deviation of dynamic moment of inertia J(2) against the rotational frequency is also examined.

A randomized controlled trial investigating the effects of craniosacral therapy on pain and heart rate variability in fibromyalgia patients.

PubMed

Castro-Sánchez, Adelaida María; Matarán-Peñarrocha, Guillermo A; Sánchez-Labraca, Nuria; Quesada-Rubio, José Manuel; Granero-Molina, José; Moreno-Lorenzo, Carmen

2011-01-01

Fibromyalgia is a prevalent musculoskeletal disorder associated with widespread mechanical tenderness, fatigue, non-refreshing sleep, depressed mood and pervasive dysfunction of the autonomic nervous system: tachycardia, postural intolerance, Raynaud's phenomenon and diarrhoea. To determine the effects of craniosacral therapy on sensitive tender points and heart rate variability in patients with fibromyalgia. A randomized controlled trial. Ninety-two patients with fibromyalgia were randomly assigned to an intervention group or placebo group. Patients received treatments for 20 weeks. The intervention group underwent a craniosacral therapy protocol and the placebo group received sham treatment with disconnected magnetotherapy equipment. Pain intensity levels were determined by evaluating tender points, and heart rate variability was recorded by 24-hour Holter monitoring. After 20 weeks of treatment, the intervention group showed significant reduction in pain at 13 of the 18 tender points (P < 0.05). Significant differences in temporal standard deviation of RR segments, root mean square deviation of temporal standard deviation of RR segments and clinical global impression of improvement versus baseline values were observed in the intervention group but not in the placebo group. At two months and one year post therapy, the intervention group showed significant differences versus baseline in tender points at left occiput, left-side lower cervical, left epicondyle and left greater trochanter and significant differences in temporal standard deviation of RR segments, root mean square deviation of temporal standard deviation of RR segments and clinical global impression of improvement. Craniosacral therapy improved medium-term pain symptoms in patients with fibromyalgia.

Evaluating and defining the sharpness of intraocular lenses: microedge structure of commercially available square-edged hydrophobic lenses.

PubMed

Werner, Liliana; Müller, Matthias; Tetz, Manfred

2008-02-01

To evaluate the microstructure of the edges of currently available square-edged hydrophobic intraocular lenses (IOLs) in terms of their deviation from an ideal square. Berlin Eye Research Institute, Berlin, Germany. Sixteen designs of hydrophobic acrylic or silicone IOLs were studied. For each design, a +20.0 diopter (D) IOL and a +0.0 D IOL (or the lowest available plus dioptric power) were evaluated. The IOL edge was imaged under high-magnification scanning electron microscopy using a standardized technique. The area above the lateral-posterior edge, representing the deviation from a perfect square, was measured in square microns using reference circles of 40 microm and 60 microm of radius and the AutoCAD LT 2000 system (Autodesk). The IOLs were compared with an experimental square-edged poly(methyl methacrylate) (PMMA) IOL (reference IOL) with an edge design that effectively stopped lens epithelial cell growth in culture in a preliminary study. Two round-edged silicone IOLs were used as controls. The hydrophobic IOLs used, labeled as square-edged IOLs, had an area of deviation from a perfect square ranging from 4.8 to 338.4 microm(2) (40 microm radius reference circle) and from 0.2 to 524.4 microm(2) (60 microm radius circle). The deviation area for the square-edged PMMA IOL was 34.0 microm(2) with a 40 microm radius circle and 37.5 microm(2) with a 60 microm radius circle. The respective values for the +20.0 D control silicone IOL were 729.3 microm(2) and 1525.3 microm(2) and for the +0.0 D control silicone IOL, 727.3 microm(2) and 1512.7 microm(2). Seven silicone IOLs of 5 designs had area values that were close to those of the reference square-edged PMMA IOL. Several differences in edge finishing between the IOLs analyzed were also observed. There was a large variation in the deviation area from a perfect square as well as in the edge finishing, not only between different IOL designs but also between different powers of the same design. Clinically, factors

Thin Films Formed from Conjugated Polymers with Ionic, Water-Soluble Backbones.

PubMed

Voortman, Thomas P; Chiechi, Ryan C

2015-12-30

This paper compares the morphologies of films of conjugated polymers in which the backbone (main chain) and pendant groups are varied between ionic/hydrophilic and aliphatic/hydrophobic. We observe that conjugated polymers in which the pendant groups and backbone are matched, either ionic-ionic or hydrophobic-hydrophobic, form smooth, structured, homogeneous films from water (ionic) or tetrahydrofuran (hydrophobic). Mismatched conjugated polymers, by contrast, form inhomogeneous films with rough topologies. The polymers with ionic backbone chains are conjugated polyions (conjugated polymers with closed-shell charges in the backbone), which are semiconducting materials with tunable bad-gaps, not unlike uncharged conjugated polymers.

Application of Mean of Absolute Deviation Method for the Selection of Best Nonlinear Component Based on Video Encryption

NASA Astrophysics Data System (ADS)

Anees, Amir; Khan, Waqar Ahmad; Gondal, Muhammad Asif; Hussain, Iqtadar

2013-07-01

The aim of this work is to make use of the mean of absolute deviation (MAD) method for the evaluation process of substitution boxes used in the advanced encryption standard. In this paper, we use the MAD technique to analyze some popular and prevailing substitution boxes used in encryption processes. In particular, MAD is applied to advanced encryption standard (AES), affine power affine (APA), Gray, Lui J., Residue Prime, S8 AES, SKIPJACK, and Xyi substitution boxes.

Exploring Students' Conceptions of the Standard Deviation

ERIC Educational Resources Information Center

delMas, Robert; Liu, Yan

2005-01-01

This study investigated introductory statistics students' conceptual understanding of the standard deviation. A computer environment was designed to promote students' ability to coordinate characteristics of variation of values about the mean with the size of the standard deviation as a measure of that variation. Twelve students participated in an…

Forward neutral pion production in p + p and d + Au collisions at square root sNN=200 GeV.

PubMed

Adams, J; Aggarwal, M M; Ahammed, Z; Amonett, J; Anderson, B D; Arkhipkin, D; Averichev, G S; Badyal, S K; Bai, Y; Balewski, J; Barannikova, O; Barnby, L S; Baudot, J; Bekele, S; Belaga, V V; Bellingeri-Laurikainen, A; Bellwied, R; Berger, J; Bezverkhny, B I; Bharadwaj, S; Bhasin, A; Bhati, A K; Bhatia, V S; Bichsel, H; Bielcik, J; Bielcikova, J; Billmeier, A; Bland, L C; Blyth, C O; Blyth, S-L; Bonner, B E; Botje, M; Boucham, A; Bouchet, J; Brandin, A V; Bravar, A; Bystersky, M; Cadman, R V; Cai, X Z; Caines, H; Sánchez, M Calderón de la Barca; Catu, O; Cebra, D; Chajecki, Z; Chaloupka, P; Chattopadhyay, S; Chen, H F; Chen, J H; Chen, Y; Cheng, J; Cherney, M; Chikanian, A; Choi, H A; Christie, W; Coffin, J P; Cormier, T M; Cosentino, M R; Cramer, J G; Crawford, H J; Das, D; Das, S; Daugherity, M; de Moura, M M; Dedovich, T G; Dephillips, M; Derevschikov, A A; Didenko, L; Dietel, T; Dogra, S M; Dong, W J; Dong, X; Draper, J E; Du, F; Dubey, A K; Dunin, V B; Dunlop, J C; Mazumdar, M R Dutta; Eckardt, V; Edwards, W R; Efimov, L G; Emelianov, V; Engelage, J; Eppley, G; Erazmus, B; Estienne, M; Fachini, P; Faivre, J; Fatemi, R; Fedorisin, J; Filimonov, K; Filip, P; Finch, E; Fine, V; Fisyak, Y; Fornazier, K S F; Fox, B D; Fu, J; Gagliardi, C A; Gaillard, L; Gans, J; Ganti, M S; Geurts, F; Ghazikhanian, V; Ghosh, P; Gonzalez, J E; Gorbunov, Y G; Gos, H; Grachov, O; Grebenyuk, O; Grosnick, D; Guertin, S M; Guo, Y; Gupta, A; Gupta, N; Gutierrez, T D; Hallman, T J; Hamed, A; Harris, J W; Heinz, M; Henry, T W; Hepplemann, S; Hippolyte, B; Hirsch, A; Hjort, E; Hoffmann, G W; Horner, M J; Huang, H Z; Huang, S L; Hughes, E W; Humanic, T J; Igo, G; Ishihara, A; Jacobs, P; Jacobs, W W; Jiang, H; Jones, P G; Judd, E G; Kabana, S; Kang, K; Kaplan, M; Keane, D; Kechechyan, A; Khodyrev, V Yu; Kim, B C; Kiryluk, J; Kisiel, A; Kislov, E M; Klein, S R; Koetke, D D; Kollegger, T; Kopytine, M; Kotchenda, L; Kowalik, K L; Kramer, M; Kravtsov, P; Kravtsov, V I; Krueger, K; Kuhn, C; Kulikov, A I; Kumar, A; Kutuev, R Kh; Kuznetsov, A A; Lamb, R; Lamont, M A C; Landgraf, J M; Lange, S; Laue, F; Lauret, J; Lebedev, A; Lednicky, R; Lee, C-H; Lehocka, S; Levine, M J; Li, C; Li, Q; Li, Y; Lin, G; Lindenbaum, S J; Lisa, M A; Liu, F; Liu, H; Liu, J; Liu, L; Liu, Q J; Liu, Z; Ljubicic, T; Llope, W J; Long, H; Longacre, R S; Lopez-Noriega, M; Love, W A; Lu, Y; Ludlam, T; Lynn, D; Ma, G L; Ma, J G; Ma, Y G; Magestro, D; Mahajan, S; Mahapatra, D P; Majka, R; Mangotra, L K; Manweiler, R; Margetis, S; Markert, C; Martin, L; Marx, J N; Matis, H S; Matulenko, Yu A; McClain, C J; McShane, T S; Melnick, Yu; Meschanin, A; Miller, M L; Minaev, N G; Mironov, C; Mischke, A; Mishra, D K; Mitchell, J; Mioduszewski, S; Mohanty, B; Molnar, L; Moore, C F; Morozov, D A; Munhoz, M G; Nandi, B K; Nayak, S K; Nayak, T K; Nelson, J M; Netrakanti, P K; Nikitin, V A; Nogach, L V; Nurushev, S B; Odyniec, G; Ogawa, A; Okorokov, V; Oldenburg, M; Olson, D; Pal, S K; Panebratsev, Y; Panitkin, S Y; Pavlinov, A I; Pawlak, T; Peitzmann, T; Perevoztchikov, V; Perkins, C; Peryt, W; Petrov, V A; Phatak, S C; Picha, R; Planinic, M; Pluta, J; Porile, N; Porter, J; Poskanzer, A M; Potekhin, M; Potrebenikova, E; Potukuchi, B V K S; Prindle, D; Pruneau, C; Putschke, J; Rakness, G; Raniwala, R; Raniwala, S; Ravel, O; Ray, R L; Razin, S V; Reichhold, D; Reid, J G; Reinnarth, J; Renault, G; Retiere, F; Ridiger, A; Ritter, H G; Roberts, J B; Rogachevskiy, O V; Romero, J L; Rose, A; Roy, C; Ruan, L; Russcher, M J; Sahoo, R; Sakrejda, I; Salur, S; Sandweiss, J; Sarsour, M; Savin, I; Sazhin, P S; Schambach, J; Scharenberg, R P; Schmitz, N; Schweda, K; Seger, J; Selyuzhenkov, I; Seyboth, P; Shabetai, A; Shahaliev, E; Shao, M; Shao, W; Sharma, M; Shen, W Q; Shestermanov, K E; Shimanskiy, S S; Sichtermann, E; Simon, F; Singaraju, R N; Smirnov, N; Snellings, R; Sood, G; Sorensen, P; Sowinski, J; Speltz, J; Spinka, H M; Srivastava, B; Stadnik, A; Stanislaus, T D S; Stock, R; Stolpovsky, A; Strikhanov, M; Stringfellow, B; Suaide, A A P; Sugarbaker, E; Sumbera, M; Surrow, B; Swanger, M; Symons, T J M; de Toledo, A Szanto; Tai, A; Takahashi, J; Tang, A H; Tarnowsky, T; Thein, D; Thomas, J H; Timmins, A R; Timoshenko, S; Tokarev, M; Trainor, T A; Trentalange, S; Tribble, R E; Tsai, O D; Ulery, J; Ullrich, T; Underwood, D G; Buren, G Van; van der Kolk, N; van Leeuwen, M; Molen, A M Vander; Varma, R; Vasilevski, I M; Vasiliev, A N; Vernet, R; Vigdor, S E; Viyogi, Y P; Vokal, S; Voloshin, S A; Waggoner, W T; Wang, F; Wang, G; Wang, G; Wang, X L; Wang, Y; Wang, Y; Wang, Z M; Ward, H; Watson, J W; Webb, J C; Westfall, G D; Wetzler, A; Whitten, C; Wieman, H; Wissink, S W; Witt, R; Wood, J; Wu, J; Xu, N; Xu, Q H; Xu, Z; Xu, Z Z; Yepes, P; Yoo, I-K; Yurevich, V I; Zborovsky, I; Zhang, H; Zhang, W M; Zhang, Y; Zhang, Z P; Zhong, C; Zoulkarneev, R; Zoulkarneeva, Y; Zubarev, A N; Zuo, J X

2006-10-13

Measurements of the production of forward pi0 mesons from p + p and d + Au collisions at square root sNN=200 GeV are reported. The p + p yield generally agrees with next-to-leading order perturbative QCD calculations. The d + Au yield per binary collision is suppressed as eta increases, decreasing to approximately 30% of the p + p yield at eta =4.00, well below shadowing expectations. Exploratory measurements of azimuthal correlations of the forward pi0 with charged hadrons at eta approximately 0 show a recoil peak in p + p that is suppressed in d + Au at low pion energy. These observations are qualitatively consistent with a saturation picture of the low-x gluon structure of heavy nuclei.

Longitudinal double-spin asymmetry and cross section for inclusive jet production in polarized proton collisions at square root of s = 200 GeV.

PubMed

Abelev, B I; Aggarwal, M M; Ahammed, Z; Amonett, J; Anderson, B D; Anderson, M; Arkhipkin, D; Averichev, G S; Bai, Y; Balewski, J; Barannikova, O; Barnby, L S; Baudot, J; Bekele, S; Belaga, V V; Bellingeri-Laurikainen, A; Bellwied, R; Benedosso, F; Bhardwaj, S; Bhasin, A; Bhati, A K; Bichsel, H; Bielcik, J; Bielcikova, J; Bland, L C; Blyth, S-L; Bonner, B E; Botje, M; Bouchet, J; Brandin, A V; Bravar, A; Burton, T P; Bystersky, M; Cadman, R V; Cai, X Z; Caines, H; Sánchez, M Calderón de la Barca; Castillo, J; Catu, O; Cebra, D; Chajecki, Z; Chaloupka, P; Chattopadhyay, S; Chen, H F; Chen, J H; Cheng, J; Cherney, M; Chikanian, A; Christie, W; Coffin, J P; Cormier, T M; Cosentino, M R; Cramer, J G; Crawford, H J; Das, D; Das, S; Dash, S; Daugherity, M; de Moura, M M; Dedovich, T G; Dephillips, M; Derevschikov, A A; Didenko, L; Dietel, T; Djawotho, P; Dogra, S M; Dong, W J; Dong, X; Draper, J E; Du, F; Dunin, V B; Dunlop, J C; Mazumdar, M R Dutta; Eckardt, V; Edwards, W R; Efimov, L G; Emelianov, V; Engelage, J; Eppley, G; Erazmus, B; Estienne, M; Fachini, P; Fatemi, R; Fedorisin, J; Filip, P; Finch, E; Fine, V; Fisyak, Y; Fu, J; Gagliardi, C A; Gaillard, L; Ganti, M S; Ghazikhanian, V; Ghosh, P; Gonzalez, J E; Gorbunov, Y G; Gos, H; Grebenyuk, O; Grosnick, D; Guertin, S M; Guimaraes, K S F F; Gupta, N; Gutierrez, T D; Haag, B; Hallman, T J; Hamed, A; Harris, J W; He, W; Heinz, M; Henry, T W; Hepplemann, S; Hippolyte, B; Hirsch, A; Hjort, E; Hoffman, A M; Hoffmann, G W; Horner, M J; Huang, H Z; Huang, S L; Hughes, E W; Humanic, T J; Igo, G; Jacobs, P; Jacobs, W W; Jakl, P; Jia, F; Jiang, H; Jones, P G; Judd, E G; Kabana, S; Kang, K; Kapitan, J; Kaplan, M; Keane, D; Kechechyan, A; Khodyrev, V Yu; Kim, B C; Kiryluk, J; Kisiel, A; Kislov, E M; Klein, S R; Kocoloski, A; Koetke, D D; Kollegger, T; Kopytine, M; Kotchenda, L; Kouchpil, V; Kowalik, K L; Kramer, M; Kravtsov, P; Kravtsov, V I; Krueger, K; Kuhn, C; Kulikov, A I; Kumar, A; Kuznetsov, A A; Lamont, M A C; Landgraf, J M; Lange, S; LaPointe, S; Laue, F; Lauret, J; Lebedev, A; Lednicky, R; Lee, C-H; Lehocka, S; LeVine, M J; Li, C; Li, Q; Li, Y; Lin, G; Lin, X; Lindenbaum, S J; Lisa, M A; Liu, F; Liu, H; Liu, J; Liu, L; Liu, Z; Ljubicic, T; Llope, W J; Long, H; Longacre, R S; Love, W A; Lu, Y; Ludlam, T; Lynn, D; Ma, G L; Ma, J G; Ma, Y G; Magestro, D; Mahapatra, D P; Majka, R; Mangotra, L K; Manweiler, R; Margetis, S; Markert, C; Martin, L; Matis, H S; Matulenko, Yu A; McClain, C J; McShane, T S; Melnick, Yu; Meschanin, A; Millane, J; Miller, M L; Minaev, N G; Mioduszewski, S; Mironov, C; Mischke, A; Mishra, D K; Mitchell, J; Mohanty, B; Molnar, L; Moore, C F; Morozov, D A; Munhoz, M G; Nandi, B K; Nattrass, C; Nayak, T K; Nelson, J M; Netrakanti, P K; Nogach, L V; Nurushev, S B; Odyniec, G; Ogawa, A; Okorokov, V; Oldenburg, M; Olson, D; Pachr, M; Pal, S K; Panebratsev, Y; Panitkin, S Y; Pavlinov, A I; Pawlak, T; Peitzmann, T; Perevoztchikov, V; Perkins, C; Peryt, W; Phatak, S C; Picha, R; Planinic, M; Pluta, J; Poljak, N; Porile, N; Porter, J; Poskanzer, A M; Potekhin, M; Potrebenikova, E; Potukuchi, B V K S; Prindle, D; Pruneau, C; Putschke, J; Rakness, G; Raniwala, R; Raniwala, S; Ray, R L; Razin, S V; Reinnarth, J; Relyea, D; Ridiger, A; Ritter, H G; Roberts, J B; Rogachevskiy, O V; Romero, J L; Rose, A; Roy, C; Ruan, L; Russcher, M J; Sahoo, R; Sakuma, T; Salur, S; Sandweiss, J; Sarsour, M; Sazhin, P S; Schambach, J; Scharenberg, R P; Schmitz, N; Seger, J; Selyuzhenkov, I; Seyboth, P; Shabetai, A; Shahaliev, E; Shao, M; Sharma, M; Shen, W Q; Shimanskiy, S S; Sichtermann, E P; Simon, F; Singaraju, R N; Smirnov, N; Snellings, R; Sood, G; Sorensen, P; Sowinski, J; Speltz, J; Spinka, H M; Srivastava, B; Stadnik, A; Stanislaus, T D S; Stock, R; Stolpovsky, A; Strikhanov, M; Stringfellow, B; Suaide, A A P; Sugarbaker, E; Sumbera, M; Sun, Z; Surrow, B; Swanger, M; Symons, T J M; Szanto de Toledo, A; Tai, A; Takahashi, J; Tang, A H; Tarnowsky, T; Thein, D; Thomas, J H; Timmins, A R; Timoshenko, S; Tokarev, M; Trainor, T A; Trentalange, S; Tribble, R E; Tsai, O D; Ulery, J; Ullrich, T; Underwood, D G; Buren, G Van; van der Kolk, N; van Leeuwen, M; Molen, A M Vander; Varma, R; Vasilevski, I M; Vasiliev, A N; Vernet, R; Vigdor, S E; Viyogi, Y P; Vokal, S; Voloshin, S A; Waggoner, W T; Wang, F; Wang, G; Wang, J S; Wang, X L; Wang, Y; Watson, J W; Webb, J C; Westfall, G D; Wetzler, A; Whitten, C; Wieman, H; Wissink, S W; Witt, R; Wood, J; Wu, J; Xu, N; Xu, Q H; Xu, Z; Yepes, P; Yoo, I-K; Yurevich, V I; Zhan, W; Zhang, H; Zhang, W M; Zhang, Y; Zhang, Z P; Zhao, Y; Zhong, C; Zoulkarneev, R; Zoulkarneeva, Y; Zubarev, A N; Zuo, J X

2006-12-22

We report a measurement of the longitudinal double-spin asymmetry A(LL) and the differential cross section for inclusive midrapidity jet production in polarized proton collisions at square root of s = 200 GeV. The cross section data cover transverse momenta 5 < pT < 50 GeV/c and agree with next-to-leading order perturbative QCD evaluations. The A(LL) data cover 5 < pT < 17 GeV/c and disfavor at 98% C.L. maximal positive gluon polarization in the polarized nucleon.

Connectivity percolation in suspensions of attractive square-well spherocylinders.

PubMed

Dixit, Mohit; Meyer, Hugues; Schilling, Tanja

2016-01-01

We have studied the connectivity percolation transition in suspensions of attractive square-well spherocylinders by means of Monte Carlo simulation and connectedness percolation theory. In the 1980s the percolation threshold of slender fibers has been predicted to scale as the fibers' inverse aspect ratio [Phys. Rev. B 30, 3933 (1984)PRBMDO1098-012110.1103/PhysRevB.30.3933]. The main finding of our study is that the attractive spherocylinder system reaches this inverse scaling regime at much lower aspect ratios than found in suspensions of hard spherocylinders. We explain this difference by showing that third virial corrections of the pair connectedness functions, which are responsible for the deviation from the scaling regime, are less important for attractive potentials than for hard particles.

Data assimilation for groundwater flow modelling using Unbiased Ensemble Square Root Filter: Case study in Guantao, North China Plain

NASA Astrophysics Data System (ADS)

Li, N.; Kinzelbach, W.; Li, H.; Li, W.; Chen, F.; Wang, L.

2017-12-01

Data assimilation techniques are widely used in hydrology to improve the reliability of hydrological models and to reduce model predictive uncertainties. This provides critical information for decision makers in water resources management. This study aims to evaluate a data assimilation system for the Guantao groundwater flow model coupled with a one-dimensional soil column simulation (Hydrus 1D) using an Unbiased Ensemble Square Root Filter (UnEnSRF) originating from the Ensemble Kalman Filter (EnKF) to update parameters and states, separately or simultaneously. To simplify the coupling between unsaturated and saturated zone, a linear relationship obtained from analyzing inputs to and outputs from Hydrus 1D is applied in the data assimilation process. Unlike EnKF, the UnEnSRF updates parameter ensemble mean and ensemble perturbations separately. In order to keep the ensemble filter working well during the data assimilation, two factors are introduced in the study. One is called damping factor to dampen the update amplitude of the posterior ensemble mean to avoid nonrealistic values. The other is called inflation factor to relax the posterior ensemble perturbations close to prior to avoid filter inbreeding problems. The sensitivities of the two factors are studied and their favorable values for the Guantao model are determined. The appropriate observation error and ensemble size were also determined to facilitate the further analysis. This study demonstrated that the data assimilation of both model parameters and states gives a smaller model prediction error but with larger uncertainty while the data assimilation of only model states provides a smaller predictive uncertainty but with a larger model prediction error. Data assimilation in a groundwater flow model will improve model prediction and at the same time make the model converge to the true parameters, which provides a successful base for applications in real time modelling or real time controlling strategies

Suppression of hadrons with large transverse momentum in central Au+Au collisions at root square[s(NN)] = 130 GeV.

PubMed

Adcox, K; Adler, S S; Ajitanand, N N; Akiba, Y; Alexander, J; Aphecetche, L; Arai, Y; Aronson, S H; Averbeck, R; Awes, T C; Barish, K N; Barnes, P D; Barrette, J; Bassalleck, B; Bathe, S; Baublis, V; Bazilevsky, A; Belikov, S; Bellaiche, F G; Belyaev, S T; Bennett, M J; Berdnikov, Y; Botelho, S; Brooks, M L; Brown, D S; Bruner, N; Bucher, D; Buesching, H; Bumazhnov, V; Bunce, G; Burward-Hoy, J; Butsyk, S; Carey, T A; Chand, P; Chang, J; Chang, W C; Chavez, L L; Chernichenko, S; Chi, C Y; Chiba, J; Chiu, M; Choudhury, R K; Christ, T; Chujo, T; Chung, M S; Chung, P; Cianciolo, V; Cole, B A; D'Enterria, D G; David, G; Delagrange, H; Denisov, A; Deshpande, A; Desmond, E J; Dietzsch, O; Dinesh, B V; Drees, A; Durum, A; Dutta, D; Ebisu, K; Efremenko, Y V; El Chenawi, K; En'yo, H; Esumi, S; Ewell, L; Ferdousi, T; Fields, D E; Fokin, S L; Fraenkel, Z; Franz, A; Frawley, A D; Fung, S-Y; Garpman, S; Ghosh, T K; Glenn, A; Godoi, A L; Goto, Y; Greene, S V; Grosse Perdekamp, M; Gupta, S K; Guryn, W; Gustafsson, H-A; Haggerty, J S; Hamagaki, H; Hansen, A G; Hara, H; Hartouni, E P; Hayano, R; Hayashi, N; He, X; Hemmick, T K; Heuser, J M; Hibino, M; Hill, J C; Ho, D S; Homma, K; Hong, B; Hoover, A; Ichihara, T; Imai, K; Ippolitov, M S; Ishihara, M; Jacak, B V; Jang, W Y; Jia, J; Johnson, B M; Johnson, S C; Joo, K S; Kametani, S; Kang, J H; Kann, M; Kapoor, S S; Kelly, S; Khachaturov, B; Khanzadeev, A; Kikuchi, J; Kim, D J; Kim, H J; Kim, S Y; Kim, Y G; Kinnison, W W; Kistenev, E; Kiyomichi, A; Klein-Boesing, C; Klinksiek, S; Kochenda, L; Kochetkov, V; Koehler, D; Kohama, T; Kotchetkov, D; Kozlov, A; Kroon, P J; Kurita, K; Kweon, M J; Kwon, Y; Kyle, G S; Lacey, R; Lajoie, J G; Lauret, J; Lebedev, A; Lee, D M; Leitch, M J; Li, X H; Li, Z; Lim, D J; Liu, M X; Liu, X; Liu, Z; Maguire, C F; Mahon, J; Makdisi, Y I; Manko, V I; Mao, Y; Mark, S K; Markacs, S; Martinez, G; Marx, M D; Masaike, A; Matathias, F; Matsumoto, T; McGaughey, P L; Melnikov, E; Merschmeyer, M; Messer, F; Messer, M; Miake, Y; Miller, T E; Milov, A; Mioduszewski, S; Mischke, R E; Mishra, G C; Mitchell, J T; Mohanty, A K; Morrison, D P; Moss, J M; Mühlbacher, F; Muniruzzaman, M; Murata, J; Nagamiya, S; Nagasaka, Y; Nagle, J L; Nakada, Y; Nandi, B K; Newby, J; Nikkinen, L; Nilsson, P; Nishimura, S; Nyanin, A S; Nystrand, J; O'Brien, E; Ogilvie, C A; Ohnishi, H; Ojha, I D; Ono, M; Onuchin, V; Oskarsson, A; Osterman, L; Otterlund, I; Oyama, K; Paffrath, L; Palounek, A P T; Pantuev, V S; Papavassiliou, V; Pate, S F; Peitzmann, T; Petridis, A N; Pinkenburg, C; Pisani, R P; Pitukhin, P; Plasil, F; Pollack, M; Pope, K; Purschke, M L; Ravinovich, I; Read, K F; Reygers, K; Riabov, V; Riabov, Y; Rosati, M; Rose, A A; Ryu, S S; Saito, N; Sakaguchi, A; Sakaguchi, T; Sako, H; Sakuma, T; Samsonov, V; Sangster, T C; Santo, R; Sato, H D; Sato, S; Sawada, S; Schlei, B R; Schutz, Y; Semenov, V; Seto, R; Shea, T K; Shein, I; Shibata, T-A; Shigaki, K; Shiina, T; Shin, Y H; Sibiriak, I G; Silvermyr, D; Sim, K S; Simon-Gillo, J; Singh, C P; Singh, V; Sivertz, M; Soldatov, A; Soltz, R A; Sorensen, S; Stankus, P W; Starinsky, N; Steinberg, P; Stenlund, E; Ster, A; Stoll, S P; Sugioka, M; Sugitate, T; Sullivan, J P; Sumi, Y; Sun, Z; Suzuki, M; Takagui, E M; Taketani, A; Tamai, M; Tanaka, K H; Tanaka, Y; Taniguchi, E; Tannenbaum, M J; Thomas, J; Thomas, J H; Thomas, T L; Tian, W; Tojo, J; Torii, H; Towell, R S; Tserruya, I; Tsuruoka, H; Tsvetkov, A A; Tuli, S K; Tydesjö, H; Tyurin, N; Ushiroda, T; van Hecke, H W; Velissaris, C; Velkovska, J; Velkovsky, M; Vinogradov, A A; Volkov, M A; Vorobyov, A; Vznuzdaev, E; Wang, H; Watanabe, Y; White, S N; Witzig, C; Wohn, F K; Woody, C L; Xie, W; Yagi, K; Yokkaichi, S; Young, G R; Yushmanov, I E; Zajc, W A; Zhang, Z; Zhou, S

2002-01-14

Transverse momentum spectra for charged hadrons and for neutral pions in the range 1 GeV/croot square[s(NN)] = 130 GeV. At high p(T) the spectra from peripheral nuclear collisions are consistent with scaling the spectra from p+p collisions by the average number of binary nucleon-nucleon collisions. The spectra from central collisions are significantly suppressed when compared to the binary-scaled p+p expectation, and also when compared to similarly binary-scaled peripheral collisions, indicating a novel nuclear-medium effect in central nuclear collisions at RHIC energies.

Probability of stress-corrosion fracture under random loading.

NASA Technical Reports Server (NTRS)

Yang, J.-N.

1972-01-01

A method is developed for predicting the probability of stress-corrosion fracture of structures under random loadings. The formulation is based on the cumulative damage hypothesis and the experimentally determined stress-corrosion characteristics. Under both stationary and nonstationary random loadings, the mean value and the variance of the cumulative damage are obtained. The probability of stress-corrosion fracture is then evaluated using the principle of maximum entropy. It is shown that, under stationary random loadings, the standard deviation of the cumulative damage increases in proportion to the square root of time, while the coefficient of variation (dispersion) decreases in inversed proportion to the square root of time. Numerical examples are worked out to illustrate the general results.

Atomic mean-square displacement of a solid: A Green's-function approach

NASA Astrophysics Data System (ADS)

Shukla, R. C.; Hübschle, Hermann

1989-07-01

We have presented a Green's-function method of calculating the atomic mean-square displacement (MSD) of a solid. The method effectively sums a class of all anharmonic contributions to the MSD. From the point of view of perturbation theory (PT) our expression for MSD includes the lowest-order (λ2) PT contributions (cubic and quartic) with correct numerical coefficients. The numerical results obtained by this method in the high-temperature limit for a fcc nearest-neighbor Lennard-Jones-solid model are in excellent agreement with the Monte Carlo (MC) method for the same model over the entire temperature range of the solid. Highly accurate results for the order-λ2 PT contributions to MSD are obtained by eliminating the uncertainty in the convergence of the cubic contributions in the earlier work of Heiser, Shukla, and Cowly and they are now in much better agreement with the MC results but still inferior to the Green's-function method at the highest temperature.

Determination of backbone chain direction of PDA using FFM

NASA Astrophysics Data System (ADS)

Jo, Sadaharu; Okamoto, Kentaro; Takenaga, Mitsuru

2010-01-01

The effect of backbone chains on friction force was investigated on both Langmuir-Blodgett (LB) films of 10,12-heptacosadiynoic acid and the (0 1 0) surfaces of single crystals of 2,4-hexadiene-1,6-diol using friction force microscopy (FFM). It was observed that friction force decreased when the scanning direction was parallel to the [0 0 1] direction in both samples. Moreover, friction force decreased when the scanning direction was parallel to the crystallographic [1 0 2], [1 0 1], [1 0 0] and [1 0 1¯] directions in only the single crystals. For the LB films, the [0 0 1] direction corresponds to the backbone chain direction of 10,12-heptacosadiynoic acid. For the single crystals, both the [0 0 1] and [1 0 1] directions correspond to the backbone chain direction, and the [1 0 2], [1 0 0] and [1 0 1¯] directions correspond to the low-index crystallographic direction. In both the LB films and single crystals, the friction force was minimized when the directions of scanning and the backbone chain were parallel.

Due Date Assignment in a Dynamic Job Shop with the Orthogonal Kernel Least Squares Algorithm

NASA Astrophysics Data System (ADS)

Yang, D. H.; Hu, L.; Qian, Y.

2017-06-01

Meeting due dates is a key goal in the manufacturing industries. This paper proposes a method for due date assignment (DDA) by using the Orthogonal Kernel Least Squares Algorithm (OKLSA). A simulation model is built to imitate the production process of a highly dynamic job shop. Several factors describing job characteristics and system state are extracted as attributes to predict job flow-times. A number of experiments under conditions of varying dispatching rules and 90% shop utilization level have been carried out to evaluate the effectiveness of OKLSA applied for DDA. The prediction performance of OKLSA is compared with those of five conventional DDA models and back-propagation neural network (BPNN). The experimental results indicate that OKLSA is statistically superior to other DDA models in terms of mean absolute lateness and root mean squares lateness in most cases. The only exception occurs when the shortest processing time rule is used for dispatching jobs, the difference between OKLSA and BPNN is not statistically significant.

Random errors in interferometry with the least-squares method

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

Wang Qi

2011-01-20

This investigation analyzes random errors in interferometric surface profilers using the least-squares method when random noises are present. Two types of random noise are considered here: intensity noise and position noise. Two formulas have been derived for estimating the standard deviations of the surface height measurements: one is for estimating the standard deviation when only intensity noise is present, and the other is for estimating the standard deviation when only position noise is present. Measurements on simulated noisy interferometric data have been performed, and standard deviations of the simulated measurements have been compared with those theoretically derived. The relationships havemore » also been discussed between random error and the wavelength of the light source and between random error and the amplitude of the interference fringe.« less

An electric current associated with gravity sensing in maize roots

NASA Technical Reports Server (NTRS)

Bjorkman, T.; Leopold, A. C.

1987-01-01

The study of gravisensing would be greatly enhanced if physiological events associated with gravity sensing could be detected separately from subsequent growth processes. This report presents a means to discriminate sensing from the growth processes. By using a vibrating probe, we have found an electric current generated by the gravity sensing region of the root cap of maize (Zea mays cv Merit) in response to gravistimulation. On the upper surface of the root cap, the change from the endogenous current has a density of 0.55 microampere per square centimeter away from gravity. The onset of the current shift has a characteristic of lag of three to four minutes after gravistimulation, which corresponds to the presentation time for gravity sensing in this tissue. A description of the current provides some information about the sensing mechanism, as well as being a valuable means to detect gravity sensing independently of differential growth.

A Comparison of Heuristic Procedures for Minimum within-Cluster Sums of Squares Partitioning

ERIC Educational Resources Information Center

Brusco, Michael J.; Steinley, Douglas

2007-01-01

Perhaps the most common criterion for partitioning a data set is the minimization of the within-cluster sums of squared deviation from cluster centroids. Although optimal solution procedures for within-cluster sums of squares (WCSS) partitioning are computationally feasible for small data sets, heuristic procedures are required for most practical…

Deviations from LTE in a stellar atmosphere

NASA Technical Reports Server (NTRS)

Kalkofen, W.; Klein, R. I.; Stein, R. F.

1979-01-01

Deviations for LTE are investigated in an atmosphere of hydrogen atoms with one bound level, satisfying the equations of radiative, hydrostatic, and statistical equilibrium. The departure coefficient and the kinetic temperature as functions of the frequency dependence of the radiative cross section are studied analytically and numerically. Near the outer boundary of the atmosphere, the departure coefficient is smaller than unity when the radiative cross section grows with frequency faster than with the square of frequency; it exceeds unity otherwise. Far from the boundary the departure coefficient tends to exceed unity for any frequency dependence of the radiative cross section. Overpopulation always implies that the kinetic temperature in the statistical-equilibrium atmosphere is higher than the temperature in the corresponding LTE atmosphere. Upper and lower bounds on the kinetic temperature are given for an atmosphere with deviations from LTE only in the optically shallow layers when the emergent intensity can be described by a radiation temperature.

On the Performance of Maximum Likelihood versus Means and Variance Adjusted Weighted Least Squares Estimation in CFA

ERIC Educational Resources Information Center

Beauducel, Andre; Herzberg, Philipp Yorck

2006-01-01

This simulation study compared maximum likelihood (ML) estimation with weighted least squares means and variance adjusted (WLSMV) estimation. The study was based on confirmatory factor analyses with 1, 2, 4, and 8 factors, based on 250, 500, 750, and 1,000 cases, and on 5, 10, 20, and 40 variables with 2, 3, 4, 5, and 6 categories. There was no…

Plasma fluctuations in a Kaufman thruster. [root mean square magnitude, spectra and cross correlation

NASA Technical Reports Server (NTRS)

Serafini, J. S.; Terdan, F. F.

1973-01-01

Measurements of the RMS magnitude, spectra and cross-correlations for the fluctuations in the beam, discharge and neutralizer keeper currents are presented for a 30-cm diameter dished grid ion thrustor for a range of magnetic baffle currents and up to 2.0 amperes beam current. The ratio of RMS to mean ion beam current varied from 0.04 to 0.23. The spectra of the amplitudes of the beam and discharge current fluctuations were taken up to 9 MHz and show that the predominant amplitudes occur at frequencies of 10 kHz or below. The fall-off with increasing frequency is rapid. Frequencies above 100 kHz the spectral levels are 45 kb or more below the maximum peak amplitudes. The cross-correlations revealed the ion beam fluctuations to have large radial and axial scales which implied that the beam fluctuates as a whole or 'in-phase.' The cross-correlations of the beam and neutralizer keeper current fluctuations indicated the neutralizer contributions to the beam fluctuations to be small, but not negligible. The mode of operation of the thrustor (values of beam and magnetic baffle currents) was significant in determining the RMS magnitude and spectral shape of the beam fluctuations. The major oscillations were not found to be directly dependent on the power conditioner inverter frequencies.

Determinants of ocular deviation in esotropic subjects under general anesthesia.

PubMed

Daien, Vincent; Turpin, Chloé; Lignereux, François; Belghobsi, Riadh; Le Meur, Guylene; Lebranchu, Pierre; Pechereau, Alain

2013-01-01

The authors attempted to identify the determinants of ocular deviation in a population of patients with esotropia under general anesthesia. Forty-one patients with esotropia were included. Horizontal ocular deviation was evaluated by the photographic Hirschberg test both in the awakened state and under general anesthesia before surgery. Changes in ocular deviation were measured and a multivariate analysis was used to assess its clinical determinants. The mean age (± standard deviation [SD]) of study subjects was 13 ± 11 years and 51% were females. The mean spherical equivalent refraction of the right eye was 2.44 ± 2.50 diopters (D), with no significant difference between eyes (P = .26). The mean ocular deviation changed significantly, from 33.5 ± 12.5 prism diopters (PD) at preoperative examination to 8.8 ± 11.4 PD under general anesthesia (P = .0001). The changes in ocular deviation positively correlated with the pre-operative ocular deviation (correlation coefficient r = 0.59, P = .0001) and negatively correlated with patient age (correlation coefficient r = -0.53, P = .0001). These two determinants remained significant after multivariate adjustment of the following variables: preoperative ocular deviation; age; gender; spherical equivalent refraction; and number of previous strabismus surgeries (model r(2) = 0.49, P = .0001). The ocular position under general anesthesia was reported as a key factor in the surgical treatment of subjects with esotropia; therefore, its clinical determinants were assessed. The authors observed that preoperative ocular deviation and patient age were the main factors that influenced the ocular position under general anesthesia. Copyright 2013, SLACK Incorporated.

Evolution driven structural changes in CENP-E motor domain.

PubMed

Kumar, Ambuj; Kamaraj, Balu; Sethumadhavan, Rao; Purohit, Rituraj

2013-06-01

Genetic evolution corresponds to various biochemical changes that are vital development of new functional traits. Phylogenetic analysis has provided an important insight into the genetic closeness among species and their evolutionary relationships. Centromere-associated protein-E (CENP-E) protein is vital for maintaining cell cycle and checkpoint signal mechanisms are vital for recruitment process of other essential kinetochore proteins. In this study we have focussed on the evolution driven structural changes in CENP-E motor domain among primate lineage. Through molecular dynamics simulation and computational chemistry approaches we examined the changes in ATP binding affinity and conformational deviations in human CENP-E motor domain as compared to the other primates. Root mean square deviation (RMSD), Root mean square fluctuation (RMSF), Radius of gyration (Rg) and principle component analysis (PCA) results together suggested a gain in stability level as we move from tarsier towards human. This study provides a significant insight into how the cell cycle proteins and their corresponding biochemical activities are evolving and illustrates the potency of a theoretical approach for assessing, in a single study, the structural, functional, and dynamical aspects of protein evolution.

A least-squares minimization approach for model parameters estimate by using a new magnetic anomaly formula

NASA Astrophysics Data System (ADS)

Abo-Ezz, E. R.; Essa, K. S.

2016-04-01

A new linear least-squares approach is proposed to interpret magnetic anomalies of the buried structures by using a new magnetic anomaly formula. This approach depends on solving different sets of algebraic linear equations in order to invert the depth ( z), amplitude coefficient ( K), and magnetization angle ( θ) of buried structures using magnetic data. The utility and validity of the new proposed approach has been demonstrated through various reliable synthetic data sets with and without noise. In addition, the method has been applied to field data sets from USA and India. The best-fitted anomaly has been delineated by estimating the root-mean squared (rms). Judging satisfaction of this approach is done by comparing the obtained results with other available geological or geophysical information.

Mass flow rate measurements in gas-liquid flows by means of a venturi or orifice plate coupled to a void fraction sensor

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

Oliveira, Jorge Luiz Goes; Passos, Julio Cesar; Verschaeren, Ruud

Two-phase flow measurements were carried out using a resistive void fraction meter coupled to a venturi or orifice plate. The measurement system used to estimate the liquid and gas mass flow rates was evaluated using an air-water experimental facility. Experiments included upward vertical and horizontal flow, annular, bubbly, churn and slug patterns, void fraction ranging from 2% to 85%, water flow rate up to 4000 kg/h, air flow rate up to 50 kg/h, and quality up to almost 10%. The fractional root mean square (RMS) deviation of the two-phase mass flow rate in upward vertical flow through a venturi platemore » is 6.8% using the correlation of Chisholm (D. Chisholm, Pressure gradients during the flow of incompressible two-phase mixtures through pipes, venturis and orifice plates, British Chemical Engineering 12 (9) (1967) 454-457). For the orifice plate, the RMS deviation of the vertical flow is 5.5% using the correlation of Zhang et al. (H.J. Zhang, W.T. Yue, Z.Y. Huang, Investigation of oil-air two-phase mass flow rate measurement using venturi and void fraction sensor, Journal of Zhejiang University Science 6A (6) (2005) 601-606). The results show that the flow direction has no significant influence on the meters in relation to the pressure drop in the experimental operation range. Quality and slip ratio analyses were also performed. The results show a mean slip ratio lower than 1.1, when bubbly and slug flow patterns are encountered for mean void fractions lower than 70%. (author)« less

Intensity Thresholds on Raw Acceleration Data: Euclidean Norm Minus One (ENMO) and Mean Amplitude Deviation (MAD) Approaches

PubMed Central

Bakrania, Kishan; Yates, Thomas; Rowlands, Alex V.; Esliger, Dale W.; Bunnewell, Sarah; Sanders, James; Davies, Melanie; Khunti, Kamlesh; Edwardson, Charlotte L.

2016-01-01

Objectives (1) To develop and internally-validate Euclidean Norm Minus One (ENMO) and Mean Amplitude Deviation (MAD) thresholds for separating sedentary behaviours from common light-intensity physical activities using raw acceleration data collected from both hip- and wrist-worn tri-axial accelerometers; and (2) to compare and evaluate the performances between the ENMO and MAD metrics. Methods Thirty-three adults [mean age (standard deviation (SD)) = 27.4 (5.9) years; mean BMI (SD) = 23.9 (3.7) kg/m2; 20 females (60.6%)] wore four accelerometers; an ActiGraph GT3X+ and a GENEActiv on the right hip; and an ActiGraph GT3X+ and a GENEActiv on the non-dominant wrist. Under laboratory-conditions, participants performed 16 different activities (11 sedentary behaviours and 5 light-intensity physical activities) for 5 minutes each. ENMO and MAD were computed from the raw acceleration data, and logistic regression and receiver-operating-characteristic (ROC) analyses were implemented to derive thresholds for activity discrimination. Areas under ROC curves (AUROC) were calculated to summarise performances and thresholds were assessed via executing leave-one-out-cross-validations. Results For both hip and wrist monitor placements, in comparison to the ActiGraph GT3X+ monitors, the ENMO and MAD values derived from the GENEActiv devices were observed to be slightly higher, particularly for the lower-intensity activities. Monitor-specific hip and wrist ENMO and MAD thresholds showed excellent ability for separating sedentary behaviours from motion-based light-intensity physical activities (in general, AUROCs >0.95), with validation indicating robustness. However, poor classification was experienced when attempting to isolate standing still from sedentary behaviours (in general, AUROCs <0.65). The ENMO and MAD metrics tended to perform similarly across activities and accelerometer brands. Conclusions Researchers can utilise these robust monitor-specific hip and wrist ENMO and MAD

Intensity Thresholds on Raw Acceleration Data: Euclidean Norm Minus One (ENMO) and Mean Amplitude Deviation (MAD) Approaches.

PubMed

Bakrania, Kishan; Yates, Thomas; Rowlands, Alex V; Esliger, Dale W; Bunnewell, Sarah; Sanders, James; Davies, Melanie; Khunti, Kamlesh; Edwardson, Charlotte L

2016-01-01

(1) To develop and internally-validate Euclidean Norm Minus One (ENMO) and Mean Amplitude Deviation (MAD) thresholds for separating sedentary behaviours from common light-intensity physical activities using raw acceleration data collected from both hip- and wrist-worn tri-axial accelerometers; and (2) to compare and evaluate the performances between the ENMO and MAD metrics. Thirty-three adults [mean age (standard deviation (SD)) = 27.4 (5.9) years; mean BMI (SD) = 23.9 (3.7) kg/m2; 20 females (60.6%)] wore four accelerometers; an ActiGraph GT3X+ and a GENEActiv on the right hip; and an ActiGraph GT3X+ and a GENEActiv on the non-dominant wrist. Under laboratory-conditions, participants performed 16 different activities (11 sedentary behaviours and 5 light-intensity physical activities) for 5 minutes each. ENMO and MAD were computed from the raw acceleration data, and logistic regression and receiver-operating-characteristic (ROC) analyses were implemented to derive thresholds for activity discrimination. Areas under ROC curves (AUROC) were calculated to summarise performances and thresholds were assessed via executing leave-one-out-cross-validations. For both hip and wrist monitor placements, in comparison to the ActiGraph GT3X+ monitors, the ENMO and MAD values derived from the GENEActiv devices were observed to be slightly higher, particularly for the lower-intensity activities. Monitor-specific hip and wrist ENMO and MAD thresholds showed excellent ability for separating sedentary behaviours from motion-based light-intensity physical activities (in general, AUROCs >0.95), with validation indicating robustness. However, poor classification was experienced when attempting to isolate standing still from sedentary behaviours (in general, AUROCs <0.65). The ENMO and MAD metrics tended to perform similarly across activities and accelerometer brands. Researchers can utilise these robust monitor-specific hip and wrist ENMO and MAD thresholds, in order to accurately

Use of multiple picosecond high-mass molecular dynamics simulations to predict crystallographic B-factors of folded globular proteins.

PubMed

Pang, Yuan-Ping

2016-09-01

Predicting crystallographic B-factors of a protein from a conventional molecular dynamics simulation is challenging, in part because the B-factors calculated through sampling the atomic positional fluctuations in a picosecond molecular dynamics simulation are unreliable, and the sampling of a longer simulation yields overly large root mean square deviations between calculated and experimental B-factors. This article reports improved B-factor prediction achieved by sampling the atomic positional fluctuations in multiple picosecond molecular dynamics simulations that use uniformly increased atomic masses by 100-fold to increase time resolution. Using the third immunoglobulin-binding domain of protein G, bovine pancreatic trypsin inhibitor, ubiquitin, and lysozyme as model systems, the B-factor root mean square deviations (mean ± standard error) of these proteins were 3.1 ± 0.2-9 ± 1 Å 2 for Cα and 7.3 ± 0.9-9.6 ± 0.2 Å 2 for Cγ, when the sampling was done for each of these proteins over 20 distinct, independent, and 50-picosecond high-mass molecular dynamics simulations with AMBER forcefield FF12MC or FF14SB. These results suggest that sampling the atomic positional fluctuations in multiple picosecond high-mass molecular dynamics simulations may be conducive to a priori prediction of crystallographic B-factors of a folded globular protein.

Least mean square fourth based microgrid state estimation algorithm using the internet of things technology.

PubMed

Rana, Md Masud

2017-01-01

This paper proposes an innovative internet of things (IoT) based communication framework for monitoring microgrid under the condition of packet dropouts in measurements. First of all, the microgrid incorporating the renewable distributed energy resources is represented by a state-space model. The IoT embedded wireless sensor network is adopted to sense the system states. Afterwards, the information is transmitted to the energy management system using the communication network. Finally, the least mean square fourth algorithm is explored for estimating the system states. The effectiveness of the developed approach is verified through numerical simulations.

Solution, solid phase and computational structures of apicidin and its backbone-reduced analogs.

PubMed

Kranz, Michael; Murray, Peter John; Taylor, Stephen; Upton, Richard J; Clegg, William; Elsegood, Mark R J

2006-06-01

The recently isolated broad-spectrum antiparasitic apicidin (1) is one of the few naturally occurring cyclic tetrapeptides (CTP). Depending on the solvent, the backbone of 1 exhibits two gamma-turns (in CH(2)Cl(2)) or a beta-turn (in DMSO), differing solely in the rotation of the plane of one of the amide bonds. In the X-ray crystal structure, the peptidic C==Os and NHs are on opposite sides of the backbone plane, giving rise to infinite stacks of cyclotetrapeptides connected by three intermolecular hydrogen bonds between the backbones. Conformational searches (Amber force field) on a truncated model system of 1 confirm all three backbone conformations to be low-energy states. The previously synthesized analogs of 1 containing a reduced amide bond exhibit the same backbone conformation as 1 in DMSO, which is confirmed further by the X-ray crystal structure of a model system of the desoxy analogs of 1. This similarity helps in explaining why the desoxy analogs retain some of the antiprotozoal activities of apicidin. The backbone-reduction approach designed to facilitate the cyclization step of the acyclic precursors of the CTPs seems to retain the conformational preferences of the parent peptide backbone.

Lower Bound on the Mean Square Displacement of Particles in the Hard Disk Model

NASA Astrophysics Data System (ADS)

Richthammer, Thomas

2016-08-01

The hard disk model is a 2D Gibbsian process of particles interacting via pure hard core repulsion. At high particle density the model is believed to show orientational order, however, it is known not to exhibit positional order. Here we investigate to what extent particle positions may fluctuate. We consider a finite volume version of the model in a box of dimensions 2 n × 2 n with arbitrary boundary configuration, and we show that the mean square displacement of particles near the center of the box is bounded from below by c log n. The result generalizes to a large class of models with fairly arbitrary interaction.

Effects of finite-size particles on the turbulent flows in a square duct

NASA Astrophysics Data System (ADS)

Yu, Zhaosheng; Lin, Zhaowu; Shao, Xueming; Wang, Lian-Ping

2015-11-01

Fully resolved numerical simulations of the particle-laden turbulent flows in a square duct are performed with a direct-forcing fictitious domain method. The effects of the finite-size particles on the mean and root-mean-square (RMS) velocities are investigated at the friction Reynolds number of 150 (based on the friction velocity and half duct width) and the particle volume fractions ranging from 0.78% to 7.07%. For the neutrally buoyant case, our results show that the mean secondary flow is enhanced and its circulation center shifts closer to the center of the duct cross-section when the particles are added. The reason for the particle effect on the mean secondary flow is analyzed by examining the terms in the mean streamwise vorticity equation. The particles enhance the wall-tangential component of the RMS velocity (i.e. Reynolds normal stress) more than its wall-normal component in the near-wall region near the corners, resulting in the enhancement in the gradients of the normal stress difference, which we think is mainly responsible for the enhancement in the mean secondary flow. The particles accumulate preferentially in the near-corner region in the neutrally buoyant case. In addition, the effects of particle sedimentation are examined at different Shields numbers. The work was supported by the National Natural Science Foundation of China (11372275) and Research Fund for the Doctoral Program of Higher Education of China (20130101110035).

Correlation of published data on the solubility of methane in H/sub 2/O-NaCl solutions

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

Coco, L.T.; Johnson, A.E. Jr.; Bebout, D.G.

1981-01-01

A new correlation of the available published data for the solubility of methane in water was developed, based on fundamental thermodynamic relationships. An empirical relationship for the salting-out coefficient of NaCl for methane solubility in water was determined as a function of temperature. Root mean square and average deviations for the new correlation, the Haas correlation, and the revised Blount equation are compared.

Expression and Interaction Analysis among Saffron ALDHs and Crocetin Dialdehyde.

PubMed

Gómez-Gómez, Lourdes; Pacios, Luis F; Diaz-Perales, Araceli; Garrido-Arandia, María; Argandoña, Javier; Rubio-Moraga, Ángela; Ahrazem, Oussama

2018-05-09

In saffron, the cleavage of zeaxanthin by means of CCD2 generates crocetin dialdehyde, which is then converted by an unknown aldehyde dehydrogenase to crocetin. A proteome from saffron stigma was released recently and, based on the expression pattern and correlation analyses, five aldehyde dehydrogenases (ALDHs) were suggested as possible candidates to generate crocetin from crocetin dialdehydes. We selected four of the suggested ALDHs and analyzed their expression in different tissues, determined their activity over crocetin dialdehyde, and performed structure modeling and docking calculation to find their specificity. All the ALDHs were able to convert crocetin dialdehyde to crocetin, but two of them were stigma tissue-specific. Structure modeling and docking analyses revealed that, in all cases, there was a high coverage of residues in the models. All of them showed a very close conformation, indicated by the low root-mean-square deviation (RMSD) values of backbone atoms, which indicate a high similarity among them. However, low affinity between the enzymes and the crocetin dialdehyde were observed. Phylogenetic analysis and binding affinities calculations, including some ALDHs from Gardenia jasmonoides , Crocus sieberi , and Buddleja species that accumulate crocetin and Bixa orellana synthetizing the apocarotenoid bixin selected on their expression pattern matching with the accumulation of either crocins or bixin, pointed out that family 2 C4 members might be involved in the conversion of crocetin dialdehyde to crocetin with high specificity.

Testing of Lagrange multiplier damped least-squares control algorithm for woofer-tweeter adaptive optics

PubMed Central

Zou, Weiyao; Burns, Stephen A.

2012-01-01

A Lagrange multiplier-based damped least-squares control algorithm for woofer-tweeter (W-T) dual deformable-mirror (DM) adaptive optics (AO) is tested with a breadboard system. We show that the algorithm can complementarily command the two DMs to correct wavefront aberrations within a single optimization process: the woofer DM correcting the high-stroke, low-order aberrations, and the tweeter DM correcting the low-stroke, high-order aberrations. The optimal damping factor for a DM is found to be the median of the eigenvalue spectrum of the influence matrix of that DM. Wavefront control accuracy is maximized with the optimized control parameters. For the breadboard system, the residual wavefront error can be controlled to the precision of 0.03 μm in root mean square. The W-T dual-DM AO has applications in both ophthalmology and astronomy. PMID:22441462

A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. I. Backbone potentials of coarse-grained polypeptide chains

NASA Astrophysics Data System (ADS)

Sieradzan, Adam K.; Makowski, Mariusz; Augustynowicz, Antoni; Liwo, Adam

2017-03-01

A general and systematic method for the derivation of the functional expressions for the effective energy terms in coarse-grained force fields of polymer chains is proposed. The method is based on the expansion of the potential of mean force of the system studied in the cluster-cumulant series and expanding the all-atom energy in the Taylor series in the squares of interatomic distances about the squares of the distances between coarse-grained centers, to obtain approximate analytical expressions for the cluster cumulants. The primary degrees of freedom to average about are the angles for collective rotation of the atoms contained in the coarse-grained interaction sites about the respective virtual-bond axes. The approach has been applied to the revision of the virtual-bond-angle, virtual-bond-torsional, and backbone-local-and-electrostatic correlation potentials for the UNited RESidue (UNRES) model of polypeptide chains, demonstrating the strong dependence of the torsional and correlation potentials on virtual-bond angles, not considered in the current UNRES. The theoretical considerations are illustrated with the potentials calculated from the ab initio potential-energy surface of terminally blocked alanine by numerical integration and with the statistical potentials derived from known protein structures. The revised torsional potentials correctly indicate that virtual-bond angles close to 90° result in the preference for the turn and helical structures, while large virtual-bond angles result in the preference for polyproline II and extended backbone geometry. The revised correlation potentials correctly reproduce the preference for the formation of β-sheet structures for large values of virtual-bond angles and for the formation of α-helical structures for virtual-bond angles close to 90°.

Detection of Tetracycline in Milk using NIR Spectroscopy and Partial Least Squares

NASA Astrophysics Data System (ADS)

Wu, Nan; Xu, Chenshan; Yang, Renjie; Ji, Xinning; Liu, Xinyuan; Yang, Fan; Zeng, Ming

2018-02-01

The feasibility of measuring tetracycline in milk was investigated by near infrared (NIR) spectroscopic technique combined with partial least squares (PLS) method. The NIR transmittance spectra of 40 pure milk samples and 40 tetracycline adulterated milk samples with different concentrations (from 0.005 to 40 mg/L) were obtained. The pure milk and tetracycline adulterated milk samples were properly assigned to the categories with 100% accuracy in the calibration set, and the rate of correct classification of 96.3% was obtained in the prediction set. For the quantitation of tetracycline in adulterated milk, the root mean squares errors for calibration and prediction models were 0.61 mg/L and 4.22 mg/L, respectively. The PLS model had good fitting effect in calibration set, however its predictive ability was limited, especially for low tetracycline concentration samples. Totally, this approach can be considered as a promising tool for discrimination of tetracycline adulterated milk, as a supplement to high performance liquid chromatography.

An approximate fluvial equilibrium topography for the Alps

NASA Astrophysics Data System (ADS)

Stüwe, K.; Hergarten, S.

2012-04-01

This contribution addresses the question whether the present topography of the Alps can be approximated by a fluvial equilibrium topography and whether this can be used to determine uplift rates. Based on a statistical analysis of the present topography we use a stream-power approach for erosion where the erosion rate is proportional to the square root of the catchment size for catchment sizes larger than 12 square kilometers and a logarithmic dependence to mimic slope processes at smaller catchment sizes. If we assume a homogeneous uplift rate over the entire region (block uplift), the best-fit fluvial equilibrium topography differs from the real topography by about 500 m RMS (root mean square) with a strong systematic deviation. Regions of low elevation are too high in the equilibrium topography, while high-mountain regions are too low. The RMS difference significantly decreases if a spatially variable uplift function is allowed. If a strong variation of the uplift rate on a scale of 5 km is allowed, the systematic deviation becomes rather small, and the RMS difference decreases to about 150 m. A significant part of the remaining deviation apparently arises from glacially-shaped valleys, while another part may result from prematurity of the relief (Hergarten, Wagner & Stüwe, EPSL 297:453, 2010). The best-fit uplift function can probably be used for forward or backward simulation of the landform evolution.

ExScal Backbone Network Architecture

DTIC Science & Technology

2005-01-01

802.11 battery powered nodes was laid over the sensor network. We adopted the Stargate platform for the backbone tier to serve as the basis for...its head. XSS Hardware and Network: XSS stands for eXtreme Scaling Stargate . A stargate is a linux-based single board computer. It has a 400 MHz

Adaptive Square-Root Cubature-Quadrature Kalman Particle Filter for satellite attitude determination using vector observations

NASA Astrophysics Data System (ADS)

Kiani, Maryam; Pourtakdoust, Seid H.

2014-12-01

A novel algorithm is presented in this study for estimation of spacecraft's attitudes and angular rates from vector observations. In this regard, a new cubature-quadrature particle filter (CQPF) is initially developed that uses the Square-Root Cubature-Quadrature Kalman Filter (SR-CQKF) to generate the importance proposal distribution. The developed CQPF scheme avoids the basic limitation of particle filter (PF) with regards to counting the new measurements. Subsequently, CQPF is enhanced to adjust the sample size at every time step utilizing the idea of confidence intervals, thus improving the efficiency and accuracy of the newly proposed adaptive CQPF (ACQPF). In addition, application of the q-method for filter initialization has intensified the computation burden as well. The current study also applies ACQPF to the problem of attitude estimation of a low Earth orbit (LEO) satellite. For this purpose, the undertaken satellite is equipped with a three-axis magnetometer (TAM) as well as a sun sensor pack that provide noisy geomagnetic field data and Sun direction measurements, respectively. The results and performance of the proposed filter are investigated and compared with those of the extended Kalman filter (EKF) and the standard particle filter (PF) utilizing a Monte Carlo simulation. The comparison demonstrates the viability and the accuracy of the proposed nonlinear estimator.

N2/O2/H2 Dual-Pump Cars: Validation Experiments

NASA Technical Reports Server (NTRS)

OByrne, S.; Danehy, P. M.; Cutler, A. D.

2003-01-01

The dual-pump coherent anti-Stokes Raman spectroscopy (CARS) method is used to measure temperature and the relative species densities of N2, O2 and H2 in two experiments. Average values and root-mean-square (RMS) deviations are determined. Mean temperature measurements in a furnace containing air between 300 and 1800 K agreed with thermocouple measurements within 26 K on average, while mean mole fractions agree to within 1.6 % of the expected value. The temperature measurement standard deviation averaged 64 K while the standard deviation of the species mole fractions averaged 7.8% for O2 and 3.8% for N2, based on 200 single-shot measurements. Preliminary measurements have also been performed in a flat-flame burner for fuel-lean and fuel-rich flames. Temperature standard deviations of 77 K were measured, and the ratios of H2 to N2 and O2 to N2 respectively had standard deviations from the mean value of 12.3% and 10% of the measured ratio.

Diffuse ultraviolet erythemal irradiance on inclined planes: a comparison of experimental and modeled data.

PubMed

Utrillas, María P; Marín, María J; Esteve, Anna R; Estellés, Victor; Tena, Fernando; Cañada, Javier; Martínez-Lozano, José A

2009-01-01

Values of measured and modeled diffuse UV erythemal irradiance (UVER) for all sky conditions are compared on planes inclined at 40 degrees and oriented north, south, east and west. The models used for simulating diffuse UVER are of the geometric-type, mainly the Isotropic, Klucher, Hay, Muneer, Reindl and Schauberger models. To analyze the precision of the models, some statistical estimators were used such as root mean square deviation, mean absolute deviation and mean bias deviation. It was seen that all the analyzed models reproduce adequately the diffuse UVER on the south-facing plane, with greater discrepancies for the other inclined planes. When the models are applied to cloud-free conditions, the errors obtained are higher because the anisotropy of the sky dome acquires more importance and the models do not provide the estimation of diffuse UVER accurately.

Underestimated Halogen Bonds Forming with Protein Backbone in Protein Data Bank.

PubMed

Zhang, Qian; Xu, Zhijian; Shi, Jiye; Zhu, Weiliang

2017-07-24

Halogen bonds (XBs) are attracting increasing attention in biological systems. Protein Data Bank (PDB) archives experimentally determined XBs in biological macromolecules. However, no software for structure refinement in X-ray crystallography takes into account XBs, which might result in the weakening or even vanishing of experimentally determined XBs in PDB. In our previous study, we showed that side-chain XBs forming with protein side chains are underestimated in PDB on the basis of the phenomenon that the proportion of side-chain XBs to overall XBs decreases as structural resolution becomes lower and lower. However, whether the dominant backbone XBs forming with protein backbone are overlooked is still a mystery. Here, with the help of the ratio (R F ) of the observed XBs' frequency of occurrence to their frequency expected at random, we demonstrated that backbone XBs are largely overlooked in PDB, too. Furthermore, three cases were discovered possessing backbone XBs in high resolution structures while losing the XBs in low resolution structures. In the last two cases, even at 1.80 Å resolution, the backbone XBs were lost, manifesting the urgent need to consider XBs in the refinement process during X-ray crystallography study.

LETTER TO THE EDITOR: Backbones of traffic jams

NASA Astrophysics Data System (ADS)

Shikhar Gupta, Himadri; Ramaswamy, Ramakrishna

1996-11-01

We study the jam phase of the deterministic traffic model in two dimensions. Within the jam phase, there is a phase transition, from a self-organized jam (formed by initial synchronization followed by jamming), to a random-jam structure. The backbone of the jam is defined and used to analyse self-organization in the jam. The fractal dimension and interparticle correlations on the backbone indicate a continous phase transition at density 0305-4470/29/21/003/img1 with critical exponent 0305-4470/29/21/003/img2, which are characterized through simulations.

The Graphical Representation of the Digital Astronaut Physiology Backbone

NASA Technical Reports Server (NTRS)

Briers, Demarcus

2010-01-01

This report summarizes my internship project with the NASA Digital Astronaut Project to analyze the Digital Astronaut (DA) physiology backbone model. The Digital Astronaut Project (DAP) applies integrated physiology models to support space biomedical operations, and to assist NASA researchers in closing knowledge gaps related to human physiologic responses to space flight. The DA physiology backbone is a set of integrated physiological equations and functions that model the interacting systems of the human body. The current release of the model is HumMod (Human Model) version 1.5 and was developed over forty years at the University of Mississippi Medical Center (UMMC). The physiology equations and functions are scripted in an XML schema specifically designed for physiology modeling by Dr. Thomas G. Coleman at UMMC. Currently it is difficult to examine the physiology backbone without being knowledgeable of the XML schema. While investigating and documenting the tags and algorithms used in the XML schema, I proposed a standard methodology for a graphical representation. This standard methodology may be used to transcribe graphical representations from the DA physiology backbone. In turn, the graphical representations can allow examination of the physiological functions and equations without the need to be familiar with the computer programming languages or markup languages used by DA modeling software.

Rapidity dependence of antiproton-to-proton ratios in Au+Au collisions at square root of (sNN) = 130 GeV.

PubMed

Bearden, I G; Beavis, D; Besliu, C; Blyakhman, Y; Brzychczyk, J; Budick, B; Bøggild, H; Chasman, C; Christensen, C H; Christiansen, P; Cibor, J; Debbe, R; Gaardhøje, J J; Grotowski, K; Hagel, K; Hansen, O; Holm, A; Holme, A K; Ito, H; Jakobsen, E; Jipa, A; Jørdre, J I; Jundt, F; Jørgensen, C E; Keutgen, T; Kim, E J; Kozik, T; Larsen, T M; Lee, J H; Lee, Y K; Løvhøiden, G L; Majka, Z; Makeev, A; McBreen, B; Murray, M; Natowitz, J; Nielsen, B S; Olchanski, K; Olness, J; Ouerdane, D; Planeta, R; Rami, F; Röhrich, D; Samset, B H; Sanders, S J; Sheetz, R A; Sosin, Z; Staszel, P; Thorsteinsen, T F; Tveter, T S; Videbaek, F; Wada, R; Wieloch, A; Zgura, I S

2001-09-10

Measurements, with the BRAHMS detector, of the antiproton-to-proton ratio at midrapidities and forward rapidities, are presented for Au+Au reactions at square root of [s(NN)] = 130 GeV, and for three different collision centralities. For collisions in the 0%-40% centrality range, we find N(&pmacr;)/N(p) = 0.64+/-0.04((stat))+/-0.06((syst)) at y approximately 0, 0.66+/-0.03+/-0.06 at y approximately 0.7, and 0.41+/-0.04+/-0.06 at y approximately 2. The ratios are found to be nearly independent of collision centrality and transverse momentum. The antiproton and proton rapidity densities vary differently with rapidity, and indicate a significant degree of collision transparency, although a net-baryon free midrapidity plateau (Bjorken limit) is not yet reached.

Characterizing the zenithal night sky brightness in large territories: how many samples per square kilometre are needed?

NASA Astrophysics Data System (ADS)

Bará, Salvador

2018-01-01

A recurring question arises when trying to characterize, by means of measurements or theoretical calculations, the zenithal night sky brightness throughout a large territory: how many samples per square kilometre are needed? The optimum sampling distance should allow reconstructing, with sufficient accuracy, the continuous zenithal brightness map across the whole region, whilst at the same time avoiding unnecessary and redundant oversampling. This paper attempts to provide some tentative answers to this issue, using two complementary tools: the luminance structure function and the Nyquist-Shannon spatial sampling theorem. The analysis of several regions of the world, based on the data from the New world atlas of artificial night sky brightness, suggests that, as a rule of thumb, about one measurement per square kilometre could be sufficient for determining the zenithal night sky brightness of artificial origin at any point in a region to within ±0.1 magV arcsec-2 (in the root-mean-square sense) of its true value in the Johnson-Cousins V band. The exact reconstruction of the zenithal night sky brightness maps from samples taken at the Nyquist rate seems to be considerably more demanding.

Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction.

PubMed

Mai, Uyen; Sayyari, Erfan; Mirarab, Siavash

2017-01-01

Phylogenetic trees inferred using commonly-used models of sequence evolution are unrooted, but the root position matters both for interpretation and downstream applications. This issue has been long recognized; however, whether the potential for discordance between the species tree and gene trees impacts methods of rooting a phylogenetic tree has not been extensively studied. In this paper, we introduce a new method of rooting a tree based on its branch length distribution; our method, which minimizes the variance of root to tip distances, is inspired by the traditional midpoint rerooting and is justified when deviations from the strict molecular clock are random. Like midpoint rerooting, the method can be implemented in a linear time algorithm. In extensive simulations that consider discordance between gene trees and the species tree, we show that the new method is more accurate than midpoint rerooting, but its relative accuracy compared to using outgroups to root gene trees depends on the size of the dataset and levels of deviations from the strict clock. We show high levels of error for all methods of rooting estimated gene trees due to factors that include effects of gene tree discordance, deviations from the clock, and gene tree estimation error. Our simulations, however, did not reveal significant differences between two equivalent methods for species tree estimation that use rooted and unrooted input, namely, STAR and NJst. Nevertheless, our results point to limitations of existing scalable rooting methods.

Minimum variance rooting of phylogenetic trees and implications for species tree reconstruction

PubMed Central

Sayyari, Erfan; Mirarab, Siavash

2017-01-01

Phylogenetic trees inferred using commonly-used models of sequence evolution are unrooted, but the root position matters both for interpretation and downstream applications. This issue has been long recognized; however, whether the potential for discordance between the species tree and gene trees impacts methods of rooting a phylogenetic tree has not been extensively studied. In this paper, we introduce a new method of rooting a tree based on its branch length distribution; our method, which minimizes the variance of root to tip distances, is inspired by the traditional midpoint rerooting and is justified when deviations from the strict molecular clock are random. Like midpoint rerooting, the method can be implemented in a linear time algorithm. In extensive simulations that consider discordance between gene trees and the species tree, we show that the new method is more accurate than midpoint rerooting, but its relative accuracy compared to using outgroups to root gene trees depends on the size of the dataset and levels of deviations from the strict clock. We show high levels of error for all methods of rooting estimated gene trees due to factors that include effects of gene tree discordance, deviations from the clock, and gene tree estimation error. Our simulations, however, did not reveal significant differences between two equivalent methods for species tree estimation that use rooted and unrooted input, namely, STAR and NJst. Nevertheless, our results point to limitations of existing scalable rooting methods. PMID:28800608

Modulatory effects by neodymium-doped yttrium aluminum garnet laser on fibroblast attachment to single rooted tooth surfaces following ultrasonic scaling and root planning: An in vitro study

PubMed Central

Negi, Shanta; Krishnamurthy, Malathi; Ganji, Kiran Kumar; Pendor, Sunil

2015-01-01

Context: One of the most important goals of periodontal therapy is connective tissue reattachment to previously diseased root surfaces. In the recent years, laser therapy has been considered as an important tool in improving the treatment of periodontal disease. Aims: To evaluate the neodymium-doped yttrium aluminum garnet (Nd: YAG) lasers effects on root surfaces affected by periodontal disease and compare this treatment with scaling and root planning (SRP) in terms of fibroblast attachment. Materials and Methods: A sample of 30 single-rooted human teeth extracted because of advanced periodontal disease was used in this study. Sixty specimens obtained by longitudinal sectioning were randomly divided in three groups. Group A control (untreated); Group B SRP; Group C laser (Nd: YAG) and ultrasonic scaling. All specimens were incubated with fibroblast suspension and then fixed and observed under scanning electron microscope. Results: With a median of 8, the control group (Group A) exhibited the least number of total fibroblasts among all the three groups. The laser and scaling - treated group (Group C) showed the highest number of fibroblasts (median = 49, mean ± standard deviation [SD] = 48.28 ± 17.18), followed by SRP only (Group B, median = 22, mean ± SD = 22.24 ± 8.67). Conclusions: Nd: YAG laser irradiation at specific energy densities can be used as a useful tool to condition the root surfaces, enhancing fibroblast attachment. Hence aiding in re-establishment of the connective tissue attachment to the root surfaces of previously diseased teeth. PMID:25810589

Molecular dynamics simulation analysis of Focal Adhesive Kinase (FAK) docked with solanesol as an anti-cancer agent.

PubMed

Daneial, Betty; Joseph, Jacob Paul Vazhappilly; Ramakrishna, Guruprasad

2017-01-01

Focal adhesion kinase (FAK) plays a primary role in regulating the activity of many signaling molecules. Increased FAK expression has been associated in a series of cellular processes like cell migration and survival. FAK inhibition by an anti cancer agent is critical. Therefore, it is of interest to identify, modify, design, improve and develop molecules to inhibit FAK. Solanesol is known to have inhibitory activity towards FAK. However, the molecular principles of its binding with FAK is unknown. Solanesol is a highly flexible ligand (25 rotatable bonds). Hence, ligand-protein docking was completed using AutoDock with a modified contact based scoring function. The FAK-solanesol complex model was further energy minimized and simulated in GROMOS96 (53a6) force field followed by post simulation analysis such as Root mean square deviation (RMSD), root mean square fluctuations (RMSF) and solvent accessible surface area (SASA) calculations to explain solanesol-FAK binding.

Least mean square fourth based microgrid state estimation algorithm using the internet of things technology

PubMed Central

2017-01-01

This paper proposes an innovative internet of things (IoT) based communication framework for monitoring microgrid under the condition of packet dropouts in measurements. First of all, the microgrid incorporating the renewable distributed energy resources is represented by a state-space model. The IoT embedded wireless sensor network is adopted to sense the system states. Afterwards, the information is transmitted to the energy management system using the communication network. Finally, the least mean square fourth algorithm is explored for estimating the system states. The effectiveness of the developed approach is verified through numerical simulations. PMID:28459848

Unweighted least squares phase unwrapping by means of multigrid techniques

NASA Astrophysics Data System (ADS)

Pritt, Mark D.

1995-11-01

We present a multigrid algorithm for unweighted least squares phase unwrapping. This algorithm applies Gauss-Seidel relaxation schemes to solve the Poisson equation on smaller, coarser grids and transfers the intermediate results to the finer grids. This approach forms the basis of our multigrid algorithm for weighted least squares phase unwrapping, which is described in a separate paper. The key idea of our multigrid approach is to maintain the partial derivatives of the phase data in separate arrays and to correct these derivatives at the boundaries of the coarser grids. This maintains the boundary conditions necessary for rapid convergence to the correct solution. Although the multigrid algorithm is an iterative algorithm, we demonstrate that it is nearly as fast as the direct Fourier-based method. We also describe how to parallelize the algorithm for execution on a distributed-memory parallel processor computer or a network-cluster of workstations.

Relationship between dental anomalies and orthodontic root resorption of upper incisors.

PubMed

Van Parys, Katrien; Aartman, Irene H A; Kuitert, Reinder; Zentner, Andrej

2012-10-01

The aim of this study was to examine the potential relationship between the occurrence of orthodontic root resorption and presence of dental anomalies such as tooth agenesis and pipette-shaped roots. Dental anomalies and root resorption were assessed on dental panoramic tomographs (DPT) of 88 subjects, 27 males and 61 females, mean age 28.4 (SD = 11.3 years), selected from orthodontic patients on the basis of the following exclusion criteria: previous fixed appliance treatment, bad quality of the DPTs and no visibility of the periodontal ligament of every tooth, and younger than 15 years of age at the onset of treatment with fixed edgewise appliance lasting at least 18 months. A pipette-shaped root was identified as defined by a drawing. Tooth agenesis was assessed on DPTs and from subjects' dental history. Root resorption was calculated as the difference between the root length before and after treatment, with and without a correction factor (crown length post-treatment/crown length pre-treatment). If one of the four upper incisors showed root resorption of ≥2.3 mm with both formulas, the patient was scored as having root resorption. Chi-square tests indicated that there was no relationship between orthodontic root resorption and agenesis (P = 0.885) nor between orthodontic root resorption and pipette-shaped roots (P = 0.800). There was no relationship between having one of the anomalies and root resorption either (P = 0.750). In the present study, it was not possible to confirm on DPTs a relationship between orthodontic root resorption and dental anomalies, such as agenesis and pipette-shaped roots.

Cooperative UAV-Based Communications Backbone for Sensor Networks

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

Roberts, R S

2001-10-07

The objective of this project is to investigate the use of unmanned air vehicles (UAVs) as mobile, adaptive communications backbones for ground-based sensor networks. In this type of network, the UAVs provide communication connectivity to sensors that cannot communicate with each other because of terrain, distance, or other geographical constraints. In these situations, UAVs provide a vertical communication path for the sensors, thereby mitigating geographic obstacles often imposed on networks. With the proper use of UAVs, connectivity to a widely disbursed sensor network in rugged terrain is readily achieved. Our investigation has focused on networks where multiple cooperating UAVs aremore » used to form a network backbone. The advantage of using multiple UAVs to form the network backbone is parallelization of sensor connectivity. Many widely spaced or isolated sensors can be connected to the network at once using this approach. In these networks, the UAVs logically partition the sensor network into sub-networks (subnets), with one UAV assigned per subnet. Partitioning the network into subnets allows the UAVs to service sensors in parallel thereby decreasing the sensor-to-network connectivity. A UAV services sensors in its subnet by flying a route (path) through the subnet, uplinking data collected by the sensors, and forwarding the data to a ground station. An additional advantage of using multiple UAVs in the network is that they provide redundancy in the communications backbone, so that the failure of a single UAV does not necessarily imply the loss of the network.« less

Nonribosomal biosynthesis of backbone-modified peptides

NASA Astrophysics Data System (ADS)

Niquille, David L.; Hansen, Douglas A.; Mori, Takahiro; Fercher, David; Kries, Hajo; Hilvert, Donald

2018-03-01

Biosynthetic modification of nonribosomal peptide backbones represents a potentially powerful strategy to modulate the structure and properties of an important class of therapeutics. Using a high-throughput assay for catalytic activity, we show here that an L-Phe-specific module of an archetypal nonribosomal peptide synthetase can be reprogrammed to accept and process the backbone-modified amino acid (S)-β-Phe with near-native specificity and efficiency. A co-crystal structure with a non-hydrolysable aminoacyl-AMP analogue reveals the origins of the 40,000-fold α/β-specificity switch, illuminating subtle but precise remodelling of the active site. When the engineered catalyst was paired with downstream module(s), (S)-β-Phe-containing peptides were produced at preparative scale in vitro (~1 mmol) and high titres in vivo (~100 mg l-1), highlighting the potential of biosynthetic pathway engineering for the construction of novel nonribosomal β-frameworks.

Overcoming deep roots, fast rates, and short internodes to resolve the ancient rapid radiation of eupolypod II ferns.

PubMed

Rothfels, Carl J; Larsson, Anders; Kuo, Li-Yaung; Korall, Petra; Chiou, Wen-Liang; Pryer, Kathleen M

2012-05-01

Backbone relationships within the large eupolypod II clade, which includes nearly a third of extant fern species, have resisted elucidation by both molecular and morphological data. Earlier studies suggest that much of the phylogenetic intractability of this group is due to three factors: (i) a long root that reduces apparent levels of support in the ingroup; (ii) long ingroup branches subtended by a series of very short backbone internodes (the "ancient rapid radiation" model); and (iii) significantly heterogeneous lineage-specific rates of substitution. To resolve the eupolypod II phylogeny, with a particular emphasis on the backbone internodes, we assembled a data set of five plastid loci (atpA, atpB, matK, rbcL, and trnG-R) from a sample of 81 accessions selected to capture the deepest divergences in the clade. We then evaluated our phylogenetic hypothesis against potential confounding factors, including those induced by rooting, ancient rapid radiation, rate heterogeneity, and the Bayesian star-tree paradox artifact. While the strong support we inferred for the backbone relationships proved robust to these potential problems, their investigation revealed unexpected model-mediated impacts of outgroup composition, divergent effects of methods for countering the star-tree paradox artifact, and gave no support to concerns about the applicability of the unrooted model to data sets with heterogeneous lineage-specific rates of substitution. This study is among few to investigate these factors with empirical data, and the first to compare the performance of the two primary methods for overcoming the Bayesian star-tree paradox artifact. Among the significant phylogenetic results is the near-complete support along the eupolypod II backbone, the demonstrated paraphyly of Woodsiaceae as currently circumscribed, and the well-supported placement of the enigmatic genera Homalosorus, Diplaziopsis, and Woodsia.

Atomic motion from the mean square displacement in a monatomic liquid

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

Wallace, Duane C.; De Lorenzi-Venneri, Giulia; Chisolm, Eric D.

V-T theory is constructed in the many-body Hamiltonian formulation, and is being developed as a novel approach to liquid dynamics theory. In this theory the liquid atomic motion consists of two contributions, normal mode vibrations in a single representative potential energy valley, and transits, which carry the system across boundaries between valleys. The mean square displacement time correlation function (the MSD) is a direct measure of the atomic motion, and our goal is to determine if the V-T formalism can produce a physically sensible account of this motion. We employ molecular dynamics (MD) data for a system representing liquid Na,more » and find the motion evolves in three successive time intervals: on the first 'vibrational' interval, the vibrational motion alone gives a highly accurate account of the MD data; on the second 'crossover' interval, the vibrational MSD saturates to a constant while the transit motion builds up from zero; on the third 'random walk' interval, the transit motion produces a purely diffusive random walk of the vibrational equilibrium positions. Furthermore, this motional evolution agrees with, and adds refinement to, the MSD atomic motion as described by current liquid dynamics theories.« less

Atomic motion from the mean square displacement in a monatomic liquid

DOE PAGES

Wallace, Duane C.; De Lorenzi-Venneri, Giulia; Chisolm, Eric D.

2016-04-08

V-T theory is constructed in the many-body Hamiltonian formulation, and is being developed as a novel approach to liquid dynamics theory. In this theory the liquid atomic motion consists of two contributions, normal mode vibrations in a single representative potential energy valley, and transits, which carry the system across boundaries between valleys. The mean square displacement time correlation function (the MSD) is a direct measure of the atomic motion, and our goal is to determine if the V-T formalism can produce a physically sensible account of this motion. We employ molecular dynamics (MD) data for a system representing liquid Na,more » and find the motion evolves in three successive time intervals: on the first 'vibrational' interval, the vibrational motion alone gives a highly accurate account of the MD data; on the second 'crossover' interval, the vibrational MSD saturates to a constant while the transit motion builds up from zero; on the third 'random walk' interval, the transit motion produces a purely diffusive random walk of the vibrational equilibrium positions. Furthermore, this motional evolution agrees with, and adds refinement to, the MSD atomic motion as described by current liquid dynamics theories.« less

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

PubMed

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

2015-11-19

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

Exploring the mechanistic insights of Cas scaffolding protein family member 4 with protein tyrosine kinase 2 in Alzheimer's disease by evaluating protein interactions through molecular docking and dynamic simulations.

PubMed

Hassan, Mubashir; Shahzadi, Saba; Alashwal, Hany; Zaki, Nazar; Seo, Sung-Yum; Moustafa, Ahmed A

2018-05-22

Cas scaffolding protein family member 4 and protein tyrosine kinase 2 are signaling proteins, which are involved in neuritic plaques burden, neurofibrillary tangles, and disruption of synaptic connections in Alzheimer's disease. In the current study, a computational approach was employed to explore the active binding sites of Cas scaffolding protein family member 4 and protein tyrosine kinase 2 proteins and their significant role in the activation of downstream signaling pathways. Sequential and structural analyses were performed on Cas scaffolding protein family member 4 and protein tyrosine kinase 2 to identify their core active binding sites. Molecular docking servers were used to predict the common interacting residues in both Cas scaffolding protein family member 4 and protein tyrosine kinase 2 and their involvement in Alzheimer's disease-mediated pathways. Furthermore, the results from molecular dynamic simulation experiment show the stability of targeted proteins. In addition, the generated root mean square deviations and fluctuations, solvent-accessible surface area, and gyration graphs also depict their backbone stability and compactness, respectively. A better understanding of CAS and their interconnected protein signaling cascade may help provide a treatment for Alzheimer's disease. Further, Cas scaffolding protein family member 4 could be used as a novel target for the treatment of Alzheimer's disease by inhibiting the protein tyrosine kinase 2 pathway.

An iteratively reweighted least-squares approach to adaptive robust adjustment of parameters in linear regression models with autoregressive and t-distributed deviations

NASA Astrophysics Data System (ADS)

Kargoll, Boris; Omidalizarandi, Mohammad; Loth, Ina; Paffenholz, Jens-André; Alkhatib, Hamza

2018-03-01

In this paper, we investigate a linear regression time series model of possibly outlier-afflicted observations and autocorrelated random deviations. This colored noise is represented by a covariance-stationary autoregressive (AR) process, in which the independent error components follow a scaled (Student's) t-distribution. This error model allows for the stochastic modeling of multiple outliers and for an adaptive robust maximum likelihood (ML) estimation of the unknown regression and AR coefficients, the scale parameter, and the degree of freedom of the t-distribution. This approach is meant to be an extension of known estimators, which tend to focus only on the regression model, or on the AR error model, or on normally distributed errors. For the purpose of ML estimation, we derive an expectation conditional maximization either algorithm, which leads to an easy-to-implement version of iteratively reweighted least squares. The estimation performance of the algorithm is evaluated via Monte Carlo simulations for a Fourier as well as a spline model in connection with AR colored noise models of different orders and with three different sampling distributions generating the white noise components. We apply the algorithm to a vibration dataset recorded by a high-accuracy, single-axis accelerometer, focusing on the evaluation of the estimated AR colored noise model.

Development of a transformation model to derive general population-based utility: Mapping the pruritus-visual analog scale (VAS) to the EQ-5D utility.

PubMed

Park, Sun-Young; Park, Eun-Ja; Suh, Hae Sun; Ha, Dongmun; Lee, Eui-Kyung

2017-08-01

Although nonpreference-based disease-specific measures are widely used in clinical studies, they cannot generate utilities for economic evaluation. A solution to this problem is to estimate utilities from disease-specific instruments using the mapping function. This study aimed to develop a transformation model for mapping the pruritus-visual analog scale (VAS) to the EuroQol 5-Dimension 3-Level (EQ-5D-3L) utility index in pruritus. A cross-sectional survey was conducted with a sample (n = 268) drawn from the general population of South Korea. Data were randomly divided into 2 groups, one for estimating and the other for validating mapping models. To select the best model, we developed and compared 3 separate models using demographic information and the pruritus-VAS as independent variables. The predictive performance was assessed using the mean absolute deviation and root mean square error in a separate dataset. Among the 3 models, model 2 using age, age squared, sex, and the pruritus-VAS as independent variables had the best performance based on the goodness of fit and model simplicity, with a log likelihood of 187.13. The 3 models had similar precision errors based on mean absolute deviation and root mean square error in the validation dataset. No statistically significant difference was observed between the mean observed and predicted values in all models. In conclusion, model 2 was chosen as the preferred mapping model. Outcomes measured as the pruritus-VAS can be transformed into the EQ-5D-3L utility index using this mapping model, which makes an economic evaluation possible when only pruritus-VAS data are available. © 2017 John Wiley & Sons, Ltd.

Temperature effect on the structure and conformational fluctuations in two zinc knuckles from the mouse mammary tumor virus.

PubMed

Nedjoua, Drici; Krallafa, Abdelghani Mohamed

2018-06-01

Zinc fingers are small protein domains in which zinc plays a structural role, contributing to the stability of the zinc-peptide complex. Zinc fingers are structurally diverse and are present in proteins that perform a broad range of functions in various cellular processes, such as replication and repair, transcription and translation, metabolism and signaling, cell proliferation, and apoptosis. Zinc fingers typically function as interaction modules and bind to a wide variety of compounds, such as nucleic acids, proteins, and small molecules. In this study, we investigated the structural properties, in solution, of the proximal and distal zinc knuckles of the nucleocapsid (NC) protein from the mouse mammary tumor virus (MMTV) (MMTV NC). For this purpose, we performed a series of molecular dynamics simulations in aqueous solution at 300 K, 333 K, and 348 K. The temperature effect was evaluated in terms of root mean square deviation of the backbone atoms and root mean square fluctuation of the coordinating residue atoms. The stability of the zinc coordination sphere was analyzed based upon the time profile of the interatomic distances between the zinc ions and the chelator atoms. The results indicate that the hydrophobic character of the proximal zinc finger is dominant at 333 K. The low mobility of the coordinating residues suggests that the strong electrostatic effect exerted by the zinc ion on its coordinating residues is not influenced by the increase in temperature. The evolution of the structural parameters of the coordination sphere of the distal zinc finger at 300 K gives us a reasonable picture of the unfolding pathway, as proposed by Bombarda and coworkers (Bombarda et al., 2005), which can predict the binding order of the four conserved ligand-binding residues. Our results support the conclusion that the structural features can vary significantly between the two zinc knuckles of MMTV NC. Copyright © 2018 Elsevier Ltd. All rights reserved.

Application of the Polynomial-Based Least Squares and Total Least Squares Models for the Attenuated Total Reflection Fourier Transform Infrared Spectra of Binary Mixtures of Hydroxyl Compounds.

PubMed

Shan, Peng; Peng, Silong; Zhao, Yuhui; Tang, Liang

2016-03-01

An analysis of binary mixtures of hydroxyl compound by Attenuated Total Reflection Fourier transform infrared spectroscopy (ATR FT-IR) and classical least squares (CLS) yield large model error due to the presence of unmodeled components such as H-bonded components. To accommodate these spectral variations, polynomial-based least squares (LSP) and polynomial-based total least squares (TLSP) are proposed to capture the nonlinear absorbance-concentration relationship. LSP is based on assuming that only absorbance noise exists; while TLSP takes both absorbance noise and concentration noise into consideration. In addition, based on different solving strategy, two optimization algorithms (limited-memory Broyden-Fletcher-Goldfarb-Shanno (LBFGS) algorithm and Levenberg-Marquardt (LM) algorithm) are combined with TLSP and then two different TLSP versions (termed as TLSP-LBFGS and TLSP-LM) are formed. The optimum order of each nonlinear model is determined by cross-validation. Comparison and analyses of the four models are made from two aspects: absorbance prediction and concentration prediction. The results for water-ethanol solution and ethanol-ethyl lactate solution show that LSP, TLSP-LBFGS, and TLSP-LM can, for both absorbance prediction and concentration prediction, obtain smaller root mean square error of prediction than CLS. Additionally, they can also greatly enhance the accuracy of estimated pure component spectra. However, from the view of concentration prediction, the Wilcoxon signed rank test shows that there is no statistically significant difference between each nonlinear model and CLS. © The Author(s) 2016.

Testing of Lagrange multiplier damped least-squares control algorithm for woofer-tweeter adaptive optics.

PubMed

Zou, Weiyao; Burns, Stephen A

2012-03-20

A Lagrange multiplier-based damped least-squares control algorithm for woofer-tweeter (W-T) dual deformable-mirror (DM) adaptive optics (AO) is tested with a breadboard system. We show that the algorithm can complementarily command the two DMs to correct wavefront aberrations within a single optimization process: the woofer DM correcting the high-stroke, low-order aberrations, and the tweeter DM correcting the low-stroke, high-order aberrations. The optimal damping factor for a DM is found to be the median of the eigenvalue spectrum of the influence matrix of that DM. Wavefront control accuracy is maximized with the optimized control parameters. For the breadboard system, the residual wavefront error can be controlled to the precision of 0.03 μm in root mean square. The W-T dual-DM AO has applications in both ophthalmology and astronomy. © 2012 Optical Society of America

Chemical characteristics and antithrombotic effect of chondroitin sulfates from sturgeon skull and sturgeon backbone.

PubMed

Gui, Meng; Song, Juyi; Zhang, Lu; Wang, Shun; Wu, Ruiyun; Ma, Changwei; Li, Pinglan

2015-06-05

Chondroitin sulfates (CSs) were extracted from sturgeon skull and backbone, and their chemical composition, anticoagulant, anti-platelet and thrombolysis activities were evaluated. The average molecular weights of CS from sturgeon skull and backbone were 38.5kDa and 49.2kDa, respectively. Disaccharide analysis indicated that the sturgeon backbone CS was primarily composed of disaccharide monosulfated in position four of the GalNAc (37.8%) and disaccharide monosulfated in position six of the GalNAc (59.6%) while sturgeon skull CS was primarily composed of nonsulfated disaccharide (74.2%). Sturgeon backbone CS showed stronger antithrombotic effect than sturgeon skull CS. Sturgeon backbone CS could significantly prolong activated partial thromboplastin time (APTT) and thrombin time (TT), inhibited ADP-induced platelet aggregation and dissolved platelet plasma clots in vitro. The results suggested that sturgeon backbone CS can be explored as a functional food with antithrombotic function. Copyright © 2015 Elsevier Ltd. All rights reserved.

Statistical Characterization of Altitude Matrices by Computer. Report 4. Frequency Distributions of Gradient.

DTIC Science & Technology

1977-01-01

balanced at the mean, with the central part steeper ( platykurtic : broad mode or truncated tails) -r flatter (leptokurtic: peaked mode or extended...and NUPUR, have negative kurtosis (they are platykurtic , with truncated tails and/or broad modes relative to their standard deviations) FERRO, on the...the other areas, and its gradients are platykurtic but almost unskewed. Hence the square root of sine transformation (Fig,15) and the log tangent

Estimating contraction level using root mean square amplitude in control subjects and patients with neuromuscular disorders.

PubMed

Boe, Shaun G; Rice, Charles L; Doherty, Timothy J

2008-04-01

To assess the utility of the surface electromyographic signal as a means of estimating the level of muscle force during quantitative electromyography studies by examining the relationship between muscle force and the amplitude of the surface electromyographic activity signal; and to determine the impact of a reduction in the number of motor units on this relationship, through inclusion of a sample of patients with neuromuscular disease. Cross-sectional, cohort study design. Tertiary care, ambulatory, electromyography laboratory. A volunteer, convenience sample of healthy control subjects (n=10), patients with amyotrophic lateral sclerosis (n=9), and patients with Charcot-Marie-Tooth disease type X (n=5). Not applicable. The first dorsal interosseous (FDI) and biceps brachii muscles were examined. Force values (at 10% increments) were calculated from two 4-second maximal voluntary contractions (MVCs). Surface electromyographic activity was recorded during separate 4-second voluntary contractions at 9 force increments (10% -90% of MVC). Additionally, a motor unit number estimate was derived for each subject to quantify the degree of motor unit loss in patients relative to control subjects. The relationships between force and surface electromyographic activity for both muscles (controls and patients) were best fit by a linear function. The variability about the grouped regression lines was quantified by 95% confidence intervals and found to be +/-6.7% (controls) and +/-8.5% (patients) for the FDI and +/-5% (controls) and +/-6.1% (patients) for the biceps brachii. These results suggest that the amplitude of the surface electromyographic activity signal may be used as a means of estimating the level of muscle force during quantitative electromyography studies. Future studies should be directed at examining if the variability associated with these force and surface electromyographic activity relationships is acceptable in replacing previous methods of measuring muscle

Modeling 15N NMR chemical shift changes in protein backbone with pressure

NASA Astrophysics Data System (ADS)

La Penna, Giovanni; Mori, Yoshiharu; Kitahara, Ryo; Akasaka, Kazuyuki; Okamoto, Yuko

2016-08-01

Nitrogen chemical shift is a useful parameter for determining the backbone three-dimensional structure of proteins. Empirical models for fast calculation of N chemical shift are improving their reliability, but there are subtle effects that cannot be easily interpreted. Among these, the effects of slight changes in hydrogen bonds, both intramolecular and with water molecules in the solvent, are particularly difficult to predict. On the other hand, these hydrogen bonds are sensitive to changes in protein environment. In this work, the change of N chemical shift with pressure for backbone segments in the protein ubiquitin is correlated with the change in the population of hydrogen bonds involving the backbone amide group. The different extent of interaction of protein backbone with the water molecules in the solvent is put in evidence.

Rooting depth varies differentially in trees and grasses as a function of mean annual rainfall in an African savanna.

PubMed

Holdo, Ricardo M; Nippert, Jesse B; Mack, Michelle C

2018-01-01

A significant fraction of the terrestrial biosphere comprises biomes containing tree-grass mixtures. Forecasting vegetation dynamics in these environments requires a thorough understanding of how trees and grasses use and compete for key belowground resources. There is disagreement about the extent to which tree-grass vertical root separation occurs in these ecosystems, how this overlap varies across large-scale environmental gradients, and what these rooting differences imply for water resource availability and tree-grass competition and coexistence. To assess the extent of tree-grass rooting overlap and how tree and grass rooting patterns vary across resource gradients, we examined landscape-level patterns of tree and grass functional rooting depth along a mean annual precipitation (MAP) gradient extending from ~ 450 to ~ 750 mm year -1 in Kruger National Park, South Africa. We used stable isotopes from soil and stem water to make inferences about relative differences in rooting depth between these two functional groups. We found clear differences in rooting depth between grasses and trees across the MAP gradient, with grasses generally exhibiting shallower rooting profiles than trees. We also found that trees tended to become more shallow-rooted as a function of MAP, to the point that trees and grasses largely overlapped in terms of rooting depth at the wettest sites. Our results reconcile previously conflicting evidence for rooting overlap in this system, and have important implications for understanding tree-grass dynamics under altered precipitation scenarios.

On estimating gravity anomalies: A comparison of least squares collocation with least squares techniques

NASA Technical Reports Server (NTRS)

Argentiero, P.; Lowrey, B.

1976-01-01

The least squares collocation algorithm for estimating gravity anomalies from geodetic data is shown to be an application of the well known regression equations which provide the mean and covariance of a random vector (gravity anomalies) given a realization of a correlated random vector (geodetic data). It is also shown that the collocation solution for gravity anomalies is equivalent to the conventional least-squares-Stokes' function solution when the conventional solution utilizes properly weighted zero a priori estimates. The mathematical and physical assumptions underlying the least squares collocation estimator are described, and its numerical properties are compared with the numerical properties of the conventional least squares estimator.

Light-regulated gravitropism in seedling roots of maize

NASA Technical Reports Server (NTRS)

Feldman, L. J.; Briggs, W. R.

1987-01-01

Red light-induced changes in the gravitropism of roots of Zea mays variety Merit is a very low fluence response with a threshold of 10(-9) moles per square meter and is not reversible by far red light. Blue light also affects root gravitropism but the sensitivity of roots to blue is 50 to 100 times less than to an equal fluence of red. In Z. mays Merit we conclude that phytochrome is the sole pigment associated with light-induced changes in root gravitropism.

Analysis of Nonlinear Dynamics by Square Matrix Method

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

Yu, Li Hua

The nonlinear dynamics of a system with periodic structure can be analyzed using a square matrix. In this paper, we show that because the special property of the square matrix constructed for nonlinear dynamics, we can reduce the dimension of the matrix from the original large number for high order calculation to low dimension in the first step of the analysis. Then a stable Jordan decomposition is obtained with much lower dimension. The transformation to Jordan form provides an excellent action-angle approximation to the solution of the nonlinear dynamics, in good agreement with trajectories and tune obtained from tracking. Andmore » more importantly, the deviation from constancy of the new action-angle variable provides a measure of the stability of the phase space trajectories and their tunes. Thus the square matrix provides a novel method to optimize the nonlinear dynamic system. The method is illustrated by many examples of comparison between theory and numerical simulation. Finally, in particular, we show that the square matrix method can be used for optimization to reduce the nonlinearity of a system.« less

Efficient Levenberg-Marquardt minimization of the maximum likelihood estimator for Poisson deviates

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

Laurence, T; Chromy, B

2009-11-10

for Poisson deviates. However, since there is a simple, analytical formula for the appropriate MLE measure for Poisson deviates, it is inexcusable that least squares estimators are used almost exclusively when fitting event counting histograms. There have been ways found to use successive non-linear least squares fitting to obtain similarly unbiased results, but this procedure is justified by simulation, must be re-tested when conditions change significantly, and requires two successive fits. There is a great need for a fitting routine for the MLE estimator for Poisson deviates that has convergence domains and rates comparable to the non-linear least squares L-M fitting. We show in this report that a simple way to achieve that goal is to use the L-M fitting procedure not to minimize the least squares measure, but the MLE for Poisson deviates.« less

Descendant root volume varies as a function of root type: estimation of root biomass lost during uprooting in Pinus pinaster.

PubMed

Danjon, Frédéric; Caplan, Joshua S; Fortin, Mathieu; Meredieu, Céline

2013-01-01

Root systems of woody plants generally display a strong relationship between the cross-sectional area or cross-sectional diameter (CSD) of a root and the dry weight of biomass (DWd) or root volume (Vd) that has grown (i.e., is descendent) from a point. Specification of this relationship allows one to quantify root architectural patterns and estimate the amount of material lost when root systems are extracted from the soil. However, specifications of this relationship generally do not account for the fact that root systems are comprised of multiple types of roots. We assessed whether the relationship between CSD and Vd varies as a function of root type. Additionally, we sought to identify a more accurate and time-efficient method for estimating missing root volume than is currently available. We used a database that described the 3D root architecture of Pinus pinaster root systems (5, 12, or 19 years) from a stand in southwest France. We determined the relationship between CSD and Vd for 10,000 root segments from intact root branches. Models were specified that did and did not account for root type. The relationships were then applied to the diameters of 11,000 broken root ends to estimate the volume of missing roots. CSD was nearly linearly related to the square root of Vd, but the slope of the curve varied greatly as a function of root type. Sinkers and deep roots tapered rapidly, as they were limited by available soil depth. Distal shallow roots tapered gradually, as they were less limited spatially. We estimated that younger trees lost an average of 17% of root volume when excavated, while older trees lost 4%. Missing volumes were smallest in the central parts of root systems and largest in distal shallow roots. The slopes of the curves for each root type are synthetic parameters that account for differentiation due to genetics, soil properties, or mechanical stimuli. Accounting for this differentiation is critical to estimating root loss accurately.

Descendant root volume varies as a function of root type: estimation of root biomass lost during uprooting in Pinus pinaster

PubMed Central

Danjon, Frédéric; Caplan, Joshua S.; Fortin, Mathieu; Meredieu, Céline

2013-01-01

Root systems of woody plants generally display a strong relationship between the cross-sectional area or cross-sectional diameter (CSD) of a root and the dry weight of biomass (DWd) or root volume (Vd) that has grown (i.e., is descendent) from a point. Specification of this relationship allows one to quantify root architectural patterns and estimate the amount of material lost when root systems are extracted from the soil. However, specifications of this relationship generally do not account for the fact that root systems are comprised of multiple types of roots. We assessed whether the relationship between CSD and Vd varies as a function of root type. Additionally, we sought to identify a more accurate and time-efficient method for estimating missing root volume than is currently available. We used a database that described the 3D root architecture of Pinus pinaster root systems (5, 12, or 19 years) from a stand in southwest France. We determined the relationship between CSD and Vd for 10,000 root segments from intact root branches. Models were specified that did and did not account for root type. The relationships were then applied to the diameters of 11,000 broken root ends to estimate the volume of missing roots. CSD was nearly linearly related to the square root of Vd, but the slope of the curve varied greatly as a function of root type. Sinkers and deep roots tapered rapidly, as they were limited by available soil depth. Distal shallow roots tapered gradually, as they were less limited spatially. We estimated that younger trees lost an average of 17% of root volume when excavated, while older trees lost 4%. Missing volumes were smallest in the central parts of root systems and largest in distal shallow roots. The slopes of the curves for each root type are synthetic parameters that account for differentiation due to genetics, soil properties, or mechanical stimuli. Accounting for this differentiation is critical to estimating root loss accurately. PMID

Development and evaluation of a soft wearable weight support device for reducing muscle fatigue on shoulder.

PubMed

Park, Daegeun; Cho, Kyu-Jin

2017-01-01

Compensating the weight of human limbs is important in reducing muscle fatigue experienced by manual laborers. In this study, a compact and lightweight soft wearable weight support device was developed and evaluated. The device supports gravitational force on the shoulder at any arm posture, although there are some limitations in its assistive performance. The device actuator consists of a cam-rod structure, a tendon-driven mechanism, and a rubber band. The desired assistive torque is translated to the shoulder joint along a tendon routing structure. Device performance was evaluated by measuring muscle activation in with-assist and without-assist conditions. Muscle activation on the deltoid was measured by surface electromyography. An experimental protocol consisting of a series of exercises was executed with six healthy subjects. The subjects raised and lowered their arm from 0 to 100 degrees for 30 times under eight conditions, which were combined with-assist and without-assist conditions, and holding the horizontal angle of the arm at 0, 30, 60, or 90 degrees against the sagittal plane. Surface electromyography data were pre-processed and analyzed using a root mean square method. When muscle fatigue occurs, the root mean square of the surface electromyography increases nonlinearly. This was calculated using the standard deviation of the root mean square. Three of six subjects showed decreased variation of the root mean square between the exercises in the with-assist condition. One subject's result was significantly reduced (by about 57.6%) in the with-assist condition. In contrast, two subjects did not show significant difference between measurements taken in the with-assist and without-assist conditions. One subject was dropped from the experiment because the device did not fit the subject's body. In conclusion, the effectiveness of the soft wearable weight support device in supporting shoulder movements was verified through the decreased variation of muscle

Development and evaluation of a soft wearable weight support device for reducing muscle fatigue on shoulder

PubMed Central

Cho, Kyu-Jin

2017-01-01

Compensating the weight of human limbs is important in reducing muscle fatigue experienced by manual laborers. In this study, a compact and lightweight soft wearable weight support device was developed and evaluated. The device supports gravitational force on the shoulder at any arm posture, although there are some limitations in its assistive performance. The device actuator consists of a cam-rod structure, a tendon-driven mechanism, and a rubber band. The desired assistive torque is translated to the shoulder joint along a tendon routing structure. Device performance was evaluated by measuring muscle activation in with-assist and without-assist conditions. Muscle activation on the deltoid was measured by surface electromyography. An experimental protocol consisting of a series of exercises was executed with six healthy subjects. The subjects raised and lowered their arm from 0 to 100 degrees for 30 times under eight conditions, which were combined with-assist and without-assist conditions, and holding the horizontal angle of the arm at 0, 30, 60, or 90 degrees against the sagittal plane. Surface electromyography data were pre-processed and analyzed using a root mean square method. When muscle fatigue occurs, the root mean square of the surface electromyography increases nonlinearly. This was calculated using the standard deviation of the root mean square. Three of six subjects showed decreased variation of the root mean square between the exercises in the with-assist condition. One subject’s result was significantly reduced (by about 57.6%) in the with-assist condition. In contrast, two subjects did not show significant difference between measurements taken in the with-assist and without-assist conditions. One subject was dropped from the experiment because the device did not fit the subject’s body. In conclusion, the effectiveness of the soft wearable weight support device in supporting shoulder movements was verified through the decreased variation of

Phytoremediation of palm oil mill secondary effluent (POMSE) by Chrysopogon zizanioides (L.) using artificial neural networks.

PubMed

Darajeh, Negisa; Idris, Azni; Fard Masoumi, Hamid Reza; Nourani, Abolfazl; Truong, Paul; Rezania, Shahabaldin

2017-05-04

Artificial neural networks (ANNs) have been widely used to solve the problems because of their reliable, robust, and salient characteristics in capturing the nonlinear relationships between variables in complex systems. In this study, ANN was applied for modeling of Chemical Oxygen Demand (COD) and biodegradable organic matter (BOD) removal from palm oil mill secondary effluent (POMSE) by vetiver system. The independent variable, including POMSE concentration, vetiver slips density, and removal time, has been considered as input parameters to optimize the network, while the removal percentage of COD and BOD were selected as output. To determine the number of hidden layer nodes, the root mean squared error of testing set was minimized, and the topologies of the algorithms were compared by coefficient of determination and absolute average deviation. The comparison indicated that the quick propagation (QP) algorithm had minimum root mean squared error and absolute average deviation, and maximum coefficient of determination. The importance values of the variables was included vetiver slips density with 42.41%, time with 29.8%, and the POMSE concentration with 27.79%, which showed none of them, is negligible. Results show that the ANN has great potential ability in prediction of COD and BOD removal from POMSE with residual standard error (RSE) of less than 0.45%.

Modeling protein conformational changes by iterative fitting of distance constraints using reoriented normal modes.

PubMed

Zheng, Wenjun; Brooks, Bernard R

2006-06-15

Recently we have developed a normal-modes-based algorithm that predicts the direction of protein conformational changes given the initial state crystal structure together with a small number of pairwise distance constraints for the end state. Here we significantly extend this method to accurately model both the direction and amplitude of protein conformational changes. The new protocol implements a multisteps search in the conformational space that is driven by iteratively minimizing the error of fitting the given distance constraints and simultaneously enforcing the restraint of low elastic energy. At each step, an incremental structural displacement is computed as a linear combination of the lowest 10 normal modes derived from an elastic network model, whose eigenvectors are reorientated to correct for the distortions caused by the structural displacements in the previous steps. We test this method on a list of 16 pairs of protein structures for which relatively large conformational changes are observed (root mean square deviation >3 angstroms), using up to 10 pairwise distance constraints selected by a fluctuation analysis of the initial state structures. This method has achieved a near-optimal performance in almost all cases, and in many cases the final structural models lie within root mean square deviation of 1 approximately 2 angstroms from the native end state structures.

A molecular dynamics study of Beta-Glucosidase B upon small substrate binding.

PubMed

Mazlan, Nur Shima Fadhilah; Ahmad Khairudin, Nurul Bahiyah

2016-07-01

Paenibacillus polymyxa β-glucosidase B (BglB), belongs to a GH family 1, is a monomeric enzyme that acts as an exo-β-glucosidase hydrolysing cellobiose and cellodextrins of higher degree of polymerization using retaining mechanism. A molecular dynamics (MD) simulation was performed at 300 K under periodic boundary condition for 5 ns using the complexes structure obtained from previous docking study, namely BglB-Beta-d-glucose and BglB-Cellobiose. From the root-mean-square deviation analysis, both enzyme complexes were reported to deviate from the initial structure in the early part of the simulation but it was stable afterwards. The root-mean-square fluctuation analysis revealed that the most flexible regions comprised of the residues from 26 to 29, 43 to 53, 272 to 276, 306 to 325 and 364 to 367. The radius of gyration analysis had shown the structure of BglB without substrate became more compact towards the end of the simulation compare to other two complexes. The residues His122 and Trp410 were observed to form stable hydrogen bond with occupancy higher than 10%. In conclusion, the behaviour of BglB enzyme towards the substrate binding was successfully explored via MD simulation approaches.

Ordinary Least Squares and Quantile Regression: An Inquiry-Based Learning Approach to a Comparison of Regression Methods

ERIC Educational Resources Information Center

Helmreich, James E.; Krog, K. Peter

2018-01-01

We present a short, inquiry-based learning course on concepts and methods underlying ordinary least squares (OLS), least absolute deviation (LAD), and quantile regression (QR). Students investigate squared, absolute, and weighted absolute distance functions (metrics) as location measures. Using differential calculus and properties of convex…

Predicting root zone soil moisture with soil properties and satellite near-surface moisture data across the conterminous United States

NASA Astrophysics Data System (ADS)

Baldwin, D.; Manfreda, S.; Keller, K.; Smithwick, E. A. H.

2017-03-01

Satellite-based near-surface (0-2 cm) soil moisture estimates have global coverage, but do not capture variations of soil moisture in the root zone (up to 100 cm depth) and may be biased with respect to ground-based soil moisture measurements. Here, we present an ensemble Kalman filter (EnKF) hydrologic data assimilation system that predicts bias in satellite soil moisture data to support the physically based Soil Moisture Analytical Relationship (SMAR) infiltration model, which estimates root zone soil moisture with satellite soil moisture data. The SMAR-EnKF model estimates a regional-scale bias parameter using available in situ data. The regional bias parameter is added to satellite soil moisture retrievals before their use in the SMAR model, and the bias parameter is updated continuously over time with the EnKF algorithm. In this study, the SMAR-EnKF assimilates in situ soil moisture at 43 Soil Climate Analysis Network (SCAN) monitoring locations across the conterminous U.S. Multivariate regression models are developed to estimate SMAR parameters using soil physical properties and the moderate resolution imaging spectroradiometer (MODIS) evapotranspiration data product as covariates. SMAR-EnKF root zone soil moisture predictions are in relatively close agreement with in situ observations when using optimal model parameters, with root mean square errors averaging 0.051 [cm3 cm-3] (standard error, s.e. = 0.005). The average root mean square error associated with a 20-fold cross-validation analysis with permuted SMAR parameter regression models increases moderately (0.082 [cm3 cm-3], s.e. = 0.004). The expected regional-scale satellite correction bias is negative in four out of six ecoregions studied (mean = -0.12 [-], s.e. = 0.002), excluding the Great Plains and Eastern Temperate Forests (0.053 [-], s.e. = 0.001). With its capability of estimating regional-scale satellite bias, the SMAR-EnKF system can predict root zone soil moisture over broad extents and has

Evaluation of surface roughness of orthodontic wires by means of atomic force microscopy.

PubMed

D'Antò, Vincenzo; Rongo, Roberto; Ametrano, Gianluca; Spagnuolo, Gianrico; Manzo, Paolo; Martina, Roberto; Paduano, Sergio; Valletta, Rosa

2012-09-01

To compare the surface roughness of different orthodontic archwires. Four nickel-titanium wires (Sentalloy(®), Sentalloy(®) High Aesthetic, Titanium Memory ThermaTi Lite(®), and Titanium Memory Esthetic(®)), three β-titanium wires (TMA(®), Colored TMA(®), and Beta Titanium(®)), and one stainless-steel wire (Stainless Steel(®)) were considered for this study. Three samples for each wire were analyzed by atomic force microscopy (AFM). Three-dimensional images were processed using Gwiddion software, and the roughness average (Ra), the root mean square (Rms), and the maximum height (Mh) values of the scanned surface profile were recorded. Statistical analysis was performed by one-way analysis of variance (ANOVA) followed by Tukey's post hoc test (P < .05). The Ra, Rms, and Mh values were expressed as the mean ± standard deviation. Among as-received archwires, the Stainless Steel (Ra  =  36.6 ± 5.8; Rms  =  48 ± 7.7; Mh  =  328.1 ± 64) archwire was less rough than the others (ANOVA, P < .05). The Sentalloy High Aesthetic was the roughest (Ra  =  133.5 ± 10.8; Rms  =  165.8 ± 9.8; Mh  =  949.6 ± 192.1) of the archwires. The surface quality of the wires investigated differed significantly. Ion implantation effectively reduced the roughness of TMA. Moreover, Teflon(®)-coated Titanium Memory Esthetic was less rough than was ion-implanted Sentalloy High Aesthetic.

Molecular dynamics simulation analysis of Focal Adhesive Kinase (FAK) docked with solanesol as an anti-cancer agent

PubMed Central

Daneial, Betty; Joseph, Jacob Paul Vazhappilly; Ramakrishna, Guruprasad

2017-01-01

Focal adhesion kinase (FAK) plays a primary role in regulating the activity of many signaling molecules. Increased FAK expression has been associated in a series of cellular processes like cell migration and survival. FAK inhibition by an anti cancer agent is critical. Therefore, it is of interest to identify, modify, design, improve and develop molecules to inhibit FAK. Solanesol is known to have inhibitory activity towards FAK. However, the molecular principles of its binding with FAK is unknown. Solanesol is a highly flexible ligand (25 rotatable bonds). Hence, ligand-protein docking was completed using AutoDock with a modified contact based scoring function. The FAK-solanesol complex model was further energy minimized and simulated in GROMOS96 (53a6) force field followed by post simulation analysis such as Root mean square deviation (RMSD), root mean square fluctuations (RMSF) and solvent accessible surface area (SASA) calculations to explain solanesol-FAK binding. PMID:29081606

vmdICE: a plug-in for rapid evaluation of molecular dynamics simulations using VMD.

PubMed

Knapp, Bernhard; Lederer, Nadja; Omasits, Ulrich; Schreiner, Wolfgang

2010-12-01

Molecular dynamics (MD) is a powerful in silico method to investigate the interactions between biomolecules. It solves Newton's equations of motion for atoms over a specified period of time and yields a trajectory file, containing the different spatial arrangements of atoms during the simulation. The movements and energies of each single atom are recorded. For evaluating of these simulation trajectories with regard to biomedical implications, several methods are available. Three well-known ones are the root mean square deviation (RMSD), the root mean square fluctuation (RMSF) and solvent accessible surface area (SASA). Herein, we present a novel plug-in for the software "visual molecular dynamics" (VMD) that allows an interactive 3D representation of RMSD, RMSF, and SASA, directly on the molecule. On the one hand, our plug-in is easy to handle for inexperienced users, and on the other hand, it provides a fast and flexible graphical impression of the spatial dynamics of a system for experts in the field. © 2010 Wiley Periodicals, Inc.

Characterization of the Interaction between Gallic Acid and Lysozyme by Molecular Dynamics Simulation and Optical Spectroscopy

PubMed Central

Zhan, Minzhong; Guo, Ming; Jiang, Yanke; Wang, Xiaomeng

2015-01-01

The binding interaction between gallic acid (GA) and lysozyme (LYS) was investigated and compared by molecular dynamics (MD) simulation and spectral techniques. The results from spectroscopy indicate that GA binds to LYS to generate a static complex. The binding constants and thermodynamic parameters were calculated. MD simulation revealed that the main driving forces for GA binding to LYS are hydrogen bonding and hydrophobic interactions. The root-mean-square deviation verified that GA and LYS bind to form a stable complex, while the root-mean-square fluctuation results showed that the stability of the GA-LYS complex at 298 K was higher than that at 310 K. The calculated free binding energies from the molecular mechanics/Poisson-Boltzmann surface area method showed that van der Waals forces and electrostatic interactions are the predominant intermolecular forces. The MD simulation was consistent with the spectral experiments. This study provides a reference for future study of the pharmacological mechanism of GA. PMID:26140374

Characterization of the Interaction between Gallic Acid and Lysozyme by Molecular Dynamics Simulation and Optical Spectroscopy.

PubMed

Zhan, Minzhong; Guo, Ming; Jiang, Yanke; Wang, Xiaomeng

2015-07-01

The binding interaction between gallic acid (GA) and lysozyme (LYS) was investigated and compared by molecular dynamics (MD) simulation and spectral techniques. The results from spectroscopy indicate that GA binds to LYS to generate a static complex. The binding constants and thermodynamic parameters were calculated. MD simulation revealed that the main driving forces for GA binding to LYS are hydrogen bonding and hydrophobic interactions. The root-mean-square deviation verified that GA and LYS bind to form a stable complex, while the root-mean-square fluctuation results showed that the stability of the GA-LYS complex at 298 K was higher than that at 310 K. The calculated free binding energies from the molecular mechanics/Poisson-Boltzmann surface area method showed that van der Waals forces and electrostatic interactions are the predominant intermolecular forces. The MD simulation was consistent with the spectral experiments. This study provides a reference for future study of the pharmacological mechanism of GA.

Measurement of inclusive jet cross sections in Z/gamma*(-->e+e-) + jets production in pp[over ] collisions at square root s = 1.96 TeV.

PubMed

Aaltonen, T; Adelman, J; Akimoto, T; Albrow, M G; Alvarez González, B; Amerio, S; Amidei, D; Anastassov, A; Annovi, A; Antos, J; Aoki, M; Apollinari, G; Apresyan, A; Arisawa, T; Artikov, A; Ashmanskas, W; Attal, A; Aurisano, A; Azfar, F; Azzi-Bacchetta, P; Azzurri, P; Bacchetta, N; Badgett, W; Barbaro-Galtieri, A; Barnes, V E; Barnett, B A; Baroiant, S; Bartsch, V; Bauer, G; Beauchemin, P-H; Bedeschi, F; Bednar, P; Behari, S; Bellettini, G; Bellinger, J; Belloni, A; Benjamin, D; Beretvas, A; Beringer, J; Berry, T; Bhatti, A; Binkley, M; Bisello, D; Bizjak, I; Blair, R E; Blocker, C; Blumenfeld, B; Bocci, A; Bodek, A; Boisvert, V; Bolla, G; Bolshov, A; Bortoletto, D; Boudreau, J; Boveia, A; Brau, B; Bridgeman, A; Brigliadori, L; Bromberg, C; Brubaker, E; Budagov, J; Budd, H S; Budd, S; Burkett, K; Busetto, G; Bussey, P; Buzatu, A; Byrum, K L; Cabrera, S; Campanelli, M; Campbell, M; Canelli, F; Canepa, A; Carlsmith, D; Carosi, R; Carrillo, S; Carron, S; Casal, B; Casarsa, M; Castro, A; Catastini, P; Cauz, D; Cavalli-Sforza, M; Cerri, A; Cerrito, L; Chang, S H; Chen, Y C; Chertok, M; Chiarelli, G; Chlachidze, G; Chlebana, F; Cho, K; Chokheli, D; Chou, J P; Choudalakis, G; Chuang, S H; Chung, K; Chung, W H; Chung, Y S; Ciobanu, C I; Ciocci, M A; Clark, A; Clark, D; Compostella, G; Convery, M E; Conway, J; Cooper, B; Copic, K; Cordelli, M; Cortiana, G; Crescioli, F; Cuenca Almenar, C; Cuevas, J; Culbertson, R; Cully, J C; Dagenhart, D; Datta, M; Davies, T; de Barbaro, P; De Cecco, S; Deisher, A; De Lentdecker, G; De Lorenzo, G; Dell'orso, M; Demortier, L; Deng, J; Deninno, M; De Pedis, D; Derwent, P F; Di Giovanni, G P; Dionisi, C; Di Ruzza, B; Dittmann, J R; D'Onofrio, M; Donati, S; Dong, P; Donini, J; Dorigo, T; Dube, S; Efron, J; Erbacher, R; Errede, D; Errede, S; Eusebi, R; Fang, H C; Farrington, S; Fedorko, W T; Feild, R G; Feindt, M; Fernandez, J P; Ferrazza, C; Field, R; Flanagan, G; Forrest, R; Forrester, S; Franklin, M; Freeman, J C; Furic, I; Gallinaro, M; Galyardt, J; Garberson, F; Garcia, J E; Garfinkel, A F; Gerberich, H; Gerdes, D; Giagu, S; Giakoumopolou, V; Giannetti, P; Gibson, K; Gimmell, J L; Ginsburg, C M; Giokaris, N; Giordani, M; Giromini, P; Giunta, M; Glagolev, V; Glenzinski, D; Gold, M; Goldschmidt, N; Golossanov, A; Gomez, G; Gomez-Ceballos, G; Goncharov, M; González, O; Gorelov, I; Goshaw, A T; Goulianos, K; Gresele, A; Grinstein, S; Grosso-Pilcher, C; Grundler, U; Guimaraes da Costa, J; Gunay-Unalan, Z; Haber, C; Hahn, K; Hahn, S R; Halkiadakis, E; Hamilton, A; Han, B-Y; Han, J Y; Handler, R; Happacher, F; Hara, K; Hare, D; Hare, M; Harper, S; Harr, R F; Harris, R M; Hartz, M; Hatakeyama, K; Hauser, J; Hays, C; Heck, M; Heijboer, A; Heinemann, B; Heinrich, J; Henderson, C; Herndon, M; Heuser, J; Hewamanage, S; Hidas, D; Hill, C S; Hirschbuehl, D; Hocker, A; Hou, S; Houlden, M; Hsu, S-C; Huffman, B T; Hughes, R E; Husemann, U; Huston, J; Incandela, J; Introzzi, G; Iori, M; Ivanov, A; Iyutin, B; James, E; Jayatilaka, B; Jeans, D; Jeon, E J; Jindariani, S; Johnson, W; Jones, M; Joo, K K; Jun, S Y; Jung, J E; Junk, T R; Kamon, T; Kar, D; Karchin, P E; Kato, Y; Kephart, R; Kerzel, U; Khotilovich, V; Kilminster, B; Kim, D H; Kim, H S; Kim, J E; Kim, M J; Kim, S B; Kim, S H; Kim, Y K; Kimura, N; Kirsch, L; Klimenko, S; Klute, M; Knuteson, B; Ko, B R; Koay, S A; Kondo, K; Kong, D J; Konigsberg, J; Korytov, A; Kotwal, A V; Kraus, J; Kreps, M; Kroll, J; Krumnack, N; Kruse, M; Krutelyov, V; Kubo, T; Kuhlmann, S E; Kuhr, T; Kulkarni, N P; Kusakabe, Y; Kwang, S; Laasanen, A T; Lai, S; Lami, S; Lammel, S; Lancaster, M; Lander, R L; Lannon, K; Lath, A; Latino, G; Lazzizzera, I; Lecompte, T; Lee, J; Lee, J; Lee, Y J; Lee, S W; Lefèvre, R; Leonardo, N; Leone, S; Levy, S; Lewis, J D; Lin, C; Lin, C S; Linacre, J; Lindgren, M; Lipeles, E; Lister, A; Litvintsev, D O; Liu, T; Lockyer, N S; Loginov, A; Loreti, M; Lovas, L; Lu, R-S; Lucchesi, D; Lueck, J; Luci, C; Lujan, P; Lukens, P; Lungu, G; Lyons, L; Lys, J; Lysak, R; Lytken, E; Mack, P; Macqueen, D; Madrak, R; Maeshima, K; Makhoul, K; Maki, T; Maksimovic, P; Malde, S; Malik, S; Manca, G; Manousakis, A; Margaroli, F; Marino, C; Marino, C P; Martin, A; Martin, M; Martin, V; Martínez, M; Martínez-Ballarín, R; Maruyama, T; Mastrandrea, P; Masubuchi, T; Mattson, M E; Mazzanti, P; McFarland, K S; McIntyre, P; McNulty, R; Mehta, A; Mehtala, P; Menzemer, S; Menzione, A; Merkel, P; Mesropian, C; Messina, A; Miao, T; Miladinovic, N; Miles, J; Miller, R; Mills, C; Milnik, M; Mitra, A; Mitselmakher, G; Miyake, H; Moed, S; Moggi, N; Moon, C S; Moore, R; Morello, M; Movilla Fernandez, P; Mülmenstädt, J; Mukherjee, A; Muller, Th; Mumford, R; Murat, P; Mussini, M; Nachtman, J; Nagai, Y; Nagano, A; Naganoma, J; Nakamura, K; Nakano, I; Napier, A; Necula, V; Neu, C; Neubauer, M S; Nielsen, J; Nodulman, L; Norman, M; Norniella, O; Nurse, E; Oh, S H; Oh, Y D; Oksuzian, I; Okusawa, T; Oldeman, R; Orava, R; Osterberg, K; Pagan Griso, S; Pagliarone, C; Palencia, E; Papadimitriou, V; Papaikonomou, A; Paramonov, A A; Parks, B; Pashapour, S; Patrick, J; Pauletta, G; Paulini, M; Paus, C; Pellett, D E; Penzo, A; Phillips, T J; Piacentino, G; Piedra, J; Pinera, L; Pitts, K; Plager, C; Pondrom, L; Portell, X; Poukhov, O; Pounder, N; Prakoshyn, F; Pronko, A; Proudfoot, J; Ptohos, F; Punzi, G; Pursley, J; Rademacker, J; Rahaman, A; Ramakrishnan, V; Ranjan, N; Redondo, I; Reisert, B; Rekovic, V; Renton, P; Rescigno, M; Richter, S; Rimondi, F; Ristori, L; Robson, A; Rodrigo, T; Rogers, E; Rolli, S; Roser, R; Rossi, M; Rossin, R; Roy, P; Ruiz, A; Russ, J; Rusu, V; Saarikko, H; Safonov, A; Sakumoto, W K; Salamanna, G; Saltó, O; Santi, L; Sarkar, S; Sartori, L; Sato, K; Savoy-Navarro, A; Scheidle, T; Schlabach, P; Schmidt, E E; Schmidt, M A; Schmidt, M P; Schmitt, M; Schwarz, T; Scodellaro, L; Scott, A L; Scribano, A; Scuri, F; Sedov, A; Seidel, S; Seiya, Y; Semenov, A; Sexton-Kennedy, L; Sfyria, A; Shalhout, S Z; Shapiro, M D; Shears, T; Shepard, P F; Sherman, D; Shimojima, M; Shochet, M; Shon, Y; Shreyber, I; Sidoti, A; Sinervo, P; Sisakyan, A; Slaughter, A J; Slaunwhite, J; Sliwa, K; Smith, J R; Snider, F D; Snihur, R; Soderberg, M; Soha, A; Somalwar, S; Sorin, V; Spalding, J; Spinella, F; Spreitzer, T; Squillacioti, P; Stanitzki, M; St Denis, R; Stelzer, B; Stelzer-Chilton, O; Stentz, D; Strologas, J; Stuart, D; Suh, J S; Sukhanov, A; Sun, H; Suslov, I; Suzuki, T; Taffard, A; Takashima, R; Takeuchi, Y; Tanaka, R; Tecchio, M; Teng, P K; Terashi, K; Thom, J; Thompson, A S; Thompson, G A; Thomson, E; Tipton, P; Tiwari, V; Tkaczyk, S; Toback, D; Tokar, S; Tollefson, K; Tomura, T; Tonelli, D; Torre, S; Torretta, D; Tourneur, S; Trischuk, W; Tu, Y; Turini, N; Ukegawa, F; Uozumi, S; Vallecorsa, S; van Remortel, N; Varganov, A; Vataga, E; Vázquez, F; Velev, G; Vellidis, C; Veszpremi, V; Vidal, M; Vidal, R; Vila, I; Vilar, R; Vine, T; Vogel, M; Volobouev, I; Volpi, G; Würthwein, F; Wagner, P; Wagner, R G; Wagner, R L; Wagner-Kuhr, J; Wagner, W; Wakisaka, T; Wallny, R; Wang, S M; Warburton, A; Waters, D; Weinberger, M; Wester, W C; Whitehouse, B; Whiteson, D; Wicklund, A B; Wicklund, E; Williams, G; Williams, H H; Wilson, P; Winer, B L; Wittich, P; Wolbers, S; Wolfe, C; Wright, T; Wu, X; Wynne, S M; Yagil, A; Yamamoto, K; Yamaoka, J; Yamashita, T; Yang, C; Yang, U K; Yang, Y C; Yao, W M; Yeh, G P; Yoh, J; Yorita, K; Yoshida, T; Yu, G B; Yu, I; Yu, S S; Yun, J C; Zanello, L; Zanetti, A; Zaw, I; Zhang, X; Zheng, Y; Zucchelli, S

2008-03-14

Inclusive jet cross sections in Z/gamma* events, with Z/gamma* decaying into an electron-positron pair, are measured as a function of jet transverse momentum and jet multiplicity in pp[over ] collisions at square root s = 1.96 TeV with the upgraded Collider Detector at Fermilab in run II, based on an integrated luminosity of 1.7 fb(-1). The measurements cover the rapidity region |y(jet)|<2.1 and the transverse momentum range p(T)(jet)>30 GeV/c. Next-to-leading order perturbative QCD predictions are in good agreement with the measured cross sections.

Online Soft Sensor of Humidity in PEM Fuel Cell Based on Dynamic Partial Least Squares

PubMed Central

Long, Rong; Chen, Qihong; Zhang, Liyan; Ma, Longhua; Quan, Shuhai

2013-01-01

Online monitoring humidity in the proton exchange membrane (PEM) fuel cell is an important issue in maintaining proper membrane humidity. The cost and size of existing sensors for monitoring humidity are prohibitive for online measurements. Online prediction of humidity using readily available measured data would be beneficial to water management. In this paper, a novel soft sensor method based on dynamic partial least squares (DPLS) regression is proposed and applied to humidity prediction in PEM fuel cell. In order to obtain data of humidity and test the feasibility of the proposed DPLS-based soft sensor a hardware-in-the-loop (HIL) test system is constructed. The time lag of the DPLS-based soft sensor is selected as 30 by comparing the root-mean-square error in different time lag. The performance of the proposed DPLS-based soft sensor is demonstrated by experimental results. PMID:24453923

Application of partial least squares near-infrared spectral classification in diabetic identification

NASA Astrophysics Data System (ADS)

Yan, Wen-juan; Yang, Ming; He, Guo-quan; Qin, Lin; Li, Gang

2014-11-01

In order to identify the diabetic patients by using tongue near-infrared (NIR) spectrum - a spectral classification model of the NIR reflectivity of the tongue tip is proposed, based on the partial least square (PLS) method. 39sample data of tongue tip's NIR spectra are harvested from healthy people and diabetic patients , respectively. After pretreatment of the reflectivity, the spectral data are set as the independent variable matrix, and information of classification as the dependent variables matrix, Samples were divided into two groups - i.e. 53 samples as calibration set and 25 as prediction set - then the PLS is used to build the classification model The constructed modelfrom the 53 samples has the correlation of 0.9614 and the root mean square error of cross-validation (RMSECV) of 0.1387.The predictions for the 25 samples have the correlation of 0.9146 and the RMSECV of 0.2122.The experimental result shows that the PLS method can achieve good classification on features of healthy people and diabetic patients.

A hybrid least squares support vector machines and GMDH approach for river flow forecasting

NASA Astrophysics Data System (ADS)

Samsudin, R.; Saad, P.; Shabri, A.

2010-06-01

This paper proposes a novel hybrid forecasting model, which combines the group method of data handling (GMDH) and the least squares support vector machine (LSSVM), known as GLSSVM. The GMDH is used to determine the useful input variables for LSSVM model and the LSSVM model which works as time series forecasting. In this study the application of GLSSVM for monthly river flow forecasting of Selangor and Bernam River are investigated. The results of the proposed GLSSVM approach are compared with the conventional artificial neural network (ANN) models, Autoregressive Integrated Moving Average (ARIMA) model, GMDH and LSSVM models using the long term observations of monthly river flow discharge. The standard statistical, the root mean square error (RMSE) and coefficient of correlation (R) are employed to evaluate the performance of various models developed. Experiment result indicates that the hybrid model was powerful tools to model discharge time series and can be applied successfully in complex hydrological modeling.

Recursive least squares estimation and its application to shallow trench isolation

NASA Astrophysics Data System (ADS)

Wang, Jin; Qin, S. Joe; Bode, Christopher A.; Purdy, Matthew A.

2003-06-01

In recent years, run-to-run (R2R) control technology has received tremendous interest in semiconductor manufacturing. One class of widely used run-to-run controllers is based on the exponentially weighted moving average (EWMA) statistics to estimate process deviations. Using an EWMA filter to smooth the control action on a linear process has been shown to provide good results in a number of applications. However, for a process with severe drifts, the EWMA controller is insufficient even when large weights are used. This problem becomes more severe when there is measurement delay, which is almost inevitable in semiconductor industry. In order to control drifting processes, a predictor-corrector controller (PCC) and a double EWMA controller have been developed. Chen and Guo (2001) show that both PCC and double-EWMA controller are in effect Integral-double-Integral (I-II) controllers, which are able to control drifting processes. However, since offset is often within the noise of the process, the second integrator can actually cause jittering. Besides, tuning the second filter is not as intuitive as a single EWMA filter. In this work, we look at an alternative way Recursive Least Squares (RLS), to estimate and control the drifting process. EWMA and double-EWMA are shown to be the least squares estimate for locally constant mean model and locally constant linear trend model. Then the recursive least squares with exponential factor is applied to shallow trench isolation etch process to predict the future etch rate. The etch process, which is a critical process in the flash memory manufacturing, is known to suffer from significant etch rate drift due to chamber seasoning. In order to handle the metrology delay, we propose a new time update scheme. RLS with the new time update method gives very good result. The estimate error variance is smaller than that from EWMA, and mean square error decrease more than 10% compared to that from EWMA.

Computed tomography assessment of the efficiency of different techniques for removal of root canal filling material.

PubMed

Dall'Agnol, Cristina; Hartmann, Mateus Silveira Martins; Barletta, Fernando Branco

2008-01-01

This study evaluated the efficiency of different techniques for removal of filling material from root canals, using computed tomography (CT). Sixty mesial roots from extracted human mandibular molars were used. Root canals were filled and, after 6 months, the teeth were randomly assigned to 3 groups, according to the root-filling removal technique: Group A - hand instrumentation with K-type files; Group B - reciprocating instrumentation with engine-driven K-type files; and Group C rotary instrumentation with engine-driven ProTaper system. CT scans were used to assess the volume of filling material inside the root canals before and after the removal procedure. In both moments, the area of filling material was outlined by an experienced radiologist and the volume of filling material was automatically calculated by the CT software program. Based on the volume of initial and residual filling material of each specimen, the percentage of filling material removed from the root canals by the different techniques was calculated. Data were analyzed statistically by ANOVA and chi-square test for linear trend (?=0.05). No statistically significant difference (p=0.36) was found among the groups regarding the percent means of removed filling material. The analysis of the association between the percentage of filling material removal (high or low) and the proposed techniques by chi-square test showed statistically significant difference (p=0.015), as most cases in group B (reciprocating technique) presented less than 50% of filling material removed (low percent removal). In conclusion, none of the techniques evaluated in this study was effective in providing complete removal of filling material from the root canals.

Uganda's National Transmission Backbone Infrastructure Project: Technical Challenges and the Way Forward

NASA Astrophysics Data System (ADS)

Bulega, T.; Kyeyune, A.; Onek, P.; Sseguya, R.; Mbabazi, D.; Katwiremu, E.

2011-10-01

Several publications have identified technical challenges facing Uganda's National Transmission Backbone Infrastructure project. This research addresses the technical limitations of the National Transmission Backbone Infrastructure project, evaluates the goals of the project, and compares the results against the technical capability of the backbone. The findings of the study indicate a bandwidth deficit, which will be addressed by using dense wave division multiplexing repeaters, leasing bandwidth from private companies. Microwave links for redundancy, a Network Operation Center for operation and maintenance, and deployment of wireless interoperability for microwave access as a last-mile solution are also suggested.

Hierarchical mean-field approach to the J1-J2 Heisenberg model on a square lattice

NASA Astrophysics Data System (ADS)

Isaev, L.; Ortiz, G.; Dukelsky, J.

2009-01-01

We study the quantum phase diagram and excitation spectrum of the frustrated J1-J2 spin-1/2 Heisenberg Hamiltonian. A hierarchical mean-field approach, at the heart of which lies the idea of identifying relevant degrees of freedom, is developed. Thus, by performing educated, manifestly symmetry-preserving mean-field approximations, we unveil fundamental properties of the system. We then compare various coverings of the square lattice with plaquettes, dimers, and other degrees of freedom, and show that only the symmetric plaquette covering, which reproduces the original Bravais lattice, leads to the known phase diagram. The intermediate quantum paramagnetic phase is shown to be a (singlet) plaquette crystal, connected with the neighboring Néel phase by a continuous phase transition. We also introduce fluctuations around the hierarchical mean-field solutions, and demonstrate that in the paramagnetic phase the ground and first excited states are separated by a finite gap, which closes in the Néel and columnar phases. Our results suggest that the quantum phase transition between Néel and paramagnetic phases can be properly described within the Ginzburg-Landau-Wilson paradigm.

Hierarchical mean-field approach to the J1-J2 Heisenberg model on a square lattice

NASA Astrophysics Data System (ADS)

Isaev, Leonid; Ortiz, Gerardo; Dukelsky, Jorge

2009-03-01

We study the quantum phase diagram and excitation spectrum of the frustrated J1-J2 spin-1/2 Heisenberg Hamiltonian. A hierarchical mean-field approach, at the heart of which lies the idea of identifying relevant degrees of freedom, is developed. Thus, by performing educated, manifestly symmetry preserving mean-field approximations, we unveil fundamental properties of the system. We then compare various coverings of the square lattice with plaquettes, dimers and other degrees of freedom, and show that only the symmetric plaquette covering, which reproduces the original Bravais lattice, leads to the known phase diagram. The intermediate quantum paramagnetic phase is shown to be a (singlet) plaquette crystal, connected with the neighbouring N'eel phase by a continuous phase transition. We also introduce fluctuations around the hierarchical mean-field solutions, and demonstrate that in the paramagnetic phase the ground and first excited states are separated by a finite gap, which closes in the N'eel and columnar phases. Our results suggest that the quantum phase transition between N'eel and paramagnetic phases can be properly described within the Ginzburg-Landau-Wilson paradigm.

Severe root resorption resulting from orthodontic treatment: prevalence and risk factors.

PubMed

Maués, Caroline Pelagio Raick; do Nascimento, Rizomar Ramos; Vilella, Oswaldo de Vasconcellos

2015-01-01

To assess the prevalence of severe external root resorption and its potential risk factors resulting from orthodontic treatment. A randomly selected sample was used. It comprised conventional periapical radiographs taken in the same radiology center for maxillary and mandibular incisors before and after active orthodontic treatment of 129 patients, males and females, treated by means of the Standard Edgewise technique. Two examiners measured and defined root resorption according to the index proposed by Levander et al. The degree of external apical root resorption was registered defining resorption in four degrees of severity. To assess intra and inter-rater reproducibility, kappa coefficient was used. Chi-square test was used to assess the relationship between the amount of root resorption and patient's sex, dental arch (maxillary or mandibular), treatment with or without extractions, treatment duration, root apex stage (open or closed), root shape, as well as overjet and overbite at treatment onset. Maxillary central incisors had the highest percentage of severe root resorption, followed by maxillary lateral incisors and mandibular lateral incisors. Out of 959 teeth, 28 (2.9%) presented severe root resorption. The following risk factors were observed: anterior maxillary teeth, overjet greater than or equal to 5 mm at treatment onset, treatment with extractions, prolonged therapy, and degree of apex formation at treatment onset. This study showed that care must be taken in orthodontic treatment involving extractions, great retraction of maxillary incisors, prolonged therapy, and/or completely formed apex at orthodontic treatment onset.

Barley root hair growth and morphology in soil, sand, and water solution media and relationship with nickel toxicity.

PubMed

Lin, Yanqing; Allen, Herbert E; Di Toro, Dominic M

2016-08-01

Barley, Hordeum vulgare (Doyce), was grown in the 3 media of soil, hydroponic sand solution (sand), and hydroponic water solution (water) culture at the same environmental conditions for 4 d. Barley roots were scanned, and root morphology was analyzed. Plants grown in the 3 media had different root morphology and nickel (Ni) toxicity response. Root elongations and total root lengths followed the sequence soil > sand > water. Plants grown in water culture were more sensitive to Ni toxicity and had greater root hair length than those from soil and sand cultures, which increased root surface area. The unit root surface area as root surface area per centimeter of length of root followed the sequence water > sand > soil and was found to be related with root elongation. Including the unit root surface area, the difference in root elongation and 50% effective concentration were diminished, and percentage of root elongations can be improved with a root mean square error approximately 10% for plants grown in different media. Because the unit root surface area of plants in sand culture is closer to that in soil culture, the sand culture method, not water culture, is recommended for toxicity parameter estimation. Environ Toxicol Chem 2016;35:2125-2133. © 2016 SETAC. © 2016 SETAC.

Modeling {sup 15}N NMR chemical shift changes in protein backbone with pressure

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

La Penna, Giovanni, E-mail: glapenna@iccom.cnr.it; Mori, Yoshiharu, E-mail: ymori@ims.ac.jp; Kitahara, Ryo, E-mail: ryo@ph.ritsumei.ac.jp

2016-08-28

Nitrogen chemical shift is a useful parameter for determining the backbone three-dimensional structure of proteins. Empirical models for fast calculation of N chemical shift are improving their reliability, but there are subtle effects that cannot be easily interpreted. Among these, the effects of slight changes in hydrogen bonds, both intramolecular and with water molecules in the solvent, are particularly difficult to predict. On the other hand, these hydrogen bonds are sensitive to changes in protein environment. In this work, the change of N chemical shift with pressure for backbone segments in the protein ubiquitin is correlated with the change inmore » the population of hydrogen bonds involving the backbone amide group. The different extent of interaction of protein backbone with the water molecules in the solvent is put in evidence.« less

Comparing biomarker measurements to a normal range: when to use standard error of the mean (SEM) or standard deviation (SD) confidence intervals tests.

PubMed

Pleil, Joachim D

2016-01-01

This commentary is the second of a series outlining one specific concept in interpreting biomarkers data. In the first, an observational method was presented for assessing the distribution of measurements before making parametric calculations. Here, the discussion revolves around the next step, the choice of using standard error of the mean or the calculated standard deviation to compare or predict measurement results.

Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility.

PubMed

Schueler-Furman, Ora; Wang, Chu; Baker, David

2005-08-01

RosettaDock uses real-space Monte Carlo minimization (MCM) on both rigid-body and side-chain degrees of freedom to identify the lowest free energy docked arrangement of 2 protein structures. An improved version of the method that uses gradient-based minimization for off-rotamer side-chain optimization and includes information from unbound structures was used to create predictions for Rounds 4 and 5 of CAPRI. First, large numbers of independent MCM trajectories were carried out and the lowest free energy docked configurations identified. Second, new trajectories were started from these lowest energy structures to thoroughly sample the surrounding conformation space, and the lowest energy configurations were submitted as predictions. For all cases in which there were no significant backbone conformational changes, a small number of very low-energy configurations were identified in the first, global search and subsequently found to be close to the center of the basin of attraction in the free energy landscape in the second, local search. Following the release of the experimental coordinates, it was found that the centers of these free energy minima were remarkably close to the native structures in not only the rigid-body orientation but also the detailed conformations of the side-chains. Out of 8 targets, the lowest energy models had interface root-mean-square deviations (RMSDs) less than 1.1 A from the correct structures for 6 targets, and interface RMSDs less than 0.4 A for 3 targets. The predictions were top submissions to CAPRI for Targets 11, 12, 14, 15, and 19. The close correspondence of the lowest free energy structures found in our searches to the experimental structures suggests that our free energy function is a reasonable representation of the physical chemistry, and that the real space search with full side-chain flexibility to some extent solves the protein-protein docking problem in the absence of significant backbone conformational changes. On the

Real-time estimation of BDS/GPS high-rate satellite clock offsets using sequential least squares

NASA Astrophysics Data System (ADS)

Fu, Wenju; Yang, Yuanxi; Zhang, Qin; Huang, Guanwen

2018-07-01

The real-time precise satellite clock product is one of key prerequisites for real-time Precise Point Positioning (PPP). The accuracy of the 24-hour predicted satellite clock product with 15 min sampling interval and an update of 6 h provided by the International GNSS Service (IGS) is only 3 ns, which could not meet the needs of all real-time PPP applications. The real-time estimation of high-rate satellite clock offsets is an efficient method for improving the accuracy. In this paper, the sequential least squares method to estimate real-time satellite clock offsets with high sample rate is proposed to improve the computational speed by applying an optimized sparse matrix operation to compute the normal equation and using special measures to take full advantage of modern computer power. The method is first applied to BeiDou Navigation Satellite System (BDS) and provides real-time estimation with a 1 s sample rate. The results show that the amount of time taken to process a single epoch is about 0.12 s using 28 stations. The Standard Deviation (STD) and Root Mean Square (RMS) of the real-time estimated BDS satellite clock offsets are 0.17 ns and 0.44 ns respectively when compared to German Research Center for Geosciences (GFZ) final clock products. The positioning performance of the real-time estimated satellite clock offsets is evaluated. The RMSs of the real-time BDS kinematic PPP in east, north, and vertical components are 7.6 cm, 6.4 cm and 19.6 cm respectively. The method is also applied to Global Positioning System (GPS) with a 10 s sample rate and the computational time of most epochs is less than 1.5 s with 75 stations. The STD and RMS of the real-time estimated GPS satellite clocks are 0.11 ns and 0.27 ns, respectively. The accuracies of 5.6 cm, 2.6 cm and 7.9 cm in east, north, and vertical components are achieved for the real-time GPS kinematic PPP.

Light-Regulated Gravitropism in Seedling Roots of Maize 1

PubMed Central

Feldman, Lewis J.; Briggs, Winslow R.

1987-01-01

Red light-induced changes in the gravitropism of roots of Zea mays variety Merit is a very low fluence response with a threshold of 10−9 moles per square meter and is not reversible by far red light. Blue light also affects root gravitropism but the sensitivity of roots to blue is 50 to 100 times less than to an equal fluence of red. In Z. mays Merit we conclude that phytochrome is the sole pigment associated with light-induced changes in root gravitropism. PMID:11539030

An exhaustive survey of regular peptide conformations using a new metric for backbone handedness (h)

PubMed Central

2017-01-01

The Ramachandran plot is important to structural biology as it describes a peptide backbone in the context of its dominant degrees of freedom—the backbone dihedral angles φ and ψ (Ramachandran, Ramakrishnan & Sasisekharan, 1963). Since its introduction, the Ramachandran plot has been a crucial tool to characterize protein backbone features. However, the conformation or twist of a backbone as a function of φ and ψ has not been completely described for both cis and trans backbones. Additionally, little intuitive understanding is available about a peptide’s conformation simply from knowing the φ and ψ values of a peptide (e.g., is the regular peptide defined by φ = ψ =  − 100°  left-handed or right-handed?). This report provides a new metric for backbone handedness (h) based on interpreting a peptide backbone as a helix with axial displacement d and angular displacement θ, both of which are derived from a peptide backbone’s internal coordinates, especially dihedral angles φ, ψ and ω. In particular, h equals sin(θ)d∕|d|, with range [−1, 1] and negative (or positive) values indicating left(or right)-handedness. The metric h is used to characterize the handedness of every region of the Ramachandran plot for both cis (ω = 0°) and trans (ω = 180°) backbones, which provides the first exhaustive survey of twist handedness in Ramachandran (φ, ψ) space. These maps fill in the ‘dead space’ within the Ramachandran plot, which are regions that are not commonly accessed by structured proteins, but which may be accessible to intrinsically disordered proteins, short peptide fragments, and protein mimics such as peptoids. Finally, building on the work of (Zacharias & Knapp, 2013), this report presents a new plot based on d and θ that serves as a universal and intuitive alternative to the Ramachandran plot. The universality arises from the fact that the co-inhabitants of such a plot include every possible peptide backbone including cis

Does standard deviation matter? Using "standard deviation" to quantify security of multistage testing.

PubMed

Wang, Chun; Zheng, Yi; Chang, Hua-Hua

2014-01-01

With the advent of web-based technology, online testing is becoming a mainstream mode in large-scale educational assessments. Most online tests are administered continuously in a testing window, which may post test security problems because examinees who take the test earlier may share information with those who take the test later. Researchers have proposed various statistical indices to assess the test security, and one most often used index is the average test-overlap rate, which was further generalized to the item pooling index (Chang & Zhang, 2002, 2003). These indices, however, are all defined as the means (that is, the expected proportion of common items among examinees) and they were originally proposed for computerized adaptive testing (CAT). Recently, multistage testing (MST) has become a popular alternative to CAT. The unique features of MST make it important to report not only the mean, but also the standard deviation (SD) of test overlap rate, as we advocate in this paper. The standard deviation of test overlap rate adds important information to the test security profile, because for the same mean, a large SD reflects that certain groups of examinees share more common items than other groups. In this study, we analytically derived the lower bounds of the SD under MST, with the results under CAT as a benchmark. It is shown that when the mean overlap rate is the same between MST and CAT, the SD of test overlap tends to be larger in MST. A simulation study was conducted to provide empirical evidence. We also compared the security of MST under the single-pool versus the multiple-pool designs; both analytical and simulation studies show that the non-overlapping multiple-pool design will slightly increase the security risk.

Analysis of uncertainties and convergence of the statistical quantities in turbulent wall-bounded flows by means of a physically based criterion

NASA Astrophysics Data System (ADS)

Andrade, João Rodrigo; Martins, Ramon Silva; Thompson, Roney Leon; Mompean, Gilmar; da Silveira Neto, Aristeu

2018-04-01

The present paper provides an analysis of the statistical uncertainties associated with direct numerical simulation (DNS) results and experimental data for turbulent channel and pipe flows, showing a new physically based quantification of these errors, to improve the determination of the statistical deviations between DNSs and experiments. The analysis is carried out using a recently proposed criterion by Thompson et al. ["A methodology to evaluate statistical errors in DNS data of plane channel flows," Comput. Fluids 130, 1-7 (2016)] for fully turbulent plane channel flows, where the mean velocity error is estimated by considering the Reynolds stress tensor, and using the balance of the mean force equation. It also presents how the residual error evolves in time for a DNS of a plane channel flow, and the influence of the Reynolds number on its convergence rate. The root mean square of the residual error is shown in order to capture a single quantitative value of the error associated with the dimensionless averaging time. The evolution in time of the error norm is compared with the final error provided by DNS data of similar Reynolds numbers available in the literature. A direct consequence of this approach is that it was possible to compare different numerical results and experimental data, providing an improved understanding of the convergence of the statistical quantities in turbulent wall-bounded flows.

Computation-Guided Backbone Grafting of a Discontinuous Motif onto a Protein Scaffold

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

Azoitei, Mihai L.; Correia, Bruno E.; Ban, Yih-En Andrew

2012-02-07

The manipulation of protein backbone structure to control interaction and function is a challenge for protein engineering. We integrated computational design with experimental selection for grafting the backbone and side chains of a two-segment HIV gp120 epitope, targeted by the cross-neutralizing antibody b12, onto an unrelated scaffold protein. The final scaffolds bound b12 with high specificity and with affinity similar to that of gp120, and crystallographic analysis of a scaffold bound to b12 revealed high structural mimicry of the gp120-b12 complex structure. The method can be generalized to design other functional proteins through backbone grafting.

Solvation thermodynamics of amino acid side chains on a short peptide backbone

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

Hajari, Timir; Vegt, Nico F. A. van der, E-mail: vandervegt@csi.tu-darmstadt.de

The hydration process of side chain analogue molecules differs from that of the actual amino acid side chains in peptides and proteins owing to the effects of the peptide backbone on the aqueous solvent environment. A recent molecular simulation study has provided evidence that all nonpolar side chains, attached to a short peptide backbone, are considerably less hydrophobic than the free side chain analogue molecules. In contrast to this, the hydrophilicity of the polar side chains is hardly affected by the backbone. To analyze the origin of these observations, we here present a molecular simulation study on temperature dependent solvationmore » free energies of nonpolar and polar side chains attached to a short peptide backbone. The estimated solvation entropies and enthalpies of the various amino acid side chains are compared with existing side chain analogue data. The solvation entropies and enthalpies of the polar side chains are negative, but in absolute magnitude smaller compared with the corresponding analogue data. The observed differences are large; however, owing to a nearly perfect enthalpy-entropy compensation, the solvation free energies of polar side chains remain largely unaffected by the peptide backbone. We find that a similar compensation does not apply to the nonpolar side chains; while the backbone greatly reduces the unfavorable solvation entropies, the solvation enthalpies are either more favorable or only marginally affected. This results in a very small unfavorable free energy cost, or even free energy gain, of solvating the nonpolar side chains in strong contrast to solvation of small hydrophobic or nonpolar molecules in bulk water. The solvation free energies of nonpolar side chains have been furthermore decomposed into a repulsive cavity formation contribution and an attractive dispersion free energy contribution. We find that cavity formation next to the peptide backbone is entropically favored over formation of similar sized nonpolar

Solvation thermodynamics of amino acid side chains on a short peptide backbone

NASA Astrophysics Data System (ADS)

Hajari, Timir; van der Vegt, Nico F. A.

2015-04-01

The hydration process of side chain analogue molecules differs from that of the actual amino acid side chains in peptides and proteins owing to the effects of the peptide backbone on the aqueous solvent environment. A recent molecular simulation study has provided evidence that all nonpolar side chains, attached to a short peptide backbone, are considerably less hydrophobic than the free side chain analogue molecules. In contrast to this, the hydrophilicity of the polar side chains is hardly affected by the backbone. To analyze the origin of these observations, we here present a molecular simulation study on temperature dependent solvation free energies of nonpolar and polar side chains attached to a short peptide backbone. The estimated solvation entropies and enthalpies of the various amino acid side chains are compared with existing side chain analogue data. The solvation entropies and enthalpies of the polar side chains are negative, but in absolute magnitude smaller compared with the corresponding analogue data. The observed differences are large; however, owing to a nearly perfect enthalpy-entropy compensation, the solvation free energies of polar side chains remain largely unaffected by the peptide backbone. We find that a similar compensation does not apply to the nonpolar side chains; while the backbone greatly reduces the unfavorable solvation entropies, the solvation enthalpies are either more favorable or only marginally affected. This results in a very small unfavorable free energy cost, or even free energy gain, of solvating the nonpolar side chains in strong contrast to solvation of small hydrophobic or nonpolar molecules in bulk water. The solvation free energies of nonpolar side chains have been furthermore decomposed into a repulsive cavity formation contribution and an attractive dispersion free energy contribution. We find that cavity formation next to the peptide backbone is entropically favored over formation of similar sized nonpolar side

Statistical analysis of solid waste composition data: Arithmetic mean, standard deviation and correlation coefficients.

PubMed

Edjabou, Maklawe Essonanawe; Martín-Fernández, Josep Antoni; Scheutz, Charlotte; Astrup, Thomas Fruergaard

2017-11-01

Data for fractional solid waste composition provide relative magnitudes of individual waste fractions, the percentages of which always sum to 100, thereby connecting them intrinsically. Due to this sum constraint, waste composition data represent closed data, and their interpretation and analysis require statistical methods, other than classical statistics that are suitable only for non-constrained data such as absolute values. However, the closed characteristics of waste composition data are often ignored when analysed. The results of this study showed, for example, that unavoidable animal-derived food waste amounted to 2.21±3.12% with a confidence interval of (-4.03; 8.45), which highlights the problem of the biased negative proportions. A Pearson's correlation test, applied to waste fraction generation (kg mass), indicated a positive correlation between avoidable vegetable food waste and plastic packaging. However, correlation tests applied to waste fraction compositions (percentage values) showed a negative association in this regard, thus demonstrating that statistical analyses applied to compositional waste fraction data, without addressing the closed characteristics of these data, have the potential to generate spurious or misleading results. Therefore, ¨compositional data should be transformed adequately prior to any statistical analysis, such as computing mean, standard deviation and correlation coefficients. Copyright © 2017 Elsevier Ltd. All rights reserved.

Search for new physics in high-mass electron-positron events in pp[over] collisions at square root s = 1.96 TeV.

PubMed

Aaltonen, T; Abulencia, A; Adelman, J; Affolder, T; Akimoto, T; Albrow, M G; Amerio, S; Amidei, D; Anastassov, A; Anikeev, K; Annovi, A; Antos, J; Aoki, M; Apollinari, G; Arisawa, T; Artikov, A; Ashmanskas, W; Attal, A; Aurisano, A; Azfar, F; Azzi-Bacchetta, P; Azzurri, P; Bacchetta, N; Badgett, W; Barbaro-Galtieri, A; Barnes, V E; Barnett, B A; Baroiant, S; Bartsch, V; Bauer, G; Beauchemin, P-H; Bedeschi, F; Behari, S; Bellettini, G; Bellinger, J; Belloni, A; Benjamin, D; Beretvas, A; Beringer, J; Berry, T; Bhatti, A; Binkley, M; Bisello, D; Bizjak, I; Blair, R E; Blocker, C; Blumenfeld, B; Bocci, A; Bodek, A; Boisvert, V; Bolla, G; Bolshov, A; Bortoletto, D; Boudreau, J; Boveia, A; Brau, B; Brigliadori, L; Bromberg, C; Brubaker, E; Budagov, J; Budd, H S; Budd, S; Burkett, K; Busetto, G; Bussey, P; Buzatu, A; Byrum, K L; Cabrera, S; Campanelli, M; Campbell, M; Canelli, F; Canepa, A; Carrillo, S; Carlsmith, D; Carosi, R; Carron, S; Casal, B; Casarsa, M; Castro, A; Catastini, P; Cauz, D; Cavalli-Sforza, M; Cerri, A; Cerrito, L; Chang, S H; Chen, Y C; Chertok, M; Chiarelli, G; Chlachidze, G; Chlebana, F; Cho, I; Cho, K; Chokheli, D; Chou, J P; Choudalakis, G; Chuang, S H; Chung, K; Chung, W H; Chung, Y S; Cilijak, M; Ciobanu, C I; Ciocci, M A; Clark, A; Clark, D; Coca, M; Compostella, G; Convery, M E; Conway, J; Cooper, B; Copic, K; Cordelli, M; Cortiana, G; Crescioli, F; Cuenca Almenar, C; Cuevas, J; Culbertson, R; Cully, J C; DaRonco, S; Datta, M; D'Auria, S; Davies, T; Dagenhart, D; de Barbaro, P; De Cecco, S; Deisher, A; De Lentdecker, G; De Lorenzo, G; Dell'Orso, M; Delli Paoli, F; Demortier, L; Deng, J; Deninno, M; De Pedis, D; Derwent, P F; Di Giovanni, G P; Dionisi, C; Di Ruzza, B; Dittmann, J R; D'Onofrio, M; Dörr, C; Donati, S; Dong, P; Donini, J; Dorigo, T; Dube, S; Efron, J; Erbacher, R; Errede, D; Errede, S; Eusebi, R; Fang, H C; Farrington, S; Fedorko, I; Fedorko, W T; Feild, R G; Feindt, M; Fernandez, J P; Field, R; Flanagan, G; Forrest, R; Forrester, S; Franklin, M; Freeman, J C; Furic, I; Gallinaro, M; Galyardt, J; Garcia, J E; Garberson, F; Garfinkel, A F; Gay, C; Gerberich, H; Gerdes, D; Giagu, S; Giannetti, P; Gibson, K; Gimmell, J L; Ginsburg, C; Giokaris, N; Giordani, M; Giromini, P; Giunta, M; Giurgiu, G; Glagolev, V; Glenzinski, D; Gold, M; Goldschmidt, N; Goldstein, J; Golossanov, A; Gomez, G; Gomez-Ceballos, G; Goncharov, M; González, O; Gorelov, I; Goshaw, A T; Goulianos, K; Gresele, A; Grinstein, S; Grosso-Pilcher, C; Grundler, U; Guimaraes da Costa, J; Gunay-Unalan, Z; Haber, C; Hahn, K; Hahn, S R; Halkiadakis, E; Hamilton, A; Han, B-Y; Han, J Y; Handler, R; Happacher, F; Hara, K; Hare, D; Hare, M; Harper, S; Harr, R F; Harris, R M; Hartz, M; Hatakeyama, K; Hauser, J; Hays, C; Heck, M; Heijboer, A; Heinemann, B; Heinrich, J; Henderson, C; Herndon, M; Heuser, J; Hidas, D; Hill, C S; Hirschbuehl, D; Hocker, A; Holloway, A; Hou, S; Houlden, M; Hsu, S-C; Huffman, B T; Hughes, R E; Husemann, U; Huston, J; Incandela, J; Introzzi, G; Iori, M; Ivanov, A; Iyutin, B; James, E; Jang, D; Jayatilaka, B; Jeans, D; Jeon, E J; Jindariani, S; Johnson, W; Jones, M; Joo, K K; Jun, S Y; Jung, J E; Junk, T R; Kamon, T; Karchin, P E; Kato, Y; Kemp, Y; Kephart, R; Kerzel, U; Khotilovich, V; Kilminster, B; Kim, D H; Kim, H S; Kim, J E; Kim, M J; Kim, S B; Kim, S H; Kim, Y K; Kimura, N; Kirsch, L; Klimenko, S; Klute, M; Knuteson, B; Ko, B R; Kondo, K; Kong, D J; Konigsberg, J; Korytov, A; Kotwal, A V; Kraan, A C; Kraus, J; Kreps, M; Kroll, J; Krumnack, N; Kruse, M; Krutelyov, V; Kubo, T; Kuhlmann, S E; Kuhr, T; Kulkarni, N P; Kusakabe, Y; Kwang, S; Laasanen, A T; Lai, S; Lami, S; Lammel, S; Lancaster, M; Lander, R L; Lannon, K; Lath, A; Latino, G; Lazzizzera, I; Lecompte, T; Lee, J; Lee, J; Lee, Y J; Lee, S W; Lefèvre, R; Leonardo, N; Leone, S; Levy, S; Lewis, J D; Lin, C; Lin, C S; Lindgren, M; Lipeles, E; Lister, A; Litvintsev, D O; Liu, T; Lockyer, N S; Loginov, A; Loreti, M; Lu, R-S; Lucchesi, D; Lujan, P; Lukens, P; Lungu, G; Lyons, L; Lys, J; Lysak, R; Lytken, E; Mack, P; Macqueen, D; Madrak, R; Maeshima, K; Makhoul, K; Maki, T; Maksimovic, P; Malde, S; Malik, S; Manca, G; Manousakis, A; Margaroli, F; Marginean, R; Marino, C; Marino, C P; Martin, A; Martin, M; Martin, V; Martínez, M; Martínez-Ballarín, R; Maruyama, T; Mastrandrea, P; Masubuchi, T; Matsunaga, H; Mattson, M E; Mazini, R; Mazzanti, P; McFarland, K S; McIntyre, P; McNulty, R; Mehta, A; Mehtala, P; Menzemer, S; Menzione, A; Merkel, P; Mesropian, C; Messina, A; Miao, T; Miladinovic, N; Miles, J; Miller, R; Mills, C; Milnik, M; Mitra, A; Mitselmakher, G; Miyamoto, A; Moed, S; Moggi, N; Mohr, B; Moon, C S; Moore, R; Morello, M; Fernandez, P Movilla; Mülmenstädt, J; Mukherjee, A; Muller, Th; Mumford, R; Murat, P; Mussini, M; Nachtman, J; Nagano, A; Naganoma, J; Nakamura, K; Nakano, I; Napier, A; Necula, V; Neu, C; Neubauer, M S; Nielsen, J; Nodulman, L; Norniella, O; Nurse, E; Oh, S H; Oh, Y D; Oksuzian, I; Okusawa, T; Oldeman, R; Orava, R; Osterberg, K; Pagliarone, C; Palencia, E; Papadimitriou, V; Papaikonomou, A; Paramonov, A A; Parks, B; Pashapour, S; Patrick, J; Pauletta, G; Paulini, M; Paus, C; Pellett, D E; Penzo, A; Phillips, T J; Piacentino, G; Piedra, J; Pinera, L; Pitts, K; Plager, C; Pondrom, L; Portell, X; Poukhov, O; Pounder, N; Prakoshyn, F; Pronko, A; Proudfoot, J; Ptohos, F; Punzi, G; Pursley, J; Rademacker, J; Rahaman, A; Ramakrishnan, V; Ranjan, N; Redondo, I; Reisert, B; Rekovic, V; Renton, P; Rescigno, M; Richter, S; Rimondi, F; Ristori, L; Robson, A; Rodrigo, T; Rogers, E; Rolli, S; Roser, R; Rossi, M; Rossin, R; Roy, P; Ruiz, A; Russ, J; Rusu, V; Saarikko, H; Safonov, A; Sakumoto, W K; Salamanna, G; Saltó, O; Santi, L; Sarkar, S; Sartori, L; Sato, K; Savard, P; Savoy-Navarro, A; Scheidle, T; Schlabach, P; Schmidt, E E; Schmidt, M P; Schmitt, M; Schwarz, T; Scodellaro, L; Scott, A L; Scribano, A; Scuri, F; Sedov, A; Seidel, S; Seiya, Y; Semenov, A; Sexton-Kennedy, L; Sfyrla, A; Shalhout, S Z; Shapiro, M D; Shears, T; Shepard, P F; Sherman, D; Shimojima, M; Shochet, M; Shon, Y; Shreyber, I; Sidoti, A; Sinervo, P; Sisakyan, A; Slaughter, A J; Slaunwhite, J; Sliwa, K; Smith, J R; Snider, F D; Snihur, R; Soderberg, M; Soha, A; Somalwar, S; Sorin, V; Spalding, J; Spinella, F; Spreitzer, T; Squillacioti, P; Stanitzki, M; Staveris-Polykalas, A; St Denis, R; Stelzer, B; Stelzer-Chilton, O; Stentz, D; Strologas, J; Stuart, D; Suh, J S; Sukhanov, A; Sun, H; Suslov, I; Suzuki, T; Taffard, A; Takashima, R; Takeuchi, Y; Tanaka, R; Tecchio, M; Teng, P K; Terashi, K; Thom, J; Thompson, A S; Thomson, E; Tipton, P; Tiwari, V; Tkaczyk, S; Toback, D; Tokar, S; Tollefson, K; Tomura, T; Tonelli, D; Torre, S; Torretta, D; Tourneur, S; Trischuk, W; Tsuno, S; Tu, Y; Turini, N; Ukegawa, F; Uozumi, S; Vallecorsa, S; van Remortel, N; Varganov, A; Vataga, E; Vazquez, F; Velev, G; Vellidis, C; Veramendi, G; Veszpremi, V; Vidal, M; Vidal, R; Vila, I; Vilar, R; Vine, T; Vogel, M; Vollrath, I; Volobouev, I; Volpi, G; Würthwein, F; Wagner, P; Wagner, R G; Wagner, R L; Wagner, J; Wagner, W; Wallny, R; Wang, S M; Warburton, A; Waters, D; Weinberger, M; Wester, W C; Whitehouse, B; Whiteson, D; Wicklund, A B; Wicklund, E; Williams, G; Williams, H H; Wilson, P; Winer, B L; Wittich, P; Wolbers, S; Wolfe, C; Wright, T; Wu, X; Wynne, S M; Yagil, A; Yamamoto, K; Yamaoka, J; Yamashita, T; Yang, C; Yang, U K; Yang, Y C; Yao, W M; Yeh, G P; Yoh, J; Yorita, K; Yoshida, T; Yu, G B; Yu, I; Yu, S S; Yun, J C; Zanello, L; Zanetti, A; Zaw, I; Zhang, X; Zhou, J; Zucchelli, S

2007-10-26

We report the results of a search for a narrow resonance in electron-positron events in the invariant mass range of 150-950 GeV/c(2) using 1.3 fb(-1) of pp[over] collision data at square root s = 1.96 TeV collected by the CDF II detector at Fermilab. No significant evidence of such a resonance is observed and we interpret the results to exclude the standard-model-like Z' with a mass below 923 GeV/c(2) and the Randall-Sundrum graviton with a mass below 807 GeV/c(2) for k/M[over](pl) = 0.1, both at the 95% confidence level. Combining with diphoton data excludes the Randall-Sundrum graviton for masses below 889 GeV/c(2) for k/M[over](pl) = 0.1.

Simultaneous estimation of cross-validation errors in least squares collocation applied for statistical testing and evaluation of the noise variance components

NASA Astrophysics Data System (ADS)

Behnabian, Behzad; Mashhadi Hossainali, Masoud; Malekzadeh, Ahad

2018-02-01

The cross-validation technique is a popular method to assess and improve the quality of prediction by least squares collocation (LSC). We present a formula for direct estimation of the vector of cross-validation errors (CVEs) in LSC which is much faster than element-wise CVE computation. We show that a quadratic form of CVEs follows Chi-squared distribution. Furthermore, a posteriori noise variance factor is derived by the quadratic form of CVEs. In order to detect blunders in the observations, estimated standardized CVE is proposed as the test statistic which can be applied when noise variances are known or unknown. We use LSC together with the methods proposed in this research for interpolation of crustal subsidence in the northern coast of the Gulf of Mexico. The results show that after detection and removing outliers, the root mean square (RMS) of CVEs and estimated noise standard deviation are reduced about 51 and 59%, respectively. In addition, RMS of LSC prediction error at data points and RMS of estimated noise of observations are decreased by 39 and 67%, respectively. However, RMS of LSC prediction error on a regular grid of interpolation points covering the area is only reduced about 4% which is a consequence of sparse distribution of data points for this case study. The influence of gross errors on LSC prediction results is also investigated by lower cutoff CVEs. It is indicated that after elimination of outliers, RMS of this type of errors is also reduced by 19.5% for a 5 km radius of vicinity. We propose a method using standardized CVEs for classification of dataset into three groups with presumed different noise variances. The noise variance components for each of the groups are estimated using restricted maximum-likelihood method via Fisher scoring technique. Finally, LSC assessment measures were computed for the estimated heterogeneous noise variance model and compared with those of the homogeneous model. The advantage of the proposed method is the

[Application of near infrared spectroscopy combined with particle swarm optimization based least square support vactor machine to rapid quantitative analysis of Corni Fructus].

PubMed

Liu, Xue-song; Sun, Fen-fang; Jin, Ye; Wu, Yong-jiang; Gu, Zhi-xin; Zhu, Li; Yan, Dong-lan

2015-12-01

A novel method was developed for the rapid determination of multi-indicators in corni fructus by means of near infrared (NIR) spectroscopy. Particle swarm optimization (PSO) based least squares support vector machine was investigated to increase the levels of quality control. The calibration models of moisture, extractum, morroniside and loganin were established using the PSO-LS-SVM algorithm. The performance of PSO-LS-SVM models was compared with partial least squares regression (PLSR) and back propagation artificial neural network (BP-ANN). The calibration and validation results of PSO-LS-SVM were superior to both PLS and BP-ANN. For PSO-LS-SVM models, the correlation coefficients (r) of calibrations were all above 0.942. The optimal prediction results were also achieved by PSO-LS-SVM models with the RMSEP (root mean square error of prediction) and RSEP (relative standard errors of prediction) less than 1.176 and 15.5% respectively. The results suggest that PSO-LS-SVM algorithm has a good model performance and high prediction accuracy. NIR has a potential value for rapid determination of multi-indicators in Corni Fructus.

On estimating gravity anomalies - A comparison of least squares collocation with conventional least squares techniques

NASA Technical Reports Server (NTRS)

Argentiero, P.; Lowrey, B.

1977-01-01

The least squares collocation algorithm for estimating gravity anomalies from geodetic data is shown to be an application of the well known regression equations which provide the mean and covariance of a random vector (gravity anomalies) given a realization of a correlated random vector (geodetic data). It is also shown that the collocation solution for gravity anomalies is equivalent to the conventional least-squares-Stokes' function solution when the conventional solution utilizes properly weighted zero a priori estimates. The mathematical and physical assumptions underlying the least squares collocation estimator are described.

Statistical properties of the anomalous scaling exponent estimator based on time-averaged mean-square displacement

NASA Astrophysics Data System (ADS)

Sikora, Grzegorz; Teuerle, Marek; Wyłomańska, Agnieszka; Grebenkov, Denis

2017-08-01

The most common way of estimating the anomalous scaling exponent from single-particle trajectories consists of a linear fit of the dependence of the time-averaged mean-square displacement on the lag time at the log-log scale. We investigate the statistical properties of this estimator in the case of fractional Brownian motion (FBM). We determine the mean value, the variance, and the distribution of the estimator. Our theoretical results are confirmed by Monte Carlo simulations. In the limit of long trajectories, the estimator is shown to be asymptotically unbiased, consistent, and with vanishing variance. These properties ensure an accurate estimation of the scaling exponent even from a single (long enough) trajectory. As a consequence, we prove that the usual way to estimate the diffusion exponent of FBM is correct from the statistical point of view. Moreover, the knowledge of the estimator distribution is the first step toward new statistical tests of FBM and toward a more reliable interpretation of the experimental histograms of scaling exponents in microbiology.

No-Enclave Percolation Corresponds to Holes in the Cluster Backbone.

PubMed

Hu, Hao; Ziff, Robert M; Deng, Youjin

2016-10-28

The no-enclave percolation (NEP) model introduced recently by Sheinman et al. can be mapped to a problem of holes within a standard percolation backbone, and numerical measurements of such holes give the same size-distribution exponent τ=1.82(1) as found for the NEP model. An argument is given that τ=1+d_{B}/2≈1.822 for backbone holes, where d_{B} is the backbone dimension. On the other hand, a model of simple holes within a percolation cluster yields τ=1+d_{f}/2=187/96≈1.948, where d_{f} is the fractal dimension of the cluster, and this value is consistent with the experimental results of gel collapse of Sheinman et al., which give τ=1.91(6). This suggests that the gel clusters are of the universality class of percolation cluster holes. Both models give a discontinuous maximum hole size at p_{c}, signifying explosive percolation behavior.

Band head spin assignment of superdeformed bands in Hg isotopes through power index formula

NASA Astrophysics Data System (ADS)

Sharma, Honey; Mittal, H. M.

2018-05-01

The power index formula has been used to obtain the band head spin (I 0) of all the superdeformed (SD) bands in Hg isotopes. A least squares fitting approach is used. The root mean square deviations between the determined and the observed transition energies are calculated by extracting the model parameters using the power index formula. Whenever definite spins are available, the determined and the observed transition energies are in accordance with each other. The computed values of dynamic moment of inertia J (2) obtained by using the power index formula and its deviation with the rotational frequency is also studied. Excellent agreement is shown between the calculated and the experimental results for J (2) versus the rotational frequency. Hence, the power index formula works very well for all the SD bands in Hg isotopes expect for 195Hg(2, 3, 4).

An augmented classical least squares method for quantitative Raman spectral analysis against component information loss.

PubMed

Zhou, Yan; Cao, Hui

2013-01-01

We propose an augmented classical least squares (ACLS) calibration method for quantitative Raman spectral analysis against component information loss. The Raman spectral signals with low analyte concentration correlations were selected and used as the substitutes for unknown quantitative component information during the CLS calibration procedure. The number of selected signals was determined by using the leave-one-out root-mean-square error of cross-validation (RMSECV) curve. An ACLS model was built based on the augmented concentration matrix and the reference spectral signal matrix. The proposed method was compared with partial least squares (PLS) and principal component regression (PCR) using one example: a data set recorded from an experiment of analyte concentration determination using Raman spectroscopy. A 2-fold cross-validation with Venetian blinds strategy was exploited to evaluate the predictive power of the proposed method. The one-way variance analysis (ANOVA) was used to access the predictive power difference between the proposed method and existing methods. Results indicated that the proposed method is effective at increasing the robust predictive power of traditional CLS model against component information loss and its predictive power is comparable to that of PLS or PCR.

Measurement of the Lambda b0 lifetime in Lambda b0-->J/psi Lambda 0 in pp collisions at square root s=1.96 TeV.

PubMed

Abulencia, A; Adelman, J; Affolder, T; Akimoto, T; Albrow, M G; Ambrose, D; Amerio, S; Amidei, D; Anastassov, A; Anikeev, K; Annovi, A; Antos, J; Aoki, M; Apollinari, G; Arguin, J-F; Arisawa, T; Artikov, A; Ashmanskas, W; Attal, A; Azfar, F; Azzi-Bacchetta, P; Azzurri, P; Bacchetta, N; Badgett, W; Barbaro-Galtieri, A; Barnes, V E; Barnett, B A; Baroiant, S; Bartsch, V; Bauer, G; Bedeschi, F; Behari, S; Belforte, S; Bellettini, G; Bellinger, J; Belloni, A; Benjamin, D; Beretvas, A; Beringer, J; Berry, T; Bhatti, A; Binkley, M; Bisello, D; Blair, R E; Blocker, C; Blumenfeld, B; Bocci, A; Bodek, A; Boisvert, V; Bolla, G; Bolshov, A; Bortoletto, D; Boudreau, J; Boveia, A; Brau, B; Brigliadori, L; Bromberg, C; Brubaker, E; Budagov, J; Budd, H S; Budd, S; Budroni, S; Burkett, K; Busetto, G; Bussey, P; Byrum, K L; Cabrera, S; Campanelli, M; Campbell, M; Canelli, F; Canepa, A; Carrillo, S; Carlsmith, D; Carosi, R; Carron, S; Casarsa, M; Castro, A; Catastini, P; Cauz, D; Cavalli-Sforza, M; Cerri, A; Cerrito, L; Chang, S H; Chen, Y C; Chertok, M; Chiarelli, G; Chlachidze, G; Chlebana, F; Cho, I; Cho, K; Chokheli, D; Chou, J P; Choudalakis, G; Chuang, S H; Chung, K; Chung, W H; Chung, Y S; Ciljak, M; Ciobanu, C I; Ciocci, M A; Clark, A; Clark, D; Coca, M; Compostella, G; Convery, M E; Conway, J; Cooper, B; Copic, K; Cordelli, M; Cortiana, G; Crescioli, F; Cuenca Almenar, C; Cuevas, J; Culbertson, R; Cully, J C; Cyr, D; DaRonco, S; D'Auria, S; Davies, T; D'Onofrio, M; Dagenhart, D; de Barbaro, P; De Cecco, S; Deisher, A; De Lentdecker, G; Dell'Orso, M; Delli Paoli, F; Demortier, L; Deng, J; Deninno, M; De Pedis, D; Derwent, P F; Di Giovanni, G P; Dionisi, C; Di Ruzza, B; Dittmann, J R; DiTuro, P; Dörr, C; Donati, S; Donega, M; Dong, P; Donini, J; Dorigo, T; Dube, S; Efron, J; Erbacher, R; Errede, D; Errede, S; Eusebi, R; Fang, H C; Farrington, S; Fedorko, I; Fedorko, W T; Feild, R G; Feindt, M; Fernandez, J P; Field, R; Flanagan, G; Foland, A; Forrester, S; Foster, G W; Franklin, M; Freeman, J C; Furic, I; Gallinaro, M; Galyardt, J; Garcia, J E; Garberson, F; Garfinkel, A F; Gay, C; Gerberich, H; Gerdes, D; Giagu, S; Giannetti, P; Gibson, A; Gibson, K; Gimmell, J L; Ginsburg, C; Giokaris, N; Giordani, M; Giromini, P; Giunta, M; Giurgiu, G; Glagolev, V; Glenzinski, D; Gold, M; Goldschmidt, N; Goldstein, J; Gomez, G; Gomez-Ceballos, G; Goncharov, M; González, O; Gorelov, I; Goshaw, A T; Goulianos, K; Gresele, A; Griffiths, M; Grinstein, S; Grosso-Pilcher, C; Group, R C; Grundler, U; Guimaraes da Costa, J; Gunay-Unalan, Z; Haber, C; Hahn, K; Hahn, S R; Halkiadakis, E; Hamilton, A; Han, B-Y; Han, J Y; Handler, R; Happacher, F; Hara, K; Hare, M; Harper, S; Harr, R F; Harris, R M; Hartz, M; Hatakeyama, K; Hauser, J; Heijboer, A; Heinemann, B; Heinrich, J; Henderson, C; Herndon, M; Heuser, J; Hidas, D; Hill, C S; Hirschbuehl, D; Hocker, A; Holloway, A; Hou, S; Houlden, M; Hsu, S-C; Huffman, B T; Hughes, R E; Husemann, U; Huston, J; Incandela, J; Introzzi, G; Iori, M; Ishizawa, Y; Ivanov, A; Iyutin, B; James, E; Jang, D; Jayatilaka, B; Jeans, D; Jensen, H; Jeon, E J; Jindariani, S; Jones, M; Joo, K K; Jun, S Y; Jung, J E; Junk, T R; Kamon, T; Karchin, P E; Kato, Y; Kemp, Y; Kephart, R; Kerzel, U; Khotilovich, V; Kilminster, B; Kim, D H; Kim, H S; Kim, J E; Kim, M J; Kim, S B; Kim, S H; Kim, Y K; Kimura, N; Kirsch, L; Klimenko, S; Klute, M; Knuteson, B; Ko, B R; Kondo, K; Kong, D J; Konigsberg, J; Korytov, A; Kotwal, A V; Kovalev, A; Kraan, A C; Kraus, J; Kravchenko, I; Kreps, M; Kroll, J; Krumnack, N; Kruse, M; Krutelyov, V; Kubo, T; Kuhlmann, S E; Kuhr, T; Kusakabe, Y; Kwang, S; Laasanen, A T; Labarga, L; Lai, S; Lami, S; Lammel, S; Lancaster, M; Lander, R L; Lannon, K; Lath, A; Latino, G; Lazzizzera, I; LeCompte, T; Lee, J; Lee, J; Lee, Y J; Lee, S W; Lefèvre, R; Leonardo, N; Leone, S; Levy, S; Lewis, J D; Lin, C; Lin, C S; Lindgren, M; Lipeles, E; Liss, T M; Lister, A; Litvintsev, D O; Liu, T; Lockyer, N S; Loginov, A; Loreti, M; Loverre, P; Lu, R-S; Lucchesi, D; Lujan, P; Lukens, P; Lungu, G; Lyons, L; Lys, J; Lysak, R; Lytken, E; Mack, P; MacQueen, D; Madrak, R; Maeshima, K; Makhoul, K; Maki, T; Maksimovic, P; Malde, S; Manca, G; Margaroli, F; Marginean, R; Marino, C; Marino, C P; Martin, A; Martin, M; Martin, V; Martínez, M; Maruyama, T; Mastrandrea, P; Masubuchi, T; Matsunaga, H; Mattson, M E; Mazini, R; Mazzanti, P; McFarland, K S; McIntyre, P; McNulty, R; Mehta, A; Mehtala, P; Menzemer, S; Menzione, A; Merkel, P; Mesropian, C; Messina, A; Miao, T; Miladinovic, N; Miles, J; Miller, R; Mills, C; Milnik, M; Mitra, A; Mitselmakher, G; Miyamoto, A; Moed, S; Moggi, N; Mohr, B; Moore, R; Morello, M; Movilla Fernandez, P; Mülmenstädt, J; Mukherjee, A; Muller, Th; Mumford, R; Murat, P; Nachtman, J; Nagano, A; Naganoma, J; Nahn, S; Nakano, I; Napier, A; Necula, V; Neu, C; Neubauer, M S; Nielsen, J; Nigmanov, T; Nodulman, L; Norniella, O; Nurse, E; Oh, S H; Oh, Y D; Oksuzian, I; Okusawa, T; Oldeman, R; Orava, R; Osterberg, K; Pagliarone, C; Palencia, E; Papadimitriou, V; Paramonov, A A; Parks, B; Pashapour, S; Patrick, J; Pauletta, G; Paulini, M; Paus, C; Pellett, D E; Penzo, A; Phillips, T J; Piacentino, G; Piedra, J; Pinera, L; Pitts, K; Plager, C; Pondrom, L; Portell, X; Poukhov, O; Pounder, N; Prokoshin, F; Pronko, A; Proudfoot, J; Ptochos, F; Punzi, G; Pursley, J; Rademacker, J; Rahaman, A; Ranjan, N; Rappoccio, S; Reisert, B; Rekovic, V; Renton, P; Rescigno, M; Richter, S; Rimondi, F; Ristori, L; Robson, A; Rodrigo, T; Rogers, E; Rolli, S; Roser, R; Rossi, M; Rossin, R; Ruiz, A; Russ, J; Rusu, V; Saarikko, H; Sabik, S; Safonov, A; Sakumoto, W K; Salamanna, G; Saltó, O; Saltzberg, D; Sánchez, C; Santi, L; Sarkar, S; Sartori, L; Sato, K; Savard, P; Savoy-Navarro, A; Scheidle, T; Schlabach, P; Schmidt, E E; Schmidt, M P; Schmitt, M; Schwarz, T; Scodellaro, L; Scott, A L; Scribano, A; Scuri, F; Sedov, A; Seidel, S; Seiya, Y; Semenov, A; Sexton-Kennedy, L; Sfyrla, A; Shapiro, M D; Shears, T; Shepard, P F; Sherman, D; Shimojima, M; Shochet, M; Shon, Y; Shreyber, I; Sidoti, A; Sinervo, P; Sisakyan, A; Sjolin, J; Slaughter, A J; Slaunwhite, J; Sliwa, K; Smith, J R; Snider, F D; Snihur, R; Soderberg, M; Soha, A; Somalwar, S; Sorin, V; Spalding, J; Spinella, F; Spreitzer, T; Squillacioti, P; Stanitzki, M; Staveris-Polykalas, A; St Denis, R; Stelzer, B; Stelzer-Chilton, O; Stentz, D; Strologas, J; Stuart, D; Suh, J S; Sukhanov, A; Sun, H; Suzuki, T; Taffard, A; Takashima, R; Takeuchi, Y; Takikawa, K; Tanaka, M; Tanaka, R; Tecchio, M; Teng, P K; Terashi, K; Tesarek, R J; Thom, J; Thompson, A S; Thomson, E; Tipton, P; Tiwari, V; Tkaczyk, S; Toback, D; Tokar, S; Tollefson, K; Tomura, T; Tonelli, D; Torre, S; Torretta, D; Tourneur, S; Trischuk, W; Tsuchiya, R; Tsuno, S; Turini, N; Ukegawa, F; Unverhau, T; Uozumi, S; Usynin, D; Vallecorsa, S; van Remortel, N; Varganov, A; Vataga, E; Vázquez, F; Velev, G; Veramendi, G; Veszpremi, V; Vidal, R; Vila, I; Vilar, R; Vine, T; Vollrath, I; Volobouev, I; Volpi, G; Würthwein, F; Wagner, P; Wagner, R G; Wagner, R L; Wagner, J; Wagner, W; Wallny, R; Wang, S M; Warburton, A; Waschke, S; Waters, D; Weinberger, M; Wester, W C; Whitehouse, B; Whiteson, D; Wicklund, A B; Wicklund, E; Williams, G; Williams, H H; Wilson, P; Winer, B L; Wittich, P; Wolbers, S; Wolfe, C; Wright, T; Wu, X; Wynne, S M; Yagil, A; Yamamoto, K; Yamaoka, J; Yamashita, T; Yang, C; Yang, U K; Yang, Y C; Yao, W M; Yeh, G P; Yoh, J; Yorita, K; Yoshida, T; Yu, G B; Yu, I; Yu, S S; Yun, J C; Zanello, L; Zanetti, A; Zaw, I; Zhang, X; Zhou, J; Zucchelli, S

2007-03-23

We report a measurement of the Lambda b0 lifetime in the exclusive decay Lambda b0-->J/psi Lambda 0 in pp collisions at square root s=1.96 TeV using an integrated luminosity of 1.0 fb-1 of data collected by the CDF II detector at the Fermilab Tevatron. Using fully reconstructed decays, we measure tau(Lambda b0)=1.593(-0.078)(+0.083)(stat)+/-0.033(syst) ps. This is the single most precise measurement of tau(Lambda b0) and is 3.2sigma higher than the current world average.

A component prediction method for flue gas of natural gas combustion based on nonlinear partial least squares method.

PubMed

Cao, Hui; Yan, Xingyu; Li, Yaojiang; Wang, Yanxia; Zhou, Yan; Yang, Sanchun

2014-01-01

Quantitative analysis for the flue gas of natural gas-fired generator is significant for energy conservation and emission reduction. The traditional partial least squares method may not deal with the nonlinear problems effectively. In the paper, a nonlinear partial least squares method with extended input based on radial basis function neural network (RBFNN) is used for components prediction of flue gas. For the proposed method, the original independent input matrix is the input of RBFNN and the outputs of hidden layer nodes of RBFNN are the extension term of the original independent input matrix. Then, the partial least squares regression is performed on the extended input matrix and the output matrix to establish the components prediction model of flue gas. A near-infrared spectral dataset of flue gas of natural gas combustion is used for estimating the effectiveness of the proposed method compared with PLS. The experiments results show that the root-mean-square errors of prediction values of the proposed method for methane, carbon monoxide, and carbon dioxide are, respectively, reduced by 4.74%, 21.76%, and 5.32% compared to those of PLS. Hence, the proposed method has higher predictive capabilities and better robustness.

Perceptions of midline deviations among different facial types.

PubMed

Williams, Ryan P; Rinchuse, Daniel J; Zullo, Thomas G

2014-02-01

The correction of a deviated midline can involve complicated mechanics and a protracted treatment. The threshold below which midline deviations are considered acceptable might depend on multiple factors. The objective of this study was to evaluate the effect of facial type on laypersons' perceptions of various degrees of midline deviation. Smiling photographs of male and female subjects were altered to create 3 facial type variations (euryprosopic, mesoprosopic, and leptoprosopic) and deviations in the midline ranging from 0.0 to 4.0 mm. Evaluators rated the overall attractiveness and acceptability of each photograph. Data were collected from 160 raters. The overall threshold for the acceptability of a midline deviation was 2.92 ± 1.10 mm, with the threshold for the male subject significantly lower than that for the female subject. The euryprosopic facial type showed no decrease in mean attractiveness until the deviations were 2 mm or more. All other facial types were rated as decreasingly attractive from 1 mm onward. Among all facial types, the attractiveness of the male subject was only affected at deviations of 2 mm or greater; for the female subject, the attractiveness scores were significantly decreased at 1 mm. The mesoprosopic facial type was most attractive for the male subject but was the least attractive for the female subject. Facial type and sex may affect the thresholds at which a midline deviation is detected and above which a midline deviation is considered unacceptable. Both the euryprosopic facial type and male sex were associated with higher levels of attractiveness at relatively small levels of deviations. Copyright © 2014 American Association of Orthodontists. Published by Mosby, Inc. All rights reserved.

Efficiently explore the energy landscape of proteins in molecular dynamics simulations by amplifying collective motions

NASA Astrophysics Data System (ADS)

He, Jianbin; Zhang, Zhiyong; Shi, Yunyu; Liu, Haiyan

2003-08-01

We describe a method for efficient sampling of the energy landscape of a protein in atomic molecular dynamics simulations. A simulation is divided into alternatively occurring relaxation phases and excitation phases. In the relaxation phase (conventional simulation), we use a frequently updated reference structure and deviations from this reference structure to mark whether the system has been trapped in a local minimum. In that case, the simulation enters the excitation phase, during which a few slow collective modes of the system are coupled to a higher temperature bath. After the system has escaped from the minimum (also judged by deviations from the reference structure) the simulation reenters the relaxation phase. The collective modes are obtained from a coarse-grained Gaussian elastic network model. The scheme, which we call ACM-AME (amplified collective motion-assisted minimum escaping), is compared with conventional simulations as well as an alternative scheme that elevates the temperature of all degrees of freedom during the excitation phase (amplified overall motion-assisted minimum escaping, or AOM-AME). Comparison is made using simulations on four peptides starting from non-native extended or all helical structures. In terms of sampling low energy conformations and continuously sampling new conformations throughout a simulation, the ACM-AME scheme demonstrates very good performance while the AOM-AME scheme shows little improvement upon conventional simulations. Limited success is achieved in producing structures close to the native structures of the peptides: for an S-peptide analog, the ACM-AME approach is able to reproduce its native helical structure, and starting from an all-helical structure of the villin headpiece subdomain (HP-36) in implicit solvent, two out of three 150 ns ACM-AME runs are able to sample structures with 3-4 Å backbone root-mean-square deviations from the nuclear magnetic resonance structure of the protein.

Large Deviations: Advanced Probability for Undergrads

ERIC Educational Resources Information Center

Rolls, David A.

2007-01-01

In the branch of probability called "large deviations," rates of convergence (e.g. of the sample mean) are considered. The theory makes use of the moment generating function. So, particularly for sums of independent and identically distributed random variables, the theory can be made accessible to senior undergraduates after a first course in…

In Terms of the Logarithmic Mean Annual Seismicity Rate and Its Standard Deviation to Present the Gutenberg-Richter Relation

NASA Astrophysics Data System (ADS)

Chen, K. P.; Chang, W. Y.; Tsai, Y. B.

2016-12-01

The main purpose of this study is to apply an innovative approach to assess the median annual seismicity rates and their dispersions for Taiwan earthquakes in different depth ranges. This approach explicitly represents the Gutenberg-Richter (G-R) relation in terms of both the logarithmic mean annual seismicity rate and its standard deviation, instead of just the arithmetic mean. We use the high-quality seismicity data obtained by the Institute of Earth Sciences (IES) and the Central Weather Bureau (CWB) in an earthquake catalog with homogenized moment magnitudes from 1975 to 2014 for our study. The selected data set is shown to be complete for Mw>3.0. We first use it to illustrate the merits of our new approach for dampening the influence of spuriously large or small event numbers in individual years on the determination of median annual seismicity rate and its standard deviation. We further show that the logarithmic annual seismicity rates indeed possess a well-behaved lognormal distribution. The final results are summarized as follows: log10N=5.75-0.90Mw+/-(0.245-0.01Mw) for focal depth 0 300 km; log10N=5.78-0.94Mw+/-(0.195+0.01Mw) for focal depth 0-35 km; log10N=4.72-0.89Mw+/-(-0.075+0.075Mw) for focal depth 35-70 km; and log10N=4.69-0.88Mw+/-(-0.47+0.16Mw) for focal depth 70-300 km. Above results show distinctly different values for the parameters a and b in the G-R relations for Taiwan earthquakes in different depth ranges. These analytical equations can be readily used for comprehensive probabilistic seismic hazard assessment. Furthermore, a numerical table on the corresponding median annual seismicity rates and their upper and lower bounds at median +/- one standard deviation levels, as calculated from above analytical equations, is presented at the end. This table offers an overall glance of the estimated median annual seismicity rates and their dispersions for Taiwan earthquakes of various magnitudes and focal depths. It is interesting to point out that

Fine root morphological traits determine variation in root respiration of Quercus serrata.

PubMed

Makita, Naoki; Hirano, Yasuhiro; Dannoura, Masako; Kominami, Yuji; Mizoguchi, Takeo; Ishii, Hiroaki; Kanazawa, Yoichi

2009-04-01

Fine root respiration is a significant component of carbon cycling in forest ecosystems. Although fine roots differ functionally from coarse roots, these root types have been distinguished based on arbitrary diameter cut-offs (e.g., 2 or 5 mm). Fine root morphology is directly related to physiological function, but few attempts have been made to understand the relationships between morphology and respiration of fine roots. To examine relationships between respiration rates and morphological traits of fine roots (0.15-1.4 mm in diameter) of mature Quercus serrata Murr., we measured respiration of small fine root segments in the field with a portable closed static chamber system. We found a significant power relationship between mean root diameter and respiration rate. Respiration rates of roots<0.4 mm in mean diameter were high and variable, ranging from 3.8 to 11.3 nmol CO2 g(-1) s(-1), compared with those of larger diameter roots (0.4-1.4 mm), which ranged from 1.8 to 3.0 nmol CO2 g(-1) s(-1). Fine root respiration rate was positively correlated with specific root length (SRL) as well as with root nitrogen (N) concentration. For roots<0.4 mm in diameter, SRL had a wider range (11.3-80.4 m g(-1)) and was more strongly correlated with respiration rate than diameter. Our results indicate that a more detailed classification of fine roots<2.0 mm is needed to represent the heterogeneity of root respiration and to evaluate root biomass and root morphological traits.

Least-Squares Data Adjustment with Rank-Deficient Data Covariance Matrices

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

Williams, J.G.

2011-07-01

A derivation of the linear least-squares adjustment formulae is required that avoids the assumption that the covariance matrix of prior parameters can be inverted. Possible proofs are of several kinds, including: (i) extension of standard results for the linear regression formulae, and (ii) minimization by differentiation of a quadratic form of the deviations in parameters and responses. In this paper, the least-squares adjustment equations are derived in both these ways, while explicitly assuming that the covariance matrix of prior parameters is singular. It will be proved that the solutions are unique and that, contrary to statements that have appeared inmore » the literature, the least-squares adjustment problem is not ill-posed. No modification is required to the adjustment formulae that have been used in the past in the case of a singular covariance matrix for the priors. In conclusion: The linear least-squares adjustment formula that has been used in the past is valid in the case of a singular covariance matrix for the covariance matrix of prior parameters. Furthermore, it provides a unique solution. Statements in the literature, to the effect that the problem is ill-posed are wrong. No regularization of the problem is required. This has been proved in the present paper by two methods, while explicitly assuming that the covariance matrix of prior parameters is singular: i) extension of standard results for the linear regression formulae, and (ii) minimization by differentiation of a quadratic form of the deviations in parameters and responses. No modification is needed to the adjustment formulae that have been used in the past. (author)« less

Identified baryon and meson distributions at large transverse momenta from Au + Au collisions at square root sNN=200 GeV.

PubMed

Abelev, B I; Aggarwal, M M; Ahammed, Z; Anderson, B D; Anderson, M; Arkhipkin, D; Averichev, G S; Bai, Y; Balewski, J; Barannikova, O; Barnby, L S; Baudot, J; Bekele, S; Belaga, V V; Bellingeri-Laurikainen, A; Bellwied, R; Benedosso, F; Bhardwaj, S; Bhasin, A; Bhati, A K; Bichsel, H; Bielcik, J; Bielcikova, J; Bland, L C; Blyth, S-L; Bonner, B E; Botje, M; Bouchet, J; Brandin, A V; Bravar, A; Burton, T P; Bystersky, M; Cadman, R V; Cai, X Z; Caines, H; Calderón de la Barca Sánchez, M; Castillo, J; Catu, O; Cebra, D; Chajecki, Z; Chaloupka, P; Chattopadhyay, S; Chen, H F; Chen, J H; Cheng, J; Cherney, M; Chikanian, A; Christie, W; Coffin, J P; Cormier, T M; Cosentino, M R; Cramer, J G; Crawford, H J; Das, D; Das, S; Dash, S; Daugherity, M; de Moura, M M; Dedovich, T G; Dephillips, M; Derevschikov, A A; Didenko, L; Dietel, T; Djawotho, P; Dogra, S M; Dong, W J; Dong, X; Draper, J E; Du, F; Dunin, V B; Dunlop, J C; Dutta Mazumdar, M R; Eckardt, V; Edwards, W R; Efimov, L G; Emelianov, V; Engelage, J; Eppley, G; Erazmus, B; Estienne, M; Fachini, P; Fatemi, R; Fedorisin, J; Filip, P; Finch, E; Fine, V; Fisyak, Y; Fu, J; Gagliardi, C A; Gaillard, L; Ganti, M S; Ghazikhanian, V; Ghosh, P; Gonzalez, J E; Gorbunov, Y G; Gos, H; Grebenyuk, O; Grosnick, D; Guertin, S M; Guimaraes, K S F F; Gupta, N; Gutierrez, T D; Haag, B; Hallman, T J; Hamed, A; Harris, J W; He, W; Heinz, M; Henry, T W; Hepplemann, S; Hippolyte, B; Hirsch, A; Hjort, E; Hoffman, A M; Hoffmann, G W; Horner, M J; Huang, H Z; Huang, S L; Hughes, E W; Humanic, T J; Igo, G; Jacobs, P; Jacobs, W W; Jakl, P; Jia, F; Jiang, H; Jones, P G; Judd, E G; Kabana, S; Kang, K; Kapitan, J; Kaplan, M; Keane, D; Kechechyan, A; Khodyrev, V Yu; Kim, B C; Kiryluk, J; Kisiel, A; Kislov, E M; Klein, S R; Kocoloski, A; Koetke, D D; Kollegger, T; Kopytine, M; Kotchenda, L; Kouchpil, V; Kowalik, K L; Kramer, M; Kravtsov, P; Kravtsov, V I; Krueger, K; Kuhn, C; Kulikov, A I; Kumar, A; Kuznetsov, A A; Lamont, M A C; Landgraf, J M; Lange, S; Lapointe, S; Laue, F; Lauret, J; Lebedev, A; Lednicky, R; Lee, C-H; Lehocka, S; Levine, M J; Li, C; Li, Q; Li, Y; Lin, G; Lin, X; Lindenbaum, S J; Lisa, M A; Liu, F; Liu, H; Liu, J; Liu, L; Liu, Z; Ljubicic, T; Llope, W J; Long, H; Longacre, R S; Love, W A; Lu, Y; Ludlam, T; Lynn, D; Ma, G L; Ma, J G; Ma, Y G; Magestro, D; Mahapatra, D P; Majka, R; Mangotra, L K; Manweiler, R; Margetis, S; Markert, C; Martin, L; Matis, H S; Matulenko, Yu A; McClain, C J; McShane, T S; Melnick, Yu; Meschanin, A; Millane, J; Miller, M L; Minaev, N G; Mioduszewski, S; Mironov, C; Mischke, A; Mishra, D K; Mitchell, J; Mohanty, B; Molnar, L; Moore, C F; Morozov, D A; Munhoz, M G; Nandi, B K; Nattrass, C; Nayak, T K; Nelson, J M; Nepali, N S; Netrakanti, P K; Nogach, L V; Nurushev, S B; Odyniec, G; Ogawa, A; Okorokov, V; Oldenburg, M; Olson, D; Pachr, M; Pal, S K; Panebratsev, Y; Panitkin, S Y; Pavlinov, A I; Pawlak, T; Peitzmann, T; Perevoztchikov, V; Perkins, C; Peryt, W; Phatak, S C; Picha, R; Planinic, M; Pluta, J; Poljak, N; Porile, N; Porter, J; Poskanzer, A M; Potekhin, M; Potrebenikova, E; Potukuchi, B V K S; Prindle, D; Pruneau, C; Putschke, J; Rakness, G; Raniwala, R; Raniwala, S; Ray, R L; Razin, S V; Reinnarth, J; Relyea, D; Ridiger, A; Ritter, H G; Roberts, J B; Rogachevskiy, O V; Romero, J L; Rose, A; Roy, C; Ruan, L; Russcher, M J; Sahoo, R; Sakuma, T; Salur, S; Sandweiss, J; Sarsour, M; Sazhin, P S; Schambach, J; Scharenberg, R P; Schmitz, N; Seger, J; Selyuzhenkov, I; Seyboth, P; Shabetai, A; Shahaliev, E; Shao, M; Sharma, M; Shen, W Q; Shimanskiy, S S; Sichtermann, E P; Simon, F; Singaraju, R N; Smirnov, N; Snellings, R; Sood, G; Sorensen, P; Sowinski, J; Speltz, J; Spinka, H M; Srivastava, B; Stadnik, A; Stanislaus, T D S; Stock, R; Stolpovsky, A; Strikhanov, M; Stringfellow, B; Suaide, A A P; Subba, N L; Sugarbaker, E; Sumbera, M; Sun, Z; Surrow, B; Swanger, M; Symons, T J M; Szanto de Toledo, A; Tai, A; Takahashi, J; Tang, A H; Tarnowsky, T; Thein, D; Thomas, J H; Timmins, A R; Timoshenko, S; Tokarev, M; Trainor, T A; Trentalange, S; Tribble, R E; Tsai, O D; Ulery, J; Ullrich, T; Underwood, D G; Van Buren, G; van der Kolk, N; van Leeuwen, M; Vander Molen, A M; Varma, R; Vasilevski, I M; Vasiliev, A N; Vernet, R; Vigdor, S E; Viyogi, Y P; Vokal, S; Voloshin, S A; Waggoner, W T; Wang, F; Wang, G; Wang, J S; Wang, X L; Wang, Y; Watson, J W; Webb, J C; Westfall, G D; Wetzler, A; Whitten, C; Wieman, H; Wissink, S W; Witt, R; Wood, J; Wu, J; Xu, N; Xu, Q H; Xu, Z; Yepes, P; Yoo, I-K; Yurevich, V I; Zhan, W; Zhang, H; Zhang, W M; Zhang, Y; Zhang, Z P; Zhao, Y; Zhong, C; Zoulkarneev, R; Zoulkarneeva, Y; Zubarev, A N; Zuo, J X

2006-10-13

Transverse momentum spectra of pi+/-, p, and p up to 12 GeV/c at midrapidity in centrality selected Au + Au collisions at square root sNN=200 GeV are presented. In central Au + Au collisions, both pi +/- and p(p) show significant suppression with respect to binary scaling at pT approximately >4 GeV/c. Protons and antiprotons are less suppressed than pi+/-, in the range 1.5 approximately < pT approximately < 6 GeV/c. The pi-/pi+ and p/p ratios show at most a weak pT dependence and no significant centrality dependence. The p/pi ratios in central Au + Au collisions approach the values in p + p and d + Au collisions at pT approximately >5 GeV/c. The results at high pT indicate that the partonic sources of pi+/-, p, and p have similar energy loss when traversing the nuclear medium.

Phosphorus and magnesium interactively modulate the elongation and directional growth of primary roots in Arabidopsis thaliana (L.) Heynh

PubMed Central

Niu, Yaofang; Jin, Gulei; Li, Xin; Tang, Caixian; Zhang, Yongsong; Liang, Yongchao; Yu, Jingquan

2015-01-01

A balanced supply of essential nutrients is an important factor influencing root architecture in many plants, yet data related to the interactive effects of two nutrients on root growth are limited. Here, we investigated the interactive effect between phosphorus (P) and magnesium (Mg) on root growth of Arabidopsis grown in pH-buffered agar medium at different P and Mg levels. The results showed that elongation and deviation of primary roots were directly correlated with the amount of P added to the medium but could be modified by the Mg level, which was related to the root meristem activity and stem-cell division. High P enhanced while low P decreased the tip-focused fluorescence signal of auxin biosynthesis, transport, and redistribution during elongation of primary roots; these effects were greater under low Mg than under high Mg. The altered root growth in response to P and Mg supply was correlated with AUX1, PIN2, and PIN3 mRNA abundance and expression and the accumulation of the protein. Application of either auxin influx inhibitor or efflux inhibitor inhibited the elongation and increased the deviation angle of primary roots, and decreased auxin level in root tips. Furthermore, the auxin-transport mutants aux1-22 and eir1-1 displayed reduced root growth and increased the deviation angle. Our data suggest a profound effect of the combined supply of P and Mg on the development of root morphology in Arabidopsis through auxin signals that modulate the elongation and directional growth of primary root and the expression of root differentiation and development genes. PMID:25922494

Estimating solar ultraviolet irradiance (290-385 nm) by means of the spectral parametric models: SPCTRAL2 and SMARTS2

NASA Astrophysics Data System (ADS)

Foyo-Moreno, I.; Vida, J.; Olmo, F. J.; Alados-Arboledas, L.

2000-11-01

. Although SMARTS2 provide slightly worse results, both models give estimates of solar ultraviolet irradiance with mean bias deviation below 5%, and root mean square deviation close to experimental errors.

Severe root resorption resulting from orthodontic treatment: Prevalence and risk factors

PubMed Central

Maués, Caroline Pelagio Raick; do Nascimento, Rizomar Ramos; Vilella, Oswaldo de Vasconcellos

2015-01-01

OBJECTIVE: To assess the prevalence of severe external root resorption and its potential risk factors resulting from orthodontic treatment. METHODS: A randomly selected sample was used. It comprised conventional periapical radiographs taken in the same radiology center for maxillary and mandibular incisors before and after active orthodontic treatment of 129 patients, males and females, treated by means of the Standard Edgewise technique. Two examiners measured and defined root resorption according to the index proposed by Levander et al. The degree of external apical root resorption was registered defining resorption in four degrees of severity. To assess intra and inter-rater reproducibility, kappa coefficient was used. Chi-square test was used to assess the relationship between the amount of root resorption and patient's sex, dental arch (maxillary or mandibular), treatment with or without extractions, treatment duration, root apex stage (open or closed), root shape, as well as overjet and overbite at treatment onset. RESULTS: Maxillary central incisors had the highest percentage of severe root resorption, followed by maxillary lateral incisors and mandibular lateral incisors. Out of 959 teeth, 28 (2.9%) presented severe root resorption. The following risk factors were observed: anterior maxillary teeth, overjet greater than or equal to 5 mm at treatment onset, treatment with extractions, prolonged therapy, and degree of apex formation at treatment onset. CONCLUSION: This study showed that care must be taken in orthodontic treatment involving extractions, great retraction of maxillary incisors, prolonged therapy, and/or completely formed apex at orthodontic treatment onset. PMID:25741825

The Separability of Morphological Processes from Semantic Meaning and Syntactic Class in Production of Single Words: Evidence from the Hebrew Root Morpheme.

PubMed

Deutsch, Avital

2016-02-01

In the present study we investigated to what extent the morphological facilitation effect induced by the derivational root morpheme in Hebrew is independent of semantic meaning and grammatical information of the part of speech involved. Using the picture-word interference paradigm with auditorily presented distractors, Experiment 1 compared the facilitation effect induced by semantically transparent versus semantically opaque morphologically related distractor words (i.e., a shared root) on the production latency of bare nouns. The results revealed almost the same amount of facilitation for both relatedness conditions. These findings accord with the results of the few studies that have addressed this issue in production in Indo-European languages, as well as previous studies in written word perception in Hebrew. Experiment 2 compared the root's facilitation effect, induced by morphologically related nominal versus verbal distractors, on the production latency of bare nouns. The results revealed a facilitation effect of similar size induced by the shared root, regardless of the distractor's part of speech. It is suggested that the principle that governs lexical organization at the level of morphology, at least for Hebrew roots, is form-driven and independent of semantic meaning. This principle of organization crosses the linguistic domains of production and written word perception, as well as grammatical organization according to part of speech.

Mean square hydrogen fluctuations in chitosan/lecithin nanoparticles from elastic neutron scattering experiments

NASA Astrophysics Data System (ADS)

Sonvico, Fabio; Teresa Di Bari, Maria; Bove, Livia; Deriu, Antonio; Cavatorta, Fabrizio; Albanese, Gianfranco

2006-11-01

Recently, we have started a systematic study of the structure and dynamics of nano- and microparticles of interest as highly biocompatible drug carriers. For these particles, that are composed of polymeric and lipid material, a detailed understanding of the particle-solvent interactions is of key importance in order to tailor their characteristics for delivering drugs with specific chemical properties. Here we report results of elastic neutron scattering (ENS) investigations on lecithin/chitosan nanoparticles. They were first prepared by autoassembling the two components in aqueous solution; the samples were then freeze-dried and re-hydrated in a D 2O atmosphere. The experiments were performed in the temperature range of 20-50 K using the backscattering spectrometer IN13 at ILL (Grenoble, France). The comparison of samples in the dry state with similar ones at an hydration level of about 0.3-0.4 (g D 2O/g hydrated sample), indicates that the presence of an outer chitosan ‘‘coating’’ reduces the mean square fluctuations of the hydrogens in the lipid component, leading thus to a stiffer nanoparticle structure.

Micro-computed tomography analysis of post space preparation in root canals filled with carrier-based thermoplasticized gutta-percha.

PubMed

Schroeder, A A; Ford, N L; Coil, J M

2017-03-01

To determine whether post space preparation deviated from the root canal preparation in canals filled with Thermafil, GuttaCore or warm vertically compacted gutta-percha. Forty-two extracted human permanent maxillary lateral incisors were decoronated, and their root canals instrumented using a standardized protocol. Samples were divided into three groups and filled with Thermafil (Dentsply Tulsa Dental Specialties, Johnson City, TN, USA), GuttaCore (Dentsply Tulsa Dental Specialties) or warm vertically compacted gutta-percha, before post space preparation was performed with a GT Post drill (Dentsply Tulsa Dental Specialties). Teeth were scanned using micro-computed tomography after root filling and again after post space preparation. Scans were examined for number of samples with post space deviation, linear deviation of post space preparation and minimum root thickness before and after post space preparation. Parametric data were analysed with one-way analysis of variance (anova) or one-tailed paired Student's t-tests, whilst nonparametric data were analysed with Fisher's exact test. Deviation occurred in eight of forty-two teeth (19%), seven of fourteen from the Thermafil group (50%), one of fourteen from the GuttaCore group (7%), and none from the gutta-percha group. Deviation occurred significantly more often in the Thermafil group than in each of the other two groups (P < 0.05). Linear deviation of post space preparation was greater in the Thermafil group than in both of the other groups and was significantly greater than that of the gutta-percha group (P < 0.05). Minimum root thickness before post space preparation was significantly greater than it was after post space preparation for all groups (P < 0.01). The differences between the Thermafil, GuttaCore and gutta-percha groups in the number of samples with post space deviation and in linear deviation of post space preparation were associated with the presence or absence of a carrier as well as the

TANGLE: Two-Level Support Vector Regression Approach for Protein Backbone Torsion Angle Prediction from Primary Sequences

PubMed Central

Song, Jiangning; Tan, Hao; Wang, Mingjun; Webb, Geoffrey I.; Akutsu, Tatsuya

2012-01-01

Protein backbone torsion angles (Phi) and (Psi) involve two rotation angles rotating around the Cα-N bond (Phi) and the Cα-C bond (Psi). Due to the planarity of the linked rigid peptide bonds, these two angles can essentially determine the backbone geometry of proteins. Accordingly, the accurate prediction of protein backbone torsion angle from sequence information can assist the prediction of protein structures. In this study, we develop a new approach called TANGLE (Torsion ANGLE predictor) to predict the protein backbone torsion angles from amino acid sequences. TANGLE uses a two-level support vector regression approach to perform real-value torsion angle prediction using a variety of features derived from amino acid sequences, including the evolutionary profiles in the form of position-specific scoring matrices, predicted secondary structure, solvent accessibility and natively disordered region as well as other global sequence features. When evaluated based on a large benchmark dataset of 1,526 non-homologous proteins, the mean absolute errors (MAEs) of the Phi and Psi angle prediction are 27.8° and 44.6°, respectively, which are 1% and 3% respectively lower than that using one of the state-of-the-art prediction tools ANGLOR. Moreover, the prediction of TANGLE is significantly better than a random predictor that was built on the amino acid-specific basis, with the p-value<1.46e-147 and 7.97e-150, respectively by the Wilcoxon signed rank test. As a complementary approach to the current torsion angle prediction algorithms, TANGLE should prove useful in predicting protein structural properties and assisting protein fold recognition by applying the predicted torsion angles as useful restraints. TANGLE is freely accessible at http://sunflower.kuicr.kyoto-u.ac.jp/~sjn/TANGLE/. PMID:22319565

Mean individual muscle activities and ratios of total muscle activities in a selective muscle strengthening experiment: the effects of lower limb muscle activity based on mediolateral slope angles during a one-leg stance.

PubMed

Lee, Sang-Yeol

2016-09-01

[Purpose] The purpose of this study was to provide basic data for research on selective muscle strengthening by identifying mean muscle activities and calculating muscle ratios for use in developing strengthening methods. [Subjects and Methods] Twenty-one healthy volunteers were included in this study. Muscle activity was measured during a one-leg stance under 6 conditions of slope angle: 0°, 5°, 10°, 15°, 20°, and 25°. The data used in the analysis were root mean square and % total muscle activity values. [Results] There were significant differences in the root mean square of the gluteus medius, the hamstring, and the medial gastrocnemius muscles. There were significant differences in % total muscle activity of the medial gastrocnemius. [Conclusion] Future studies aimed at developing selective muscle strengthening methods are likely to yield more effective results by using muscle activity ratios based on electromyography data.

Negative Differential Conductance in Polyporphyrin Oligomers with Nonlinear Backbones.

PubMed

Kuang, Guowen; Chen, Shi Zhang; Yan, Linghao; Chen, Ke Qiu; Shang, Xuesong; Liu, Pei Nian; Lin, Nian

2018-01-17

We study negative differential conductance (NDC) effects in polyporphyrin oligomers with nonlinear backbones. Using a low-temperature scanning tunneling microscope, we selectively controlled the charge transport path in single oligomer wires. We observed robust NDC when charge passed through a T-shape junction, bistable NDC when charge passed through a 90° kink and no NDC when charge passed through a 120° kink. Aided by density functional theory with nonequilibrium Green's functions simulations, we attributed this backbone-dependent NDC to bias-modulated hybridization of the electrode states with the resonant transport molecular orbital. We argue this mechanism is generic in molecular systems, which opens a new route of designing molecular NDC devices.

Integrating Map Algebra and Statistical Modeling for Spatio- Temporal Analysis of Monthly Mean Daily Incident Photosynthetically Active Radiation (PAR) over a Complex Terrain.

PubMed

Evrendilek, Fatih

2007-12-12

This study aims at quantifying spatio-temporal dynamics of monthly mean dailyincident photosynthetically active radiation (PAR) over a vast and complex terrain such asTurkey. The spatial interpolation method of universal kriging, and the combination ofmultiple linear regression (MLR) models and map algebra techniques were implemented togenerate surface maps of PAR with a grid resolution of 500 x 500 m as a function of fivegeographical and 14 climatic variables. Performance of the geostatistical and MLR modelswas compared using mean prediction error (MPE), root-mean-square prediction error(RMSPE), average standard prediction error (ASE), mean standardized prediction error(MSPE), root-mean-square standardized prediction error (RMSSPE), and adjustedcoefficient of determination (R² adj. ). The best-fit MLR- and universal kriging-generatedmodels of monthly mean daily PAR were validated against an independent 37-year observeddataset of 35 climate stations derived from 160 stations across Turkey by the Jackknifingmethod. The spatial variability patterns of monthly mean daily incident PAR were moreaccurately reflected in the surface maps created by the MLR-based models than in thosecreated by the universal kriging method, in particular, for spring (May) and autumn(November). The MLR-based spatial interpolation algorithms of PAR described in thisstudy indicated the significance of the multifactor approach to understanding and mappingspatio-temporal dynamics of PAR for a complex terrain over meso-scales.

Radiological evaluation of the morphological changes of root canals shaped with ProTaper for hand use and the ProTaper and RaCe rotary instruments.

PubMed

Aguiar, Carlos M; Câmara, Andréa C

2008-12-01

This study evaluated, by means of the radiography examination, the occurrence of deviations in the apical third of root canals shaped with hand and rotary instruments. Sixty mandibular human molars were divided into three groups. The root canals in group 1 were instrumented with ProTaper (Dentsply/Maillefer, Ballaigues, Switzerland) for hand use, group 2 with ProTaper and group 3 with RaCe. The images obtained by double superimposition of the pre- and postoperative radiographs were evaluated by two endodontists with the aid of a magnifier-viewer and a fivefold magnifier. Statistical analysis was performed using the Fisher-Freeman-Halton. The instrumentation using the ProTaper for hand use showed 25% of the canals with a deviation in the apical third, as did the ProTaper, while the corresponding figure for the RaCe (FKG Dentaire, La-Chaux-de-Fonds, Switzerland) was 20%, but these results were not statistically significant. There was no correlation between the occurrence of deviations in the apical third and the systems used.

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. © 2013 The Protein Society.

Particle-type dependence of azimuthal anisotropy and nuclear modification of particle production in Au+Au collisions at square root of sNN=200 GeV.

PubMed

Adams, J; Adler, C; Aggarwal, M M; Ahammed, Z; Amonett, J; Anderson, B D; Anderson, M; Arkhipkin, D; Averichev, G S; Badyal, S K; Balewski, J; Barannikova, O; Barnby, L S; Baudot, J; Bekele, S; Belaga, V V; Bellwied, R; Berger, J; Bezverkhny, B I; Bhardwaj, S; Bhaskar, P; Bhati, A K; Bichsel, H; Billmeier, A; Bland, L C; Blyth, C O; Bonner, B E; Botje, M; Boucham, A; Brandin, A; Bravar, A; Cadman, R V; Cai, X Z; Caines, H; Calderón de la Barca Sánchez, M; Carroll, J; Castillo, J; Castro, M; Cebra, D; Chaloupka, P; Chattopadhyay, S; Chen, H F; Chen, Y; Chernenko, S P; Cherney, M; Chikanian, A; Choi, B; Christie, W; Coffin, J P; Cormier, T M; Cramer, J G; Crawford, H J; Das, D; Das, S; Derevschikov, A A; Didenko, L; Dietel, T; Dong, W J; Dong, X; Draper, J E; Du, F; Dubey, A K; Dunin, V B; Dunlop, J C; Dutta Majumdar, M R; Eckardt, V; Efimov, L G; Emelianov, V; Engelage, J; Eppley, G; Erazmus, B; Estienne, M; Fachini, P; Faine, V; Faivre, J; Fatemi, R; Filimonov, K; Filip, P; Finch, E; Fisyak, Y; Flierl, D; Foley, K J; Fu, J; Gagliardi, C A; Gagunashvili, N; Gans, J; Ganti, M S; Gaudichet, L; Germain, M; Geurts, F; Ghazikhanian, V; Ghosh, P; Gonzalez, J E; Grachov, O; Grigoriev, V; Gronstal, S; Grosnick, D; Guedon, M; Guertin, S M; Gupta, A; Gushin, E; Gutierrez, T D; Hallman, T J; Hardtke, D; Harris, J W; Heinz, M; Henry, T W; Heppelmann, S; Herston, T; Hippolyte, B; Hirsch, A; Hjort, E; Hoffmann, G W; Horsley, M; Huang, H Z; Huang, S L; Humanic, T J; Igo, G; Ishihara, A; Jacobs, P; Jacobs, W W; Janik, M; Jiang, H; Johnson, I; Jones, P G; Judd, E G; Kabana, S; Kaneta, M; Kaplan, M; Keane, D; Khodyrev, V Yu; Kiryluk, J; Kisiel, A; Klay, J; Klein, S R; Klyachko, A; Koetke, D D; Kollegger, T; Kopytine, M; Kotchenda, L; Kovalenko, A D; Kramer, M; Kravtsov, P; Kravtsov, V I; Krueger, K; Kuhn, C; Kulikov, A I; Kumar, A; Kunde, G J; Kunz, C L; Kutuev, R Kh; Kuznetsov, A A; Lamont, M A C; Landgraf, J M; Lange, S; Lansdell, C P; Lasiuk, B; Laue, F; Lauret, J; Lebedev, A; Lednický, R; LeVine, M J; Li, C; Li, Q; Lindenbaum, S J; Lisa, M A; Liu, F; Liu, L; Liu, Z; Liu, Q J; Ljubicic, T; Llope, W J; Long, H; Longacre, R S; Lopez-Noriega, M; Love, W A; Ludlam, T; Lynn, D; Ma, J; Ma, Y G; Magestro, D; Mahajan, S; Mangotra, L K; Mahapatra, D P; Majka, R; Manweiler, R; Margetis, S; Markert, C; Martin, L; Marx, J; Matis, H S; Matulenko, Yu A; McShane, T S; Meissner, F; Melnick, Yu; Meschanin, A; Messer, M; Miller, M L; Milosevich, Z; Minaev, N G; Mironov, C; Mishra, D; Mitchell, J; Mohanty, B; Molnar, L; Moore, C F; Mora-Corral, M J; Morozov, D A; Morozov, V; de Moura, M M; Munhoz, M G; Nandi, B K; Nayak, S K; Nayak, T K; Nelson, J M; Nevski, P; Nikitin, V A; Nogach, L V; Norman, B; Nurushev, S B; Odyniec, G; Ogawa, A; Okorokov, V; Oldenburg, M; Olson, D; Paic, G; Pandey, S U; Pal, S K; Panebratsev, Y; Panitkin, S Y; Pavlinov, A I; Pawlak, T; Perevoztchikov, V; Perkins, C; Peryt, W; Petrov, V A; Phatak, S C; Picha, R; Planinic, M; Pluta, J; Porile, N; Porter, J; Poskanzer, A M; Potekhin, M; Potrebenikova, E; Potukuchi, B V K S; Prindle, D; Pruneau, C; Putschke, J; Rai, G; Rakness, G; Raniwala, R; Raniwala, S; Ravel, O; Ray, R L; Razin, S V; Reichhold, D; Reid, J G; Renault, G; Retiere, F; Ridiger, A; Ritter, H G; Roberts, J B; Rogachevski, O V; Romero, J L; Rose, A; Roy, C; Ruan, L J; Sahoo, R; Sakrejda, I; Salur, S; Sandweiss, J; Savin, I; Schambach, J; Scharenberg, R P; Schmitz, N; Schroeder, L S; Schweda, K; Seger, J; Seliverstov, D; Seyboth, P; Shahaliev, E; Shao, M; Sharma, M; Shestermanov, K E; Shimanskii, S S; Singaraju, R N; Simon, F; Skoro, G; Smirnov, N; Snellings, R; Sood, G; Sorensen, P; Sowinski, J; Spinka, H M; Srivastava, B; Stanislaus, S; Stock, R; Stolpovsky, A; Strikhanov, M; Stringfellow, B; Struck, C; Suaide, A A P; Sugarbaker, E; Suire, C; Sumbera, M; Surrow, B; Symons, T J M; de Toledo, A Szanto; Szarwas, P; Tai, A; Takahashi, J; Tang, A H; Thein, D; Thomas, J H; Tikhomirov, V; Tokarev, M; Tonjes, M B; Trainor, T A; Trentalange, S; Tribble, R E; Trivedi, M D; Trofimov, V; Tsai, O; Ullrich, T; Underwood, D G; Van Buren, G; VanderMolen, A M; Vasiliev, A N; Vasiliev, M; Vigdor, S E; Viyogi, Y P; Voloshin, S A; Waggoner, W; Wang, F; Wang, G; Wang, X L; Wang, Z M; Ward, H; Watson, J W; Wells, R; Westfall, G D; Whitten, C; Wieman, H; Willson, R; Wissink, S W; Witt, R; Wood, J; Wu, J; Xu, N; Xu, Z; Xu, Z Z; Yamamoto, E; Yepes, P; Yurevich, V I; Zanevski, Y V; Zborovský, I; Zhang, H; Zhang, W M; Zhang, Z P; Zołnierczuk, P A; Zoulkarneev, R; Zoulkarneeva, J; Zubarev, A N

2004-02-06

We present STAR measurements of the azimuthal anisotropy parameter v(2) and the binary-collision scaled centrality ratio R(CP) for kaons and lambdas (Lambda+Lambda) at midrapidity in Au+Au collisions at square root of s(NN)=200 GeV. In combination, the v(2) and R(CP) particle-type dependencies contradict expectations from partonic energy loss followed by standard fragmentation in vacuum. We establish p(T) approximately 5 GeV/c as the value where the centrality dependent baryon enhancement ends. The K(0)(S) and Lambda+Lambda v(2) values are consistent with expectations of constituent-quark-number scaling from models of hadron formation by parton coalescence or recombination.

Unraveling the Deleterious Effects of Cancer-Driven STK11 Mutants Through Conformational Sampling Approach.

PubMed

Lopus, Merlin; Paul, D Meshach; Rajasekaran, R

2016-01-01

Tumor suppressor gene, STK11, encodes for serine-threonine kinase, which has a critical role in regulating cell growth and apoptosis. Mutations of the same lead to the inactivation of STK11, which eventually causes different types of cancer. In this study, we focused on identifying those driver mutations through analyzing structural variations of mutants, viz., D194N, E199K, L160P, and Y49D. Native and the mutants were analyzed to determine their geometrical deviations such as root-mean-square deviation, root-mean-square fluctuation, radius of gyration, potential energy, and solvent-accessible surface area using conformational sampling technique. Additionally, the global minimized structure of native and mutants was further analyzed to compute their intramolecular interactions and distribution of secondary structure. Subsequently, simulated thermal denaturation and docking studies were performed to determine their structural variations, which in turn alter the formation of active complex that comprises STK11, STRAD, and MO25. The deleterious effect of the mutants would result in a comparative loss of enzyme function due to variations in their binding energy pertaining to spatial conformation and flexibility. Hence, the structural variations in binding energy exhibited by the mutants, viz., D194N, E199K, L160P, and Y49D, to that of the native, consequently lead to pathogenesis.

Selective Weighted Least Squares Method for Fourier Transform Infrared Quantitative Analysis.

PubMed

Wang, Xin; Li, Yan; Wei, Haoyun; Chen, Xia

2017-06-01

Classical least squares (CLS) regression is a popular multivariate statistical method used frequently for quantitative analysis using Fourier transform infrared (FT-IR) spectrometry. Classical least squares provides the best unbiased estimator for uncorrelated residual errors with zero mean and equal variance. However, the noise in FT-IR spectra, which accounts for a large portion of the residual errors, is heteroscedastic. Thus, if this noise with zero mean dominates in the residual errors, the weighted least squares (WLS) regression method described in this paper is a better estimator than CLS. However, if bias errors, such as the residual baseline error, are significant, WLS may perform worse than CLS. In this paper, we compare the effect of noise and bias error in using CLS and WLS in quantitative analysis. Results indicated that for wavenumbers with low absorbance, the bias error significantly affected the error, such that the performance of CLS is better than that of WLS. However, for wavenumbers with high absorbance, the noise significantly affected the error, and WLS proves to be better than CLS. Thus, we propose a selective weighted least squares (SWLS) regression that processes data with different wavenumbers using either CLS or WLS based on a selection criterion, i.e., lower or higher than an absorbance threshold. The effects of various factors on the optimal threshold value (OTV) for SWLS have been studied through numerical simulations. These studies reported that: (1) the concentration and the analyte type had minimal effect on OTV; and (2) the major factor that influences OTV is the ratio between the bias error and the standard deviation of the noise. The last part of this paper is dedicated to quantitative analysis of methane gas spectra, and methane/toluene mixtures gas spectra as measured using FT-IR spectrometry and CLS, WLS, and SWLS. The standard error of prediction (SEP), bias of prediction (bias), and the residual sum of squares of the errors

Search for charged Higgs bosons in decays of top quarks in pp collisions at square root s = 1.96 TeV.

PubMed

Aaltonen, T; Adelman, J; Akimoto, T; Alvarez González, B; Amerio, S; Amidei, D; Anastassov, A; Annovi, A; Antos, J; Apollinari, G; Apresyan, A; Arisawa, T; Artikov, A; Ashmanskas, W; Attal, A; Aurisano, A; Azfar, F; Azzurri, P; Badgett, W; Barbaro-Galtieri, A; Barnes, V E; Barnett, B A; Bartsch, V; Bauer, G; Beauchemin, P-H; Bedeschi, F; Beecher, D; Behari, S; Bellettini, G; Bellinger, J; Benjamin, D; Beretvas, A; Beringer, J; Bhatti, A; Binkley, M; Bisello, D; Bizjak, I; Blair, R E; Blocker, C; Blumenfeld, B; Bocci, A; Bodek, A; Boisvert, V; Bolla, G; Bortoletto, D; Boudreau, J; Boveia, A; Brau, B; Bridgeman, A; Brigliadori, L; Bromberg, C; Brubaker, E; Budagov, J; Budd, H S; Budd, S; Burke, S; Burkett, K; Busetto, G; Bussey, P; Buzatu, A; Byrum, K L; Cabrera, S; Calancha, C; Campanelli, M; Campbell, M; Canelli, F; Canepa, A; Carls, B; Carlsmith, D; Carosi, R; Carrillo, S; Carron, S; Casal, B; Casarsa, M; Castro, A; Catastini, P; Cauz, D; Cavaliere, V; Cavalli-Sforza, M; Cerri, A; Cerrito, L; Chang, S H; Chen, Y C; Chertok, M; Chiarelli, G; Chlachidze, G; Chlebana, F; Cho, K; Chokheli, D; Chou, J P; Choudalakis, G; Chuang, S H; Chung, K; Chung, W H; Chung, Y S; Chwalek, T; Ciobanu, C I; Ciocci, M A; Clark, A; Clark, D; Compostella, G; Convery, M E; Conway, J; Cordelli, M; Cortiana, G; Cox, C A; Cox, D J; Crescioli, F; Cuenca Almenar, C; Cuevas, J; Culbertson, R; Cully, J C; Dagenhart, D; Datta, M; Davies, T; de Barbaro, P; De Cecco, S; Deisher, A; De Lorenzo, G; Dell'orso, M; Deluca, C; Demortier, L; Deng, J; Deninno, M; Derwent, P F; di Giovanni, G P; Dionisi, C; Di Ruzza, B; Dittmann, J R; D'Onofrio, M; Donati, S; Dong, P; Donini, J; Dorigo, T; Dube, S; Efron, J; Elagin, A; Erbacher, R; Errede, D; Errede, S; Eusebi, R; Fang, H C; Farrington, S; Fedorko, W T; Feild, R G; Feindt, M; Fernandez, J P; Ferrazza, C; Field, R; Flanagan, G; Forrest, R; Frank, M J; Franklin, M; Freeman, J C; Furic, I; Gallinaro, M; Galyardt, J; Garberson, F; Garcia, J E; Garfinkel, A F; Genser, K; Gerberich, H; Gerdes, D; Gessler, A; Giagu, S; Giakoumopoulou, V; Giannetti, P; Gibson, K; Gimmell, J L; Ginsburg, C M; Giokaris, N; Giordani, M; Giromini, P; Giunta, M; Giurgiu, G; Glagolev, V; Glenzinski, D; Gold, M; Goldschmidt, N; Golossanov, A; Gomez, G; Gomez-Ceballos, G; Goncharov, M; González, O; Gorelov, I; Goshaw, A T; Goulianos, K; Gresele, A; Grinstein, S; Grosso-Pilcher, C; Grundler, U; Guimaraes da Costa, J; Gunay-Unalan, Z; Haber, C; Hahn, K; Hahn, S R; Halkiadakis, E; Han, B-Y; Han, J Y; Happacher, F; Hara, K; Hare, D; Hare, M; Harper, S; Harr, R F; Harris, R M; Hartz, M; Hatakeyama, K; Hays, C; Heck, M; Heijboer, A; Heinrich, J; Henderson, C; Herndon, M; Heuser, J; Hewamanage, S; Hidas, D; Hill, C S; Hirschbuehl, D; Hocker, A; Hou, S; Houlden, M; Hsu, S-C; Huffman, B T; Hughes, R E; Husemann, U; Hussein, M; Huston, J; Incandela, J; Introzzi, G; Iori, M; Ivanov, A; James, E; Jang, D; Jayatilaka, B; Jeon, E J; Jha, M K; Jindariani, S; Johnson, W; Jones, M; Joo, K K; Jun, S Y; Jung, J E; Junk, T R; Kamon, T; Kar, D; Karchin, P E; Kato, Y; Kephart, R; Keung, J; Khotilovich, V; Kilminster, B; Kim, D H; Kim, H S; Kim, H W; Kim, J E; Kim, M J; Kim, S B; Kim, S H; Kim, Y K; Kimura, N; Kirsch, L; Klimenko, S; Knuteson, B; Ko, B R; Kondo, K; Kong, D J; Konigsberg, J; Korytov, A; Kotwal, A V; Kreps, M; Kroll, J; Krop, D; Krumnack, N; Kruse, M; Krutelyov, V; Kubo, T; Kuhr, T; Kulkarni, N P; Kurata, M; Kwang, S; Laasanen, A T; Lami, S; Lammel, S; Lancaster, M; Lander, R L; Lannon, K; Lath, A; Latino, G; Lazzizzera, I; Lecompte, T; Lee, E; Lee, H S; Lee, S W; Leone, S; Lewis, J D; Lin, C-S; Linacre, J; Lindgren, M; Lipeles, E; Lister, A; Litvintsev, D O; Liu, C; Liu, T; Lockyer, N S; Loginov, A; Loreti, M; Lovas, L; Lucchesi, D; Luci, C; Lueck, J; Lujan, P; Lukens, P; Lungu, G; Lyons, L; Lys, J; Lysak, R; Macqueen, D; Madrak, R; Maeshima, K; Makhoul, K; Maki, T; Maksimovic, P; Malde, S; Malik, S; Manca, G; Manousakis-Katsikakis, A; Margaroli, F; Marino, C; Marino, C P; Martin, A; Martin, V; Martínez, M; Martínez-Ballarín, R; Maruyama, T; Mastrandrea, P; Masubuchi, T; Mathis, M; Mattson, M E; Mazzanti, P; McFarland, K S; McIntyre, P; McNulty, R; Mehta, A; Mehtala, P; Menzione, A; Merkel, P; Mesropian, C; Miao, T; Miladinovic, N; Miller, R; Mills, C; Milnik, M; Mitra, A; Mitselmakher, G; Miyake, H; Moggi, N; Moon, C S; Moore, R; Morello, M J; Morlock, J; Movilla Fernandez, P; Mülmenstädt, J; Mukherjee, A; Muller, Th; Mumford, R; Murat, P; Mussini, M; Nachtman, J; Nagai, Y; Nagano, A; Naganoma, J; Nakamura, K; Nakano, I; Napier, A; Necula, V; Nett, J; Neu, C; Neubauer, M S; Neubauer, S; Nielsen, J; Nodulman, L; Norman, M; Norniella, O; Nurse, E; Oakes, L; Oh, S H; Oh, Y D; Oksuzian, I; Okusawa, T; Orava, R; Osterberg, K; Pagan Griso, S; Palencia, E; Papadimitriou, V; Papaikonomou, A; Paramonov, A A; Parks, B; Pashapour, S; Patrick, J; Pauletta, G; Paulini, M; Paus, C; Peiffer, T; Pellett, D E; Penzo, A; Phillips, T J; Piacentino, G; Pianori, E; Pinera, L; Pitts, K; Plager, C; Pondrom, L; Poukhov, O; Pounder, N; Prakoshyn, F; Pronko, A; Proudfoot, J; Ptohos, F; Pueschel, E; Punzi, G; Pursley, J; Rademacker, J; Rahaman, A; Ramakrishnan, V; Ranjan, N; Redondo, I; Renton, P; Renz, M; Rescigno, M; Richter, S; Rimondi, F; Ristori, L; Robson, A; Rodrigo, T; Rodriguez, T; Rogers, E; Rolli, S; Roser, R; Rossi, M; Rossin, R; Roy, P; Ruiz, A; Russ, J; Rusu, V; Saarikko, H; Safonov, A; Sakumoto, W K; Saltó, O; Santi, L; Sarkar, S; Sartori, L; Sato, K; Savoy-Navarro, A; Schlabach, P; Schmidt, A; Schmidt, E E; Schmidt, M A; Schmidt, M P; Schmitt, M; Schwarz, T; Scodellaro, L; Scribano, A; Scuri, F; Sedov, A; Seidel, S; Seiya, Y; Semenov, A; Sexton-Kennedy, L; Sforza, F; Sfyrla, A; Shalhout, S Z; Shears, T; Shepard, P F; Shimojima, M; Shiraishi, S; Shochet, M; Shon, Y; Shreyber, I; Sidoti, A; Sinervo, P; Sisakyan, A; Slaughter, A J; Slaunwhite, J; Sliwa, K; Smith, J R; Snider, F D; Snihur, R; Soha, A; Somalwar, S; Sorin, V; Spalding, J; Spreitzer, T; Squillacioti, P; Stanitzki, M; St Denis, R; Stelzer, B; Stelzer-Chilton, O; Stentz, D; Strologas, J; Strycker, G L; Stuart, D; Suh, J S; Sukhanov, A; Suslov, I; Suzuki, T; Taffard, A; Takashima, R; Takeuchi, Y; Tanaka, R; Tecchio, M; Teng, P K; Terashi, K; Thom, J; Thompson, A S; Thompson, G A; Thomson, E; Tipton, P; Ttito-Guzmán, P; Tkaczyk, S; Toback, D; Tokar, S; Tollefson, K; Tomura, T; Tonelli, D; Torre, S; Torretta, D; Totaro, P; Tourneur, S; Trovato, M; Tsai, S-Y; Tu, Y; Turini, N; Ukegawa, F; Vallecorsa, S; van Remortel, N; Varganov, A; Vataga, E; Vázquez, F; Velev, G; Vellidis, C; Vidal, M; Vidal, R; Vila, I; Vilar, R; Vine, T; Vogel, M; Volobouev, I; Volpi, G; Wagner, P; Wagner, R G; Wagner, R L; Wagner, W; Wagner-Kuhr, J; Wakisaka, T; Wallny, R; Wang, S M; Warburton, A; Waters, D; Weinberger, M; Weinelt, J; Wester, W C; Whitehouse, B; Whiteson, D; Wicklund, A B; Wicklund, E; Wilbur, S; Williams, G; Williams, H H; Wilson, P; Winer, B L; Wittich, P; Wolbers, S; Wolfe, C; Wright, T; Wu, X; Würthwein, F; Xie, S; Yagil, A; Yamamoto, K; Yamaoka, J; Yang, U K; Yang, Y C; Yao, W M; Yeh, G P; Yoh, J; Yorita, K; Yoshida, T; Yu, G B; Yu, I; Yu, S S; Yun, J C; Zanello, L; Zanetti, A; Zhang, X; Zheng, Y; Zucchelli, S

2009-09-04

We report on the first direct search for charged Higgs bosons decaying into cs in tt events produced by pp collisions at square root s = 1.96 TeV. The search uses a data sample corresponding to an integrated luminosity of 2.2 fb(-1) collected by the CDF II detector at Fermilab and looks for a resonance in the invariant mass distribution of two jets in the lepton + jets sample of tt candidates. We observe no evidence of charged Higgs bosons in top quark decays. Hence, 95% upper limits on the top quark decay branching ratio are placed at B(t --> H(+)b)< 0.1 to 0.3 for charged Higgs boson masses of 60 to 150 GeV/c(2) assuming B(H(+) --> cs)=1.0. The upper limits on B(t --> H(+)b) are also used as model-independent limits on the decay branching ratio of top quarks to generic scalar charged bosons beyond the standard model.

Structural Model for the Interaction of a Designed Ankyrin Repeat Protein with the Human Epidermal Growth Factor Receptor 2

PubMed Central

Epa, V. Chandana; Dolezal, Olan; Doughty, Larissa; Xiao, Xiaowen; Jost, Christian; Plückthun, Andreas; Adams, Timothy E.

2013-01-01

Designed Ankyrin Repeat Proteins are a class of novel binding proteins that can be selected and evolved to bind to targets with high affinity and specificity. We are interested in the DARPin H10-2-G3, which has been evolved to bind with very high affinity to the human epidermal growth factor receptor 2 (HER2). HER2 is found to be over-expressed in 30% of breast cancers, and is the target for the FDA-approved therapeutic monoclonal antibodies trastuzumab and pertuzumab and small molecule tyrosine kinase inhibitors. Here, we use computational macromolecular docking, coupled with several interface metrics such as shape complementarity, interaction energy, and electrostatic complementarity, to model the structure of the complex between the DARPin H10-2-G3 and HER2. We analyzed the interface between the two proteins and then validated the structural model by showing that selected HER2 point mutations at the putative interface with H10-2-G3 reduce the affinity of binding up to 100-fold without affecting the binding of trastuzumab. Comparisons made with a subsequently solved X-ray crystal structure of the complex yielded a backbone atom root mean square deviation of 0.84–1.14 Ångstroms. The study presented here demonstrates the capability of the computational techniques of structural bioinformatics in generating useful structural models of protein-protein interactions. PMID:23527120

Molecular Dynamics Simulation of WSK-3, a Computationally Designed, Water-Soluble Variant of the Integral Membrane Protein KcsA

PubMed Central

Bronson, Jonathan; Lee, One-Sun; Saven, Jeffery G.

2006-01-01

Poor solubility and low expression levels often make membrane proteins difficult to study. An alternative to the use of detergents to solubilize these aggregation-prone proteins is the partial redesign of the sequence so as to confer water solubility. Recently, computationally assisted membrane protein solubilization (CAMPS) has been reported, where exposed hydrophobic residues on a protein's surface are computationally redesigned. Herein, the structure and fluctuations of a designed, water-soluble variant of KcsA (WSK-3) were studied using molecular dynamics simulations. The root mean square deviation of the protein from its starting structure, where the backbone coordinates are those of KcsA, was 1.8 Å. The structure of salt bridges involved in structural specificity and solubility were examined. The preferred configuration of ions and water in the selectivity filter of WSK-3 was consistent with the reported preferences for KcsA. The structure of the selectivity filter was maintained, which is consistent with WSK-3 having an affinity for agitoxin2 comparable to that of wild-type KcsA. In contrast to KcsA, the central cavity's side chains were observed to reorient, allowing water diffusion through the side of the cavity wall. These simulations provide an atomistic analysis of the CAMPS strategy and its implications for further investigations of membrane proteins. PMID:16299086

Rapid search for tertiary fragments reveals protein sequence–structure relationships

PubMed Central

Zhou, Jianfu; Grigoryan, Gevorg

2015-01-01

Finding backbone substructures from the Protein Data Bank that match an arbitrary query structural motif, composed of multiple disjoint segments, is a problem of growing relevance in structure prediction and protein design. Although numerous protein structure search approaches have been proposed, methods that address this specific task without additional restrictions and on practical time scales are generally lacking. Here, we propose a solution, dubbed MASTER, that is both rapid, enabling searches over the Protein Data Bank in a matter of seconds, and provably correct, finding all matches below a user-specified root-mean-square deviation cutoff. We show that despite the potentially exponential time complexity of the problem, running times in practice are modest even for queries with many segments. The ability to explore naturally plausible structural and sequence variations around a given motif has the potential to synthesize its design principles in an automated manner; so we go on to illustrate the utility of MASTER to protein structural biology. We demonstrate its capacity to rapidly establish structure–sequence relationships, uncover the native designability landscapes of tertiary structural motifs, identify structural signatures of binding, and automatically rewire protein topologies. Given the broad utility of protein tertiary fragment searches, we hope that providing MASTER in an open-source format will enable novel advances in understanding, predicting, and designing protein structure. PMID:25420575

RCD+: Fast loop modeling server.

PubMed

López-Blanco, José Ramón; Canosa-Valls, Alejandro Jesús; Li, Yaohang; Chacón, Pablo

2016-07-08

Modeling loops is a critical and challenging step in protein modeling and prediction. We have developed a quick online service (http://rcd.chaconlab.org) for ab initio loop modeling combining a coarse-grained conformational search with a full-atom refinement. Our original Random Coordinate Descent (RCD) loop closure algorithm has been greatly improved to enrich the sampling distribution towards near-native conformations. These improvements include a new workflow optimization, MPI-parallelization and fast backbone angle sampling based on neighbor-dependent Ramachandran probability distributions. The server starts by efficiently searching the vast conformational space from only the loop sequence information and the environment atomic coordinates. The generated closed loop models are subsequently ranked using a fast distance-orientation dependent energy filter. Top ranked loops are refined with the Rosetta energy function to obtain accurate all-atom predictions that can be interactively inspected in an user-friendly web interface. Using standard benchmarks, the average root mean squared deviation (RMSD) is 0.8 and 1.4 Å for 8 and 12 residues loops, respectively, in the challenging modeling scenario in where the side chains of the loop environment are fully remodeled. These results are not only very competitive compared to those obtained with public state of the art methods, but also they are obtained ∼10-fold faster. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Inferences from structural comparison: flexibility, secondary structure wobble and sequence alignment optimization.

PubMed

Zhang, Gaihua; Su, Zhen

2012-01-01

Work on protein structure prediction is very useful in biological research. To evaluate their accuracy, experimental protein structures or their derived data are used as the 'gold standard'. However, as proteins are dynamic molecular machines with structural flexibility such a standard may be unreliable. To investigate the influence of the structure flexibility, we analysed 3,652 protein structures of 137 unique sequences from 24 protein families. The results showed that (1) the three-dimensional (3D) protein structures were not rigid: the root-mean-square deviation (RMSD) of the backbone Cα of structures with identical sequences was relatively large, with the average of the maximum RMSD from each of the 137 sequences being 1.06 Å; (2) the derived data of the 3D structure was not constant, e.g. the highest ratio of the secondary structure wobble site was 60.69%, with the sequence alignments from structural comparisons of two proteins in the same family sometimes being completely different. Proteins may have several stable conformations and the data derived from resolved structures as a 'gold standard' should be optimized before being utilized as criteria to evaluate the prediction methods, e.g. sequence alignment from structural comparison. Helix/β-sheet transition exists in normal free proteins. The coil ratio of the 3D structure could affect its resolution as determined by X-ray crystallography.

Soil moisture depletion under simulated drought in the Amazon: impacts on deep root uptake.

PubMed

Markewitz, Daniel; Devine, Scott; Davidson, Eric A; Brando, Paulo; Nepstad, Daniel C

2010-08-01

*Deep root water uptake in tropical Amazonian forests has been a major discovery during the last 15 yr. However, the effects of extended droughts, which may increase with climate change, on deep soil moisture utilization remain uncertain. *The current study utilized a 1999-2005 record of volumetric water content (VWC) under a throughfall exclusion experiment to calibrate a one-dimensional model of the hydrologic system to estimate VWC, and to quantify the rate of root uptake through 11.5 m of soil. *Simulations with root uptake compensation had a relative root mean square error (RRMSE) of 11% at 0-40 cm and < 5% at 350-1150 cm. The simulated contribution of deep root uptake under the control was c. 20% of water demand from 250 to 550 cm and c. 10% from 550 to 1150 cm. Furthermore, in years 2 (2001) and 3 (2002) of throughfall exclusion, deep root uptake increased as soil moisture was available but then declined to near zero in deep layers in 2003 and 2004. *Deep root uptake was limited despite high VWC (i.e. > 0.30 cm(3) cm(-3)). This limitation may partly be attributable to high residual water contents (theta(r)) in these high-clay (70-90%) soils or due to high soil-to-root resistance. The ability of deep roots and soils to contribute increasing amounts of water with extended drought will be limited.

Insights into the folding pathway of the Engrailed Homeodomain protein using replica exchange molecular dynamics simulations.

PubMed

Koulgi, Shruti; Sonavane, Uddhavesh; Joshi, Rajendra

2010-11-01

Protein folding studies were carried out by performing microsecond time scale simulations on the ultrafast/fast folding protein Engrailed Homeodomain (EnHD) from Drosophila melanogaster. It is a three-helix bundle protein consisting of 54 residues (PDB ID: 1ENH). The positions of the helices are 8-20 (Helix I), 26-36 (Helix II) and 40-53 (Helix III). The second and third helices together form a Helix-Turn-Helix (HTH) motif which belongs to the family of DNA binding proteins. The molecular dynamics (MD) simulations were performed using replica exchange molecular dynamics (REMD). REMD is a method that involves simulating a protein at different temperatures and performing exchanges at regular time intervals. These exchanges were accepted or rejected based on the Metropolis criterion. REMD was performed using the AMBER FF03 force field with the generalised Born solvation model for the temperature range 286-373 K involving 30 replicas. The extended conformation of the protein was used as the starting structure. A simulation of 600 ns per replica was performed resulting in an overall simulation time of 18 μs. The protein was seen to fold close to the native state with backbone root mean square deviation (RMSD) of 3.16 Å. In this low RMSD structure, the Helix I was partially formed with a backbone RMSD of 3.37 Å while HTH motif had an RMSD of 1.81 Å. Analysis suggests that EnHD folds to its native structure via an intermediate in which the HTH motif is formed. The secondary structure development occurs first followed by tertiary packing. The results were in good agreement with the experimental findings. Copyright © 2010 Elsevier Inc. All rights reserved.

An exhaustive survey of regular peptide conformations using a new metric for backbone handedness ( h )

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

Mannige, Ranjan V.

The Ramachandran plot is important to structural biology as it describes a peptide backbone in the context of its dominant degrees of freedom—the backbone dihedral anglesφandψ(Ramachandran, Ramakrishnan & Sasisekharan, 1963). Since its introduction, the Ramachandran plot has been a crucial tool to characterize protein backbone features. However, the conformation or twist of a backbone as a function ofφandψhas not been completely described for bothcisandtransbackbones. Additionally, little intuitive understanding is available about a peptide’s conformation simply from knowing theφandψvalues of a peptide (e.g., is the regular peptide defined byφ = ψ =  - 100°  left-handed or right-handed?). This report provides a new metric for backbone handednessmore » (h) based on interpreting a peptide backbone as a helix with axial displacementdand angular displacementθ, both of which are derived from a peptide backbone’s internal coordinates, especially dihedral anglesφ,ψandω. In particular,hequals sin(θ)d/d|, with range [-1, 1] and negative (or positive) values indicating left(or right)-handedness. The metrichis used to characterize the handedness of every region of the Ramachandran plot for bothcis(ω = 0°) and trans (ω = 180°) backbones, which provides the first exhaustive survey of twist handedness in Ramachandran (φ,ψ) space. These maps fill in the ‘dead space’ within the Ramachandran plot, which are regions that are not commonly accessed by structured proteins, but which may be accessible to intrinsically disordered proteins, short peptide fragments, and protein mimics such as peptoids. Finally, building on the work of (Zacharias & Knapp, 2013), this report presents a new plot based ondandθthat serves as a universal and intuitive alternative to the Ramachandran plot. The universality arises from the fact that the co-inhabitants of such a plot include every possible peptide backbone includingcisandtransbackbones. The intuitiveness

An exhaustive survey of regular peptide conformations using a new metric for backbone handedness ( h )

DOE PAGES

Mannige, Ranjan V.

2017-05-16

The Ramachandran plot is important to structural biology as it describes a peptide backbone in the context of its dominant degrees of freedom—the backbone dihedral anglesφandψ(Ramachandran, Ramakrishnan & Sasisekharan, 1963). Since its introduction, the Ramachandran plot has been a crucial tool to characterize protein backbone features. However, the conformation or twist of a backbone as a function ofφandψhas not been completely described for bothcisandtransbackbones. Additionally, little intuitive understanding is available about a peptide’s conformation simply from knowing theφandψvalues of a peptide (e.g., is the regular peptide defined byφ = ψ =  - 100°  left-handed or right-handed?). This report provides a new metric for backbone handednessmore » (h) based on interpreting a peptide backbone as a helix with axial displacementdand angular displacementθ, both of which are derived from a peptide backbone’s internal coordinates, especially dihedral anglesφ,ψandω. In particular,hequals sin(θ)d/d|, with range [-1, 1] and negative (or positive) values indicating left(or right)-handedness. The metrichis used to characterize the handedness of every region of the Ramachandran plot for bothcis(ω = 0°) and trans (ω = 180°) backbones, which provides the first exhaustive survey of twist handedness in Ramachandran (φ,ψ) space. These maps fill in the ‘dead space’ within the Ramachandran plot, which are regions that are not commonly accessed by structured proteins, but which may be accessible to intrinsically disordered proteins, short peptide fragments, and protein mimics such as peptoids. Finally, building on the work of (Zacharias & Knapp, 2013), this report presents a new plot based ondandθthat serves as a universal and intuitive alternative to the Ramachandran plot. The universality arises from the fact that the co-inhabitants of such a plot include every possible peptide backbone includingcisandtransbackbones. The intuitiveness

SMERGE: A multi-decadal root-zone soil moisture product for CONUS

NASA Astrophysics Data System (ADS)

Crow, W. T.; Dong, J.; Tobin, K. J.; Torres, R.

2017-12-01

Multi-decadal root-zone soil moisture products are of value for a range of water resource and climate applications. The NASA-funded root-zone soil moisture merging project (SMERGE) seeks to develop such products through the optimal merging of land surface model predictions with surface soil moisture retrievals acquired from multi-sensor remote sensing products. This presentation will describe the creation and validation of a daily, multi-decadal (1979-2015), vertically-integrated (both surface to 40 cm and surface to 100 cm), 0.125-degree root-zone product over the contiguous United States (CONUS). The modeling backbone of the system is based on hourly root-zone soil moisture simulations generated by the Noah model (v3.2) operating within the North American Land Data Assimilation System (NLDAS-2). Remotely-sensed surface soil moisture retrievals are taken from the multi-sensor European Space Agency Climate Change Initiative soil moisture data set (ESA CCI SM). In particular, the talk will detail: 1) the exponential smoothing approach used to convert surface ESA CCI SM retrievals into root-zone soil moisture estimates, 2) the averaging technique applied to merge (temporally-sporadic) remotely-sensed with (continuous) NLDAS-2 land surface model estimates of root-zone soil moisture into the unified SMERGE product, and 3) the validation of the SMERGE product using long-term, ground-based soil moisture datasets available within CONUS.

Baseline correction combined partial least squares algorithm and its application in on-line Fourier transform infrared quantitative analysis.

PubMed

Peng, Jiangtao; Peng, Silong; Xie, Qiong; Wei, Jiping

2011-04-01

In order to eliminate the lower order polynomial interferences, a new quantitative calibration algorithm "Baseline Correction Combined Partial Least Squares (BCC-PLS)", which combines baseline correction and conventional PLS, is proposed. By embedding baseline correction constraints into PLS weights selection, the proposed calibration algorithm overcomes the uncertainty in baseline correction and can meet the requirement of on-line attenuated total reflectance Fourier transform infrared (ATR-FTIR) quantitative analysis. The effectiveness of the algorithm is evaluated by the analysis of glucose and marzipan ATR-FTIR spectra. BCC-PLS algorithm shows improved prediction performance over PLS. The root mean square error of cross-validation (RMSECV) on marzipan spectra for the prediction of the moisture is found to be 0.53%, w/w (range 7-19%). The sugar content is predicted with a RMSECV of 2.04%, w/w (range 33-68%). Copyright © 2011 Elsevier B.V. All rights reserved.

The Predisposing Factors between Dental Caries and Deviations from Normal Weight.

PubMed

Chopra, Amandeep; Rao, Nanak Chand; Gupta, Nidhi; Vashisth, Shelja; Lakhanpal, Manav

2015-04-01

Dental caries and deviations from normal weight are two conditions which share several broadly predisposing factors. So it's important to understand any relationship between dental state and body weight if either is to be managed appropriately. The study was done to find out the correlation between body mass index (BMI), diet, and dental caries among 12-15-year-old schoolgoing children in Panchkula District. A multistage sample of 12-15-year-old school children (n = 810) in Panchkula district, Haryana was considered. Child demographic details and diet history for 5 days was recorded. Data regarding dental caries status was collected using World Health Organization (1997) format. BMI was calculated and categorized according to the World Health Organization classification system for BMI. The data were subjected to statistical analysis using chi-square test and binomial regression developed using the Statistical Package for Social Sciences (SPSS) 20.0. The mean Decayed Missing Filled Teeth (DMFT) score was found to be 1.72 with decayed, missing, and filled teeth to be 1.22, 0.04, and 0.44, respectively. When the sample was assessed based on type of diet, it was found that vegetarians had higher mean DMFT (1.72) as compared to children having mixed diet. Overweight children had highest DMFT (3.21) which was followed by underweight (2.31) and obese children (2.23). Binomial regression revealed that females were 1.293 times at risk of developing caries as compared to males. Fair and poor Simplified-Oral Hygiene Index (OHI-S) showed 3.920 and 4.297 times risk of developing caries as compared to good oral hygiene, respectively. Upper high socioeconomic status (SES) is at most risk of developing caries. Underweight, overweight, and obese are at 2.7, 2.5, and 3 times risk of developing caries as compared to children with normal BMI, respectively. Dental caries and deviations from normal weight are two conditions which share several broadly predisposing factors such as diet

Bio-inspired optimization algorithms for optical parameter extraction of dielectric materials: A comparative study

NASA Astrophysics Data System (ADS)

Ghulam Saber, Md; Arif Shahriar, Kh; Ahmed, Ashik; Hasan Sagor, Rakibul

2016-10-01

Particle swarm optimization (PSO) and invasive weed optimization (IWO) algorithms are used for extracting the modeling parameters of materials useful for optics and photonics research community. These two bio-inspired algorithms are used here for the first time in this particular field to the best of our knowledge. The algorithms are used for modeling graphene oxide and the performances of the two are compared. Two objective functions are used for different boundary values. Root mean square (RMS) deviation is determined and compared.

Geometrical Solutions of Some Quadratic Equations with Non-Real Roots

ERIC Educational Resources Information Center

Pathak, H. K.; Grewal, A. S.

2002-01-01

This note gives geometrical/graphical methods of finding solutions of the quadratic equation ax[squared] + bx + c = 0, a [not equal to] 0, with non-real roots. Three different cases which give rise to non-real roots of the quadratic equation have been discussed. In case I a geometrical construction and its proof for finding the solutions of the…

Hypoglycemia Early Alarm Systems Based on Recursive Autoregressive Partial Least Squares Models

PubMed Central

Bayrak, Elif Seyma; Turksoy, Kamuran; Cinar, Ali; Quinn, Lauretta; Littlejohn, Elizabeth; Rollins, Derrick

2013-01-01

Background Hypoglycemia caused by intensive insulin therapy is a major challenge for artificial pancreas systems. Early detection and prevention of potential hypoglycemia are essential for the acceptance of fully automated artificial pancreas systems. Many of the proposed alarm systems are based on interpretation of recent values or trends in glucose values. In the present study, subject-specific linear models are introduced to capture glucose variations and predict future blood glucose concentrations. These models can be used in early alarm systems of potential hypoglycemia. Methods A recursive autoregressive partial least squares (RARPLS) algorithm is used to model the continuous glucose monitoring sensor data and predict future glucose concentrations for use in hypoglycemia alarm systems. The partial least squares models constructed are updated recursively at each sampling step with a moving window. An early hypoglycemia alarm algorithm using these models is proposed and evaluated. Results Glucose prediction models based on real-time filtered data has a root mean squared error of 7.79 and a sum of squares of glucose prediction error of 7.35% for six-step-ahead (30 min) glucose predictions. The early alarm systems based on RARPLS shows good performance. A sensitivity of 86% and a false alarm rate of 0.42 false positive/day are obtained for the early alarm system based on six-step-ahead predicted glucose values with an average early detection time of 25.25 min. Conclusions The RARPLS models developed provide satisfactory glucose prediction with relatively smaller error than other proposed algorithms and are good candidates to forecast and warn about potential hypoglycemia unless preventive action is taken far in advance. PMID:23439179

Hypoglycemia early alarm systems based on recursive autoregressive partial least squares models.

PubMed

Bayrak, Elif Seyma; Turksoy, Kamuran; Cinar, Ali; Quinn, Lauretta; Littlejohn, Elizabeth; Rollins, Derrick

2013-01-01

Hypoglycemia caused by intensive insulin therapy is a major challenge for artificial pancreas systems. Early detection and prevention of potential hypoglycemia are essential for the acceptance of fully automated artificial pancreas systems. Many of the proposed alarm systems are based on interpretation of recent values or trends in glucose values. In the present study, subject-specific linear models are introduced to capture glucose variations and predict future blood glucose concentrations. These models can be used in early alarm systems of potential hypoglycemia. A recursive autoregressive partial least squares (RARPLS) algorithm is used to model the continuous glucose monitoring sensor data and predict future glucose concentrations for use in hypoglycemia alarm systems. The partial least squares models constructed are updated recursively at each sampling step with a moving window. An early hypoglycemia alarm algorithm using these models is proposed and evaluated. Glucose prediction models based on real-time filtered data has a root mean squared error of 7.79 and a sum of squares of glucose prediction error of 7.35% for six-step-ahead (30 min) glucose predictions. The early alarm systems based on RARPLS shows good performance. A sensitivity of 86% and a false alarm rate of 0.42 false positive/day are obtained for the early alarm system based on six-step-ahead predicted glucose values with an average early detection time of 25.25 min. The RARPLS models developed provide satisfactory glucose prediction with relatively smaller error than other proposed algorithms and are good candidates to forecast and warn about potential hypoglycemia unless preventive action is taken far in advance. © 2012 Diabetes Technology Society.

Protein simulation using coarse-grained two-bead multipole force field with polarizable water models.

PubMed

Li, Min; Zhang, John Z H

2017-02-14

A recently developed two-bead multipole force field (TMFF) is employed in coarse-grained (CG) molecular dynamics (MD) simulation of proteins in combination with polarizable CG water models, the Martini polarizable water model, and modified big multipole water model. Significant improvement in simulated structures and dynamics of proteins is observed in terms of both the root-mean-square deviations (RMSDs) of the structures and residue root-mean-square fluctuations (RMSFs) from the native ones in the present simulation compared with the simulation result with Martini's non-polarizable water model. Our result shows that TMFF simulation using CG water models gives much stable secondary structures of proteins without the need for adding extra interaction potentials to constrain the secondary structures. Our result also shows that by increasing the MD time step from 2 fs to 6 fs, the RMSD and RMSF results are still in excellent agreement with those from all-atom simulations. The current study demonstrated clearly that the application of TMFF together with a polarizable CG water model significantly improves the accuracy and efficiency for CG simulation of proteins.

[Application of genetic algorithm in blending technology for extractions of Cortex Fraxini].

PubMed

Yang, Ming; Zhou, Yinmin; Chen, Jialei; Yu, Minying; Shi, Xiufeng; Gu, Xijun

2009-10-01

To explore the feasibility of genetic algorithm (GA) on multiple objective blending technology for extractions of Cortex Fraxini. According to that the optimization objective was the combination of fingerprint similarity and the root-mean-square error of multiple key constituents, a new multiple objective optimization model of 10 batches extractions of Cortex Fraxini was built. The blending coefficient was obtained by genetic algorithm. The quality of 10 batches extractions of Cortex Fraxini that after blending was evaluated with the finger print similarity and root-mean-square error as indexes. The quality of 10 batches extractions of Cortex Fraxini that after blending was well improved. Comparing with the fingerprint of the control sample, the similarity was up, but the degree of variation is down. The relative deviation of the key constituents was less than 10%. It is proved that genetic algorithm works well on multiple objective blending technology for extractions of Cortex Fraxini. This method can be a reference to control the quality of extractions of Cortex Fraxini. Genetic algorithm in blending technology for extractions of Chinese medicines is advisable.

Protein simulation using coarse-grained two-bead multipole force field with polarizable water models

NASA Astrophysics Data System (ADS)

Li, Min; Zhang, John Z. H.

2017-02-01

A recently developed two-bead multipole force field (TMFF) is employed in coarse-grained (CG) molecular dynamics (MD) simulation of proteins in combination with polarizable CG water models, the Martini polarizable water model, and modified big multipole water model. Significant improvement in simulated structures and dynamics of proteins is observed in terms of both the root-mean-square deviations (RMSDs) of the structures and residue root-mean-square fluctuations (RMSFs) from the native ones in the present simulation compared with the simulation result with Martini's non-polarizable water model. Our result shows that TMFF simulation using CG water models gives much stable secondary structures of proteins without the need for adding extra interaction potentials to constrain the secondary structures. Our result also shows that by increasing the MD time step from 2 fs to 6 fs, the RMSD and RMSF results are still in excellent agreement with those from all-atom simulations. The current study demonstrated clearly that the application of TMFF together with a polarizable CG water model significantly improves the accuracy and efficiency for CG simulation of proteins.

Structural test of the parameterized-backbone method for protein design.

PubMed

Plecs, Joseph J; Harbury, Pehr B; Kim, Peter S; Alber, Tom

2004-09-03

Designing new protein folds requires a method for simultaneously optimizing the conformation of the backbone and the side-chains. One approach to this problem is the use of a parameterized backbone, which allows the systematic exploration of families of structures. We report the crystal structure of RH3, a right-handed, three-helix coiled coil that was designed using a parameterized backbone and detailed modeling of core packing. This crystal structure was determined using another rationally designed feature, a metal-binding site that permitted experimental phasing of the X-ray data. RH3 adopted the intended fold, which has not been observed previously in biological proteins. Unanticipated structural asymmetry in the trimer was a principal source of variation within the RH3 structure. The sequence of RH3 differs from that of a previously characterized right-handed tetramer, RH4, at only one position in each 11 amino acid sequence repeat. This close similarity indicates that the design method is sensitive to the core packing interactions that specify the protein structure. Comparison of the structures of RH3 and RH4 indicates that both steric overlap and cavity formation provide strong driving forces for oligomer specificity.

Impact of aggregation on scaling behavior of Internet backbone traffic

NASA Astrophysics Data System (ADS)

Zhang, Zhi-Li; Ribeiro, Vinay J.; Moon, Sue B.; Diot, Christophe

2002-07-01

We study the impact of aggregation on the scaling behavior of Internet backbone tra ffic, based on traces collected from OC3 and OC12 links in a tier-1 ISP. We make two striking observations regarding the sub-second small time scaling behaviors of Internet backbone traffic: 1) for a majority of these traces, the Hurst parameters at small time scales (1ms - 100ms) are fairly close to 0.5. Hence the traffic at these time scales are nearly uncorrelated; 2) the scaling behaviors at small time scales are link-dependent, and stay fairly invariant over changing utilization and time. To understand the scaling behavior of network traffic, we develop analytical models and employ them to demonstrate how traffic composition -- aggregation of traffic with different characteristics -- affects the small-time scalings of network traffic. The degree of aggregation and burst correlation structure are two major factors in traffic composition. Our trace-based data analysis confirms this. Furthermore, we discover that traffic composition on a backbone link stays fairly consistent over time and changing utilization, which we believe is the cause for the invariant small-time scalings we observe in the traces.

Dealing with missing standard deviation and mean values in meta-analysis of continuous outcomes: a systematic review.

PubMed

Weir, Christopher J; Butcher, Isabella; Assi, Valentina; Lewis, Stephanie C; Murray, Gordon D; Langhorne, Peter; Brady, Marian C

2018-03-07

Rigorous, informative meta-analyses rely on availability of appropriate summary statistics or individual participant data. For continuous outcomes, especially those with naturally skewed distributions, summary information on the mean or variability often goes unreported. While full reporting of original trial data is the ideal, we sought to identify methods for handling unreported mean or variability summary statistics in meta-analysis. We undertook two systematic literature reviews to identify methodological approaches used to deal with missing mean or variability summary statistics. Five electronic databases were searched, in addition to the Cochrane Colloquium abstract books and the Cochrane Statistics Methods Group mailing list archive. We also conducted cited reference searching and emailed topic experts to identify recent methodological developments. Details recorded included the description of the method, the information required to implement the method, any underlying assumptions and whether the method could be readily applied in standard statistical software. We provided a summary description of the methods identified, illustrating selected methods in example meta-analysis scenarios. For missing standard deviations (SDs), following screening of 503 articles, fifteen methods were identified in addition to those reported in a previous review. These included Bayesian hierarchical modelling at the meta-analysis level; summary statistic level imputation based on observed SD values from other trials in the meta-analysis; a practical approximation based on the range; and algebraic estimation of the SD based on other summary statistics. Following screening of 1124 articles for methods estimating the mean, one approximate Bayesian computation approach and three papers based on alternative summary statistics were identified. Illustrative meta-analyses showed that when replacing a missing SD the approximation using the range minimised loss of precision and generally

A new characterization of three-dimensional conductivity backbone above and below the percolation threshold

NASA Astrophysics Data System (ADS)

Skal, Asya S.

1996-08-01

A new definition of three-dimensional conductivity backbone, obtained from a distribution function of Joule heat and the Hall coefficient is introduced. The fractal dimension d fB = d - ( {g}/{v}) = 2.25 of conductivity backbone for both sides of the threshold is obtained from a critical exponent of the Hall coefficient g = 0.6. This allows one to construct, below the threshold, a new order parameter of metal-conductor transition—the two-component infinite conductivity back-bone and tested scaling relation, proposed by Alexander and Orbach [ J. Phys. Rev. Lett.43, 1982, L625] for both sides of a threshold.

Directional virtual backbone based data aggregation scheme for Wireless Visual Sensor Networks.

PubMed

Zhang, Jing; Liu, Shi-Jian; Tsai, Pei-Wei; Zou, Fu-Min; Ji, Xiao-Rong

2018-01-01

Data gathering is a fundamental task in Wireless Visual Sensor Networks (WVSNs). Features of directional antennas and the visual data make WVSNs more complex than the conventional Wireless Sensor Network (WSN). The virtual backbone is a technique, which is capable of constructing clusters. The version associating with the aggregation operation is also referred to as the virtual backbone tree. In most of the existing literature, the main focus is on the efficiency brought by the construction of clusters that the existing methods neglect local-balance problems in general. To fill up this gap, Directional Virtual Backbone based Data Aggregation Scheme (DVBDAS) for the WVSNs is proposed in this paper. In addition, a measurement called the energy consumption density is proposed for evaluating the adequacy of results in the cluster-based construction problems. Moreover, the directional virtual backbone construction scheme is proposed by considering the local-balanced factor. Furthermore, the associated network coding mechanism is utilized to construct DVBDAS. Finally, both the theoretical analysis of the proposed DVBDAS and the simulations are given for evaluating the performance. The experimental results prove that the proposed DVBDAS achieves higher performance in terms of both the energy preservation and the network lifetime extension than the existing methods.

Influence of occlusal plane inclination and mandibular deviation on esthetics

PubMed Central

Corte, Cristiane Cherobini Dalla; da Silveira, Bruno Lopes; Marquezan, Mariana

2015-01-01

Objective: The aim of this study was to assess the degree of perception of occlusal plane inclination and mandibular deviation in facial esthetics, assessed by laypeople, dentists and orthodontists. Methods: A woman with 5.88° of inclination and 5.54 mm of mandibular deviation was selected and, based on her original photograph, four new images were created correcting the deviations and creating more symmetric faces and smiles. Examiners assessed the images by means of a questionnaire. Their opinions were compared by qualitative and quantitative analyses. Results: A total of 45 laypeople, 27 dentists and 31 orthodontists filled out the questionnaires. All groups were able to perceive the asymmetry; however, orthodontists were more sensitive, identifying asymmetries as from 4.32° of occlusal plane inclination and 4.155 mm of mandibular deviation (p< 0.05). The other categories of evaluators identified asymmetries and assigned significantly lower grades, starting from 5.88° of occlusal plane inclination and 5.54 mm of mandibular deviation (p< 0.05). Conclusion: Occlusal plane inclination and mandibular deviation were perceived by all groups, but orthodontists presented higher perception of deviations. PMID:26560821

A Note on Standard Deviation and Standard Error

ERIC Educational Resources Information Center

Hassani, Hossein; Ghodsi, Mansoureh; Howell, Gareth

2010-01-01

Many students confuse the standard deviation and standard error of the mean and are unsure which, if either, to use in presenting data. In this article, we endeavour to address these questions and cover some related ambiguities about these quantities.

Azimuthal anisotropy and correlations at large transverse momenta in p + p and Au + Au collisions at square root sNN=200 GeV.

PubMed

Adams, J; Aggarwal, M M; Ahammed, Z; Amonett, J; Anderson, B D; Arkhipkin, D; Averichev, G S; Badyal, S K; Bai, Y; Balewski, J; Barannikova, O; Barnby, L S; Baudot, J; Bekele, S; Belaga, V V; Bellwied, R; Berger, J; Bezverkhny, B I; Bharadwaj, S; Bhasin, A; Bhati, A K; Bhatia, V S; Bichsel, H; Billmeier, A; Bland, L C; Blyth, C O; Bonner, B E; Botje, M; Boucham, A; Brandin, A V; Bravar, A; Bystersky, M; Cadman, R V; Cai, X Z; Caines, H; Calderón de la Barca Sánchez, M; Carroll, J; Castillo, J; Cebra, D; Chajecki, Z; Chaloupka, P; Chattopdhyay, S; Chen, H F; Chen, Y; Cheng, J; Cherney, M; Chikanian, A; Christie, W; Coffin, J P; Cormier, T M; Cramer, J G; Crawford, H J; Das, D; Das, S; de Moura, M M; Derevschikov, A A; Didenko, L; Dietel, T; Dogra, S M; Dong, W J; Dong, X; Draper, J E; Du, F; Dubey, A K; Dunin, V B; Dunlop, J C; Dutta Mazumdar, M R; Eckardt, V; Edwards, W R; Efimov, L G; Emelianov, V; Engelage, J; Eppley, G; Erazmus, B; Estienne, M; Fachini, P; Faivre, J; Fatemi, R; Fedorisin, J; Filimonov, K; Filip, P; Finch, E; Fine, V; Fisyak, Y; Foley, K J; Fomenko, K; Fu, J; Gagliardi, C A; Gans, J; Ganti, M S; Gaudichet, L; Geurts, F; Ghazikhanian, V; Ghosh, P; Gonzalez, J E; Grachov, O; Grebenyuk, O; Grosnick, D; Guertin, S M; Guo, Y; Gupta, A; Gutierrez, T D; Hallman, T J; Hamed, A; Hardtke, D; Harris, J W; Heinz, M; Henry, T W; Hepplemann, S; Hippolyte, B; Hirsch, A; Hjort, E; Hoffmann, G W; Huang, H Z; Huang, S L; Hughes, E W; Humanic, T J; Igo, G; Ishihara, A; Jacobs, P; Jacobs, W W; Janik, M; Jiang, H; Jones, P G; Judd, E G; Kabana, S; Kang, K; Kaplan, M; Keane, D; Khodyrev, V Yu; Kiryluk, J; Kisiel, A; Kislov, E M; Klay, J; Klein, S R; Klyachko, A; Koetke, D D; Kollegger, T; Kopytine, M; Kotchenda, L; Kramer, M; Kravtsov, P; Kravtsov, V I; Krueger, K; Kuhn, C; Kulikov, A I; Kumar, A; Kunz, C L; Kutuev, R Kh; Kuznetsov, A A; Lamont, M A C; Landgraf, J M; Lange, S; Laue, F; Lauret, J; Lebedev, A; Lednicky, R; Lehocka, S; LeVine, M J; Li, C; Li, Q; Li, Y; Lindenbaum, S J; Lisa, M A; Liu, F; Liu, L; Liu, Q J; Liu, Z; Ljubicic, T; Llope, W J; Long, H; Longacre, R S; Lopez-Noriega, M; Love, W A; Lu, Y; Ludlam, T; Lynn, D; Ma, G L; Ma, J G; Ma, Y G; Magestro, D; Mahajan, S; Mahapatra, D P; Majka, R; Mangotra, L K; Manweiler, R; Margetis, S; Markert, C; Martin, L; Marx, J N; Matis, H S; Matulenko, Yu A; McClain, C J; McShane, T S; Meissner, F; Melnick, Yu; Meschanin, A; Miller, M L; Milosevich, Z; Minaev, N G; Mironov, C; Mischke, A; Mishra, D K; Mitchell, J; Mohanty, B; Molnar, L; Moore, C F; Morozov, D A; Munhoz, M G; Nandi, B K; Nayak, S K; Nayak, T K; Nelson, J M; Netrakanti, P K; Nikitin, V A; Nogach, L V; Nurushev, S B; Odyniec, G; Ogawa, A; Okorokov, V; Oldenburg, M; Olson, D; Pal, S K; Panebratsev, Y; Panitkin, S Y; Pavlinov, A I; Pawlak, T; Peitzmann, T; Perevoztchikov, V; Perkins, C; Peryt, W; Petrov, V A; Phatak, S C; Picha, R; Planinic, M; Pluta, J; Porile, N; Porter, J; Poskanzer, A M; Potekhin, M; Potrebenikova, E; Potukuchi, B V K S; Prindle, D; Pruneau, C; Putschke, J; Rai, G; Rakness, G; Raniwala, R; Raniwala, S; Ravel, O; Ray, R L; Razin, S V; Reichhold, D; Reid, J G; Renault, G; Retiere, F; Ridiger, A; Ritter, H G; Roberts, J B; Rogachevskiy, O V; Romero, J L; Rose, A; Roy, C; Ruan, L; Sahoo, R; Sakrejda, I; Salur, S; Sandweiss, J; Savin, I; Sazhin, P S; Schambach, J; Scharenberg, R P; Schmitz, N; Schroeder, L S; Schweda, K; Seger, J; Seyboth, P; Shahaliev, E; Shao, M; Shao, W; Sharma, M; Shen, W Q; Shestermanov, K E; Shimanskiy, S S; Sichtermann, E; Simon, F; Singaraju, R N; Skoro, G; Smirnov, N; Snellings, R; Sood, G; Sorensen, P; Sowinski, J; Speltz, J; Spinka, H M; Srivastava, B; Stadnik, A; Stanislaus, T D S; Stock, R; Stolpovsky, A; Strikhanov, M; Stringfellow, B; Suaide, A A P; Sugarbaker, E; Suire, C; Sumbera, M; Surrow, B; Symons, T J M; Szanto de Toledo, A; Szarwas, P; Tai, A; Takahashi, J; Tang, A H; Tarnowsky, T; Thein, D; Thomas, J H; Timoshenko, S; Tokarev, M; Trentalange, S; Tribble, R E; Tsai, O D; Ulery, J; Ullrich, T; Underwood, D G; Urkinbaev, A; Van Buren, G; van Leeuwen, M; Vander Molen, A M; Varma, R; Vasilevski, I M; Vasiliev, A N; Vernet, R; Vigdor, S E; Viyogi, Y P; Vokal, S; Voloshin, S A; Vznuzdaev, M; Waggoner, W T; Wang, F; Wang, G; Wang, G; Wang, X L; Wang, Y; Wang, Y; Wang, Z M; Ward, H; Watson, J W; Webb, J C; Wells, R; Westfall, G D; Wetzler, A; Whitten, C; Wieman, H; Wissink, S W; Witt, R; Wood, J; Wu, J; Xu, N; Xu, Z; Xu, Z Z; Yamamoto, E; Yepes, P; Yurevich, V I; Zanevsky, Y V; Zhang, H; Zhang, W M; Zhang, Z P; Zolnierczuk, P A; Zoulkarneev, R; Zoulkarneeva, Y; Zubarev, A N

2004-12-17

Results on high transverse momentum charged particle emission with respect to the reaction plane are presented for Au + Au collisions at square root s(NN)=200 GeV. Two- and four-particle correlations results are presented as well as a comparison of azimuthal correlations in Au + Au collisions to those in p + p at the same energy. The elliptic anisotropy v(2) is found to reach its maximum at p(t) approximately 3 GeV/c, then decrease slowly and remain significant up to p(t) approximately 7-10 GeV/c. Stronger suppression is found in the back-to-back high-p(t) particle correlations for particles emitted out of plane compared to those emitted in plane. The centrality dependence of v(2) at intermediate p(t) is compared to simple models based on jet quenching.

On Nth roots of positive operators

NASA Technical Reports Server (NTRS)

Brown, D. R.; Omalley, M. J.

1978-01-01

A bounded operator A on a Hilbert space H was positive. These operators were symmetric, and as such constitute a natural generalization of nonnegative real diagonal matrices. The following result is thus both well known and not surprising: A positive operator has a unique positive square root (under operator composition).

Mapping the functional roles of cap cells in the response of Arabidopsis primary roots to gravity

NASA Technical Reports Server (NTRS)

Blancaflor, E. B.; Fasano, J. M.; Gilroy, S.; Evans, M. L. (Principal Investigator)

1998-01-01

The cap is widely accepted to be the site of gravity sensing in roots because removal of the cap abolishes root curvature. Circumstantial evidence favors the columella cells as the gravisensory cells because amyloplasts (and often other cellular components) are polarized with respect to the gravity vector. However, there has been no functional confirmation of their role. To address this problem, we used laser ablation to remove defined cells in the cap of Arabidopsis primary roots and quantified the response of the roots to gravity using three parameters: time course of curvature, presentation time, and deviation from vertical growth. Ablation of the peripheral cap cells and tip cells did not alter root curvature. Ablation of the innermost columella cells caused the strongest inhibitory effect on root curvature without affecting growth rates. Many of these roots deviated significantly from vertical growth and had a presentation time 6-fold longer than the controls. Among the two inner columella stories, the central cells of story 2 contributed the most to root gravitropism. These cells also exhibited the largest amyloplast sedimentation velocities. Therefore, these results are consistent with the starch-statolith sedimentation hypothesis for gravity sensing.