Relationship between the species-representative phenotype and intraspecific variation in Ranunculaceae floral organ and Asteraceae flower numbers.

PubMed

Kitazawa, Miho S; Fujimoto, Koichi

2016-04-01

Phenotypic variation in floral morphologies contributes to speciation by testing various morphologies that might have higher adaptivity, leading eventually to phylogenetic diversity. Species diversity has been recognized, however, by modal morphologies where the variation is averaged out, so little is known about the relationship between the variation and the diversity. We analysed quantitatively the intraspecific variation of the organ numbers within flowers of Ranunculaceae, a family which branched near the monocot-eudicot separation, and the numbers of flowers within the capitula of Asteraceae, one of the most diverse families of eudicots. We used four elementary statistical quantities: mean, standard deviation (s.d.), degree of symmetry (skewness) and steepness (kurtosis). While these four quantities vary among populations, we found a common relationship between s.d. and the mean number of petals and sepals in Ranunculaceae and number of flowers per capitulum in Asteraceae. The s.d. is equal to the square root of the difference between the mean and specific number, showing robustness: for example, 3 in Ficaria sepals, 5 in Ranunculus petals and Anemone tepals, and 13 in Farfugium ray florets. This square-root relationship was not applicable to Eranthis petals which show little correlation between the s.d. and mean, and the stamens and carpels of Ranunculaceae whose s.d. is proportional to the mean. The specific values found in the square-root relationship provide a novel way to find the species-representative phenotype among varied morphologies. The representative phenotype is, in most cases, unique to the species or genus level, despite intraspecific differences of average phenotype among populations. The type of variation shown by the statistical quantities indicates not only the robustness of the morphologies but also how flowering plants changed during evolution among representative phenotypes that eventually led to phylogenetic diversification. © The Author 2016. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Relationship between the species-representative phenotype and intraspecific variation in Ranunculaceae floral organ and Asteraceae flower numbers

PubMed Central

Kitazawa, Miho S.; Fujimoto, Koichi

2016-01-01

Background and Aims Phenotypic variation in floral morphologies contributes to speciation by testing various morphologies that might have higher adaptivity, leading eventually to phylogenetic diversity. Species diversity has been recognized, however, by modal morphologies where the variation is averaged out, so little is known about the relationship between the variation and the diversity. Methods We analysed quantitatively the intraspecific variation of the organ numbers within flowers of Ranunculaceae, a family which branched near the monocot–eudicot separation, and the numbers of flowers within the capitula of Asteraceae, one of the most diverse families of eudicots. We used four elementary statistical quantities: mean, standard deviation (s.d.), degree of symmetry (skewness) and steepness (kurtosis). Key Results While these four quantities vary among populations, we found a common relationship between s.d. and the mean number of petals and sepals in Ranunculaceae and number of flowers per capitulum in Asteraceae. The s.d. is equal to the square root of the difference between the mean and specific number, showing robustness: for example, 3 in Ficaria sepals, 5 in Ranunculus petals and Anemone tepals, and 13 in Farfugium ray florets. This square-root relationship was not applicable to Eranthis petals which show little correlation between the s.d. and mean, and the stamens and carpels of Ranunculaceae whose s.d. is proportional to the mean. The specific values found in the square-root relationship provide a novel way to find the species-representative phenotype among varied morphologies. Conclusions The representative phenotype is, in most cases, unique to the species or genus level, despite intraspecific differences of average phenotype among populations. The type of variation shown by the statistical quantities indicates not only the robustness of the morphologies but also how flowering plants changed during evolution among representative phenotypes that eventually led to phylogenetic diversification. PMID:27052344

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.

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

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.

Neural network versus classical time series forecasting models

NASA Astrophysics Data System (ADS)

Nor, Maria Elena; Safuan, Hamizah Mohd; Shab, Noorzehan Fazahiyah Md; Asrul, Mohd; Abdullah, Affendi; Mohamad, Nurul Asmaa Izzati; Lee, Muhammad Hisyam

2017-05-01

Artificial neural network (ANN) has advantage in time series forecasting as it has potential to solve complex forecasting problems. This is because ANN is data driven approach which able to be trained to map past values of a time series. In this study the forecast performance between neural network and classical time series forecasting method namely seasonal autoregressive integrated moving average models was being compared by utilizing gold price data. Moreover, the effect of different data preprocessing on the forecast performance of neural network being examined. The forecast accuracy was evaluated using mean absolute deviation, root mean square error and mean absolute percentage error. It was found that ANN produced the most accurate forecast when Box-Cox transformation was used as data preprocessing.

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.

Determining the Uncertainty of X-Ray Absorption Measurements

PubMed Central

Wojcik, Gary S.

2004-01-01

X-ray absorption (or more properly, x-ray attenuation) techniques have been applied to study the moisture movement in and moisture content of materials like cement paste, mortar, and wood. An increase in the number of x-ray counts with time at a location in a specimen may indicate a decrease in moisture content. The uncertainty of measurements from an x-ray absorption system, which must be known to properly interpret the data, is often assumed to be the square root of the number of counts, as in a Poisson process. No detailed studies have heretofore been conducted to determine the uncertainty of x-ray absorption measurements or the effect of averaging data on the uncertainty. In this study, the Poisson estimate was found to adequately approximate normalized root mean square errors (a measure of uncertainty) of counts for point measurements and profile measurements of water specimens. The Poisson estimate, however, was not reliable in approximating the magnitude of the uncertainty when averaging data from paste and mortar specimens. Changes in uncertainty from differing averaging procedures were well-approximated by a Poisson process. The normalized root mean square errors decreased when the x-ray source intensity, integration time, collimator size, and number of scanning repetitions increased. Uncertainties in mean paste and mortar count profiles were kept below 2 % by averaging vertical profiles at horizontal spacings of 1 mm or larger with counts per point above 4000. Maximum normalized root mean square errors did not exceed 10 % in any of the tests conducted. PMID:27366627

Nonlinear filtering properties of detrended fluctuation analysis

NASA Astrophysics Data System (ADS)

Kiyono, Ken; Tsujimoto, Yutaka

2016-11-01

Detrended fluctuation analysis (DFA) has been widely used for quantifying long-range correlation and fractal scaling behavior. In DFA, to avoid spurious detection of scaling behavior caused by a nonstationary trend embedded in the analyzed time series, a detrending procedure using piecewise least-squares fitting has been applied. However, it has been pointed out that the nonlinear filtering properties involved with detrending may induce instabilities in the scaling exponent estimation. To understand this issue, we investigate the adverse effects of the DFA detrending procedure on the statistical estimation. We show that the detrending procedure using piecewise least-squares fitting results in the nonuniformly weighted estimation of the root-mean-square deviation and that this property could induce an increase in the estimation error. In addition, for comparison purposes, we investigate the performance of a centered detrending moving average analysis with a linear detrending filter and sliding window DFA and show that these methods have better performance than the standard DFA.

[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.

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.

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.

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.

Three-Dimensional Assessment of Temporomandibular Joint Using MRI-CBCT Image Registration

PubMed Central

Lagravere, Manuel; Boulanger, Pierre; Jaremko, Jacob L.; Major, Paul W.

2017-01-01

Purpose To introduce a new approach to reconstruct a 3D model of the TMJ using magnetic resonance imaging (MRI) and cone-beam computed tomography (CBCT) registered images, and to evaluate the intra-examiner reproducibility values of reconstructing the 3D models of the TMJ. Methods MRI and CBCT images of five patients (10 TMJs) were obtained. Multiple MRIs and CBCT images were registered using a mutual information based algorithm. The articular disc, condylar head and glenoid fossa were segmented at two different occasions, at least one-week apart, by one investigator, and 3D models were reconstructed. Differences between the segmentation at two occasions were automatically measured using the surface contours (Average Perpendicular Distance) and the volume overlap (Dice Similarity Index) of the 3D models. Descriptive analysis of the changes at 2 occasions, including means and standard deviation (SD) were reported to describe the intra-examiner reproducibility. Results The automatic segmentation of the condyle revealed maximum distance change of 1.9±0.93 mm, similarity index of 98% and root mean squared distance of 0.1±0.08 mm, and the glenoid fossa revealed maximum distance change of 2±0.52 mm, similarity index of 96% and root mean squared distance of 0.2±0.04 mm. The manual segmentation of the articular disc revealed maximum distance change of 3.6±0.32 mm, similarity index of 80% and root mean squared distance of 0.3±0.1 mm. Conclusion The MRI-CBCT registration provides a reliable tool to reconstruct 3D models of the TMJ’s soft and hard tissues, allows quantification of the articular disc morphology and position changes with associated differences of the condylar head and glenoid fossa, and facilitates measuring tissue changes over time. PMID:28095486

Three-Dimensional Assessment of Temporomandibular Joint Using MRI-CBCT Image Registration.

PubMed

Al-Saleh, Mohammed A Q; Punithakumar, Kumaradevan; Lagravere, Manuel; Boulanger, Pierre; Jaremko, Jacob L; Major, Paul W

2017-01-01

To introduce a new approach to reconstruct a 3D model of the TMJ using magnetic resonance imaging (MRI) and cone-beam computed tomography (CBCT) registered images, and to evaluate the intra-examiner reproducibility values of reconstructing the 3D models of the TMJ. MRI and CBCT images of five patients (10 TMJs) were obtained. Multiple MRIs and CBCT images were registered using a mutual information based algorithm. The articular disc, condylar head and glenoid fossa were segmented at two different occasions, at least one-week apart, by one investigator, and 3D models were reconstructed. Differences between the segmentation at two occasions were automatically measured using the surface contours (Average Perpendicular Distance) and the volume overlap (Dice Similarity Index) of the 3D models. Descriptive analysis of the changes at 2 occasions, including means and standard deviation (SD) were reported to describe the intra-examiner reproducibility. The automatic segmentation of the condyle revealed maximum distance change of 1.9±0.93 mm, similarity index of 98% and root mean squared distance of 0.1±0.08 mm, and the glenoid fossa revealed maximum distance change of 2±0.52 mm, similarity index of 96% and root mean squared distance of 0.2±0.04 mm. The manual segmentation of the articular disc revealed maximum distance change of 3.6±0.32 mm, similarity index of 80% and root mean squared distance of 0.3±0.1 mm. The MRI-CBCT registration provides a reliable tool to reconstruct 3D models of the TMJ's soft and hard tissues, allows quantification of the articular disc morphology and position changes with associated differences of the condylar head and glenoid fossa, and facilitates measuring tissue changes over time.

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.

Protein solubility modeling

NASA Technical Reports Server (NTRS)

Agena, S. M.; Pusey, M. L.; Bogle, I. D.

1999-01-01

A thermodynamic framework (UNIQUAC model with temperature dependent parameters) is applied to model the salt-induced protein crystallization equilibrium, i.e., protein solubility. The framework introduces a term for the solubility product describing protein transfer between the liquid and solid phase and a term for the solution behavior describing deviation from ideal solution. Protein solubility is modeled as a function of salt concentration and temperature for a four-component system consisting of a protein, pseudo solvent (water and buffer), cation, and anion (salt). Two different systems, lysozyme with sodium chloride and concanavalin A with ammonium sulfate, are investigated. Comparison of the modeled and experimental protein solubility data results in an average root mean square deviation of 5.8%, demonstrating that the model closely follows the experimental behavior. Model calculations and model parameters are reviewed to examine the model and protein crystallization process. Copyright 1999 John Wiley & Sons, Inc.

Water quality management using statistical analysis and time-series prediction model

NASA Astrophysics Data System (ADS)

Parmar, Kulwinder Singh; Bhardwaj, Rashmi

2014-12-01

This paper deals with water quality management using statistical analysis and time-series prediction model. The monthly variation of water quality standards has been used to compare statistical mean, median, mode, standard deviation, kurtosis, skewness, coefficient of variation at Yamuna River. Model validated using R-squared, root mean square error, mean absolute percentage error, maximum absolute percentage error, mean absolute error, maximum absolute error, normalized Bayesian information criterion, Ljung-Box analysis, predicted value and confidence limits. Using auto regressive integrated moving average model, future water quality parameters values have been estimated. It is observed that predictive model is useful at 95 % confidence limits and curve is platykurtic for potential of hydrogen (pH), free ammonia, total Kjeldahl nitrogen, dissolved oxygen, water temperature (WT); leptokurtic for chemical oxygen demand, biochemical oxygen demand. Also, it is observed that predicted series is close to the original series which provides a perfect fit. All parameters except pH and WT cross the prescribed limits of the World Health Organization /United States Environmental Protection Agency, and thus water is not fit for drinking, agriculture and industrial use.

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.

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…

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.

Is an intuitive convergence definition of molecular dynamics simulations solely based on the root mean square deviation possible?

PubMed

Knapp, B; Frantal, S; Cibena, M; Schreiner, W; Bauer, P

2011-08-01

Molecular dynamics is a commonly used technique in computational biology. One key issue of each molecular dynamics simulation is: When does this simulation reach equilibrium state? A widely used way to determine this is the visual and intuitive inspection of root mean square deviation (RMSD) plots of the simulation. Although this technique has been criticized several times, it is still often used. Therefore, we present a study proving that this method is not reliable at all. We conducted a survey with participants from the field in which we illustrated different RMSD plots to scientists in the field of molecular dynamics. These plots were randomized and repeated, using a statistical model and different variants of the plots. We show that there is no mutual consent about the point of equilibrium. The decisions are severely biased by different parameters. Therefore, we conclude that scientists should not discuss the equilibration of a molecular dynamics simulation on the basis of a RMSD plot.

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…

A 45-ns molecular dynamics simulation of hemoglobin in water by vectorizing and parallelizing COSMOS90 on the earth simulator: dynamics of tertiary and quaternary structures.

PubMed

Saito, Minoru; Okazaki, Isao

2007-04-30

Molecular dynamics (MD) simulations of human adult hemoglobin (HbA) were carried out for 45 ns in water with all degrees of freedom including bond stretching and without any artificial constraints. To perform such large-scale simulations, one of the authors (M.S.) accelerated his own software COSMOS90 on the Earth Simulator by vectorization and parallelization. The dynamical features of HbA were investigated by evaluating root-mean-square deviations from the initial X-ray structure (an oxy T-state hemoglobin with PDB code: 1GZX) and root-mean-square fluctuations around the average structure from the simulation trajectories. The four subunits (alpha(1), alpha(2), beta(1), and beta(2)) of HbA maintained structures close to their respective X-ray structures during the simulations even though no constraints were applied to HbA in the simulations. Dimers alpha(1)beta(1) and alpha(2)beta(2) also maintained structures close to their respective X-ray structures while they moved relative to each other like two stacks of dumbbells. The distance between the two dimers (alpha(1)beta(1) and alpha(2)beta(2)) increased by 2 A (7.4%) in the initial 15 ns and stably fluctuated at the distance with the standard deviation 0.2 A. The relative orientation of the two dimers fluctuated between the initial X-ray angle -100 degrees and about -105 degrees with intervals of a few tens of nanoseconds.

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 Generic Force Field for Protein Coarse-Grained Molecular Dynamics Simulation

PubMed Central

Gu, Junfeng; Bai, Fang; Li, Honglin; Wang, Xicheng

2012-01-01

Coarse-grained (CG) force fields have become promising tools for studies of protein behavior, but the balance of speed and accuracy is still a challenge in the research of protein coarse graining methodology. In this work, 20 CG beads have been designed based on the structures of amino acid residues, with which an amino acid can be represented by one or two beads, and a CG solvent model with five water molecules was adopted to ensure the consistence with the protein CG beads. The internal interactions in protein were classified according to the types of the interacting CG beads, and adequate potential functions were chosen and systematically parameterized to fit the energy distributions. The proposed CG force field has been tested on eight proteins, and each protein was simulated for 1000 ns. Even without any extra structure knowledge of the simulated proteins, the Cα root mean square deviations (RMSDs) with respect to their experimental structures are close to those of relatively short time all atom molecular dynamics simulations. However, our coarse grained force field will require further refinement to improve agreement with and persistence of native-like structures. In addition, the root mean square fluctuations (RMSFs) relative to the average structures derived from the simulations show that the conformational fluctuations of the proteins can be sampled. PMID:23203075

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.

A comparative study of satellite estimation for solar insolation in Albania with ground measurements

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

Mitrushi, Driada, E-mail: driadamitrushi@yahoo.com; Berberi, Pëllumb, E-mail: pellumb.berberi@gmail.com; Muda, Valbona, E-mail: vmuda@hotmail.com

The main objective of this study is to compare data provided by Database of NASA with available ground data for regions covered by national meteorological net NASA estimates that their measurements of average daily solar radiation have a root-mean-square deviation RMSD error of 35 W/m{sup 2} (roughly 20% inaccuracy). Unfortunately valid data from meteorological stations for regions of interest are quite rare in Albania. In these cases, use of Solar Radiation Database of NASA would be a satisfactory solution for different case studies. Using a statistical method allows to determine most probable margins between to sources of data. Comparison of meanmore » insulation data provided by NASA with ground data of mean insulation provided by meteorological stations show that ground data for mean insolation results, in all cases, to be underestimated compared with data provided by Database of NASA. Converting factor is 1.149.« less

[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.

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 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.

UK audit of analysis of quantitative parameters from renography data generated using a physical phantom.

PubMed

Nijran, Kuldip S; Houston, Alex S; Fleming, John S; Jarritt, Peter H; Heikkinen, Jari O; Skrypniuk, John V

2014-07-01

In this second UK audit of quantitative parameters obtained from renography, phantom simulations were used in cases in which the 'true' values could be estimated, allowing the accuracy of the parameters measured to be assessed. A renal physical phantom was used to generate a set of three phantom simulations (six kidney functions) acquired on three different gamma camera systems. A total of nine phantom simulations and three real patient studies were distributed to UK hospitals participating in the audit. Centres were asked to provide results for the following parameters: relative function and time-to-peak (whole kidney and cortical region). As with previous audits, a questionnaire collated information on methodology. Errors were assessed as the root mean square deviation from the true value. Sixty-one centres responded to the audit, with some hospitals providing multiple sets of results. Twenty-one centres provided a complete set of parameter measurements. Relative function and time-to-peak showed a reasonable degree of accuracy and precision in most UK centres. The overall average root mean squared deviation of the results for (i) the time-to-peak measurement for the whole kidney and (ii) the relative function measurement from the true value was 7.7 and 4.5%, respectively. These results showed a measure of consistency in the relative function and time-to-peak that was similar to the results reported in a previous renogram audit by our group. Analysis of audit data suggests a reasonable degree of accuracy in the quantification of renography function using relative function and time-to-peak measurements. However, it is reasonable to conclude that the objectives of the audit could not be fully realized because of the limitations of the mechanical phantom in providing true values for renal parameters.

Month-to-month and year-to-year reproducibility of high frequency QRS ECG signals

NASA Technical Reports Server (NTRS)

Batdorf, Niles J.; Feiveson, Alan H.; Schlegel, Todd T.

2004-01-01

High frequency electrocardiography analyzing the entire QRS complex in the frequency range of 150 to 250 Hz may prove useful in the detection of coronary artery disease, yet the long-term stability of these waveforms has not been fully characterized. Therefore, we prospectively investigated the reproducibility of the root mean squared voltage, kurtosis, and the presence versus absence of reduced amplitude zones in signal averaged 12-lead high frequency QRS recordings acquired in the supine position one month apart in 16 subjects and one year apart in 27 subjects. Reproducibility of root mean squared voltage and kurtosis was excellent over these time intervals in the limb leads, and acceptable in the precordial leads using both the V-lead and CR-lead derivations. The relative error of root mean squared voltage was 12% month-to-month and 16% year-to-year in the serial recordings when averaged over all 12 leads. Reduced amplitude zones were also reproducible up to a rate of 87% and 81%, respectively, for the month-to-month and year-to-year recordings. We conclude that 12-lead high frequency QRS electrocardiograms are sufficiently reproducible for clinical use.

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.

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…

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...

Application of Visible and Near-Infrared Hyperspectral Imaging to Determine Soluble Protein Content in Oilseed Rape Leaves

PubMed Central

Zhang, Chu; Liu, Fei; Kong, Wenwen; He, Yong

2015-01-01

Visible and near-infrared hyperspectral imaging covering spectral range of 380–1030 nm as a rapid and non-destructive method was applied to estimate the soluble protein content of oilseed rape leaves. Average spectrum (500–900 nm) of the region of interest (ROI) of each sample was extracted, and four samples out of 128 samples were defined as outliers by Monte Carlo-partial least squares (MCPLS). Partial least squares (PLS) model using full spectra obtained dependable performance with the correlation coefficient (rp) of 0.9441, root mean square error of prediction (RMSEP) of 0.1658 mg/g and residual prediction deviation (RPD) of 2.98. The weighted regression coefficient (Bw), successive projections algorithm (SPA) and genetic algorithm-partial least squares (GAPLS) selected 18, 15, and 16 sensitive wavelengths, respectively. SPA-PLS model obtained the best performance with rp of 0.9554, RMSEP of 0.1538 mg/g and RPD of 3.25. Distribution of protein content within the rape leaves were visualized and mapped on the basis of the SPA-PLS model. The overall results indicated that hyperspectral imaging could be used to determine and visualize the soluble protein content of rape leaves. PMID:26184198

Statistical behavior of post-shock overpressure past grid turbulence

NASA Astrophysics Data System (ADS)

Sasoh, Akihiro; Harasaki, Tatsuya; Kitamura, Takuya; Takagi, Daisuke; Ito, Shigeyoshi; Matsuda, Atsushi; Nagata, Kouji; Sakai, Yasuhiko

2014-09-01

When a shock wave ejected from the exit of a 5.4-mm inner diameter, stainless steel tube propagated through grid turbulence across a distance of 215 mm, which is 5-15 times larger than its integral length scale , and was normally incident onto a flat surface; the peak value of post-shock overpressure, , at a shock Mach number of 1.0009 on the flat surface experienced a standard deviation of up to about 9 % of its ensemble average. This value was more than 40 times larger than the dynamic pressure fluctuation corresponding to the maximum value of the root-mean-square velocity fluctuation, . By varying and , the statistical behavior of was obtained after at least 500 runs were performed for each condition. The standard deviation of due to the turbulence was almost proportional to . Although the overpressure modulations at two points 200 mm apart were independent of each other, we observed a weak positive correlation between the peak overpressure difference and the relative arrival time difference.

Accelerometer Data Analysis and Presentation Techniques

NASA Technical Reports Server (NTRS)

Rogers, Melissa J. B.; Hrovat, Kenneth; McPherson, Kevin; Moskowitz, Milton E.; Reckart, Timothy

1997-01-01

The NASA Lewis Research Center's Principal Investigator Microgravity Services project analyzes Orbital Acceleration Research Experiment and Space Acceleration Measurement System data for principal investigators of microgravity experiments. Principal investigators need a thorough understanding of data analysis techniques so that they can request appropriate analyses to best interpret accelerometer data. Accelerometer data sampling and filtering is introduced along with the related topics of resolution and aliasing. Specific information about the Orbital Acceleration Research Experiment and Space Acceleration Measurement System data sampling and filtering is given. Time domain data analysis techniques are discussed and example environment interpretations are made using plots of acceleration versus time, interval average acceleration versus time, interval root-mean-square acceleration versus time, trimmean acceleration versus time, quasi-steady three dimensional histograms, and prediction of quasi-steady levels at different locations. An introduction to Fourier transform theory and windowing is provided along with specific analysis techniques and data interpretations. The frequency domain analyses discussed are power spectral density versus frequency, cumulative root-mean-square acceleration versus frequency, root-mean-square acceleration versus frequency, one-third octave band root-mean-square acceleration versus frequency, and power spectral density versus frequency versus time (spectrogram). Instructions for accessing NASA Lewis Research Center accelerometer data and related information using the internet are provided.

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.

Personal coronary risk profiles modify autonomic nervous system responses to air pollution.

PubMed

Chen, Jiu-Chiuan; Stone, Peter H; Verrier, Richard L; Nearing, Bruce D; MacCallum, Gail; Kim, Jee-Young; Herrick, Robert F; You, Jinhong; Zhou, Haibo; Christiani, David C

2006-11-01

We investigated whether PM2.5-mediated autonomic modulation depends on individual coronary risk profiles. Five-minute average heart rate (HR) and heart rate variability (HRV, including standard deviation of normal-to-normal intervals [SDNN], square root of the mean squared differences of successive NN intervals [rMSSD], high frequency [HF]) were measured from 24-hour ambulatory electrocardiograms, and personal PM(2.5) exposures were monitored in a prospective study of 10 male boilermakers (aged 34.3 +/- 8.1 years). We used the Framingham score to classify individuals into low (score = 1-3) and high (score = 5-6) risk categories. Mixed-effect models were used for statistical analyses. Each 1-mg/m(3) increase in the preceding 4-hour moving average PM(2.5) was associated with HR increase (5.3 beats/min) and HRV reduction (11.7%, confidence interval [CI] = 6.2-17.1% for SDNN; 11.1%, CI = 3.1-19.1% for rMSSD; 16.6%, CI = 1.5-31.7% for HF). Greater responses (2- to 4-fold differences) were observed in high-risk subjects than in low-risk subjects. Our study suggests that adverse autonomic responses to metal particulate are aggravated in workers with higher coronary risk profiles.

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...

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.

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.

A comparison of performance of several artificial intelligence methods for predicting the dynamic viscosity of TiO2/SAE 50 nano-lubricant

NASA Astrophysics Data System (ADS)

Hemmat Esfe, Mohammad; Tatar, Afshin; Ahangar, Mohammad Reza Hassani; Rostamian, Hossein

2018-02-01

Since the conventional thermal fluids such as water, oil, and ethylene glycol have poor thermal properties, the tiny solid particles are added to these fluids to increase their heat transfer improvement. As viscosity determines the rheological behavior of a fluid, studying the parameters affecting the viscosity is crucial. Since the experimental measurement of viscosity is expensive and time consuming, predicting this parameter is the apt method. In this work, three artificial intelligence methods containing Genetic Algorithm-Radial Basis Function Neural Networks (GA-RBF), Least Square Support Vector Machine (LS-SVM) and Gene Expression Programming (GEP) were applied to predict the viscosity of TiO2/SAE 50 nano-lubricant with Non-Newtonian power-law behavior using experimental data. The correlation factor (R2), Average Absolute Relative Deviation (AARD), Root Mean Square Error (RMSE), and Margin of Deviation were employed to investigate the accuracy of the proposed models. RMSE values of 0.58, 1.28, and 6.59 and R2 values of 0.99998, 0.99991, and 0.99777 reveal the accuracy of the proposed models for respective GA-RBF, CSA-LSSVM, and GEP methods. Among the developed models, the GA-RBF shows the best accuracy.

The effect of regularization in motion compensated PET image reconstruction: a realistic numerical 4D simulation study.

PubMed

Tsoumpas, C; Polycarpou, I; Thielemans, K; Buerger, C; King, A P; Schaeffter, T; Marsden, P K

2013-03-21

Following continuous improvement in PET spatial resolution, respiratory motion correction has become an important task. Two of the most common approaches that utilize all detected PET events to motion-correct PET data are the reconstruct-transform-average method (RTA) and motion-compensated image reconstruction (MCIR). In RTA, separate images are reconstructed for each respiratory frame, subsequently transformed to one reference frame and finally averaged to produce a motion-corrected image. In MCIR, the projection data from all frames are reconstructed by including motion information in the system matrix so that a motion-corrected image is reconstructed directly. Previous theoretical analyses have explained why MCIR is expected to outperform RTA. It has been suggested that MCIR creates less noise than RTA because the images for each separate respiratory frame will be severely affected by noise. However, recent investigations have shown that in the unregularized case RTA images can have fewer noise artefacts, while MCIR images are more quantitatively accurate but have the common salt-and-pepper noise. In this paper, we perform a realistic numerical 4D simulation study to compare the advantages gained by including regularization within reconstruction for RTA and MCIR, in particular using the median-root-prior incorporated in the ordered subsets maximum a posteriori one-step-late algorithm. In this investigation we have demonstrated that MCIR with proper regularization parameters reconstructs lesions with less bias and root mean square error and similar CNR and standard deviation to regularized RTA. This finding is reproducible for a variety of noise levels (25, 50, 100 million counts), lesion sizes (8 mm, 14 mm diameter) and iterations. Nevertheless, regularized RTA can also be a practical solution for motion compensation as a proper level of regularization reduces both bias and mean square error.

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.

Evaluation of a pointwise microcirculation assessment method using liquid and multilayered tissue simulating phantoms

NASA Astrophysics Data System (ADS)

Fredriksson, Ingemar; Saager, Rolf B.; Durkin, Anthony J.; Strömberg, Tomas

2017-11-01

A fiber-optic probe-based instrument, designed for assessment of parameters related to microcirculation, red blood cell tissue fraction (fRBC), oxygen saturation (S), and speed resolved perfusion, has been evaluated using state-of-the-art tissue phantoms. The probe integrates diffuse reflectance spectroscopy (DRS) at two source-detector separations and laser Doppler flowmetry, using an inverse Monte Carlo method for identifying the parameters of a multilayered tissue model. Here, we characterize the accuracy of the DRS aspect of the instrument using (1) liquid blood phantoms containing yeast and (2) epidermis-dermis mimicking solid-layered phantoms fabricated from polydimethylsiloxane, titanium oxide, hemoglobin, and coffee. The root-mean-square (RMS) deviations for fRBC for the two liquid phantoms were 11% and 5.3%, respectively, and 11% for the solid phantoms with highest hemoglobin signatures. The RMS deviation for S was 5.2% and 2.9%, respectively, for the liquid phantoms, and 2.9% for the solid phantoms. RMS deviation for the reduced scattering coefficient (μs‧), for the solid phantoms was 15% (475 to 850 nm). For the liquid phantoms, the RMS deviation in average vessel diameter (D) was 1 μm. In conclusion, the skin microcirculation parameters fRBC and S, as well as, μs‧ and D are estimated with reasonable accuracy.

Entanglement Entropy of Eigenstates of Quantum Chaotic Hamiltonians.

PubMed

Vidmar, Lev; Rigol, Marcos

2017-12-01

In quantum statistical mechanics, it is of fundamental interest to understand how close the bipartite entanglement entropy of eigenstates of quantum chaotic Hamiltonians is to maximal. For random pure states in the Hilbert space, the average entanglement entropy is known to be nearly maximal, with a deviation that is, at most, a constant. Here we prove that, in a system that is away from half filling and divided in two equal halves, an upper bound for the average entanglement entropy of random pure states with a fixed particle number and normally distributed real coefficients exhibits a deviation from the maximal value that grows with the square root of the volume of the system. Exact numerical results for highly excited eigenstates of a particle number conserving quantum chaotic model indicate that the bound is saturated with increasing system size.

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.

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.

Repeatability of paired counts.

PubMed

Alexander, Neal; Bethony, Jeff; Corrêa-Oliveira, Rodrigo; Rodrigues, Laura C; Hotez, Peter; Brooker, Simon

2007-08-30

The Bland and Altman technique is widely used to assess the variation between replicates of a method of clinical measurement. It yields the repeatability, i.e. the value within which 95 per cent of repeat measurements lie. The valid use of the technique requires that the variance is constant over the data range. This is not usually the case for counts of items such as CD4 cells or parasites, nor is the log transformation applicable to zero counts. We investigate the properties of generalized differences based on Box-Cox transformations. For an example, in a data set of hookworm eggs counted by the Kato-Katz method, the square root transformation is found to stabilize the variance. We show how to back-transform the repeatability on the square root scale to the repeatability of the counts themselves, as an increasing function of the square mean root egg count, i.e. the square of the average of square roots. As well as being more easily interpretable, the back-transformed results highlight the dependence of the repeatability on the sample volume used.

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.

Accuracy assessment of TanDEM-X IDEM using airborne LiDAR on the area of Poland

NASA Astrophysics Data System (ADS)

Woroszkiewicz, Małgorzata; Ewiak, Ireneusz; Lulkowska, Paulina

2017-06-01

The TerraSAR-X add-on for Digital Elevation Measurement (TanDEM-X) mission launched in 2010 is another programme - after the Shuttle Radar Topography Mission (SRTM) in 2000 - that uses space-borne radar interferometry to build a global digital surface model. This article presents the accuracy assessment of the TanDEM-X intermediate Digital Elevation Model (IDEM) provided by the German Aerospace Center (DLR) under the project "Accuracy assessment of a Digital Elevation Model based on TanDEM-X data" for the southwestern territory of Poland. The study area included: open terrain, urban terrain and forested terrain. Based on a set of 17,498 reference points acquired by airborne laser scanning, the mean errors of average heights and standard deviations were calculated for areas with a terrain slope below 2 degrees, between 2 and 6 degrees and above 6 degrees. The absolute accuracy of the IDEM data for the analysed area, expressed as a root mean square error (Total RMSE), was 0.77 m.

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.

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.

Uncertainty Quantification of GEOS-5 L-band Radiative Transfer Model Parameters Using Bayesian Inference and SMOS Observations

NASA Technical Reports Server (NTRS)

DeLannoy, Gabrielle J. M.; Reichle, Rolf H.; Vrugt, Jasper A.

2013-01-01

Uncertainties in L-band (1.4 GHz) radiative transfer modeling (RTM) affect the simulation of brightness temperatures (Tb) over land and the inversion of satellite-observed Tb into soil moisture retrievals. In particular, accurate estimates of the microwave soil roughness, vegetation opacity and scattering albedo for large-scale applications are difficult to obtain from field studies and often lack an uncertainty estimate. Here, a Markov Chain Monte Carlo (MCMC) simulation method is used to determine satellite-scale estimates of RTM parameters and their posterior uncertainty by minimizing the misfit between long-term averages and standard deviations of simulated and observed Tb at a range of incidence angles, at horizontal and vertical polarization, and for morning and evening overpasses. Tb simulations are generated with the Goddard Earth Observing System (GEOS-5) and confronted with Tb observations from the Soil Moisture Ocean Salinity (SMOS) mission. The MCMC algorithm suggests that the relative uncertainty of the RTM parameter estimates is typically less than 25 of the maximum a posteriori density (MAP) parameter value. Furthermore, the actual root-mean-square-differences in long-term Tb averages and standard deviations are found consistent with the respective estimated total simulation and observation error standard deviations of m3.1K and s2.4K. It is also shown that the MAP parameter values estimated through MCMC simulation are in close agreement with those obtained with Particle Swarm Optimization (PSO).

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 muscle activation. PMID:28291825

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 activation.

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

EARLINET Single Calculus Chain - technical - Part 2: Calculation of optical products

NASA Astrophysics Data System (ADS)

Mattis, Ina; D'Amico, Giuseppe; Baars, Holger; Amodeo, Aldo; Madonna, Fabio; Iarlori, Marco

2016-07-01

In this paper we present the automated software tool ELDA (EARLINET Lidar Data Analyzer) for the retrieval of profiles of optical particle properties from lidar signals. This tool is one of the calculus modules of the EARLINET Single Calculus Chain (SCC) which allows for the analysis of the data of many different lidar systems of EARLINET in an automated, unsupervised way. ELDA delivers profiles of particle extinction coefficients from Raman signals as well as profiles of particle backscatter coefficients from combinations of Raman and elastic signals or from elastic signals only. Those analyses start from pre-processed signals which have already been corrected for background, range dependency and hardware specific effects. An expert group reviewed all algorithms and solutions for critical calculus subsystems which are used within EARLINET with respect to their applicability for automated retrievals. Those methods have been implemented in ELDA. Since the software was designed in a modular way, it is possible to add new or alternative methods in future. Most of the implemented algorithms are well known and well documented, but some methods have especially been developed for ELDA, e.g., automated vertical smoothing and temporal averaging or the handling of effective vertical resolution in the case of lidar ratio retrievals, or the merging of near-range and far-range products. The accuracy of the retrieved profiles was tested following the procedure of the EARLINET-ASOS algorithm inter-comparison exercise which is based on the analysis of synthetic signals. Mean deviations, mean relative deviations, and normalized root-mean-square deviations were calculated for all possible products and three height layers. In all cases, the deviations were clearly below the maximum allowed values according to the EARLINET quality requirements.

Theoretical modeling and experimental analysis of solar still integrated with evacuated tubes

NASA Astrophysics Data System (ADS)

Panchal, Hitesh; Awasthi, Anuradha

2017-06-01

In this present research work, theoretical modeling of single slope, single basin solar still integrated with evacuated tubes has been performed based on energy balance equations. Major variables like water temperature, inner glass cover temperature and distillate output has been computed based on theoretical modeling. The experimental setup has been made from locally available materials and installed at Gujarat Power Engineering and Research Institute, Mehsana, Gujarat, India (23.5880°N, 72.3693°E) with 0.04 m depth during 6 months of time interval. From the series of experiments, it is found considerable increment in average distillate output of a solar still when integrated with evacuated tubes not only during daytime but also from night time. In all experimental cases, the correlation of coefficient (r) and root mean square percentage deviation of theoretical modeling and experimental study found good agreement with 0.97 < r < 0.98 and 10.22 < e < 38.4% respectively.

Advanced image fusion algorithms for Gamma Knife treatment planning. Evaluation and proposal for clinical use.

PubMed

Apostolou, N; Papazoglou, Th; Koutsouris, D

2006-01-01

Image fusion is a process of combining information from multiple sensors. It is a useful tool implemented in the treatment planning programme of Gamma Knife Radiosurgery. In this paper we evaluate advanced image fusion algorithms for Matlab platform and head images. We develop nine level grayscale image fusion methods: average, principal component analysis (PCA), discrete wavelet transform (DWT) and Laplacian, filter - subtract - decimate (FSD), contrast, gradient, morphological pyramid and a shift invariant discrete wavelet transform (SIDWT) method in Matlab platform. We test these methods qualitatively and quantitatively. The quantitative criteria we use are the Root Mean Square Error (RMSE), the Mutual Information (MI), the Standard Deviation (STD), the Entropy (H), the Difference Entropy (DH) and the Cross Entropy (CEN). The qualitative are: natural appearance, brilliance contrast, presence of complementary features and enhancement of common features. Finally we make clinically useful suggestions.

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.

Simulation Study Using a New Type of Sample Variance

NASA Technical Reports Server (NTRS)

Howe, D. A.; Lainson, K. J.

1996-01-01

We evaluate with simulated data a new type of sample variance for the characterization of frequency stability. The new statistic (referred to as TOTALVAR and its square root TOTALDEV) is a better predictor of long-term frequency variations than the present sample Allan deviation. The statistical model uses the assumption that a time series of phase or frequency differences is wrapped (periodic) with overall frequency difference removed. We find that the variability at long averaging times is reduced considerably for the five models of power-law noise commonly encountered with frequency standards and oscillators.

Volatilization of organic compounds from streams

USGS Publications Warehouse

Rathburn, R.E.; Tai, D.Y.

1982-01-01

Mass-transfer coefficients for the volatilization of ethylene and propane were correlated with the hydraulic and geometric properties of seven streams, and predictive equations were developed. The equations were evaluated using a normalized root-mean-square error as the criterion of comparison. The two best equations were a two-variable equation containing the energy dissipated per unit mass per unit time and the average depth of flow and a three-variable equation containing the average velocity, the average depth of flow, and the slope of the stream. Procedures for adjusting the ethylene and propane coefficients for other organic compounds were evaluated. These procedures are based on molecular diffusivity, molecular diameter, or molecular weight. Because of limited data, none of these procedures have been extensively verified. Therefore, until additional data become available, it is suggested that the mass-transfer coefficient be assumed to be inversely proportional to the square root of the molecular weight.

Intelligent Ensemble Forecasting System of Stock Market Fluctuations Based on Symetric and Asymetric Wavelet Functions

NASA Astrophysics Data System (ADS)

Lahmiri, Salim; Boukadoum, Mounir

2015-08-01

We present a new ensemble system for stock market returns prediction where continuous wavelet transform (CWT) is used to analyze return series and backpropagation neural networks (BPNNs) for processing CWT-based coefficients, determining the optimal ensemble weights, and providing final forecasts. Particle swarm optimization (PSO) is used for finding optimal weights and biases for each BPNN. To capture symmetry/asymmetry in the underlying data, three wavelet functions with different shapes are adopted. The proposed ensemble system was tested on three Asian stock markets: The Hang Seng, KOSPI, and Taiwan stock market data. Three statistical metrics were used to evaluate the forecasting accuracy; including, mean of absolute errors (MAE), root mean of squared errors (RMSE), and mean of absolute deviations (MADs). Experimental results showed that our proposed ensemble system outperformed the individual CWT-ANN models each with different wavelet function. In addition, the proposed ensemble system outperformed the conventional autoregressive moving average process. As a result, the proposed ensemble system is suitable to capture symmetry/asymmetry in financial data fluctuations for better prediction accuracy.

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.

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.

Decomposition Analyses Applied to a Complex Ultradian Biorhythm: The Oscillating NADH Oxidase Activity of Plasma Membranes Having a Potential Time-Keeping (Clock) Function

PubMed Central

Foster, Ken; Anwar, Nasim; Pogue, Rhea; Morré, Dorothy M.; Keenan, T. W.; Morré, D. James

2003-01-01

Seasonal decomposition analyses were applied to the statistical evaluation of an oscillating activity for a plasma membrane NADH oxidase activity with a temperature compensated period of 24 min. The decomposition fits were used to validate the cyclic oscillatory pattern. Three measured values, average percentage error (MAPE), a measure of the periodic oscillation, mean average deviation (MAD), a measure of the absolute average deviations from the fitted values, and mean standard deviation (MSD), the measure of standard deviation from the fitted values plus R-squared and the Henriksson-Merton p value were used to evaluate accuracy. Decomposition was carried out by fitting a trend line to the data, then detrending the data if necessary, by subtracting the trend component. The data, with or without detrending, were then smoothed by subtracting a centered moving average of length equal to the period length determined by Fourier analysis. Finally, the time series were decomposed into cyclic and error components. The findings not only validate the periodic nature of the major oscillations but suggest, as well, that the minor intervening fluctuations also recur within each period with a reproducible pattern of recurrence. PMID:19330112

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.

A Historical Study to Understand Students' Current Difficulties about RMS Values

ERIC Educational Resources Information Center

Khantine-Langlois, Françoise; Munier, Valérie

2016-01-01

Several studies show that students experience more and more difficulties managing the measurements of electrical values in alternating current and that they have trouble making links between theory and practice. They find it difficult to give meaning to root mean square (RMS; or effective) values, which are not understood as average values and are…

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).

Validation of the thermophysiological model by Fiala for prediction of local skin temperatures

NASA Astrophysics Data System (ADS)

Martínez, Natividad; Psikuta, Agnes; Kuklane, Kalev; Quesada, José Ignacio Priego; de Anda, Rosa María Cibrián Ortiz; Soriano, Pedro Pérez; Palmer, Rosario Salvador; Corberán, José Miguel; Rossi, René Michel; Annaheim, Simon

2016-12-01

The most complete and realistic physiological data are derived from direct measurements during human experiments; however, they present some limitations such as ethical concerns, time and cost burden. Thermophysiological models are able to predict human thermal response in a wide range of environmental conditions, but their use is limited due to lack of validation. The aim of this work was to validate the thermophysiological model by Fiala for prediction of local skin temperatures against a dedicated database containing 43 different human experiments representing a wide range of conditions. The validation was conducted based on root-mean-square deviation (rmsd) and bias. The thermophysiological model by Fiala showed a good precision when predicting core and mean skin temperature (rmsd 0.26 and 0.92 °C, respectively) and also local skin temperatures for most body sites (average rmsd for local skin temperatures 1.32 °C). However, an increased deviation of the predictions was observed for the forehead skin temperature (rmsd of 1.63 °C) and for the thigh during exercising exposures (rmsd of 1.41 °C). Possible reasons for the observed deviations are lack of information on measurement circumstances (hair, head coverage interference) or an overestimation of the sweat evaporative cooling capacity for the head and thigh, respectively. This work has highlighted the importance of collecting details about the clothing worn and how and where the sensors were attached to the skin for achieving more precise results in the simulations.

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.

Electrocardiographic signal-averaging during atrial pacing and effect of cycle length on the terminal QRS in patients with and without inducible ventricular tachycardia.

PubMed

Kremers, M S; Black, W H; Lange, R; Wells, P J; Solo, M

1990-11-01

Electrocardiographic signal-averaging during sinus rhythm (61 to 99 beats/min) and atrial pacing (100 to 171 beats/min) were performed to determine the effect of heart rate on late potentials in 15 patients without (group 1) and 7 patients with (group 2) inducible sustained ventricular tachycardia (VT). In sinus rhythm (79 +/- 12 vs 77 +/- 12 beats/min, difference not significant), the duration of the low-amplitude signal less than 40 microV was longer in group 2 than group 1 (43 +/- 21 vs 26 +/- 8 ms, p = 0.034) and more patients had late potentials (57 vs 7%, p = 0.021), but QRS duration (121 +/- 32 vs 98 +/- 19 ms) and terminal voltage (33 +/- 33 vs 50 +/- 26 ms) were not significantly different. With atrial pacing in group 1 (128 +/- 16 beats/min), 3 patients developed a simultaneous decrease in terminal voltage and an increase in terminal QRS duration consistent with a late potential, but mean total and terminal durations were unchanged. Terminal voltage increased (50 +/- 26 to 59 +/- 40) but not significantly. With atrial pacing in group 2 (119 +/- 12 beats/min) all patients either had a late potential or developed a simultaneous decrease in terminal voltage and an increase in terminal QRS duration (p = 0.001 vs group 1). Root mean square (p = 0.001 vs group 1). Root mean square voltage decreased (33 +/- 23 to 22 +/- 23) and became significantly different from group 1 (p = 0.017). Mean QRS duration, root mean square terminal voltage and low-amplitude terminal QRS duration, however, were unchanged.(ABSTRACT TRUNCATED AT 250 WORDS)

Statistical fluctuations in cooperative cyclotron radiation

NASA Astrophysics Data System (ADS)

Anishchenko, S. V.; Baryshevsky, V. G.

2018-01-01

Shot noise is the cause of statistical fluctuations in cooperative cyclotron radiation generated by an ensemble of electrons oscillating in magnetic field. Autophasing time - the time required for the cooperative cyclotron radiation power to peak - is the critical parameter characterizing the dynamics of electron-oscillators interacting via the radiation field. It is shown that premodulation of charged particles leads to a considerable narrowing of the autophasing time distribution function for which the analytic expression is obtained. When the number of particles Ne exceeds a certain value that depends on the degree to which the particles have been premodulated, the relative root-mean-square deviation (RMSD) of the autophasing time δT changes from a logarithmic dependence on Ne (δT ∼ 1 / lnNe) to square-root (δT ∼ 1 /√{Ne }). A slight energy spread (∼4%) results in a twofold drop of the maximum attainable power of cooperative cyclotron radiation.

Applications of laser-induced breakdown spectroscopy in the aluminum electrolysis industry

NASA Astrophysics Data System (ADS)

Sun, Lanxiang; Yu, Haibin; Cong, Zhibo; Lu, Hui; Cao, Bin; Zeng, Peng; Dong, Wei; Li, Yang

2018-04-01

The industrial aluminum reduction cell is an electrochemistry reactor that operates under high temperatures and corrosive conditions. Monitoring the molten aluminum and electrolyte components is very important for controlling the chemical reaction process. Due to the lack of fast methods to monitor the components, controlling aluminum reduction cells is difficult. In this work, laser-induced breakdown spectroscopy (LIBS) was applied to aluminum electrolysis. A new method for calculating the molecular ratio, which is an important control parameter that represents the acidity of the electrolyte, was proposed. Experiments were first performed on solid electrolyte samples to test the performance of the proposed method. Using this method, the average relative standard deviation (RSD) of the molecular ratio measurement was 0.39%, and the average root mean square error (RMSE) was 0.0236. These results prove that LIBS can accurately measure the molecular ratio. Then, in situ measurements of the molten aluminum and electrolyte were performed in industrial aluminum induction cells using the developed LIBS equipment. The spectra of the molten electrolyte were successfully obtained and were consistent with the spectra of the solid electrolyte.

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.

Measurement and correlation of the solubility of gossypol acetic acid and gossypol acetic acid of optical activity in different solvents

NASA Astrophysics Data System (ADS)

Zhang, B.; Tang, H.; Liu, X. Y.; Zhai, X.; Yao, X. C.

2018-01-01

The equilibrium method was used to measure the solubility of gossypol acetic acid and gossypol acetic acid of optical activity in isopropyl alcohol, ethanol, acetic acid and ethyl acetate at temperature from 288.15 to 315.15. The Empirical equation and the Apelblat equation model were adopted to correlate the experimental data. For gossypol acetic acid, the root-mean-square deviations (RMSD) were observed in the range of 0.023-4.979 and 0.0112-0.614 for the Empirical equation and the Apelblat equation, respectively. For gossypol acetic acid of optical activity, the RMSD were observed in the range of 0.021-2.211 and 0.021-2.243 for the Empirical equation and the Apelblat equation, individually. And the maximum relative average deviation was 7.5%. Both equations offered an accurate mathematical expression of the experimental results. The calculated solubility showed a good relationship with the experimental solubility for most of solvents. This study provided valuable datas not only for optimizing the process of purification of gossypol acetic acid of optical activity in industry but also for further theoretical studies.

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

The U.S. Geological Survey (USGS) maintains approximately 148 real-time streamgages in Iowa for which daily mean streamflow information is available, but daily mean streamflow data commonly are needed at locations where no streamgages are present. Therefore, the USGS conducted a study as part of a larger project in cooperation with the Iowa Department of Natural Resources to develop methods to estimate daily mean streamflow at locations in ungaged watersheds in Iowa by using two regression-based statistical methods. The regression equations for the statistical methods were developed from historical daily mean streamflow and basin characteristics from streamgages within the study area, which includes the entire State of Iowa and adjacent areas within a 50-mile buffer of Iowa in neighboring states. Results of this study can be used with other techniques to determine the best method for application in Iowa and can be used to produce a Web-based geographic information system tool to compute streamflow estimates automatically. The Flow Anywhere statistical method is a variation of the drainage-area-ratio method, which transfers same-day streamflow information from a reference streamgage to another location by using the daily mean streamflow at the reference streamgage and the drainage-area ratio of the two locations. The Flow Anywhere method modifies the drainage-area-ratio method in order to regionalize the equations for Iowa and determine the best reference streamgage from which to transfer same-day streamflow information to an ungaged location. Data used for the Flow Anywhere method were retrieved for 123 continuous-record streamgages located in Iowa and within a 50-mile buffer of Iowa. The final regression equations were computed by using either left-censored regression techniques with a low limit threshold set at 0.1 cubic feet per second (ft3/s) and the daily mean streamflow for the 15th day of every other month, or by using an ordinary-least-squares multiple linear regression method and the daily mean streamflow for the 15th day of every other month. The Flow Duration Curve Transfer method was used to estimate unregulated daily mean streamflow from the physical and climatic characteristics of gaged basins. For the Flow Duration Curve Transfer method, daily mean streamflow quantiles at the ungaged site were estimated with the parameter-based regression model, which results in a continuous daily flow-duration curve (the relation between exceedance probability and streamflow for each day of observed streamflow) at the ungaged site. By the use of a reference streamgage, the Flow Duration Curve Transfer is converted to a time series. Data used in the Flow Duration Curve Transfer method were retrieved for 113 continuous-record streamgages in Iowa and within a 50-mile buffer of Iowa. The final statewide regression equations for Iowa were computed by using a weighted-least-squares multiple linear regression method and were computed for the 0.01-, 0.05-, 0.10-, 0.15-, 0.20-, 0.30-, 0.40-, 0.50-, 0.60-, 0.70-, 0.80-, 0.85-, 0.90-, and 0.95-exceedance probability statistics determined from the daily mean streamflow with a reporting limit set at 0.1 ft3/s. The final statewide regression equation for Iowa computed by using left-censored regression techniques was computed for the 0.99-exceedance probability statistic determined from the daily mean streamflow with a low limit threshold and a reporting limit set at 0.1 ft3/s. For the Flow Anywhere method, results of the validation study conducted by using six streamgages show that differences between the root-mean-square error and the mean absolute error ranged from 1,016 to 138 ft3/s, with the larger value signifying a greater occurrence of outliers between observed and estimated streamflows. Root-mean-square-error values ranged from 1,690 to 237 ft3/s. Values of the percent root-mean-square error ranged from 115 percent to 26.2 percent. The logarithm (base 10) streamflow percent root-mean-square 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 estimated streamflow, streamflows appear to be substantially underestimated for much of the time period. Estimated cumulative streamflow for the period October 1, 2004, to September 30, 2009, are underestimated by -9.3 and -22.7 percent for the closest and poorest comparisons, respectively.

Smooth diamond films as low friction, long wear surfaces

DOEpatents

Gruen, Dieter M.; Krauss, Alan R.; Erdemir, Ali; Bindal, Cuma; Zuiker, Christopher D.

1999-01-01

An article and method of manufacture of a nanocrystalline diamond film. The nanocrystalline film is prepared by forming a carbonaceous vapor, providing an inert gas containing gas stream and combining the gas stream with the carbonaceous containing vapor. A plasma of the combined vapor and gas stream is formed in a chamber and fragmented carbon species are deposited onto a substrate to form the nanocrystalline diamond film having a root mean square flatness of about 50 nm deviation from flatness in the as deposited state.

The Rydberg constant and proton size from atomic hydrogen

NASA Astrophysics Data System (ADS)

Beyer, Axel; Maisenbacher, Lothar; Matveev, Arthur; Pohl, Randolf; Khabarova, Ksenia; Grinin, Alexey; Lamour, Tobias; Yost, Dylan C.; Hänsch, Theodor W.; Kolachevsky, Nikolai; Udem, Thomas

2017-10-01

At the core of the “proton radius puzzle” is a four-standard deviation discrepancy between the proton root-mean-square charge radii (rp) determined from the regular hydrogen (H) and the muonic hydrogen (µp) atoms. Using a cryogenic beam of H atoms, we measured the 2S-4P transition frequency in H, yielding the values of the Rydberg constant R∞ = 10973731.568076(96) per meterand rp = 0.8335(95) femtometer. Our rp value is 3.3 combined standard deviations smaller than the previous H world data, but in good agreement with the µp value. We motivate an asymmetric fit function, which eliminates line shifts from quantum interference of neighboring atomic resonances.

Building on crossvalidation for increasing the quality of geostatistical modeling

USGS Publications Warehouse

Olea, R.A.

2012-01-01

The random function is a mathematical model commonly used in the assessment of uncertainty associated with a spatially correlated attribute that has been partially sampled. There are multiple algorithms for modeling such random functions, all sharing the requirement of specifying various parameters that have critical influence on the results. The importance of finding ways to compare the methods and setting parameters to obtain results that better model uncertainty has increased as these algorithms have grown in number and complexity. Crossvalidation has been used in spatial statistics, mostly in kriging, for the analysis of mean square errors. An appeal of this approach is its ability to work with the same empirical sample available for running the algorithms. This paper goes beyond checking estimates by formulating a function sensitive to conditional bias. Under ideal conditions, such function turns into a straight line, which can be used as a reference for preparing measures of performance. Applied to kriging, deviations from the ideal line provide sensitivity to the semivariogram lacking in crossvalidation of kriging errors and are more sensitive to conditional bias than analyses of errors. In terms of stochastic simulation, in addition to finding better parameters, the deviations allow comparison of the realizations resulting from the applications of different methods. Examples show improvements of about 30% in the deviations and approximately 10% in the square root of mean square errors between reasonable starting modelling and the solutions according to the new criteria. ?? 2011 US Government.

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.

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.

[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.

Superimposition of protein structures with dynamically weighted RMSD.

PubMed

Wu, Di; Wu, Zhijun

2010-02-01

In protein modeling, one often needs to superimpose a group of structures for a protein. A common way to do this is to translate and rotate the structures so that the square root of the sum of squares of coordinate differences of the atoms in the structures, called the root-mean-square deviation (RMSD) of the structures, is minimized. While it has provided a general way of aligning a group of structures, this approach has not taken into account the fact that different atoms may have different properties and they should be compared differently. For this reason, when superimposed with RMSD, the coordinate differences of different atoms should be evaluated with different weights. The resulting RMSD is called the weighted RMSD (wRMSD). Here we investigate the use of a special wRMSD for superimposing a group of structures with weights assigned to the atoms according to certain thermal motions of the atoms. We call such an RMSD the dynamically weighted RMSD (dRMSD). We show that the thermal motions of the atoms can be obtained from several sources such as the mean-square fluctuations that can be estimated by Gaussian network model analysis. We show that the superimposition of structures with dRMSD can successfully identify protein domains and protein motions, and that it has important implications in practice, e.g., in aligning the ensemble of structures determined by nuclear magnetic resonance.

The contribution of transient counterion imbalances to DNA bending fluctuations.

PubMed

Manning, Gerald S

2006-05-01

A two-sided model for DNA is employed to analyze fluctuations of the spatial distribution of condensed counterions and the effect of these fluctuations on transient bending. We analyze two classes of fluctuations. In the first, the number of condensed counterions on one side of the DNA remains at its average value, while on the other side, counterions are lost to bulk solution or gained from it. The second class of fluctuations is characterized by movement of some counterions from one side of the DNA to the other. The root-mean-square fluctuation for each class is calculated from counterion condensation theory. The amplitude of the root-mean-square fluctuation depends on the ionic strength as well as the length of the segment considered and is of the order 5-10%. Both classes of fluctuation result in transient bends toward the side of greater counterion density. The bending amplitudes are approximately 15% of the total root-mean-square bends associated with the persistence length of DNA. We are thus led to suggest that asymmetric fluctuations of counterion density contribute modestly but significantly toward the aggregate of thermalized solvent fluctuations that cause bending deformations of DNA free in solution. The calculations support the idea that counterions may exert some modulating influence on the fine structure of DNA.

Binding mode analysis, dynamic simulation and binding free energy calculations of the MurF ligase from Acinetobacter baumannii.

PubMed

Ahmad, Sajjad; Raza, Saad; Uddin, Reaz; Azam, Syed Sikander

2017-10-01

MurF ligase catalyzes the final cytoplasmic step of bacterial peptidoglycan biosynthesis and, as such, is a validated target for therapeutic intervention. Herein, we performed molecular docking to identify putative inhibitors of Acinetobacter baumannii MurF (AbMurF). Based on comparative docking analysis, compound 114 (ethyl pyridine substituted 3-cyanothiophene) was predicted to potentially be the most active ligand. Computational pharmacokinetic characterization of drug-likeness of the compound showed it to fulfil all the parameters of Muegge and the MDDR rule. A molecular dynamic simulation of 114 indicated the complex to be stable on the basis of an average root mean square deviation (RMSD) value of 2.09Å for the ligand. The stability of the complex was further supported by root mean square fluctuation (RMSF), beta factor and radius of gyration values. Analyzing the complex using radial distribution function (RDF) and a novel analytical tool termed the axial frequency distribution (AFD) illustrated that after simulation the ligand is positioned in close vicinity of the protein active site where Thr42 and Asp43 participate in hydrogen bonding and stabilization of the complex. Binding free energy calculations based on the Poisson-Boltzmann or Generalized-Born Surface Area Continuum Solvation (MM(PB/GB)SA) method indicated the van der Waals contribution to the overall binding energy of the complex to be dominant along with electrostatic contributions involving the hot spot amino acids from the protein active site. The present results indicate that the screened compound 114 may act as a parent structure for designing potent derivatives against AbMurF in specific and MurF of other bacterial pathogens in general. Copyright © 2017 Elsevier Inc. All rights reserved.

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.

Heat-resistant cytosolic malate dehydrogenases (cMDHs) of thermophilic intertidal snails (genus Echinolittorina): protein underpinnings of tolerance to body temperatures reaching 55°C.

PubMed

Liao, Ming-Ling; Zhang, Shu; Zhang, Guang-Ya; Chu, Yun-Meng; Somero, George N; Dong, Yun-Wei

2017-06-01

Snails of the genus Echinolittorina are among the most heat-tolerant animals; they experience average body temperatures near 41-44°C in summer and withstand temperatures up to at least 55°C. Here, we demonstrate that heat stability of function (indexed by the Michaelis-Menten constant of the cofactor NADH, K M NADH ) and structure (indexed by rate of denaturation) of cytosolic malate dehydrogenases (cMDHs) of two congeners ( E. malaccana and E. radiata ) exceeds values previously found for orthologs of this protein from less thermophilic species. The ortholog of E. malaccana is more heat stable than that of E. radiata , in keeping with the congeners' thermal environments. Only two inter-congener differences in amino acid sequence in these 332 residue proteins were identified. In both cases (positions 48 and 114), a glycine in the E. malaccana ortholog is replaced by a serine in the E. radiata protein. To explore the relationship between structure and function and to characterize how amino acid substitutions alter stability of different regions of the enzyme, we used molecular dynamics simulation methods. These computational methods allow determination of thermal effects on fine-scale movements of protein components, for example, by estimating the root mean square deviation in atom position over time and the root mean square fluctuation for individual residues. The minor changes in amino acid sequence favor temperature-adaptive change in flexibility of regions in and around the active sites. Interspecific differences in effects of temperature on fine-scale protein movements are consistent with the differences in thermal effects on binding and rates of heat denaturation. © 2017. Published by The Company of Biologists Ltd.

Combining Ratio Estimation for Low Density Parity Check (LDPC) Coding

NASA Technical Reports Server (NTRS)

Mahmoud, Saad; Hi, Jianjun

2012-01-01

The Low Density Parity Check (LDPC) Code decoding algorithm make use of a scaled receive signal derived from maximizing the log-likelihood ratio of the received signal. The scaling factor (often called the combining ratio) in an AWGN channel is a ratio between signal amplitude and noise variance. Accurately estimating this ratio has shown as much as 0.6 dB decoding performance gain. This presentation briefly describes three methods for estimating the combining ratio: a Pilot-Guided estimation method, a Blind estimation method, and a Simulation-Based Look-Up table. The Pilot Guided Estimation method has shown that the maximum likelihood estimates of signal amplitude is the mean inner product of the received sequence and the known sequence, the attached synchronization marker (ASM) , and signal variance is the difference of the mean of the squared received sequence and the square of the signal amplitude. This method has the advantage of simplicity at the expense of latency since several frames worth of ASMs. The Blind estimation method s maximum likelihood estimator is the average of the product of the received signal with the hyperbolic tangent of the product combining ratio and the received signal. The root of this equation can be determined by an iterative binary search between 0 and 1 after normalizing the received sequence. This method has the benefit of requiring one frame of data to estimate the combining ratio which is good for faster changing channels compared to the previous method, however it is computationally expensive. The final method uses a look-up table based on prior simulated results to determine signal amplitude and noise variance. In this method the received mean signal strength is controlled to a constant soft decision value. The magnitude of the deviation is averaged over a predetermined number of samples. This value is referenced in a look up table to determine the combining ratio that prior simulation associated with the average magnitude of the deviation. This method is more complicated than the Pilot-Guided Method due to the gain control circuitry, but does not have the real-time computation complexity of the Blind Estimation method. Each of these methods can be used to provide an accurate estimation of the combining ratio, and the final selection of the estimation method depends on other design constraints.

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.

Feasibility of Coherent and Incoherent Backscatter Experiments from the AMPS Laboratory. Technical Section

NASA Technical Reports Server (NTRS)

Mozer, F. S.

1976-01-01

A computer program simulated the spectrum which resulted when a radar signal was transmitted into the ionosphere for a finite time and received for an equal finite interval. The spectrum derived from this signal is statistical in nature because the signal is scattered from the ionosphere, which is statistical in nature. Many estimates of any property of the ionosphere can be made. Their average value will approach the average property of the ionosphere which is being measured. Due to the statistical nature of the spectrum itself, the estimators will vary about this average. The square root of the variance about this average is called the standard deviation, an estimate of the error which exists in any particular radar measurement. In order to determine the feasibility of the space shuttle radar, the magnitude of these errors for measurements of physical interest must be understood.

Molecular dynamics simulation of polyacrylamides in potassium montmorillonite clay hydrates

NASA Astrophysics Data System (ADS)

Zhang, Junfang; Rivero, Mayela; Choi, S. K.

2007-02-01

We present molecular dynamics simulation results for polyacrylamide in potassium montmorillonite clay-aqueous systems. Interlayer molecular structure and dynamics properties are investigated. The number density profile, radial distribution function, root-mean-square deviation (RMSD), mean-square displacement (MSD) and diffusion coefficient are reported. The calculations are conducted in constant NVT ensembles, at T = 300 K and with layer spacing of 40 Å. Our simulation results showed that polyacrylamides had little impact on the structure of interlayer water. Density profiles and radial distribution function indicated that hydration shells were formed. In the presence of polyacrylamides more potassium counterions move close to the clay surface while water molecules move away, indicating that potassium counterions are hydrated to a lesser extent than the system in which no polyacrylamides were added. The diffusion coefficients for potassium and water decreased when polyacrylamides were added.

Exploration of Structural and Functional Variations Owing to Point Mutations in α-NAGA.

PubMed

Meshach Paul, D; Rajasekaran, R

2018-03-01

Schindler disease is a lysosomal storage disorder caused due to deficiency or defective activity of alpha-N-acetylgalactosaminidase (α-NAGA). Mutations in gene encoding α-NAGA cause wide range of diseases, characterized with mild to severe clinical features. Molecular effects of these mutations are yet to be explored in detail. Therefore, this study was focused on four missense mutations of α-NAGA namely, S160C, E325K, R329Q and R329W. Native and mutant structures of α-NAGA were analysed to determine geometrical deviations such as the contours of root mean square deviation, root mean square fluctuation, percentage of residues in allowed regions of Ramachandran plot and solvent accessible surface area, using conformational sampling technique. Additionally, global energy-minimized structures of native and mutants were further analysed to compute their intra-molecular interactions, hydrogen bond dilution and distribution of secondary structure. In addition, docking studies were also performed to determine variations in binding energies between native and mutants. The deleterious effects of mutants were evident due to variations in their active site residues pertaining to spatial conformation and flexibility, comparatively. Hence, variations exhibited by mutants, namely S160C, E325K, R329Q and R329W to that of native, consequently, lead to the detrimental effects causing Schindler disease. This study computationally explains the underlying reasons for the pathogenesis of the disease, thereby aiding future researchers in drug development and disease management.

Interest rate next-day variation prediction based on hybrid feedforward neural network, particle swarm optimization, and multiresolution techniques

NASA Astrophysics Data System (ADS)

Lahmiri, Salim

2016-02-01

Multiresolution analysis techniques including continuous wavelet transform, empirical mode decomposition, and variational mode decomposition are tested in the context of interest rate next-day variation prediction. In particular, multiresolution analysis techniques are used to decompose interest rate actual variation and feedforward neural network for training and prediction. Particle swarm optimization technique is adopted to optimize its initial weights. For comparison purpose, autoregressive moving average model, random walk process and the naive model are used as main reference models. In order to show the feasibility of the presented hybrid models that combine multiresolution analysis techniques and feedforward neural network optimized by particle swarm optimization, we used a set of six illustrative interest rates; including Moody's seasoned Aaa corporate bond yield, Moody's seasoned Baa corporate bond yield, 3-Month, 6-Month and 1-Year treasury bills, and effective federal fund rate. The forecasting results show that all multiresolution-based prediction systems outperform the conventional reference models on the criteria of mean absolute error, mean absolute deviation, and root mean-squared error. Therefore, it is advantageous to adopt hybrid multiresolution techniques and soft computing models to forecast interest rate daily variations as they provide good forecasting performance.

Activation of N-methyl-d-aspartate receptors reduces heart rate variability and facilitates atrial fibrillation in rats.

PubMed

Shi, Shaobo; Liu, Tao; Wang, Dandan; Zhang, Yan; Liang, Jinjun; Yang, Bo; Hu, Dan

2017-07-01

The goal of this study was to assess the effects of N-methyl-d-aspartate (NMDA) receptors activation on heart rate variability (HRV) and susceptibility to atrial fibrillation (AF). Rats were randomized for treatment with saline, NMDA (agonist of NMDA receptors), or NMDA plus MK-801 (antagonist of NMDA receptors) for 2 weeks. Heart rate variability was evaluated by using implantable electrocardiogram telemeters. Atrial fibrillation susceptibility was assessed with programmed stimulation in isolated hearts. Compared with the controls, the NMDA-treated rats displayed a decrease in the standard deviation of normal RR intervals, the standard deviation of the average RR intervals, the mean of the 5-min standard deviations of RR intervals, the root mean square of successive differences, and high frequency (HF); and an increase in low frequency (LF) and LF/HF (all P< 0.01). Additionally, the NMDA-treated rats showed prolonged activation latency and reduced effective refractory period (all P< 0.01). Importantly, AF was induced in all NMDA-treated rats. While atrial fibrosis developed, connexin40 downgraded and metalloproteinase 9 upgraded in the NMDA-treated rats (all P< 0.01). Most of the above alterations were mitigated by co-administering with MK-801. These results indicate that NMDA receptors activation reduces HRV and enhances AF inducibility, with cardiac autonomic imbalance, atrial fibrosis, and degradation of gap junction protein identified as potential mechanistic contributors. Published on behalf of the European Society of Cardiology. All rights reserved. © The Author 2016. For permissions please email: journals.permissions@oup.com.

Using Fit Indexes to Select a Covariance Model for Longitudinal Data

ERIC Educational Resources Information Center

Liu, Siwei; Rovine, Michael J.; Molenaar, Peter C. M.

2012-01-01

This study investigated the performance of fit indexes in selecting a covariance structure for longitudinal data. Data were simulated to follow a compound symmetry, first-order autoregressive, first-order moving average, or random-coefficients covariance structure. We examined the ability of the likelihood ratio test (LRT), root mean square error…

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.

On the radiated EMI current extraction of dc transmission line based on corona current statistical measurements

NASA Astrophysics Data System (ADS)

Yi, Yong; Chen, Zhengying; Wang, Liming

2018-05-01

Corona-originated discharge of DC transmission lines is the main reason for the radiated electromagnetic interference (EMI) field in the vicinity of transmission lines. A joint time-frequency analysis technique was proposed to extract the radiated EMI current (excitation current) of DC corona based on corona current statistical measurements. A reduced-scale experimental platform was setup to measure the statistical distributions of current waveform parameters of aluminum conductor steel reinforced. Based on the measured results, the peak value, root-mean-square value and average value with 9 kHz and 200 Hz band-with of 0.5 MHz radiated EMI current were calculated by the technique proposed and validated with conventional excitation function method. Radio interference (RI) was calculated based on the radiated EMI current and a wire-to-plate platform was built for the validity of the RI computation results. The reason for the certain deviation between the computations and measurements was detailed analyzed.

Initial geomagnetic field model from Magsat vector data

NASA Technical Reports Server (NTRS)

Langel, R. A.; Mead, G. D.; Lancaster, E. R.; Estes, R. H.; Fabiano, E. B.

1980-01-01

Magsat data from the magnetically quiet days of November 5-6, 1979, were used to derive a thirteenth degree and order spherical harmonic geomagnetic field model, MGST(6/80). The model utilized both scalar and high-accuracy vector data and fit that data with root-mean-square deviations of 8.2, 6.9, 7.6 and 7.4 nT for the scalar magnitude, B(r), B(theta), and B(phi), respectively. The model includes the three first-order coefficients of the external field. Comparison with averaged Dst indicates that zero Dst corresponds with 25 nT of horizontal field from external sources. When compared with earlier models, the earth's dipole moment continues to decrease at a rate of about 26 nT/yr. Evaluation of earlier models with Magsat data shows that the scalar field at the Magsat epoch is best predicted by the POGO(2/72) model but that the WC80, AWC/75 and IGS/75 are better for predicting vector fields.

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.

The change in spatial distribution of upper trapezius muscle activity is correlated to contraction duration.

PubMed

Farina, Dario; Leclerc, Frédéric; Arendt-Nielsen, Lars; Buttelli, Olivier; Madeleine, Pascal

2008-02-01

The aim of the study was to confirm the hypothesis that the longer a contraction is sustained, the larger are the changes in the spatial distribution of muscle activity. For this purpose, surface electromyographic (EMG) signals were recorded with a 13 x 5 grid of electrodes from the upper trapezius muscle of 11 healthy male subjects during static contractions with shoulders 90 degrees abducted until endurance. The entropy (degree of uniformity) and center of gravity of the EMG root mean square map were computed to assess spatial inhomogeneity in muscle activation and changes over time in EMG amplitude spatial distribution. At the endurance time, entropy decreased (mean+/-SD, percent change 2.0+/-1.6%; P<0.0001) and the center of gravity moved in the cranial direction (shift 11.2+/-6.1mm; P<0.0001) with respect to the beginning of the contraction. The shift in the center of gravity was positively correlated with endurance time (R(2)=0.46, P<0.05), thus subjects with larger shift in the activity map showed longer endurance time. The percent variation in average (over the grid) root mean square was positively correlated with the shift in the center of gravity (R(2)=0.51, P<0.05). Moreover, the shift in the center of gravity was negatively correlated to both initial and final (at the endurance) entropy (R(2)=0.54 and R(2)=0.56, respectively; P<0.01 in both cases), indicating that subjects with less uniform root mean square maps had larger shift of the center of gravity over time. The spatial changes in root mean square EMG were likely due to spatially-dependent changes in motor unit activation during the sustained contraction. It was concluded that the changes in spatial muscle activity distribution play a role in the ability to maintain a static contraction.

Determination of a transient heat transfer property of acrylic using thermochromic liquid crystals

NASA Technical Reports Server (NTRS)

Heidmann, James D.

1994-01-01

An experiment was performed to determine a transient heat transfer property of acrylic. The experiment took advantage of the known analytical solution for heat conduction in a homogeneous semi-infinite solid with a constant surface heat flux. Thermochromic liquid crystals were used to measure the temperature nonintrusively. The relevant property in this experiment was the transient thermal conduction coefficient h(sub t), which is the square root of the product of density p, specific heat c(sub p), and thermal conductivity k (i.e., square root of pc(sub p)k). A value of 595.6 W square root of s/sq m K was obtained for h(sub t), with a standard deviation of 5.1 W square root of s/sq m K. Although there is no generally accepted value for h(sub t), a commonly used one is 580 W square root of s/sq m K, which is almost 3 percent less than the h(sub t) value obtained in this experiment. Since these results were highly repeatable and since there is no definitive value for h(sub t), the new value is recommended for future use.

Evaluation of LiDAR-acquired bathymetric and topographic data accuracy in various hydrogeomorphic settings in the Deadwood and South Fork Boise Rivers, West-Central Idaho, 2007

USGS Publications Warehouse

Skinner, Kenneth D.

2011-01-01

High-quality elevation data in riverine environments are important for fisheries management applications and the accuracy of such data needs to be determined for its proper application. The Experimental Advanced Airborne Research LiDAR (Light Detection and Ranging)-or EAARL-system was used to obtain topographic and bathymetric data along the Deadwood and South Fork Boise Rivers in west-central Idaho. The EAARL data were post-processed into bare earth and bathymetric raster and point datasets. Concurrently with the EAARL surveys, real-time kinematic global positioning system surveys were made in three areas along each of the rivers to assess the accuracy of the EAARL elevation data in different hydrogeomorphic settings. The accuracies of the EAARL-derived raster elevation values, determined in open, flat terrain, to provide an optimal vertical comparison surface, had root mean square errors ranging from 0.134 to 0.347 m. Accuracies in the elevation values for the stream hydrogeomorphic settings had root mean square errors ranging from 0.251 to 0.782 m. The greater root mean square errors for the latter data are the result of complex hydrogeomorphic environments within the streams, such as submerged aquatic macrophytes and air bubble entrainment; and those along the banks, such as boulders, woody debris, and steep slopes. These complex environments reduce the accuracy of EAARL bathymetric and topographic measurements. Steep banks emphasize the horizontal location discrepancies between the EAARL and ground-survey data and may not be good representations of vertical accuracy. The EAARL point to ground-survey comparisons produced results with slightly higher but similar root mean square errors than those for the EAARL raster to ground-survey comparisons, emphasizing the minimized horizontal offset by using interpolated values from the raster dataset at the exact location of the ground-survey point as opposed to an actual EAARL point within a 1-meter distance. The average error for the wetted stream channel surface areas was -0.5 percent, while the average error for the wetted stream channel volume was -8.3 percent. The volume of the wetted river channel was underestimated by an average of 31 percent in half of the survey areas, and overestimated by an average of 14 percent in the remainder of the survey areas. The EAARL system is an efficient way to obtain topographic and bathymetric data in large areas of remote terrain. The elevation accuracy of the EAARL system varies throughout the area depending upon the hydrogeomorphic setting, preventing the use of a single accuracy value to describe the EAARL system. The elevation accuracy variations should be kept in mind when using the data, such as for hydraulic modeling or aquatic habitat assessments.

Liquid fuel spray processes in high-pressure gas flow

NASA Technical Reports Server (NTRS)

Ingebo, R. D.

1985-01-01

Atomization of single liquid jets injected downstream in high pressure and high velocity airflow was investigated to determine the effect of airstream pressure on mean drop size as measured with a scanning radiometer. For aerodynamic - wave breakup of liquid jets, the ratio of orifice diameter D sub o to measured mean drop diameter D sub m which is assumed equal to D sub 32 or Sauter mean diameter, was correlated with the product of the Weber and Reynolds numbers WeRe and the dimensionless group G1/square root of c, where G is the gravitational acceleration, 1 the mean free molecular path, and square root of C the root mean square velocity, as follows; D sub o/D sub 32 = 1.2 (WeRe) to the 0.4 (G1/square root of c) to the 0.15 for values of WeRe 1 million and an airstream pressure range of 0.10 to 2.10 MPa.

Liquid fuel spray processes in high-pressure gas flow

NASA Technical Reports Server (NTRS)

Ingebo, R. D.

1986-01-01

Atomization of single liquid jets injected downstream in high pressure and high velocity airflow was investigated to determine the effect of airstream pressure on mean drop size as measured with a scanning radiometer. For aerodynamic - wave breakup of liquid jets, the ratio of orifice diameter D sub o to measured mean drop diameter D sub m which is assumed equal to D sub 32 or Sauter mean diameter, was correlated with the product of the Weber and Reynolds numbers WeRe and the dimensionless group G1/square root of c, where G is the gravitational acceleration, 1 the mean free molecular path, and square root of C the root mean square velocity, as follows; D sub o/D sub 32 = 1.2 (WeRe) to the 0.4 (G1/square root of c) to the 0.15 for values of WeRe 1 million and an airstream pressure range of 0.10 to 2.10 MPa.

Improving the distinguishable cluster results: spin-component scaling

NASA Astrophysics Data System (ADS)

Kats, Daniel

2018-06-01

The spin-component scaling is employed in the energy evaluation to improve the distinguishable cluster approach. SCS-DCSD reaction energies reproduce reference values with a root-mean-squared deviation well below 1 kcal/mol, the interaction energies are three to five times more accurate than DCSD, and molecular systems with a large amount of static electron correlation are still described reasonably well. SCS-DCSD represents a pragmatic approach to achieve chemical accuracy with a simple method without triples, which can also be applied to multi-configurational molecular systems.

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.

Temperature dependence of Ti 1s near-edge spectra in Ti-based perovskites: theory and experiment

NASA Astrophysics Data System (ADS)

Shirley, Eric; Cockayne, Eric; Ravel, Bruce; Woicik, Joseph

Ti 1s near-edge spectra (around 4970 eV) in SrTiO3 and PbTiO3 reveal electric-dipole and quadrupole transitions to Ti 3d, 4p and mixed 3d-4p states. Crystal field-split pre-edge features attributed to 1s ->3d transitions are small compared to the main edge jump at the onset of the Ti 4s/4p continuum. Pre-edge and subsequent near-edge features are predicted to be weaker than what is observed, unless one accounts for ferroelectric polarization in PbTiO3 and thermal motion in both compounds. Using density-functional theory molecular dynamics simulations at various temperatures (including sampling two phases of PbTiO3), we capture the statistically averaged root-mean-square deviations of Ti4+ ions from the centers of their oxygen cages. By sampling appropriate snapshots of atomic configurations and averaging Ti 1s absorption spectra computed within a Bethe-Salpeter Equation framework, we obtain absorption spectra that agree well with experiment, including details related to ferroelectric polarization, phase transitions, and fluctuations of atomic coordinates.

Single tooth torque correction in the lower frontal area by a completely customized lingual appliance.

PubMed

Jacobs, Collin; Katzorke, Milena; Wiechmann, Dirk; Wehrbein, Heiner; Schwestka-Polly, Rainer

2017-10-10

Aim of this study was to analyze the efficacy and precision of the completely customized lingual appliance (CCLA) regarding the single tooth torque correction. The study also examined external apical root resorptions as possible side effects of torque correction and the changings of the periodontal situation. A case series of three patients were included. The patients showed a single tooth torque problem with a gingival recession and were treated with the CCLA. Plaster casts before and after treatment and plaster casts of the set up were scanned and superimposed. Deviations between the two plaster casts were analyzed at different points of interest. Changes of the gingival recession were compared before and after treatment. Relative root resorptions were measured by the orthopantomograms. Treatment times were assessed by the records of the patients. Results were presented descriptively. The mean change of the most apical part of the root reached by the orthodontic treatment was 1.8 ± 0.3 mm. The largest deviation between set up and final model was measured on the occlusal surface of the tooth 36 with 0.8 mm. Most measurement points showed a deviation of 0.5 mm or less. The depths of the gingival recession showed a significant reduction of 4.7 mm. The widths of the gingival recession were reduced by 1.1 mm. The average relative root resorption of the corrected teeth was 2.7 ± 1.5%. The average treatment time was 13.8 ± 4.5 months. This is the first study showing that the CCLA with its high precision is very effective in correcting single tooth torque problems. Orthodontic torque correction resulted in a significant reduction of gingival recessions and caused only negligible root resorptions.

The Influence of Dimensionality on Estimation in the Partial Credit Model.

ERIC Educational Resources Information Center

De Ayala, R. J.

1995-01-01

The effect of multidimensionality on partial credit model parameter estimation was studied with noncompensatory and compensatory data. Analysis results, consisting of root mean square error bias, Pearson product-moment corrections, standardized root mean squared differences, standardized differences between means, and descriptive statistics…

Comprehensive Assessment of Coronary Artery Disease by Using First-Pass Analysis Dynamic CT Perfusion: Validation in a Swine Model.

PubMed

Hubbard, Logan; Lipinski, Jerry; Ziemer, Benjamin; Malkasian, Shant; Sadeghi, Bahman; Javan, Hanna; Groves, Elliott M; Dertli, Brian; Molloi, Sabee

2018-01-01

Purpose To retrospectively validate a first-pass analysis (FPA) technique that combines computed tomographic (CT) angiography and dynamic CT perfusion measurement into one low-dose examination. Materials and Methods The study was approved by the animal care committee. The FPA technique was retrospectively validated in six swine (mean weight, 37.3 kg ± 7.5 [standard deviation]) between April 2015 and October 2016. Four to five intermediate-severity stenoses were generated in the left anterior descending artery (LAD), and 20 contrast material-enhanced volume scans were acquired per stenosis. All volume scans were used for maximum slope model (MSM) perfusion measurement, but only two volume scans were used for FPA perfusion measurement. Perfusion measurements in the LAD, left circumflex artery (LCx), right coronary artery, and all three coronary arteries combined were compared with microsphere perfusion measurements by using regression, root-mean-square error, root-mean-square deviation, Lin concordance correlation, and diagnostic outcomes analysis. The CT dose index and size-specific dose estimate per two-volume FPA perfusion measurement were also determined. Results FPA and MSM perfusion measurements (P FPA and P MSM ) in all three coronary arteries combined were related to reference standard microsphere perfusion measurements (P MICRO ), as follows: P FPA_COMBINED = 1.02 P MICRO_COMBINED + 0.11 (r = 0.96) and P MSM_COMBINED = 0.28 P MICRO_COMBINED + 0.23 (r = 0.89). The CT dose index and size-specific dose estimate per two-volume FPA perfusion measurement were 10.8 and 17.8 mGy, respectively. Conclusion The FPA technique was retrospectively validated in a swine model and has the potential to be used for accurate, low-dose vessel-specific morphologic and physiologic assessment of coronary artery disease. © RSNA, 2017.

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.

Molecular Dynamic Simulation of Space and Earth-Grown Crystal Structures of Thermostable T1 Lipase Geobacillus zalihae Revealed a Better Structure.

PubMed

Ishak, Siti Nor Hasmah; Aris, Sayangku Nor Ariati Mohamad; Halim, Khairul Bariyyah Abd; Ali, Mohd Shukuri Mohamad; Leow, Thean Chor; Kamarudin, Nor Hafizah Ahmad; Masomian, Malihe; Rahman, Raja Noor Zaliha Raja Abd

2017-09-25

Less sedimentation and convection in a microgravity environment has become a well-suited condition for growing high quality protein crystals. Thermostable T1 lipase derived from bacterium Geobacillus zalihae has been crystallized using the counter diffusion method under space and earth conditions. Preliminary study using YASARA molecular modeling structure program for both structures showed differences in number of hydrogen bond, ionic interaction, and conformation. The space-grown crystal structure contains more hydrogen bonds as compared with the earth-grown crystal structure. A molecular dynamics simulation study was used to provide insight on the fluctuations and conformational changes of both T1 lipase structures. The analysis of root mean square deviation (RMSD), radius of gyration, and root mean square fluctuation (RMSF) showed that space-grown structure is more stable than the earth-grown structure. Space-structure also showed more hydrogen bonds and ion interactions compared to the earth-grown structure. Further analysis also revealed that the space-grown structure has long-lived interactions, hence it is considered as the more stable structure. This study provides the conformational dynamics of T1 lipase crystal structure grown in space and earth condition.

Molecular Dynamics Simulation of Rap1 Myb-type domain in Saccharomyces cerevisiae

PubMed Central

Mukherjee, Koel; Pandey, Dev Mani; Vidyarthi, Ambarish Saran

2012-01-01

Telomere is a nucleoprotein complex that plays important role in stability and their maintenance and consists of random repeats of species specific motifs. In budding Saccharomyces cerevisiae, Repressor Activator Protein 1 (Rap1) is a sequence specific protein that involved in transcriptional regulation. Rap1 consist of three active domains like N-terminal BRCT-domain, DNA-binding domain and C-terminal RCT-domain. In this study the unknown 3D structure of Myb-type domain (having 61 residues) within DNAbinding domain was modeled by Modeller7, and verified using different online bioinformatics tools (ProCheck, WhatIf, Verify3D). Dynamics of Myb-type domain of Rap1was carried out through simulation studies using GROMACS software. Time dependent interactions among the molecules were analyzed by Root Mean Square Deviation (RMSD), Radius of Gyration (Rg) and Root Mean Square Fluctuation (RMSF) plots. Motional properties in reduced dimension were also performed by Principal Component Analysis (PCA). Result indicated that Rap1 interacts with DNA major groove through its Helix Turn Helix motifs. Helix 3 was rigid, less amount of fluctuation was found as it interacts with DNA major groove. Helix2 and N-terminal having considerable fluctuation in the time scale. PMID:23144544

Molecular Dynamics Simulation of Rap1 Myb-type domain in Saccharomyces cerevisiae.

PubMed

Mukherjee, Koel; Pandey, Dev Mani; Vidyarthi, Ambarish Saran

2012-01-01

Telomere is a nucleoprotein complex that plays important role in stability and their maintenance and consists of random repeats of species specific motifs. In budding Saccharomyces cerevisiae, Repressor Activator Protein 1 (Rap1) is a sequence specific protein that involved in transcriptional regulation. Rap1 consist of three active domains like N-terminal BRCT-domain, DNA-binding domain and C-terminal RCT-domain. In this study the unknown 3D structure of Myb-type domain (having 61 residues) within DNAbinding domain was modeled by Modeller7, and verified using different online bioinformatics tools (ProCheck, WhatIf, Verify3D). Dynamics of Myb-type domain of Rap1was carried out through simulation studies using GROMACS software. Time dependent interactions among the molecules were analyzed by Root Mean Square Deviation (RMSD), Radius of Gyration (Rg) and Root Mean Square Fluctuation (RMSF) plots. Motional properties in reduced dimension were also performed by Principal Component Analysis (PCA). Result indicated that Rap1 interacts with DNA major groove through its Helix Turn Helix motifs. Helix 3 was rigid, less amount of fluctuation was found as it interacts with DNA major groove. Helix2 and N-terminal having considerable fluctuation in the time scale.

Estimating accuracy of land-cover composition from two-stage cluster sampling

USGS Publications Warehouse

Stehman, S.V.; Wickham, J.D.; Fattorini, L.; Wade, T.D.; Baffetta, F.; Smith, J.H.

2009-01-01

Land-cover maps are often used to compute land-cover composition (i.e., the proportion or percent of area covered by each class), for each unit in a spatial partition of the region mapped. We derive design-based estimators of mean deviation (MD), mean absolute deviation (MAD), root mean square error (RMSE), and correlation (CORR) to quantify accuracy of land-cover composition for a general two-stage cluster sampling design, and for the special case of simple random sampling without replacement (SRSWOR) at each stage. The bias of the estimators for the two-stage SRSWOR design is evaluated via a simulation study. The estimators of RMSE and CORR have small bias except when sample size is small and the land-cover class is rare. The estimator of MAD is biased for both rare and common land-cover classes except when sample size is large. A general recommendation is that rare land-cover classes require large sample sizes to ensure that the accuracy estimators have small bias. ?? 2009 Elsevier Inc.

1- and 2-particle Microrheology of Hyaluronic Acid

NASA Astrophysics Data System (ADS)

Sagan, Austin; Kearns, Sarah; Ross, David; Das, Moumita; Thurston, George; Franklin, Scott

2015-03-01

Hyaluronic acid (also called HA or Hyaluronan) is a high molecular weight polysaccaride ubiquitous in the extracellular matrix of soft tissue such as cartilage, skin, the eye's vitreous gel and synovial fluid. It has been shown to play an important role in mechanotransduction, cell migration and proliferation, and in tissue morphodynamics. We present a confocal microrheology study of hyaluronic acid of varying concentrations. The mean squared displacement (MSD) of sub-micron colloidal tracer particles is tracked in two dimensions and shows a transition from diffusive motion at low concentrations to small-time trapping by the protein network as the concentration increases. Correlations between particle motion can be used to determine an effective mean-squared displacement which deviates from the single-particle MSD as the fluid becomes less homogeneous. The real and effective mean-squared displacements are used to probe the local and space-averaged frequency dependent rheological properties of the fluid as the concentration changes.

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.

Improving Arterial Spin Labeling by Using Deep Learning.

PubMed

Kim, Ki Hwan; Choi, Seung Hong; Park, Sung-Hong

2018-05-01

Purpose To develop a deep learning algorithm that generates arterial spin labeling (ASL) perfusion images with higher accuracy and robustness by using a smaller number of subtraction images. Materials and Methods For ASL image generation from pair-wise subtraction, we used a convolutional neural network (CNN) as a deep learning algorithm. The ground truth perfusion images were generated by averaging six or seven pairwise subtraction images acquired with (a) conventional pseudocontinuous arterial spin labeling from seven healthy subjects or (b) Hadamard-encoded pseudocontinuous ASL from 114 patients with various diseases. CNNs were trained to generate perfusion images from a smaller number (two or three) of subtraction images and evaluated by means of cross-validation. CNNs from the patient data sets were also tested on 26 separate stroke data sets. CNNs were compared with the conventional averaging method in terms of mean square error and radiologic score by using a paired t test and/or Wilcoxon signed-rank test. Results Mean square errors were approximately 40% lower than those of the conventional averaging method for the cross-validation with the healthy subjects and patients and the separate test with the patients who had experienced a stroke (P < .001). Region-of-interest analysis in stroke regions showed that cerebral blood flow maps from CNN (mean ± standard deviation, 19.7 mL per 100 g/min ± 9.7) had smaller mean square errors than those determined with the conventional averaging method (43.2 ± 29.8) (P < .001). Radiologic scoring demonstrated that CNNs suppressed noise and motion and/or segmentation artifacts better than the conventional averaging method did (P < .001). Conclusion CNNs provided superior perfusion image quality and more accurate perfusion measurement compared with those of the conventional averaging method for generation of ASL images from pair-wise subtraction images. © RSNA, 2017.

Accuracy of intraoral data acquisition in comparison to the conventional impression.

PubMed

Luthardt, R G; Loos, R; Quaas, S

2005-10-01

The achievable accuracy is a decisive parameter for the comparison of direct intraoral digitization with the conventional impression. The objective of the study was therefore to compare the accuracy of the reproduction of a model situation by intraoral digitization vs. the conventional procedure consisting of impression taking, model production, and extraoral digitization. Proceeding from a die model with a prepared tooth 16, the reference data set of the teeth 15, 16 and 17 was produced with an established procedure by means ofextraoral digitization. For the simulated intraoral data acquisition of the master model (Cerec 3D camera, Sirona, Bensheim), the camera was fastened on a stand for the measurement and the teeth digitized seven times each in defined views (occlusal, and in each case inclined by 20 degrees, from the mesio-proximal, disto-proximal, vestibular and oral aspect). Matching was automated (comparative data sets B1-B5). A clinically perfect one-step putty-and-wash impression was taken from the starting model. The model produced under defined conditions was digitized extraorally five times (digi-SCAN, comparative data sets C1-C5). The data sets B1-B5 and C1-C5 were assigned to the reference data set by means of best-fit matching and the root of the mean quadratic deviation (RMS; root mean square) calculated. The deviations were visualized, and mean positive, negative and absolute deviations calculated. The mean RMS was 27.9 microm (B1-B5) or 18.8 microm (C1-C5). The mean deviations for the prepared tooth were 18 microm/-17 microm (B1-B5) and 9 microm /-9 microm (C1-C5). For tooth 15, the mean deviations were 22 microm/-19 microm (B1-B5) and 15 microm/-16 microm (C1-C5). The intraoral method showed good results with deviations from the CAD starting model of approx. 17 microm, related to the prepared tooth 16. On the whole, in this in-vitro study, extraoral digitization with impression taking and model production showed higher accuracy than intraoral digitization. Since the inaccuracies in the conventional impression under real clinical conditions may be higher than the values determined above, a comparison under clinical conditions should be performed subsequently.

Performance metrics for the assessment of satellite data products: an ocean color case study

PubMed Central

Seegers, Bridget N.; Stumpf, Richard P.; Schaeffer, Blake A.; Loftin, Keith A.; Werdell, P. Jeremy

2018-01-01

Performance assessment of ocean color satellite data has generally relied on statistical metrics chosen for their common usage and the rationale for selecting certain metrics is infrequently explained. Commonly reported statistics based on mean squared errors, such as the coefficient of determination (r2), root mean square error, and regression slopes, are most appropriate for Gaussian distributions without outliers and, therefore, are often not ideal for ocean color algorithm performance assessment, which is often limited by sample availability. In contrast, metrics based on simple deviations, such as bias and mean absolute error, as well as pair-wise comparisons, often provide more robust and straightforward quantities for evaluating ocean color algorithms with non-Gaussian distributions and outliers. This study uses a SeaWiFS chlorophyll-a validation data set to demonstrate a framework for satellite data product assessment and recommends a multi-metric and user-dependent approach that can be applied within science, modeling, and resource management communities. PMID:29609296

GPU-Q-J, a fast method for calculating root mean square deviation (RMSD) after optimal superposition

PubMed Central

2011-01-01

Background Calculation of the root mean square deviation (RMSD) between the atomic coordinates of two optimally superposed structures is a basic component of structural comparison techniques. We describe a quaternion based method, GPU-Q-J, that is stable with single precision calculations and suitable for graphics processor units (GPUs). The application was implemented on an ATI 4770 graphics card in C/C++ and Brook+ in Linux where it was 260 to 760 times faster than existing unoptimized CPU methods. Source code is available from the Compbio website http://software.compbio.washington.edu/misc/downloads/st_gpu_fit/ or from the author LHH. Findings The Nutritious Rice for the World Project (NRW) on World Community Grid predicted de novo, the structures of over 62,000 small proteins and protein domains returning a total of 10 billion candidate structures. Clustering ensembles of structures on this scale requires calculation of large similarity matrices consisting of RMSDs between each pair of structures in the set. As a real-world test, we calculated the matrices for 6 different ensembles from NRW. The GPU method was 260 times faster that the fastest existing CPU based method and over 500 times faster than the method that had been previously used. Conclusions GPU-Q-J is a significant advance over previous CPU methods. It relieves a major bottleneck in the clustering of large numbers of structures for NRW. It also has applications in structure comparison methods that involve multiple superposition and RMSD determination steps, particularly when such methods are applied on a proteome and genome wide scale. PMID:21453553

Structural Refinement of Membrane Proteins by Restrained Molecular Dynamics and Solvent Accessibility Data

PubMed Central

Sompornpisut, Pornthep; Roux, Benoît; Perozo, Eduardo

2008-01-01

We present an approach for incorporating solvent accessibility data from electron paramagnetic resonance experiments in the structural refinement of membrane proteins through restrained molecular dynamics simulations. The restraints have been parameterized from oxygen (ΠO2) and nickel-ethylenediaminediacetic acid (ΠNiEdda) collision frequencies, as indicators of lipid or aqueous exposed spin-label sites. These are enforced through interactions between a pseudoatom representation of the covalently attached Nitroxide spin-label and virtual “solvent” particles corresponding to O2 and NiEdda in the surrounding environment. Interactions were computed using an empirical potential function, where the parameters have been optimized to account for the different accessibilities of the spin-label pseudoatoms to the surrounding environment. This approach, “pseudoatom-driven solvent accessibility refinement”, was validated by refolding distorted conformations of the Streptomyces lividans potassium channel (KcsA), corresponding to a range of 2–30 Å root mean-square deviations away from the native structure. Molecular dynamics simulations based on up to 58 electron paramagnetic resonance restraints derived from spin-label mutants were able to converge toward the native structure within 1–3 Å root mean-square deviations with minimal computational cost. The use of energy-based ranking and structure similarity clustering as selection criteria helped in the convergence and identification of correctly folded structures from a large number of simulations. This approach can be applied to a variety of integral membrane protein systems, regardless of oligomeric state, and should be particularly useful in calculating conformational changes from a known reference crystal structure. PMID:18676641

[Influence of Spectral Pre-Processing on PLS Quantitative Model of Detecting Cu in Navel Orange by LIBS].

PubMed

Li, Wen-bing; Yao, Lin-tao; Liu, Mu-hua; Huang, Lin; Yao, Ming-yin; Chen, Tian-bing; He, Xiu-wen; Yang, Ping; Hu, Hui-qin; Nie, Jiang-hui

2015-05-01

Cu in navel orange was detected rapidly by laser-induced breakdown spectroscopy (LIBS) combined with partial least squares (PLS) for quantitative analysis, then the effect on the detection accuracy of the model with different spectral data ptetreatment methods was explored. Spectral data for the 52 Gannan navel orange samples were pretreated by different data smoothing, mean centralized and standard normal variable transform. Then 319~338 nm wavelength section containing characteristic spectral lines of Cu was selected to build PLS models, the main evaluation indexes of models such as regression coefficient (r), root mean square error of cross validation (RMSECV) and the root mean square error of prediction (RMSEP) were compared and analyzed. Three indicators of PLS model after 13 points smoothing and processing of the mean center were found reaching 0. 992 8, 3. 43 and 3. 4 respectively, the average relative error of prediction model is only 5. 55%, and in one word, the quality of calibration and prediction of this model are the best results. The results show that selecting the appropriate data pre-processing method, the prediction accuracy of PLS quantitative model of fruits and vegetables detected by LIBS can be improved effectively, providing a new method for fast and accurate detection of fruits and vegetables by LIBS.

The double nucleation model for sickle cell haemoglobin polymerization: full integration and comparison with experimental data.

PubMed

Medkour, Terkia; Ferrone, Frank; Galactéros, Frédéric; Hannaert, Patrick

2008-06-01

Sickle cell haemoglobin (HbS) polymerization reduces erythrocyte deformability, causing deleterous vaso-occlusions. The double-nucleation model states that polymers grow from HbS aggregates, the nuclei, (i) in solution (homogeneous nucleation), (ii) onto existing polymers (heterogeneous nucleation). When linearized at initial HbS concentration, this model predicts early polymerization and its characteristic delay-time (Ferrone et al. J Mol Biol 183(4):591-610, 611-631, 1985). Addressing its relevance for describing complete polymerization, we constructed the full, non-linearized model (Simulink), The MathWorks). Here, we compare the simulated outputs to experimental progress curves (n = 6-8 different [HbS], 3-6 mM range, from Ferrone's group). Within 10% from start, average root mean square (rms) deviation between simulated and experimental curves is 0.04 +/- 0.01 (25 degrees C, n = 8; mean +/- standard error). Conversely, for complete progress curves, averaged rms is 0.48 +/- 0.04. This figure is improved to 0.13 +/- 0.01 by adjusting heterogeneous pathway parameters (p < 0.01): the nucleus stability (sigma(2) micro( cc ): + 40%), and the fraction of polymer surface available for nucleation (phi), from 5e(-7), (3 mM) to 13 (6 mM). Similar results are obtained at 37 degrees C. We conclude that the physico-chemical description of heterogeneous nucleation warrants refinements in order to capture the whole HbS polymerization process.

Binding affinities of the farnesoid X receptor in the D3R Grand Challenge 2 estimated by free-energy perturbation and docking

NASA Astrophysics Data System (ADS)

Olsson, Martin A.; García-Sosa, Alfonso T.; Ryde, Ulf

2018-01-01

We have studied the binding of 102 ligands to the farnesoid X receptor within the D3R Grand Challenge 2016 blind-prediction competition. First, we employed docking with five different docking software and scoring functions. The selected docked poses gave an average root-mean-squared deviation of 4.2 Å. Consensus scoring gave decent results with a Kendall's τ of 0.26 ± 0.06 and a Spearman's ρ of 0.41 ± 0.08. For a subset of 33 ligands, we calculated relative binding free energies with free-energy perturbation. Five transformations between the ligands involved a change of the net charge and we implemented and benchmarked a semi-analytic correction (Rocklin et al., J Chem Phys 139:184103, 2013) for artifacts caused by the periodic boundary conditions and Ewald summation. The results gave a mean absolute deviation of 7.5 kJ/mol compared to the experimental estimates and a correlation coefficient of R 2 = 0.1. These results were among the four best in this competition out of 22 submissions. The charge corrections were significant (7-8 kJ/mol) and always improved the results. By employing 23 intermediate states in the free-energy perturbation, there was a proper overlap between all states and the precision was 0.1-0.7 kJ/mol. However, thermodynamic cycles indicate that the sampling was insufficient in some of the perturbations.

Tantalum films with well-controlled roughness grown by oblique incidence deposition

NASA Astrophysics Data System (ADS)

Rechendorff, K.; Hovgaard, M. B.; Chevallier, J.; Foss, M.; Besenbacher, F.

2005-08-01

We have investigated how tantalum films with well-controlled surface roughness can be grown by e-gun evaporation with oblique angle of incidence between the evaporation flux and the surface normal. Due to a more pronounced shadowing effect the root-mean-square roughness increases from about 2 to 33 nm as grazing incidence is approached. The exponent, characterizing the scaling of the root-mean-square roughness with length scale (α), varies from 0.75 to 0.93, and a clear correlation is found between the angle of incidence and root-mean-square roughness.

Pulse-echo probe of rock permeability near oil wells

NASA Technical Reports Server (NTRS)

Narasimhan, K. Y.; Parthasarathy, S. P.

1978-01-01

Processing method involves sequential insonifications of borehole wall at number of different frequencies. Return signals are normalized in amplitude, and root-mean-square (rms) value of each signal is determined. Values can be processed to yield information on size and number density of microfractures at various depths in rock matrix by using averaging methods developed for pulse-echo technique.

Retrieving air humidity, global solar radiation, and reference evapotranspiration from daily temperatures: development and validation of new methods for Mexico. Part I: humidity

NASA Astrophysics Data System (ADS)

Lobit, P.; López Pérez, L.; Lhomme, J. P.; Gómez Tagle, A.

2017-07-01

This study evaluates the dew point method (Allen et al. 1998) to estimate atmospheric vapor pressure from minimum temperature, and proposes an improved model to estimate it from maximum and minimum temperature. Both methods were evaluated on 786 weather stations in Mexico. The dew point method induced positive bias in dry areas but also negative bias in coastal areas, and its average root mean square error for all evaluated stations was 0.38 kPa. The improved model assumed a bi-linear relation between estimated vapor pressure deficit (difference between saturated vapor pressure at minimum and average temperature) and measured vapor pressure deficit. The parameters of these relations were estimated from historical annual median values of relative humidity. This model removed bias and allowed for a root mean square error of 0.31 kPa. When no historical measurements of relative humidity were available, empirical relations were proposed to estimate it from latitude and altitude, with only a slight degradation on the model accuracy (RMSE = 0.33 kPa, bias = -0.07 kPa). The applicability of the method to other environments is discussed.

Conformational analysis of the chemical shifts for molecules containing diastereotopic methylene protons

NASA Astrophysics Data System (ADS)

Borowski, Piotr

2012-01-01

Quantum chemistry SCF/GIAO calculations were carried out on a set of compounds containing diastereotopic protons. Five molecules, including recently synthesized 1,3-di(2,3-epoxypropoxy)benzene, containing the chiral or pro-chiral center and the neighboring methylene group, were chosen. The rotational averages (i.e. normalized averages with respect to the rotation about the torsional angle τ with the exponential energy weight at temperature T) calculated individually for each of the methylene protons in 1,3-di(2,3-epoxypropoxy)benzene differ by ca. 0.6 ppm, which is significantly less than the value calculated for the lowest energy conformer. This value turned out to be low enough to guarantee the proper ordering of theoretical chemical shifts, supporting the interpretation of the 1H NMR spectrum of this important compound. The rotational averages of chemical shifts for methylene protons for a given type of conformer are shown to be essentially equal to the Boltzmann averages (here, the population-weighted averages for the individual conformers representing minima on the E( τ) cross-section). The calculated Boltzmann averages in the representative conformational space may exhibit completely different ordering as compared to the chemical shifts calculated for the lowest-energy conformer. This is especially true in the case of molecules, for which no significant steric effects are present. In this case, only Boltzmann averages account for the experimental pattern of proton signals. In addition, better overall agreement with experiment (lower value of the root-mean-square deviation between calculated and measured chemical shifts) is typically obtained when Boltzmann averages are used.

Determination of total phenolic compounds in compost by infrared spectroscopy.

PubMed

Cascant, M M; Sisouane, M; Tahiri, S; Krati, M El; Cervera, M L; Garrigues, S; de la Guardia, M

2016-06-01

Middle and near infrared (MIR and NIR) were applied to determine the total phenolic compounds (TPC) content in compost samples based on models built by using partial least squares (PLS) regression. The multiplicative scatter correction, standard normal variate and first derivative were employed as spectra pretreatment, and the number of latent variable were optimized by leave-one-out cross-validation. The performance of PLS-ATR-MIR and PLS-DR-NIR models was evaluated according to root mean square error of cross validation and prediction (RMSECV and RMSEP), the coefficient of determination for prediction (Rpred(2)) and residual predictive deviation (RPD) being obtained for this latter values of 5.83 and 8.26 for MIR and NIR, respectively. Copyright © 2016 Elsevier B.V. All rights reserved.

Effects of a Passive Online Software Application on Heart Rate Variability and Autonomic Nervous System Balance.

PubMed

Rubik, Beverly

2017-01-01

This study investigated whether short-term exposure to a passive online software application of purported subtle energy technology would affect heart rate variability (HRV) and associated autonomic nervous system measures. This was a randomized, double-blinded, sham-controlled clinical trial (RCT). The study took place in a nonprofit laboratory in Emeryville, California. Twenty healthy, nonsmoking subjects (16 females), aged 40-75 years, participated. Quantum Code Technology ™ (QCT), a purported subtle energy technology, was delivered through a passive software application (Heart+ App) on a smartphone placed <1 m from subjects who were seated and reading a catalog. HRV was measured for 5 min in triplicate for each condition via finger plethysmography using a Food and Drug Administration medically approved HRV measurement device. Measurements were made at baseline and 35 min following exposure to the software applications. The following parameters were calculated and analyzed: heart rate, total power, standard deviation node-to-node, root mean square sequential difference, low frequency to high frequency ratio (LF/HF), low frequency (LF), and high frequency (HF). Paired samples t-tests showed that for the Heart+ App, mean LF/HF decreased (p = 9.5 × 10 -4 ), while mean LF decreased in a trend (p = 0.06), indicating reduced sympathetic dominance. Root mean square sequential difference increased for the Heart+ App, showing a possible trend (p = 0.09). Post-pre differences in LF/HF for sham compared with the Heart+ App were also significant (p < 0.008) by independent t-test, indicating clinical relevance. Significant beneficial changes in mean LF/HF, along with possible trends in mean LF and root mean square sequential difference, were observed in subjects following 35 min exposure to the Heart+ App that was working in the background on an active smartphone untouched by the subjects. This may be the first RCT to show that specific frequencies of a purported non-Hertzian type of subtle energy conveyed by software applications broadcast from personal electronic devices can be bioactive and beneficially impact autonomic nervous system balance.

Experimental Study of Heat Transfer to Small Cylinders in a Subsonic, High-temperature Gas Stream

NASA Technical Reports Server (NTRS)

Glawe, George E; Johnson, Robert C

1957-01-01

A Nusselt-Reynolds number relation for cylindrical thermocouple wires in crossflow was obtained from the experimental determination of time constants. Tests were conducted in exhaust gas over a temperature range of 2000 to 3400 R, a Mach number range of 0.3 to 0.8, and a static-pressure range from 2/3 to 1-1/3 atmospheres, yielding a Reynolds number range of 450 to 3000. The correlation obtained is Nu=(0.428 plus or minus 0.003) times the square root of Re* with average deviations of a single observation of 8.5 percent. This relation is the same as one previously reported for room-temperature conditions.

Enhancing Students' Understanding of Square Roots

ERIC Educational Resources Information Center

Wiesman, Jeff L.

2015-01-01

Students enrolled in a middle school prealgebra or algebra course often struggle to conceptualize and understand the meaning of radical notation when it is introduced. For example, although it is important for students to approximate the decimal value of a number such as [square root of] 30 and estimate the value of a square root in the form of…

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.

Theoretical Study of Free Energy in Docking Stability of Azurin(II)-Cytochrome c551(II) Complex System

NASA Astrophysics Data System (ADS)

Yamamoto, Tetsunori; Nishikawa, Keigo; Sugiyama, Ayumu; Purqon, Acep; Mizukami, Taku; Shimahara, Hideto; Nagao, Hidemi; Nishikawa, Kiyoshi

2008-02-01

The docking structure of the Azurin-Cytochrome C551 is presented. We investigate a complex system of Azurin(II)-Cytochrome C551(II) by using molecular dynamics simulation. We estimate some physical properties, such as root-mean-square deviation (RMSD), binding energy between Azurin and Cytochrome C551, distance between Azurin(II) and Cytochrome C551(II) through center of mass and each active site. We also discuss docking stability in relation to the configuration by free energy between Azurin(II)-Cytochrome C551(II) and Azurin(I)-Cytochrome C551(III).

Analysis of tractable distortion metrics for EEG compression applications.

PubMed

Bazán-Prieto, Carlos; Blanco-Velasco, Manuel; Cárdenas-Barrera, Julián; Cruz-Roldán, Fernando

2012-07-01

Coding distortion in lossy electroencephalographic (EEG) signal compression methods is evaluated through tractable objective criteria. The percentage root-mean-square difference, which is a global and relative indicator of the quality held by reconstructed waveforms, is the most widely used criterion. However, this parameter does not ensure compliance with clinical standard guidelines that specify limits to allowable noise in EEG recordings. As a result, expert clinicians may have difficulties interpreting the resulting distortion of the EEG for a given value of this parameter. Conversely, the root-mean-square error is an alternative criterion that quantifies distortion in understandable units. In this paper, we demonstrate that the root-mean-square error is better suited to control and to assess the distortion introduced by compression methods. The experiments conducted in this paper show that the use of the root-mean-square error as target parameter in EEG compression allows both clinicians and scientists to infer whether coding error is clinically acceptable or not at no cost for the compression ratio.

Detection of small orientation changes and the precision of visual working memory.

PubMed

Salmela, Viljami R; Saarinen, Jussi

2013-01-14

We investigated the precision of orientation representations with two tasks, change detection and recall. Previously change detection has been measured only with relatively large orientation changes compared to psychophysical thresholds. In the first experiment, we measured the observers' ability (d') to detect small changes in orientation (5-30°) with 1-4 Gabor items. With one item even a 10° change was well detected (average d'=2.5). As the amount of change increased to 30°, the d' increased to 5.2. When the number of items was increased, the d's gradually decreased. In the second experiment, we used a recall task and the observers adjusted the orientation of a probe Gabor to match the orientation of a Gabor held in the memory. The standard deviation (s.d.) of errors was calculated from the Gaussian distribution fitted to the data. As the number of items increased from 1 to 6, the s.d. increased from 8.6° to 19.6°. Even with six items, the observers did not make any random adjustments. The results show a square root relation between the d'/s.d. and the number of items. The d' in change detection is directly proportional to the square root of (1/n) and the orientation change. The increase of the s.d. in recall task is inversely proportional to square root of (1/n). The results suggest that limited resources and precision of representations, without additional assumptions, determine the memory performance. Copyright © 2012 Elsevier Ltd. All rights reserved.

Simplified method for the calculation of irregular waves in the coastal zone

NASA Astrophysics Data System (ADS)

Leont'ev, I. O.

2011-04-01

A method applicable for the estimation of the wave parameters along a set bottom profile is suggested. It takes into account the principal processes having an influence on the waves in the coastal zone: the transformation, refraction, bottom friction, and breaking. The ability to use a constant mean value of the friction coefficient under conditions of sandy shores is implied. The wave breaking is interpreted from the viewpoint of the concept of the limiting wave height at a given depth. The mean and root-mean-square wave heights are determined by the height distribution function, which transforms under the effect of the breaking. The verification of the method on the basis of the natural data shows that the calculation results reproduce the observed variations of the wave heights in a wide range of conditions, including profiles with underwater bars. The deviations from the calculated values mostly do not exceed 25%, and the mean square error is 11%. The method does not require a preliminary setting and can be implemented in the form of a relatively simple calculator accessible even for an inexperienced user.

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 applications in drought predictions and other operational hydrologic modeling purposes.

Analytical model for out-of-field dose in photon craniospinal irradiation

NASA Astrophysics Data System (ADS)

Taddei, Phillip J.; Jalbout, Wassim; Howell, Rebecca M.; Khater, Nabil; Geara, Fady; Homann, Kenneth; Newhauser, Wayne D.

2013-11-01

The prediction of late effects after radiotherapy in organs outside a treatment field requires accurate estimations of out-of-field dose. However, out-of-field dose is not calculated accurately by commercial treatment planning systems (TPSs). The purpose of this study was to develop and test an analytical model for out-of-field dose during craniospinal irradiation (CSI) from photon beams produced by a linear accelerator. In two separate evaluations of the model, we measured absorbed dose for a 6 MV CSI using thermoluminescent dosimeters placed throughout an anthropomorphic phantom and fit the measured data to an analytical model of absorbed dose versus distance outside of the composite field edge. These measurements were performed in two separate clinics—the University of Texas MD Anderson Cancer Center (MD Anderson) and the American University of Beirut Medical Center (AUBMC)—using the same phantom but different linear accelerators and TPSs commissioned for patient treatments. The measurement at AUBMC also included in-field locations. Measured dose values were compared to those predicted by TPSs and parameters were fit to the model in each setting. In each clinic, 95% of the measured data were contained within a factor of 0.2 and one root mean square deviation of the model-based values. The root mean square deviations of the mathematical model were 0.91 cGy Gy-1 and 1.67 cGy Gy-1 in the MD Anderson and AUBMC clinics, respectively. The TPS predictions agreed poorly with measurements in regions of sharp dose gradient, e.g., near the field edge. At distances greater than 1 cm from the field edge, the TPS underestimated the dose by an average of 14% ± 24% and 44% ± 19% in the MD Anderson and AUBMC clinics, respectively. The in-field measured dose values of the measurement at AUBMC matched the dose values calculated by the TPS to within 2%. Dose algorithms in TPSs systematically underestimated the actual out-of-field dose. Therefore, it is important to use an improved model based on measurements when estimating out-of-field dose. The model proposed in this study performed well for this purpose in two clinics and may be applicable in other clinics with similar treatment field configurations.

MRI-based intelligence quotient (IQ) estimation with sparse learning.

PubMed

Wang, Liye; Wee, Chong-Yaw; Suk, Heung-Il; Tang, Xiaoying; Shen, Dinggang

2015-01-01

In this paper, we propose a novel framework for IQ estimation using Magnetic Resonance Imaging (MRI) data. In particular, we devise a new feature selection method based on an extended dirty model for jointly considering both element-wise sparsity and group-wise sparsity. Meanwhile, due to the absence of large dataset with consistent scanning protocols for the IQ estimation, we integrate multiple datasets scanned from different sites with different scanning parameters and protocols. In this way, there is large variability in these different datasets. To address this issue, we design a two-step procedure for 1) first identifying the possible scanning site for each testing subject and 2) then estimating the testing subject's IQ by using a specific estimator designed for that scanning site. We perform two experiments to test the performance of our method by using the MRI data collected from 164 typically developing children between 6 and 15 years old. In the first experiment, we use a multi-kernel Support Vector Regression (SVR) for estimating IQ values, and obtain an average correlation coefficient of 0.718 and also an average root mean square error of 8.695 between the true IQs and the estimated ones. In the second experiment, we use a single-kernel SVR for IQ estimation, and achieve an average correlation coefficient of 0.684 and an average root mean square error of 9.166. All these results show the effectiveness of using imaging data for IQ prediction, which is rarely done in the field according to our knowledge.

Radiometric calibration of hyper-spectral imaging spectrometer based on optimizing multi-spectral band selection

NASA Astrophysics Data System (ADS)

Sun, Li-wei; Ye, Xin; Fang, Wei; He, Zhen-lei; Yi, Xiao-long; Wang, Yu-peng

2017-11-01

Hyper-spectral imaging spectrometer has high spatial and spectral resolution. Its radiometric calibration needs the knowledge of the sources used with high spectral resolution. In order to satisfy the requirement of source, an on-orbit radiometric calibration method is designed in this paper. This chain is based on the spectral inversion accuracy of the calibration light source. We compile the genetic algorithm progress which is used to optimize the channel design of the transfer radiometer and consider the degradation of the halogen lamp, thus realizing the high accuracy inversion of spectral curve in the whole working time. The experimental results show the average root mean squared error is 0.396%, the maximum root mean squared error is 0.448%, and the relative errors at all wavelengths are within 1% in the spectral range from 500 nm to 900 nm during 100 h operating time. The design lays a foundation for the high accuracy calibration of imaging spectrometer.

Experimental and analytical studies on the vibration serviceability of long-span prestressed concrete floor

NASA Astrophysics Data System (ADS)

Cao, Liang; Liu, Jiepeng; Li, Jiang; Zhang, Ruizhi

2018-04-01

An extensive experimental and theoretical research study was undertaken to study the vibration serviceability of a long-span prestressed concrete floor system to be used in the lounge of a major airport. Specifically, jumping impact tests were carried out to obtain the floor's modal parameters, followed by an analysis of the distribution of peak accelerations. Running tests were also performed to capture the acceleration responses. The prestressed concrete floor was found to have a low fundamental natural frequency (≈ 8.86 Hz) corresponding to the average modal damping ratio of ≈ 2.17%. A coefficients β rp is proposed for convenient calculation of the maximum root-mean-square acceleration for running. In the theoretical analysis, the prestressed concrete floor under running excitation is treated as a two-span continuous anisotropic rectangular plate with simply-supported edges. The calculated analytical results (natural frequencies and root-mean-square acceleration) agree well with the experimental ones. The analytical approach is thus validated.

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

Multivariate models for prediction of rheological characteristics of filamentous fermentation broth from the size distribution.

PubMed

Petersen, Nanna; Stocks, Stuart; Gernaey, Krist V

2008-05-01

The main purpose of this article is to demonstrate that principal component analysis (PCA) and partial least squares regression (PLSR) can be used to extract information from particle size distribution data and predict rheological properties. Samples from commercially relevant Aspergillus oryzae fermentations conducted in 550 L pilot scale tanks were characterized with respect to particle size distribution, biomass concentration, and rheological properties. The rheological properties were described using the Herschel-Bulkley model. Estimation of all three parameters in the Herschel-Bulkley model (yield stress (tau(y)), consistency index (K), and flow behavior index (n)) resulted in a large standard deviation of the parameter estimates. The flow behavior index was not found to be correlated with any of the other measured variables and previous studies have suggested a constant value of the flow behavior index in filamentous fermentations. It was therefore chosen to fix this parameter to the average value thereby decreasing the standard deviation of the estimates of the remaining rheological parameters significantly. Using a PLSR model, a reasonable prediction of apparent viscosity (micro(app)), yield stress (tau(y)), and consistency index (K), could be made from the size distributions, biomass concentration, and process information. This provides a predictive method with a high predictive power for the rheology of fermentation broth, and with the advantages over previous models that tau(y) and K can be predicted as well as micro(app). Validation on an independent test set yielded a root mean square error of 1.21 Pa for tau(y), 0.209 Pa s(n) for K, and 0.0288 Pa s for micro(app), corresponding to R(2) = 0.95, R(2) = 0.94, and R(2) = 0.95 respectively. Copyright 2007 Wiley Periodicals, Inc.

Structural Variation of Alpha-synuclein with Temperature by a Coarse-grained Approach with Knowledge-based Interactions (Postprint)

DTIC Science & Technology

2015-07-01

the radius of gyration in detail as a function FIG. 5. Variation of the root mean square (RMS) displacement of the center of mass of the protein with...depends on the temperature. The global motion can be examined by analyzing the variation of the root mean square displacement (RMS) of the center of...and global physical quantities during the course of simula- tion, including the energy of each residue, its mobility, mean square displacement of the

Effects of moderate and heavy endurance exercise on nocturnal HRV.

PubMed

Hynynen, E; Vesterinen, V; Rusko, H; Nummela, A

2010-06-01

This study examined the effects of endurance exercise on nocturnal autonomic modulation. Nocturnal R-R intervals were collected after a rest day, after a moderate endurance exercise and after a marathon run in ten healthy, physically active men. Heart rate variability (HRV) was analyzed as a continuous four-hour period starting 30 min after going to bed for sleep. In relation to average nocturnal heart rate after rest day, increases to 109+/-6% and 130+/-11% of baseline were found after moderate endurance exercise and marathon, respectively. Standard deviation of R-R intervals decreased to 90+/-9% and 64+/-10%, root-mean-square of differences between adjacent R-R intervals to 87+/-10% and 55+/-16%, and high frequency power to 77+/-19% and 34+/-19% of baseline after moderate endurance exercise and marathon, respectively. Also nocturnal low frequency power decreased to 56+/-26% of baseline after the marathon. Changes in nocturnal heart rate and HRV suggest prolonged dose-response effects on autonomic modulation after exercises, which may give useful information on the extent of exercise-induced nocturnal autonomic modulation and disturbance to the homeostasis.

Three key residues form a critical contact network in a protein folding transition state

NASA Astrophysics Data System (ADS)

Vendruscolo, Michele; Paci, Emanuele; Dobson, Christopher M.; Karplus, Martin

2001-02-01

Determining how a protein folds is a central problem in structural biology. The rate of folding of many proteins is determined by the transition state, so that a knowledge of its structure is essential for understanding the protein folding reaction. Here we use mutation measurements-which determine the role of individual residues in stabilizing the transition state-as restraints in a Monte Carlo sampling procedure to determine the ensemble of structures that make up the transition state. We apply this approach to the experimental data for the 98-residue protein acylphosphatase, and obtain a transition-state ensemble with the native-state topology and an average root-mean-square deviation of 6Å from the native structure. Although about 20 residues with small positional fluctuations form the structural core of this transition state, the native-like contact network of only three of these residues is sufficient to determine the overall fold of the protein. This result reveals how a nucleation mechanism involving a small number of key residues can lead to folding of a polypeptide chain to its unique native-state structure.

Adaptive firefly algorithm: parameter analysis and its application.

PubMed

Cheung, Ngaam J; Ding, Xue-Ming; Shen, Hong-Bin

2014-01-01

As a nature-inspired search algorithm, firefly algorithm (FA) has several control parameters, which may have great effects on its performance. In this study, we investigate the parameter selection and adaptation strategies in a modified firefly algorithm - adaptive firefly algorithm (AdaFa). There are three strategies in AdaFa including (1) a distance-based light absorption coefficient; (2) a gray coefficient enhancing fireflies to share difference information from attractive ones efficiently; and (3) five different dynamic strategies for the randomization parameter. Promising selections of parameters in the strategies are analyzed to guarantee the efficient performance of AdaFa. AdaFa is validated over widely used benchmark functions, and the numerical experiments and statistical tests yield useful conclusions on the strategies and the parameter selections affecting the performance of AdaFa. When applied to the real-world problem - protein tertiary structure prediction, the results demonstrated improved variants can rebuild the tertiary structure with the average root mean square deviation less than 0.4Å and 1.5Å from the native constrains with noise free and 10% Gaussian white noise.

Adaptive Firefly Algorithm: Parameter Analysis and its Application

PubMed Central

Shen, Hong-Bin

2014-01-01

As a nature-inspired search algorithm, firefly algorithm (FA) has several control parameters, which may have great effects on its performance. In this study, we investigate the parameter selection and adaptation strategies in a modified firefly algorithm — adaptive firefly algorithm (AdaFa). There are three strategies in AdaFa including (1) a distance-based light absorption coefficient; (2) a gray coefficient enhancing fireflies to share difference information from attractive ones efficiently; and (3) five different dynamic strategies for the randomization parameter. Promising selections of parameters in the strategies are analyzed to guarantee the efficient performance of AdaFa. AdaFa is validated over widely used benchmark functions, and the numerical experiments and statistical tests yield useful conclusions on the strategies and the parameter selections affecting the performance of AdaFa. When applied to the real-world problem — protein tertiary structure prediction, the results demonstrated improved variants can rebuild the tertiary structure with the average root mean square deviation less than 0.4Å and 1.5Å from the native constrains with noise free and 10% Gaussian white noise. PMID:25397812

Discrimination of Human Forearm Motions on the Basis of Myoelectric Signals by Using Adaptive Fuzzy Inference System

NASA Astrophysics Data System (ADS)

Kiso, Atsushi; Seki, Hirokazu

This paper describes a method for discriminating of the human forearm motions based on the myoelectric signals using an adaptive fuzzy inference system. In conventional studies, the neural network is often used to estimate motion intention by the myoelectric signals and realizes the high discrimination precision. On the other hand, this study uses the fuzzy inference for a human forearm motion discrimination based on the myoelectric signals. This study designs the membership function and the fuzzy rules using the average value and the standard deviation of the root mean square of the myoelectric potential for every channel of each motion. In addition, the characteristics of the myoelectric potential gradually change as a result of the muscle fatigue. Therefore, the motion discrimination should be performed by taking muscle fatigue into consideration. This study proposes a method to redesign the fuzzy inference system such that dynamic change of the myoelectric potential because of the muscle fatigue will be taken into account. Some experiments carried out using a myoelectric hand simulator show the effectiveness of the proposed motion discrimination method.

GPCR-I-TASSER: A Hybrid Approach to G Protein-Coupled Receptor Structure Modeling and the Application to the Human Genome.

PubMed

Zhang, Jian; Yang, Jianyi; Jang, Richard; Zhang, Yang

2015-08-04

Experimental structure determination remains difficult for G protein-coupled receptors (GPCRs). We propose a new hybrid protocol to construct GPCR structure models that integrates experimental mutagenesis data with ab initio transmembrane (TM) helix assembly simulations. The method was tested on 24 known GPCRs where the ab initio TM-helix assembly procedure constructed the correct fold for 20 cases. When combined with weak homology and sparse mutagenesis restraints, the method generated correct folds for all the tested cases with an average Cα root-mean-square deviation 2.4 Å in the TM regions. The new hybrid protocol was applied to model all 1,026 GPCRs in the human genome, where 923 have a high confidence score and are expected to have correct folds; these contain many pharmaceutically important families with no previously solved structures, including Trace amine, Prostanoids, Releasing hormones, Melanocortins, Vasopressin, and Neuropeptide Y receptors. The results demonstrate new progress on genome-wide structure modeling of TM proteins. Copyright © 2015 Elsevier Ltd. All rights reserved.

Modeling of biosorption of Cu(II) by alkali-modified spent tea leaves using response surface methodology (RSM) and artificial neural network (ANN)

NASA Astrophysics Data System (ADS)

Ghosh, Arpita; Das, Papita; Sinha, Keka

2015-06-01

In the present work, spent tea leaves were modified with Ca(OH)2 and used as a new, non-conventional and low-cost biosorbent for the removal of Cu(II) from aqueous solution. Response surface methodology (RSM) and artificial neural network (ANN) were used to develop predictive models for simulation and optimization of the biosorption process. The influence of process parameters (pH, biosorbent dose and reaction time) on the biosorption efficiency was investigated through a two-level three-factor (23) full factorial central composite design with the help of Design Expert. The same design was also used to obtain a training set for ANN. Finally, both modeling methodologies were statistically compared by the root mean square error and absolute average deviation based on the validation data set. Results suggest that RSM has better prediction performance as compared to ANN. The biosorption followed Langmuir adsorption isotherm and it followed pseudo-second-order kinetic. The optimum removal efficiency of the adsorbent was found as 96.12 %.

Development of experimental design approach and ANN-based models for determination of Cr(VI) ions uptake rate from aqueous solution onto the solid biodiesel waste residue.

PubMed

Shanmugaprakash, M; Sivakumar, V

2013-11-01

In the present work, the evaluation capacities of two optimization methodologies such as RSM and ANN were employed and compared for predication of Cr(VI) uptake rate using defatted pongamia oil cake (DPOC) in both batch and column mode. The influence of operating parameters was investigated through a central composite design (CCD) of RSM using Design Expert 8.0.7.1 software. The same data was fed as input in ANN to obtain a trained the multilayer feed-forward networks back-propagation algorithm using MATLAB. The performance of the developed ANN models were compared with RSM mathematical models for Cr(VI) uptake rate in terms of the coefficient of determination (R(2)), root mean square error (RMSE) and absolute average deviation (AAD). The estimated values confirm that ANN predominates RSM representing the superiority of a trained ANN models over RSM models in order to capture the non-linear behavior of the given system. Copyright © 2013 Elsevier Ltd. All rights reserved.

Explicit correlation treatment of the six-dimensional potential energy surface and predicted infrared spectra for OCS-H2

NASA Astrophysics Data System (ADS)

Liu, Jing-Min; Zhai, Yu; Li, Hui

2017-07-01

An effective six-dimensional ab initio potential energy surface (PES) for H2-OCS which explicitly includes the intramolecular stretch normal modes of carbonyl sulfide (OCS) is presented. The electronic structure computations are carried out using the explicitly correlated coupled cluster [CCSD(T)-F12] method with the augmented correlation-consistent aug-cc-pVTZ basis set, and the accuracy is critically tested by performing a series of benchmark calculations. Analytic four-dimensional PESs are obtained by least-squares fitting vibrationally averaged interaction energies to the Morse/long-range potential model. These fits to 13 485 points have a root-mean-square deviation (RMSD) of 0.16 cm-1. The combined radial discrete variable representation/angular finite basis representation method and the Lanczos algorithm were employed to evaluate the rovibrational energy levels for five isotopic species of the OCS-hydrogen complexes. The predicted transition frequencies and intensities based on the resulting vibrationally averaged PESs are in good agreement with the available experimental values, whose RMSDs are smaller than 0.004 cm-1 for five different species of OCS-hydrogen complexes. The calculated infrared band origin shifts for all five species of OCS-hydrogen complexes are only 0.03 cm-1 smaller than the corresponding experimental values. These validate the high quality of our PESs which can be used for modeling OCS doped in hydrogen clusters to further study quantum solution and microscopic superfluidity. In addition, the analytic coordinate transformation functions between isotopologues are also derived due to the center of mass shifting of different isotope substitutes.

Estimating River Surface Elevation From ArcticDEM

NASA Astrophysics Data System (ADS)

Dai, Chunli; Durand, Michael; Howat, Ian M.; Altenau, Elizabeth H.; Pavelsky, Tamlin M.

2018-04-01

ArcticDEM is a collection of 2-m resolution, repeat digital surface models created from stereoscopic satellite imagery. To demonstrate the potential of ArcticDEM for measuring river stages and discharges, we estimate river surface heights along a reach of Tanana River near Fairbanks, Alaska, by the precise detection of river shorelines and mapping of shorelines to land surface elevation. The river height profiles over a 15-km reach agree with in situ measurements to a standard deviation less than 30 cm. The time series of ArcticDEM-derived river heights agree with the U.S. Geological Survey gage measurements with a standard deviation of 32 cm. Using the rating curve for that gage, we obtain discharges with a validation accuracy (root-mean-square error) of 234 m3/s (23% of the mean discharge). Our results demonstrate that ArcticDEM can accurately measure spatial and temporal variations of river surfaces, providing a new and powerful data set for hydrologic analysis.

In silico approaches and proportional odds model towards identifying selective ADAM17 inhibitors from anti-inflammatory natural molecules.

PubMed

Borah, Pallab Kumar; Chakraborty, Sourav; Jha, Anupam N; Rajkhowa, Sanchaita; Duary, Raj Kumar

2016-11-01

ADAM metallopeptidase domain 17 (ADAM17) is an attractive target for the development of new anti-inflammatory drugs. We aimed to identify selective inhibitors of ADAM17 against matrix metalloproteinase enzymes (MMP-1, MMP-2, MMP-3, MMP-7, MMP-8, MMP-9, MMP-13, and MMP-16) which have substantial structural similarity. Target proteins were docked with 29 anti-inflammatory natural molecule ligands and a known selective inhibitor IK682. The ligands were screened based on Lipinski rules, interaction with the ADAM17 active site cavity, and then ranked using the proportional odds model multinomial logistic regression. Silymarin was the most selective inhibitor of ADAM17 exhibiting H-bonding with Glu 406, Gly 349, Glu 398, Asn 447, Tyr 433, and Lys 432. Molecular dynamics simulations were carried out for 10ns. The root mean square deviation (RMSD), root mean squared fluctuations (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), and H-bonding indicated the induced metastability. A comparison of the principal component analysis revealed that the silymarin complex also explored lesser region compared to IK682 complex. A control study on ADAM17 protein (2OI0) is included. These observations present silymarin (widely present in plants such as milk thistle (Silybum maianum), wild artichokes (Cynara cardunculus), turmeric (Curcuma longa) roots, coriander (Coriandrum sativum) seeds, etc.) as a promising natural template for development of ADAM17 selective drugs. Copyright © 2016 Elsevier Inc. All rights reserved.

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

Li, Li; Gu, Chun; Xu, Lixin, E-mail: xulixin@ustc.edu.cn

The self-adapting algorithms are improved to optimize a beam configuration in the direct drive laser fusion system with the solid state lasers. A configuration of 32 laser beams is proposed for achieving a high uniformity illumination, with a root-mean-square deviation at 10{sup −4} level. In our optimization, the parameters such as beam number, beam arrangement, and beam intensity profile are taken into account. The illumination uniformity robustness versus the parameters such as intensity profile deviations, power imbalance, intensity profile noise, the pointing error, and the target position error is also discussed. In this study, the model is assumed a solid-spheremore » illumination, and refraction effects of incident light on the corona are not considered. Our results may have a potential application in the design of the direct-drive laser fusion of the Shen Guang-II Upgrading facility (SG-II-U, China).« less

2S-4S spectroscopy in hydrogen atom: The new value for the Rydberg constant and the proton charge radius

NASA Astrophysics Data System (ADS)

Kolachevsky, N.; Beyer, A.; Maisenbacher, L.; Matveev, A.; Pohl, R.; Khabarova, K.; Grinin, A.; Lamour, T.; Yost, D. C.; Haensch, T. W.; Udem, Th.

2018-02-01

The core of the "proton radius puzzle" is the discrepancy of four standard deviations between the proton root mean square charge radii (rp) determined from regular hydrogen (H), and the muonic hydrogen atom (μp). We have measured the 2S-4P transition frequency in H, utilizing a cryogenic beam of H and directly demonstrate that quantum interference of neighboring atomic resonances can lead to line shifts much larger than the proton radius discrepancy. Using an asymmetric fit function we obtain rp = 0.8335(95) fm and the Rydberg constant R∞ = 10 973 731.568 076 (96) m-1. The new value for rp is 3.3 combined standard deviations smaller than the latest CODATA value, but in good agreement with the value from μp.

Optical diagnosis of malaria infection in human plasma using Raman spectroscopy

NASA Astrophysics Data System (ADS)

Bilal, Muhammad; Saleem, Muhammad; Amanat, Samina Tufail; Shakoor, Huma Abdul; Rashid, Rashad; Mahmood, Arshad; Ahmed, Mushtaq

2015-01-01

We present the prediction of malaria infection in human plasma using Raman spectroscopy. Raman spectra of malaria-infected samples are compared with those of healthy and dengue virus infected ones for disease recognition. Raman spectra were acquired using a laser at 532 nm as an excitation source and 10 distinct spectral signatures that statistically differentiated malaria from healthy and dengue-infected cases were found. A multivariate regression model has been developed that utilized Raman spectra of 20 malaria-infected, 10 non-malarial with fever, 10 healthy, and 6 dengue-infected samples to optically predict the malaria infection. The model yields the correlation coefficient r2 value of 0.981 between the predicted values and clinically known results of trainee samples, and the root mean square error in cross validation was found to be 0.09; both these parameters validated the model. The model was further blindly tested for 30 unknown suspected samples and found to be 86% accurate compared with the clinical results, with the inaccuracy due to three samples which were predicted in the gray region. Standard deviation and root mean square error in prediction for unknown samples were found to be 0.150 and 0.149, which are accepted for the clinical validation of the model.

Exploration of structural stability in deleterious nsSNPs of the XPA gene: A molecular dynamics approach.

PubMed

Nagasundaram, N; Priya Doss, C George

2011-01-01

Distinguishing the deleterious from the massive number of non-functional nsSNPs that occur within a single genome is a considerable challenge in mutation research. In this approach, we have used the existing in silico methods to explore the mutation-structure-function relationship in the XPAgene. We used the Sorting Intolerant From Tolerant (SIFT), Polymorphism Phenotyping (PolyPhen), I-Mutant 2.0, and the Protein Analysis THrough Evolutionary Relationships methods to predict the effects of deleterious nsSNPs on protein function and evaluated the impact of mutation on protein stability by Molecular Dynamics simulations. By comparing the scores of all the four in silico methods, nsSNP with an ID rs104894131 at position C108F was predicted to be highly deleterious. We extended our Molecular dynamics approach to gain insight into the impact of this non-synonymous polymorphism on structural changes that may affect the activity of the XPAgene. Based on the in silico methods score, potential energy, root-mean-square deviation, and root-mean-square fluctuation, we predict that deleterious nsSNP at position C108F would play a significant role in causing disease by the XPA gene. Our approach would present the application of in silicotools in understanding the functional variation from the perspective of structure, evolution, and phenotype.

All-atom molecular dynamics simulation of a photosystem i/detergent complex.

PubMed

Harris, Bradley J; Cheng, Xiaolin; Frymier, Paul

2014-10-09

All-atom molecular dynamics (MD) simulation was used to investigate the solution structure and dynamics of the photosynthetic pigment-protein complex photosystem I (PSI) from Thermosynechococcus elongatus embedded in a toroidal belt of n-dodecyl-β-d-maltoside (DDM) detergent. Evaluation of root-mean-square deviations (RMSDs) relative to the known crystal structure show that the protein complex surrounded by DDM molecules is stable during the 200 ns simulation time, and root-mean-square fluctuation (RMSF) analysis indicates that regions of high local mobility correspond to solvent-exposed regions such as turns in the transmembrane α-helices and flexible loops on the stromal and lumenal faces. Comparing the protein-detergent complex to a pure detergent micelle, the detergent surrounding the PSI trimer is found to be less densely packed but with more ordered detergent tails, contrary to what is seen in most lipid bilayer models. We also investigated any functional implications for the observed conformational dynamics and protein-detergent interactions, discovering interesting structural changes in the psaL subunits associated with maintaining the trimeric structure of the protein. Importantly, we find that the docking of soluble electron mediators such as cytochrome c6 and ferredoxin to PSI is not significantly impacted by the solubilization of PSI in detergent.

Biologically active ligands for yersinia outer protein H (YopH): feature based pharmacophore screening, docking and molecular dynamics studies.

PubMed

Tamilvanan, Thangaraju; Hopper, Waheeta

2014-01-01

Yersinia pestis, a Gram negative bacillus, spreads via lymphatic to lymph nodes and to all organs through the bloodstream, causing plague. Yersinia outer protein H (YopH) is one of the important effector proteins, which paralyzes lymphocytes and macrophages by dephosphorylating critical tyrosine kinases and signal transduction molecules. The purpose of the study is to generate a three-dimensional (3D) pharmacophore model by using diverse sets of YopH inhibitors, which would be useful for designing of potential antitoxin. In this study, we have selected 60 biologically active inhibitors of YopH to perform Ligand based pharmacophore study to elucidate the important structural features responsible for biological activity. Pharmacophore model demonstrated the importance of two acceptors, one hydrophobic and two aromatic features toward the biological activity. Based on these features, different databases were screened to identify novel compounds and these ligands were subjected for docking, ADME properties and Binding energy prediction. Post docking validation was performed using molecular dynamics simulation for selected ligands to calculate the Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuation (RMSF). The ligands, ASN03270114, Mol_252138, Mol_31073 and ZINC04237078 may act as inhibitors against YopH of Y. pestis.

Tryptophan to Glycine mutation in the position 116 leads to protein aggregation and decreases the stability of the LITAF protein.

PubMed

Kumar, Chundi Vinay; Swetha, Rayapadi G; Ramaiah, Sudha; Anbarasu, Anand

2015-01-01

Mutations in the gene-encoding vesicle lipopolysaccharide-induced tumor necrosis factor (LITAF) protein cause Charcot-Marie-Tooth type 1C (CMT1C) disease, a neurological disorder. The LITAF gene is mapped to chromosome number 16 and can be found at cytogenetic location 16p13 of the chromosome. CMT1C-linked small integral membrane protein of lysosome/late endosome mutants are loss-of-function mutants that act in a dominant negative manner to impair endosomal trafficking, leading to prolonged extracellular signal-regulated kinases 1/2 signaling downstream of ErbB activation. Mutation W116G in the LITAF decreases the stability of the protein and also interrupts the functioning of gene. We have analyzed the single nucleotide polymorphism (SNP) results of 28 nsSNPs obtained from dbSNP. We also carried out multiple molecular dynamics simulations of 200 ns and obtained results of root-mean-square deviation, root-mean-square fluctuation, radius of gyration, solvent-accessible surface area, H-bond, and principal component analysis to check and prove the stability of both the wild type and the mutant. The protein was then checked for its aggregation and the results showed loss of helix. The loss of helix leads to the instability of the protein.

MDplot: Visualise Molecular Dynamics.

PubMed

Margreitter, Christian; Oostenbrink, Chris

2017-05-10

The MDplot package provides plotting functions to allow for automated visualisation of molecular dynamics simulation output. It is especially useful in cases where the plot generation is rather tedious due to complex file formats or when a large number of plots are generated. The graphs that are supported range from those which are standard, such as RMsD/RMsF (root-mean-square deviation and root-mean-square fluctuation, respectively) to less standard, such as thermodynamic integration analysis and hydrogen bond monitoring over time. All told, they address many commonly used analyses. In this article, we set out the MDplot package's functions, give examples of the function calls, and show the associated plots. Plotting and data parsing is separated in all cases, i.e. the respective functions can be used independently. Thus, data manipulation and the integration of additional file formats is fairly easy. Currently, the loading functions support GROMOS, GROMACS, and AMBER file formats. Moreover, we also provide a Bash interface that allows simple embedding of MDplot into Bash scripts as the final analysis step. The package can be obtained in the latest major version from CRAN (https://cran.r-project.org/package=MDplot) or in the most recent version from the project's GitHub page at https://github.com/MDplot/MDplot, where feedback is also most welcome. MDplot is published under the GPL-3 license.

Structure and function of photosystem I–[FeFe] hydrogenase protein fusions: An all-atom molecular dynamics study

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

Harris, Bradley J.; Cheng, Xiaolin; Frymier, Paul

2015-12-15

All-atom molecular dynamics (MD) simulation was used to study the solution dynamics and protein protein interactions of protein fusions of photosystem I (PSI) from Thermosynechococcus elongatus and an [FeFe]-hydrogenase (FeFe H 2ase) from Clostridium pasteurianum, a unique complex capable of photocatalytic hydrogen production. This study involved fusions of these two proteins via dithiol linkers of different length including decanedithiol, octanedithiol, and hexanedithiol, for which experimental data had previously been obtained. Evaluation of root-mean-squared deviations (RMSDs) relative to the respective crystal structures of PSI and the FeFe H 2ase shows that these fusion complexes approach stable equilibrium conformations during the MDmore » simulations. Investigating protein mobility via root-mean-squared fluctuations (RMSFs) reveals that tethering via the shortest hexanedithiol linker results in increased atomic fluctuations of both PSI and the hydrogenase in these fusion complexes. Furthermore, evaluation of the inter- and intraprotein electron transfer distances in these fusion complexes indicates that the structural changes in the FeFe H 2ase arising from ligation to PSI via the shortest hexanedithiol linker may hinder electron transport in the hydrogenase, thus providing a molecular level explanation for the observation that the medium-length octanedithiol linker gives the highest hydrogen production rate.« less

Conformation Analysis of T1 Lipase on Alcohols Solvent using Molecular Dynamics Simulation

NASA Astrophysics Data System (ADS)

Putri, A. M.; Sumaryada, T.; Wahyudi, S. T.

2017-07-01

Biodiesel usually is produced commercially via a transesterification reaction of vegetable oil with alcohol and alkali catalyst. The alkali catalyst has some drawbacks, such as the soap formation during the reaction. T1 Lipase enzyme had been known as a thermostable biocatalyst which is able to produce biodiesel through a cleaner process. In this paper the performance of T1 lipase enzyme as catalyst for transesterification reaction in pure ethanol, methanol, and water solvents were studied using a Molecular Dynamics (MD) Simulation at temperature of 300 K for 10 nanoseconds. The results have shown that in general the conformation of T1 lipase enzyme in methanol is more dynamics as shown by the value of root mean square deviation (RMSD), root mean squared fluctuation (RMSF), and radius of gyration. The highest solvent accessible surface area (SASA) total was also found in methanol due to the contribution of non-polar amino acid in the interior of the protein. Analysis of MD simulation has also revealed that the enzyme structure tend to be more rigid in ethanol environment. The analysis of electrostatic interactions have shown that Glu359-Arg270 salt-bridge pair might hold the key of thermostability of T1 lipase enzyme as shown by its strong and stable binding in all three solvents.

All-atom molecular dynamics simulation of a photosystem I/detergent complex

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

Harris, Bradley J.; Cheng, Xiaolin; Frymier, Paul

2014-09-18

All-atom molecular dynamics (MD) simulation was used to investigate the solution structure and dynamics of the photosynthetic pigment protein complex photosystem I (PSI) from Thermosynechococcus elongatus embedded in a toroidal belt of n-dodecyl-β-d-maltoside (DDM) detergent. Evaluation of root-mean-square deviations (RMSDs) relative to the known crystal structure show that the protein complex surrounded by DDM molecules is stable during the 200 ns simulation time, and root-mean-square fluctuation (RMSF) analysis indicates that regions of high local mobility correspond to solvent-exposed regions such as turns in the transmembrane α-helices and flexible loops on the stromal and lumenal faces. Comparing the protein detergent complexmore » to a pure detergent micelle, the detergent surrounding the PSI trimer is found to be less densely packed but with more ordered detergent tails, contrary to what is seen in most lipid bilayer models. We also investigated any functional implications for the observed conformational dynamics and protein detergent interactions, discovering interesting structural changes in the psaL subunits associated with maintaining the trimeric structure of the protein. Moreover, we find that the docking of soluble electron mediators such as cytochrome c 6 and ferredoxin to PSI is not significantly impacted by the solubilization of PSI in detergent.« less

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.

Near-infrared Spectroscopy as a Process Analytical Technology Tool for Monitoring the Parching Process of Traditional Chinese Medicine Based on Two Kinds of Chemical Indicators.

PubMed

Li, Kaiyue; Wang, Weiying; Liu, Yanping; Jiang, Su; Huang, Guo; Ye, Liming

2017-01-01

The active ingredients and thus pharmacological efficacy of traditional Chinese medicine (TCM) at different degrees of parching process vary greatly. Near-infrared spectroscopy (NIR) was used to develop a new method for rapid online analysis of TCM parching process, using two kinds of chemical indicators (5-(hydroxymethyl) furfural [5-HMF] content and 420 nm absorbance) as reference values which were obviously observed and changed in most TCM parching process. Three representative TCMs, Areca ( Areca catechu L.), Malt ( Hordeum Vulgare L.), and Hawthorn ( Crataegus pinnatifida Bge.), were used in this study. With partial least squares regression, calibration models of NIR were generated based on two kinds of reference values, i.e. 5-HMF contents measured by high-performance liquid chromatography (HPLC) and 420 nm absorbance measured by ultraviolet-visible spectroscopy (UV/Vis), respectively. In the optimized models for 5-HMF, the root mean square errors of prediction (RMSEP) for Areca, Malt, and Hawthorn was 0.0192, 0.0301, and 0.2600 and correlation coefficients ( R cal ) were 99.86%, 99.88%, and 99.88%, respectively. Moreover, in the optimized models using 420 nm absorbance as reference values, the RMSEP for Areca, Malt, and Hawthorn was 0.0229, 0.0096, and 0.0409 and R cal were 99.69%, 99.81%, and 99.62%, respectively. NIR models with 5-HMF content and 420 nm absorbance as reference values can rapidly and effectively identify three kinds of TCM in different parching processes. This method has great promise to replace current subjective color judgment and time-consuming HPLC or UV/Vis methods and is suitable for rapid online analysis and quality control in TCM industrial manufacturing process. Near-infrared spectroscopy.(NIR) was used to develop a new method for online analysis of traditional Chinese medicine.(TCM) parching processCalibration and validation models of Areca, Malt, and Hawthorn were generated by partial least squares regression using 5.(hydroxymethyl) furfural contents and 420.nm absorbance as reference values, respectively, which were main indicator components during parching process of most TCMThe established NIR models of three TCMs had low root mean square errors of prediction and high correlation coefficientsThe NIR method has great promise for use in TCM industrial manufacturing processes for rapid online analysis and quality control. Abbreviations used: NIR: Near-infrared Spectroscopy; TCM: Traditional Chinese medicine; Areca: Areca catechu L.; Hawthorn: Crataegus pinnatifida Bge.; Malt: Hordeum vulgare L.; 5-HMF: 5-(hydroxymethyl) furfural; PLS: Partial least squares; D: Dimension faction; SLS: Straight line subtraction, MSC: Multiplicative scatter correction; VN: Vector normalization; RMSECV: Root mean square errors of cross-validation; RMSEP: Root mean square errors of validation; R cal : Correlation coefficients; RPD: Residual predictive deviation; PAT: Process analytical technology; FDA: Food and Drug Administration; ICH: International Conference on Harmonization of Technical Requirements for Registration of Pharmaceuticals for Human Use.

Accuracy of a Radiological Evaluation Method for Thoracic and Lumbar Spinal Curvatures Using Spinous Processes.

PubMed

Marchetti, Bárbara V; Candotti, Cláudia T; Raupp, Eduardo G; Oliveira, Eduardo B C; Furlanetto, Tássia S; Loss, Jefferson F

The purpose of this study was to assess a radiographic method for spinal curvature evaluation in children, based on spinous processes, and identify its normality limits. The sample consisted of 90 radiographic examinations of the spines of children in the sagittal plane. Thoracic and lumbar curvatures were evaluated using angular (apex angle [AA]) and linear (sagittal arrow [SA]) measurements based on the spinous processes. The same curvatures were also evaluated using the Cobb angle (CA) method, which is considered the gold standard. For concurrent validity (AA vs CA), Pearson's product-moment correlation coefficient, root-mean-square error, Pitman- Morgan test, and Bland-Altman analysis were used. For reproducibility (AA, SA, and CA), the intraclass correlation coefficient, standard error of measurement, and minimal detectable change measurements were used. A significant correlation was found between CA and AA measurements, as was a low root-mean-square error. The mean difference between the measurements was 0° for thoracic and lumbar curvatures, and the mean standard deviations of the differences were ±5.9° and 6.9°, respectively. The intraclass correlation coefficients of AA and SA were similar to or higher than the gold standard (CA). The standard error of measurement and minimal detectable change of the AA were always lower than the CA. This study determined the concurrent validity, as well as intra- and interrater reproducibility, of the radiographic measurements of kyphosis and lordosis in children. Copyright © 2017. Published by Elsevier Inc.

Statistical optimization of the phytoremediation of arsenic by Ludwigia octovalvis- in a pilot reed bed using response surface methodology (RSM) versus an artificial neural network (ANN).

PubMed

Titah, Harmin Sulistiyaning; Halmi, Mohd Izuan Effendi Bin; Abdullah, Siti Rozaimah Sheikh; Hasan, Hassimi Abu; Idris, Mushrifah; Anuar, Nurina

2018-06-07

In this study, the removal of arsenic (As) by plant, Ludwigia octovalvis, in a pilot reed bed was optimized. A Box-Behnken design was employed including a comparative analysis of both Response Surface Methodology (RSM) and an Artificial Neural Network (ANN) for the prediction of maximum arsenic removal. The predicted optimum condition using the desirability function of both models was 39 mg kg -1 for the arsenic concentration in soil, an elapsed time of 42 days (the sampling day) and an aeration rate of 0.22 L/min, with the predicted values of arsenic removal by RSM and ANN being 72.6% and 71.4%, respectively. The validation of the predicted optimum point showed an actual arsenic removal of 70.6%. This was achieved with the deviation between the validation value and the predicted values being within 3.49% (RSM) and 1.87% (ANN). The performance evaluation of the RSM and ANN models showed that ANN performs better than RSM with a higher R 2 (0.97) close to 1.0 and very small Average Absolute Deviation (AAD) (0.02) and Root Mean Square Error (RMSE) (0.004) values close to zero. Both models were appropriate for the optimization of arsenic removal with ANN demonstrating significantly higher predictive and fitting ability than RSM.

Viking bistatic radar observations of the hellas basin on Mars: preliminary results.

PubMed

Simpson, R A; Tyler, G L; Brenkle, J P; Sue, M

1979-01-05

Preliminary reduction of Viking bistatic radar data gives root-mean-square surface slopes in the Hellas basin on Mars of about 4 degrees on horizontal scales averaged over 10 centimeters to 100 meters. This roughness decreases slightly with position along the ground track, south to north. The dielectric constant in this area appears to be approximately 3.1, greater than the martian average. These values are characteristic of lunar maria and are similar to those found near the Viking lander site in Chryse with the use of Earth-based radar.

An evaluation of three growth and yield simulators for even-aged hardwood forests of the mid-Appalachian region

Treesearch

John R. Brooks; Gary W. Miller

2011-01-01

Data from even-aged hardwood stands in four ecoregions across the mid-Appalachian region were used to test projection accuracy for three available growth and yield software systems: SILVAH, the Forest Vegetation Simulator, and the Stand Damage Model. Average root mean squared error (RMSE) ranged from 20 to 140 percent of actual trees per acre while RMSE ranged from 2...

Determination of the carmine content based on spectrum fluorescence spectral and PSO-SVM

NASA Astrophysics Data System (ADS)

Wang, Shu-tao; Peng, Tao; Cheng, Qi; Wang, Gui-chuan; Kong, De-ming; Wang, Yu-tian

2018-03-01

Carmine is a widely used food pigment in various food and beverage additives. Excessive consumption of synthetic pigment shall do harm to body seriously. The food is generally associated with a variety of colors. Under the simulation context of various food pigments' coexistence, we adopted the technology of fluorescence spectroscopy, together with the PSO-SVM algorithm, so that to establish a method for the determination of carmine content in mixed solution. After analyzing the prediction results of PSO-SVM, we collected a bunch of data: the carmine average recovery rate was 100.84%, the root mean square error of prediction (RMSEP) for 1.03e-04, 0.999 for the correlation coefficient between the model output and the real value of the forecast. Compared with the prediction results of reverse transmission, the correlation coefficient of PSO-SVM was 2.7% higher, the average recovery rate for 0.6%, and the root mean square error was nearly one order of magnitude lower. According to the analysis results, it can effectively avoid the interference caused by pigment with the combination of the fluorescence spectrum technique and PSO-SVM, accurately determining the content of carmine in mixed solution with an effect better than that of BP.

Evaluation of Two New Indices of Blood Pressure Variability Using Postural Change in Older Fallers.

PubMed

Goh, Choon-Hian; Ng, Siew-Cheok; Kamaruzzaman, Shahrul B; Chin, Ai-Vyrn; Poi, Philip J H; Chee, Kok Han; Imran, Z Abidin; Tan, Maw Pin

2016-05-01

To evaluate the utility of blood pressure variability (BPV) calculated using previously published and newly introduced indices using the variables falls and age as comparators.While postural hypotension has long been considered a risk factor for falls, there is currently no documented evidence on the relationship between BPV and falls.A case-controlled study involving 25 fallers and 25 nonfallers was conducted. Systolic (SBPV) and diastolic blood pressure variability (DBPV) were assessed using 5 indices: standard deviation (SD), standard deviation of most stable continuous 120 beats (staSD), average real variability (ARV), root mean square of real variability (RMSRV), and standard deviation of real variability (SDRV). Continuous beat-to-beat blood pressure was recorded during 10 minutes' supine rest and 3 minutes' standing.Standing SBPV was significantly higher than supine SBPV using 4 indices in both groups. The standing-to-supine-BPV ratio (SSR) was then computed for each subject (staSD, ARV, RMSRV, and SDRV). Standing-to-supine ratio for SBPV was significantly higher among fallers compared to nonfallers using RMSRV and SDRV (P = 0.034 and P = 0.025). Using linear discriminant analysis (LDA), 3 indices (ARV, RMSRV, and SDRV) of SSR SBPV provided accuracies of 61.6%, 61.2%, and 60.0% for the prediction of falls which is comparable with timed-up and go (TUG), 64.4%.This study suggests that SSR SBPV using RMSRV and SDRV is a potential predictor for falls among older patients, and deserves further evaluation in larger prospective studies.

Microwave Photonic Architecture for Direction Finding of LPI Emitters: Post-Processing for Angle of Arrival Estimation

DTIC Science & Technology

2016-09-01

mean- square (RMS) error of 0.29° at ə° resolution. For a P4 coded signal, the RMS error in estimating the AOA is 0.32° at 1° resolution. 14...FMCW signal, it was demonstrated that the system is capable of estimating the AOA with a root-mean- square (RMS) error of 0.29° at ə° resolution. For a...Modulator PCB printed circuit board PD photodetector RF radio frequency RMS root-mean- square xvi THIS PAGE INTENTIONALLY LEFT BLANK xvii

Calibration of a texture-based model of a ground-water flow system, western San Joaquin Valley, California

USGS Publications Warehouse

Phillips, Steven P.; Belitz, Kenneth

1991-01-01

The occurrence of selenium in agricultural drain water from the western San Joaquin Valley, California, has focused concern on the semiconfined ground-water flow system, which is underlain by the Corcoran Clay Member of the Tulare Formation. A two-step procedure is used to calibrate a preliminary model of the system for the purpose of determining the steady-state hydraulic properties. Horizontal and vertical hydraulic conductivities are modeled as functions of the percentage of coarse sediment, hydraulic conductivities of coarse-textured (Kcoarse) and fine-textured (Kfine) end members, and averaging methods used to calculate equivalent hydraulic conductivities. The vertical conductivity of the Corcoran (Kcorc) is an additional parameter to be evaluated. In the first step of the calibration procedure, the model is run by systematically varying the following variables: (1) Kcoarse/Kfine, (2) Kcoarse/Kcorc, and (3) choice of averaging methods in the horizontal and vertical directions. Root mean square error and bias values calculated from the model results are functions of these variables. These measures of error provide a means for evaluating model sensitivity and for selecting values of Kcoarse, Kfine, and Kcorc for use in the second step of the calibration procedure. In the second step, recharge rates are evaluated as functions of Kcoarse, Kcorc, and a combination of averaging methods. The associated Kfine values are selected so that the root mean square error is minimized on the basis of the results from the first step. The results of the two-step procedure indicate that the spatial distribution of hydraulic conductivity that best produces the measured hydraulic head distribution is created through the use of arithmetic averaging in the horizontal direction and either geometric or harmonic averaging in the vertical direction. The equivalent hydraulic conductivities resulting from either combination of averaging methods compare favorably to field- and laboratory-based values.

Functional Data Analysis of Spaceflight-Induced Changes in Coordination and Phase in Head Pitch Acceleration During Treadmill Walking

NASA Technical Reports Server (NTRS)

Miller, Christopher; Peters, Brian; Feiveson, Alan; Bloomberg, Jacob

2011-01-01

Astronauts returning from spaceflight experience neurovestibular disturbances during head movements and attempt to mitigate them by limiting head motion. Analyses to date of the head movements made during walking have concentrated on amplitude and variability measures extracted from ensemble averages of individual gait cycles. Phase shifts within each gait cycle can be determined by functional data analysis through the computation of time-warping functions. Large, localized variations in the timing of peaks in head kinematics may indicate changes in coordination. The purpose of this study was to determine timing changes in head pitch acceleration of astronauts during treadmill walking before and after flight. Six astronauts (5M/1F; age = 43.5+/-6.4yr) participated in the study. Subjects walked at 1.8 m/sec (4 mph) on a motorized treadmill while reading optotypes displayed on a computer screen 4 m in front of their eyes. Three-dimensional motion of the subject s head was recorded with an Inertial Measurement Unit (IMU) device. Data were recorded twice before flight and four times after landing. The head pitch acceleration was calculated by taking the time derivative of the pitch velocity data from the IMU. Data for each session with each subject were time-normalized into gait cycles, then registered to align significant features and create a mean curve. The mean curves of each postflight session for each subject were re-registered based on their preflight mean curve to create time-warping functions. The root mean squares (RMS) of these warping functions were calculated to assess the deviation of head pitch acceleration mean curves in each postflight session from the preflight mean curve. After landing, most crewmembers exhibited localized shifts within their head pitch acceleration regimes, with the greatest deviations in RMS occurring on landing day or 1 day after landing. These results show that the alteration of head pitch coordination due to spaceflight may be assessed using an analysis of time-warping functions.

Geometrical comparison of two protein structures using Wigner-D functions.

PubMed

Saberi Fathi, S M; White, Diana T; Tuszynski, Jack A

2014-10-01

In this article, we develop a quantitative comparison method for two arbitrary protein structures. This method uses a root-mean-square deviation characterization and employs a series expansion of the protein's shape function in terms of the Wigner-D functions to define a new criterion, which is called a "similarity value." We further demonstrate that the expansion coefficients for the shape function obtained with the help of the Wigner-D functions correspond to structure factors. Our method addresses the common problem of comparing two proteins with different numbers of atoms. We illustrate it with a worked example. © 2014 Wiley Periodicals, Inc.

Subjective rating scales as a workload

NASA Technical Reports Server (NTRS)

Bird, K. L.

1981-01-01

A multidimensional bipolar-adjective rating scale is employed as a subjective measure of operator workload in the performance of a one-axis tracking task. The rating scale addressed several dimensions of workload, including cognitive, physical, and perceptual task loading as well as fatigue and stress effects. Eight subjects performed a one-axis tracking task (with six levels of difficulty) and rated these tasks on several workload dimensions. Performance measures were tracking error RMS (root-mean square) and the standard deviation of control stick output. Significant relationships were observed between these performance measures and skill required, task complexity, attention level, task difficulty, task demands, and stress level.

Direct folding simulation of a long helix in explicit water

NASA Astrophysics Data System (ADS)

Gao, Ya; Lu, Xiaoliang; Duan, Lili; Zhang, Dawei; Mei, Ye; Zhang, John Z. H.

2013-05-01

A recently proposed Polarizable Hydrogen Bond (PHB) method has been employed to simulate the folding of a 53 amino acid helix (PDB ID 2KHK) in explicit water. Under PHB simulation, starting from a fully extended structure, the peptide folds into the native state as confirmed by measured time evolutions of radius of gyration, root mean square deviation (RMSD), and native hydrogen bond. Free energy and cluster analysis show that the folded helix is thermally stable under the PHB model. Comparison of simulation results under, respectively, PHB and standard nonpolarizable force field demonstrates that polarization is critical for stable folding of this long α-helix.

Conformational diversity analysis reveals three functional mechanisms in proteins

PubMed Central

Fornasari, María Silvina

2017-01-01

Protein motions are a key feature to understand biological function. Recently, a large-scale analysis of protein conformational diversity showed a positively skewed distribution with a peak at 0.5 Å C-alpha root-mean-square-deviation (RMSD). To understand this distribution in terms of structure-function relationships, we studied a well curated and large dataset of ~5,000 proteins with experimentally determined conformational diversity. We searched for global behaviour patterns studying how structure-based features change among the available conformer population for each protein. This procedure allowed us to describe the RMSD distribution in terms of three main protein classes sharing given properties. The largest of these protein subsets (~60%), which we call “rigid” (average RMSD = 0.83 Å), has no disordered regions, shows low conformational diversity, the largest tunnels and smaller and buried cavities. The two additional subsets contain disordered regions, but with differential sequence composition and behaviour. Partially disordered proteins have on average 67% of their conformers with disordered regions, average RMSD = 1.1 Å, the highest number of hinges and the longest disordered regions. In contrast, malleable proteins have on average only 25% of disordered conformers and average RMSD = 1.3 Å, flexible cavities affected in size by the presence of disordered regions and show the highest diversity of cognate ligands. Proteins in each set are mostly non-homologous to each other, share no given fold class, nor functional similarity but do share features derived from their conformer population. These shared features could represent conformational mechanisms related with biological functions. PMID:28192432

The Relationship between Root Mean Square Error of Approximation and Model Misspecification in Confirmatory Factor Analysis Models

ERIC Educational Resources Information Center

Savalei, Victoria

2012-01-01

The fit index root mean square error of approximation (RMSEA) is extremely popular in structural equation modeling. However, its behavior under different scenarios remains poorly understood. The present study generates continuous curves where possible to capture the full relationship between RMSEA and various "incidental parameters," such as…

MRI-Based Intelligence Quotient (IQ) Estimation with Sparse Learning

PubMed Central

Wang, Liye; Wee, Chong-Yaw; Suk, Heung-Il; Tang, Xiaoying; Shen, Dinggang

2015-01-01

In this paper, we propose a novel framework for IQ estimation using Magnetic Resonance Imaging (MRI) data. In particular, we devise a new feature selection method based on an extended dirty model for jointly considering both element-wise sparsity and group-wise sparsity. Meanwhile, due to the absence of large dataset with consistent scanning protocols for the IQ estimation, we integrate multiple datasets scanned from different sites with different scanning parameters and protocols. In this way, there is large variability in these different datasets. To address this issue, we design a two-step procedure for 1) first identifying the possible scanning site for each testing subject and 2) then estimating the testing subject’s IQ by using a specific estimator designed for that scanning site. We perform two experiments to test the performance of our method by using the MRI data collected from 164 typically developing children between 6 and 15 years old. In the first experiment, we use a multi-kernel Support Vector Regression (SVR) for estimating IQ values, and obtain an average correlation coefficient of 0.718 and also an average root mean square error of 8.695 between the true IQs and the estimated ones. In the second experiment, we use a single-kernel SVR for IQ estimation, and achieve an average correlation coefficient of 0.684 and an average root mean square error of 9.166. All these results show the effectiveness of using imaging data for IQ prediction, which is rarely done in the field according to our knowledge. PMID:25822851

Computationally efficient real-time interpolation algorithm for non-uniform sampled biosignals

PubMed Central

Eftekhar, Amir; Kindt, Wilko; Constandinou, Timothy G.

2016-01-01

This Letter presents a novel, computationally efficient interpolation method that has been optimised for use in electrocardiogram baseline drift removal. In the authors’ previous Letter three isoelectric baseline points per heartbeat are detected, and here utilised as interpolation points. As an extension from linear interpolation, their algorithm segments the interpolation interval and utilises different piecewise linear equations. Thus, the algorithm produces a linear curvature that is computationally efficient while interpolating non-uniform samples. The proposed algorithm is tested using sinusoids with different fundamental frequencies from 0.05 to 0.7 Hz and also validated with real baseline wander data acquired from the Massachusetts Institute of Technology University and Boston's Beth Israel Hospital (MIT-BIH) Noise Stress Database. The synthetic data results show an root mean square (RMS) error of 0.9 μV (mean), 0.63 μV (median) and 0.6 μV (standard deviation) per heartbeat on a 1 mVp–p 0.1 Hz sinusoid. On real data, they obtain an RMS error of 10.9 μV (mean), 8.5 μV (median) and 9.0 μV (standard deviation) per heartbeat. Cubic spline interpolation and linear interpolation on the other hand shows 10.7 μV, 11.6 μV (mean), 7.8 μV, 8.9 μV (median) and 9.8 μV, 9.3 μV (standard deviation) per heartbeat. PMID:27382478

Computationally efficient real-time interpolation algorithm for non-uniform sampled biosignals.

PubMed

Guven, Onur; Eftekhar, Amir; Kindt, Wilko; Constandinou, Timothy G

2016-06-01

This Letter presents a novel, computationally efficient interpolation method that has been optimised for use in electrocardiogram baseline drift removal. In the authors' previous Letter three isoelectric baseline points per heartbeat are detected, and here utilised as interpolation points. As an extension from linear interpolation, their algorithm segments the interpolation interval and utilises different piecewise linear equations. Thus, the algorithm produces a linear curvature that is computationally efficient while interpolating non-uniform samples. The proposed algorithm is tested using sinusoids with different fundamental frequencies from 0.05 to 0.7 Hz and also validated with real baseline wander data acquired from the Massachusetts Institute of Technology University and Boston's Beth Israel Hospital (MIT-BIH) Noise Stress Database. The synthetic data results show an root mean square (RMS) error of 0.9 μV (mean), 0.63 μV (median) and 0.6 μV (standard deviation) per heartbeat on a 1 mVp-p 0.1 Hz sinusoid. On real data, they obtain an RMS error of 10.9 μV (mean), 8.5 μV (median) and 9.0 μV (standard deviation) per heartbeat. Cubic spline interpolation and linear interpolation on the other hand shows 10.7 μV, 11.6 μV (mean), 7.8 μV, 8.9 μV (median) and 9.8 μV, 9.3 μV (standard deviation) per heartbeat.

Areal-averaged and Spectrally-resolved Surface Albedo from Ground-based Transmission Data Alone: Toward an Operational Retrieval

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

Kassianov, Evgueni I.; Barnard, James C.; Flynn, Connor J.

We present here a simple retrieval of the areal-averaged and spectrally resolved surface albedo using only ground-based measurements of atmospheric transmission under fully overcast conditions. Our retrieval is based on a one-line equation and widely accepted assumptions regarding the weak spectral dependence of cloud optical properties in the visible and near-infrared spectral range. The feasibility of our approach for the routine determinations of albedo is demonstrated for different landscapes with various degrees of heterogeneity using three sets of measurements:(1) spectrally resolved atmospheric transmission from Multi-Filter Rotating Shadowband Radiometer (MFRSR) at wavelength 415, 500, 615, 673, and 870 nm, (2) tower-basedmore » measurements of local surface albedo at the same wavelengths, and (3) areal-averaged surface albedo at four wavelengths (470, 560, 670 and 860 nm) from collocated and coincident Moderate Resolution Imaging Spectroradiometer (MODIS) observations. These integrated datasets cover both long (2008-2013) and short (April-May, 2010) periods at the ARM Southern Great Plains (SGP) site and the NOAA Table Mountain site, respectively. The calculated root mean square error (RMSE), which is defined here as the root mean squared difference between the MODIS-derived surface albedo and the retrieved area-averaged albedo, is quite small (RMSE≤0.01) and comparable with that obtained previously by other investigators for the shortwave broadband albedo. Good agreement between the tower-based daily averages of surface albedo for the completely overcast and non-overcast conditions is also demonstrated. This agreement suggests that our retrieval originally developed for the overcast conditions likely will work for non-overcast conditions as well.« less

Swing arm profilometer: analytical solutions of misalignment errors for testing axisymmetric optics

NASA Astrophysics Data System (ADS)

Xiong, Ling; Luo, Xiao; Liu, Zhenyu; Wang, Xiaokun; Hu, Haixiang; Zhang, Feng; Zheng, Ligong; Zhang, Xuejun

2016-07-01

The swing arm profilometer (SAP) has been playing a very important role in testing large aspheric optics. As one of most significant error sources that affects the test accuracy, misalignment error leads to low-order errors such as aspherical aberrations and coma apart from power. In order to analyze the effect of misalignment errors, the relation between alignment parameters and test results of axisymmetric optics is presented. Analytical solutions of SAP system errors from tested mirror misalignment, arm length L deviation, tilt-angle θ deviation, air-table spin error, and air-table misalignment are derived, respectively; and misalignment tolerance is given to guide surface measurement. In addition, experiments on a 2-m diameter parabolic mirror are demonstrated to verify the model; according to the error budget, we achieve the SAP test for low-order errors except power with accuracy of 0.1 μm root-mean-square.

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.

A Simulation-Based Study on the Comparison of Statistical and Time Series Forecasting Methods for Early Detection of Infectious Disease Outbreaks.

PubMed

Yang, Eunjoo; Park, Hyun Woo; Choi, Yeon Hwa; Kim, Jusim; Munkhdalai, Lkhagvadorj; Musa, Ibrahim; Ryu, Keun Ho

2018-05-11

Early detection of infectious disease outbreaks is one of the important and significant issues in syndromic surveillance systems. It helps to provide a rapid epidemiological response and reduce morbidity and mortality. In order to upgrade the current system at the Korea Centers for Disease Control and Prevention (KCDC), a comparative study of state-of-the-art techniques is required. We compared four different temporal outbreak detection algorithms: the CUmulative SUM (CUSUM), the Early Aberration Reporting System (EARS), the autoregressive integrated moving average (ARIMA), and the Holt-Winters algorithm. The comparison was performed based on not only 42 different time series generated taking into account trends, seasonality, and randomly occurring outbreaks, but also real-world daily and weekly data related to diarrhea infection. The algorithms were evaluated using different metrics. These were namely, sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), F1 score, symmetric mean absolute percent error (sMAPE), root-mean-square error (RMSE), and mean absolute deviation (MAD). Although the comparison results showed better performance for the EARS C3 method with respect to the other algorithms, despite the characteristics of the underlying time series data, Holt⁻Winters showed better performance when the baseline frequency and the dispersion parameter values were both less than 1.5 and 2, respectively.

Rapid Quantitative Determination of Squalene in Shark Liver Oils by Raman and IR Spectroscopy.

PubMed

Hall, David W; Marshall, Susan N; Gordon, Keith C; Killeen, Daniel P

2016-01-01

Squalene is sourced predominantly from shark liver oils and to a lesser extent from plants such as olives. It is used for the production of surfactants, dyes, sunscreen, and cosmetics. The economic value of shark liver oil is directly related to the squalene content, which in turn is highly variable and species-dependent. Presented here is a validated gas chromatography-mass spectrometry analysis method for the quantitation of squalene in shark liver oils, with an accuracy of 99.0 %, precision of 0.23 % (standard deviation), and linearity of >0.999. The method has been used to measure the squalene concentration of 16 commercial shark liver oils. These reference squalene concentrations were related to infrared (IR) and Raman spectra of the same oils using partial least squares regression. The resultant models were suitable for the rapid quantitation of squalene in shark liver oils, with cross-validation r (2) values of >0.98 and root mean square errors of validation of ≤4.3 % w/w. Independent test set validation of these models found mean absolute deviations of the 4.9 and 1.0 % w/w for the IR and Raman models, respectively. Both techniques were more accurate than results obtained by an industrial refractive index analysis method, which is used for rapid, cheap quantitation of squalene in shark liver oils. In particular, the Raman partial least squares regression was suited to quantitative squalene analysis. The intense and highly characteristic Raman bands of squalene made quantitative analysis possible irrespective of the lipid matrix.

Evaluating the performance of the Lee-Carter method and its variants in modelling and forecasting Malaysian mortality

NASA Astrophysics Data System (ADS)

Zakiyatussariroh, W. H. Wan; Said, Z. Mohammad; Norazan, M. R.

2014-12-01

This study investigated the performance of the Lee-Carter (LC) method and it variants in modeling and forecasting Malaysia mortality. These include the original LC, the Lee-Miller (LM) variant and the Booth-Maindonald-Smith (BMS) variant. These methods were evaluated using Malaysia's mortality data which was measured based on age specific death rates (ASDR) for 1971 to 2009 for overall population while those for 1980-2009 were used in separate models for male and female population. The performance of the variants has been examined in term of the goodness of fit of the models and forecasting accuracy. Comparison was made based on several criteria namely, mean square error (MSE), root mean square error (RMSE), mean absolute deviation (MAD) and mean absolute percentage error (MAPE). The results indicate that BMS method was outperformed in in-sample fitting for overall population and when the models were fitted separately for male and female population. However, in the case of out-sample forecast accuracy, BMS method only best when the data were fitted to overall population. When the data were fitted separately for male and female, LCnone performed better for male population and LM method is good for female population.

Aerosols optical properties in dynamic atmosphere in the northwestern part of the Indian Himalaya: A comparative study from ground and satellite based observations

NASA Astrophysics Data System (ADS)

Guleria, Raj Paul; Kuniyal, Jagdish Chandra; Rawat, Pan Singh; Thakur, Harinder Kumar; Sharma, Manum; Sharma, Nand Lal; Singh, Mahavir; Chand, Kesar; Sharma, Priyanka; Thakur, Ajay Kumar; Dhyani, Pitamber Prasad; Bhuyan, Pradip Kumar

2011-08-01

The present study deals with the aerosol optical property which carried out during April 2006 to March 2007 over Mohal (31.9°N, 77.12°E) in the northwestern Indian Himalaya. The study was conducted using ground based Multi-wavelength Radiometer (MWR) and Moderate Resolution Imaging Spectroradiometer (MODIS) sensor. The daily average aerosol optical depth (AOD) at 500 nm was found to be (mean ± standard deviation) 0.24 ± 0.10. The afternoon AOD values have been noticed to be higher than the forenoon AOD values. Spectral AOD values exhibited larger day-to-day variation in finer aerosols during the observation period. The daily average value of Ångström exponent 'α' and turbidity coefficient 'β' obtained was 1.10 ± 0.38 and 0.12 ± 0.08 respectively. Higher value of AOD ~ 0.39 ± 0.06 during summer associated with low α ~ 0.73 ± 0.28 has attributed to the increase in the relative dominance of coarse size particles. In winter α ~ 1.21 ± 0.32 indicating a considerable increase in fine size particles, attributed to the anthropogenic activities. The AOD spectra seem to be more wavelength dependent in winter as compared to summer. Comparison of MWR observation with MODIS observation indicates a good conformity between ground-based and satellite derived AOD. The root mean square deviation (RMSD), mean absolute bias deviation (MABD) and correlation coefficient have been found to be ~ 0.08, ~ 0.06 and ~ 0.77 respectively. These results suggest that the AOD retrieval through satellite can be able to characterize AOD distribution over Mohal. However, further efforts to eliminate systematic errors in the existing MODIS products are needed. During the observation period ~ 30%, ~ 47% and ~ 62% air parcels drawn at 4000, 5500 and 8000 m above ground level respectively reached at Mohal which passed through or originated from The Great Sahara. The maximum AOD at 500 nm occurred on 8 May 2006. This has caused a significant reduction in surface reaching solar irradiance by ~ 59 Wm -2. The back trajectory analysis suggested that the highest AOD during summer is due to high degree of human interference in the form of tourism and dust transport from the country lying in the northwestern part of India.

Forecasting Error Calculation with Mean Absolute Deviation and Mean Absolute Percentage Error

NASA Astrophysics Data System (ADS)

Khair, Ummul; Fahmi, Hasanul; Hakim, Sarudin Al; Rahim, Robbi

2017-12-01

Prediction using a forecasting method is one of the most important things for an organization, the selection of appropriate forecasting methods is also important but the percentage error of a method is more important in order for decision makers to adopt the right culture, the use of the Mean Absolute Deviation and Mean Absolute Percentage Error to calculate the percentage of mistakes in the least square method resulted in a percentage of 9.77% and it was decided that the least square method be worked for time series and trend data.

14 CFR Appendix G to Part 25 - Continuous Gust Design Criteria

Code of Federal Regulations, 2014 CFR

2014-01-01

...) Values of Ā (ratio of root-mean-square incremental load root-mean-square gust velocity) must be... gust velocity, ft./sec. Ω=reduced frequency, radians per foot. L=2,500 ft. (3) The limit loads must be... velocity Uσ: (i) At speed Vc: Uσ=85 fps true gust velocity in the interval 0 to 30,000 ft. altitude and is...

14 CFR Appendix G to Part 25 - Continuous Gust Design Criteria

Code of Federal Regulations, 2013 CFR

2013-01-01

...) Values of Ā (ratio of root-mean-square incremental load root-mean-square gust velocity) must be... gust velocity, ft./sec. Ω=reduced frequency, radians per foot. L=2,500 ft. (3) The limit loads must be... velocity Uσ: (i) At speed Vc: Uσ=85 fps true gust velocity in the interval 0 to 30,000 ft. altitude and is...

14 CFR Appendix G to Part 25 - Continuous Gust Design Criteria

Code of Federal Regulations, 2012 CFR

2012-01-01

...) Values of Ā (ratio of root-mean-square incremental load root-mean-square gust velocity) must be... gust velocity, ft./sec. Ω=reduced frequency, radians per foot. L=2,500 ft. (3) The limit loads must be... velocity Uσ: (i) At speed Vc: Uσ=85 fps true gust velocity in the interval 0 to 30,000 ft. altitude and is...

Pulsar-black hole binaries as a window on quantum gravity

NASA Astrophysics Data System (ADS)

Estes, John; Kavic, Michael; Lippert, Matthew; Simonetti, John H.

Pulsars (PSRs) are some of the most accurate clocks found in nature, while black holes (BHs) offer a unique arena for the study of quantum gravity. As such, PSR-BH binaries provide ideal astrophysical systems for detecting effects of quantum gravity. With the success of aLIGO and the advent of instruments like the Square Kilometer Array (SKA) and Evolved Laser Interferometer Space Antenna (eLISA), the prospects for discovery of such PSR-BH binaries are very promising. We argue that PSR-BH binaries can serve as ready-made testing grounds for proposed resolutions to the BH information paradox. We propose using timing signals from a PSR beam passing through the region near a BH event horizon as a probe of quantum gravitational effects. In particular, we demonstrate that fluctuations of the geometry outside a BH lead to an increase in the measured root-mean-square deviation of arrival times of PSR pulsar traveling near the horizon.

A Semiempirical Formula for Single-Electron-Capture Cross Sections of Multiply Charged Ions Colliding with H, H2 and He

NASA Astrophysics Data System (ADS)

Nakai, Yohta; Shirai, Toshizo; Tabata, Tatsuo; Ito, Rinsuke

1989-01-01

A universal analytic formula is given for the total cross sections of single-electron capture by multiply-charged ions colliding with H, H2 or He. Values of constants in the formula have been determined by least-squares fit to experimental data collected from the literature. The formula is applicable to ions of almost all atomic species with charge q greater than 4 (for the H and H2 targets) or 5 (for the He target) in the energy region from about 1 to 107 eV amu-1. The root-mean-square deviation of the data from the formula is 29%. The formula shows that the cross sections are proportional to q1.07 at low energies and to q2.86 at high energies. Other trends of the cross sections that can be derived from the formula are also discussed.

Pursuit gain and saccadic intrusions in first-degree relatives of probands with schizophrenia.

PubMed

Clementz, B A; Sweeney, J A; Hirt, M; Haas, G

1990-11-01

Oculomotor functioning of 26 probands with schizophrenia, 12 spectrum and 46 nonspectrum first-degree relatives, and 38 nonpsychiatric control subjects was evaluated. Spectrum relatives had more anticipatory saccades (ASs) and lower pursuit gain than nonspectrum relatives, who had more ASs and lower pursuit gain than control subjects. Probands also had lower pursuit gain than nonspectrum relatives and control subjects but did not differ from other groups on AS frequency. Control subjects had more globally accurate pursuit tracking (root mean square [RMS] error deviation) than both relative groups, whereas probands had the poorest RMS scores. Square wave jerk frequency did not differentiate the groups. Attention enhancement affected the frequency of ASs but did not affect either the other intrusive saccadic event or RMS scores. These results offer evidence that eye-movement dysfunction may serve as a biological marker for schizophrenia.

Estimating Root Mean Square Errors in Remotely Sensed Soil Moisture over Continental Scale Domains

NASA Technical Reports Server (NTRS)

Draper, Clara S.; Reichle, Rolf; de Jeu, Richard; Naeimi, Vahid; Parinussa, Robert; Wagner, Wolfgang

2013-01-01

Root Mean Square Errors (RMSE) in the soil moisture anomaly time series obtained from the Advanced Scatterometer (ASCAT) and the Advanced Microwave Scanning Radiometer (AMSR-E; using the Land Parameter Retrieval Model) are estimated over a continental scale domain centered on North America, using two methods: triple colocation (RMSETC ) and error propagation through the soil moisture retrieval models (RMSEEP ). In the absence of an established consensus for the climatology of soil moisture over large domains, presenting a RMSE in soil moisture units requires that it be specified relative to a selected reference data set. To avoid the complications that arise from the use of a reference, the RMSE is presented as a fraction of the time series standard deviation (fRMSE). For both sensors, the fRMSETC and fRMSEEP show similar spatial patterns of relatively highlow errors, and the mean fRMSE for each land cover class is consistent with expectations. Triple colocation is also shown to be surprisingly robust to representativity differences between the soil moisture data sets used, and it is believed to accurately estimate the fRMSE in the remotely sensed soil moisture anomaly time series. Comparing the ASCAT and AMSR-E fRMSETC shows that both data sets have very similar accuracy across a range of land cover classes, although the AMSR-E accuracy is more directly related to vegetation cover. In general, both data sets have good skill up to moderate vegetation conditions.

Mechanistic insights into the urea-induced denaturation of kinase domain of human integrin linked kinase.

PubMed

Syed, Sunayana Begum; Khan, Faez Iqbal; Khan, Sabab Hasan; Srivastava, Saurabha; Hasan, Gulam Mustafa; Lobb, Kevin A; Islam, Asimul; Ahmad, Faizan; Hassan, Md Imtaiyaz

2018-05-01

Integrin-linked kinase (ILK), a ubiquitously expressed intracellular Ser/Thr protein kinase, plays a major role in the oncogenesis and tumour progression. The conformational stability and unfolding of kinase domain of ILK (ILK 193-446 ) was examined in the presence of increasing concentrations of urea. The stability parameters of the urea-induced denaturation were measured by monitoring changes in [θ] 222 (mean residue ellipticity at 222nm), difference absorption coefficient at 292nm (Δε 292 ) and intrinsic fluorescence emission intensity at pH7.5 and 25±0.1°C. The urea-induced denaturation was found to be reversible. The protein unfolding transition occurred in the urea concentration range 3.0-7.0M. A coincidence of normalized denaturation curves of optical properties ([θ] 222 , Δε 292 and λ max , the wavelength of maximum emission intensity) suggested that urea-induced denaturation of kinase domain of ILK is a two-state process. We further performed molecular dynamics simulation for 100ns to see the effect of urea on structural stability of kinase domain of ILK at atomic level. Structural changes with increasing concentrations of urea were analysed, and we observed a significant increase in the root mean square deviation, root mean square fluctuations, solvent accessible surface area and radius of gyration. A correlation was observed between in vitro and in silico studies. Copyright © 2018 Elsevier B.V. All rights reserved.

A root-mean-square approach for predicting fatigue crack growth under random loading

NASA Technical Reports Server (NTRS)

Hudson, C. M.

1981-01-01

A method for predicting fatigue crack growth under random loading which employs the concept of Barsom (1976) is presented. In accordance with this method, the loading history for each specimen is analyzed to determine the root-mean-square maximum and minimum stresses, and the predictions are made by assuming the tests have been conducted under constant-amplitude loading at the root-mean-square maximum and minimum levels. The procedure requires a simple computer program and a desk-top computer. For the eleven predictions made, the ratios of the predicted lives to the test lives ranged from 2.13 to 0.82, which is a good result, considering that the normal scatter in the fatigue-crack-growth rates may range from a factor of two to four under identical loading conditions.

Effect of Liquid Surface Turbulent Motion on the Vapor Condensation in a Mixing Tank

NASA Technical Reports Server (NTRS)

Lin, C. S.; Hasan, M. M.

1991-01-01

The effect of liquid surface motion on the vapor condensation in a tank mixed by an axial turbulent jet is numerically investigated. The average value (over the interface area) of the root-mean-squared (rms) turbulent velocity at the interface is shown to be linearly increasing with decreasing liquid height and increasing jet diameter for a given tank size. The average rms turbulent velocity is incorporated in Brown et al. (1990) condensation correlation to predict the condensation of vapor on a liquid surface. The results are in good agreement with available condensation data.

Breast Tissue Characterization with Photon-counting Spectral CT Imaging: A Postmortem Breast Study

PubMed Central

Ding, Huanjun; Klopfer, Michael J.; Ducote, Justin L.; Masaki, Fumitaro

2014-01-01

Purpose To investigate the feasibility of breast tissue characterization in terms of water, lipid, and protein contents with a spectral computed tomographic (CT) system based on a cadmium zinc telluride (CZT) photon-counting detector by using postmortem breasts. Materials and Methods Nineteen pairs of postmortem breasts were imaged with a CZT-based photon-counting spectral CT system with beam energy of 100 kVp. The mean glandular dose was estimated to be in the range of 1.8–2.2 mGy. The images were corrected for pulse pile-up and other artifacts by using spectral distortion corrections. Dual-energy decomposition was then applied to characterize each breast into water, lipid, and protein contents. The precision of the three-compartment characterization was evaluated by comparing the composition of right and left breasts, where the standard error of the estimations was determined. The results of dual-energy decomposition were compared by using averaged root mean square to chemical analysis, which was used as the reference standard. Results The standard errors of the estimations of the right-left correlations obtained from spectral CT were 7.4%, 6.7%, and 3.2% for water, lipid, and protein contents, respectively. Compared with the reference standard, the average root mean square error in breast tissue composition was 2.8%. Conclusion Spectral CT can be used to accurately quantify the water, lipid, and protein contents in breast tissue in a laboratory study by using postmortem specimens. © RSNA, 2014 PMID:24814180

Molecular dynamics study of biodegradation of azo dyes via their interactions with AzrC azoreductase.

PubMed

Haghshenas, Hamed; Kay, Maryam; Dehghanian, Fariba; Tavakol, Hossein

2016-01-01

Azo dyes are one of the most important class of dyes, which have been widely used in industries. Because of the environmental pollution of azo dyes, many studies have been performed to study their biodegradation using bacterial systems. In present work, the AzrC of mesophilic gram-positive Bacillus sp. B29 has been considered to study its interaction with five common azo dyes (orange G, acid red 88, Sudan I, orange I, and methyl red). The molecular dynamics simulations have been employed to study the interaction between AzrC and azo dyes. The trajectory was confirmed using root mean square deviation and the root mean square fluctuation analyses. Then, the hydrogen bond and alanine scanning analyses were performed to reveal active site residues. Phe105 (A), Phe125 (B), Phe172 (B), and Pro132 (B) have been found as the most important hydrophobic residues whereas Asn104 (A), Tyr127 (B), and Asn187 (A) have key role in making hydrogen bond. The results of molecular mechanics Poisson-Boltzmann surface area and molecular mechanics generalized Born surface area calculations proved that the hydrophobic azo dyes like Acid red 88 binds more tightly to the AzrC protein. The calculated data suggested MR A 121 (B) I as a potential candidate for improving the AzrC-MR interactions.

Molecular dynamic of curcumin/chitosan interaction using a computational molecular approach: Emphasis on biofilm reduction.

PubMed

Khezri, Azam; Karimi, Arsalan; Yazdian, Fatemeh; Jokar, Mahmoud; Mofradnia, Soheil Rezazadeh; Rashedi, Hamid; Tavakoli, Zahra

2018-07-15

Nanotechnology-based drug delivery systems have been used to enhance bioavailability and biological activities. Chitosan incorporating curcumin can serve as a biocompatible substitute for metallic nanoparticles in preventing biofilm formation of Streptococcus mutans and plaque on teeth. The interactions between chitosan nanoparticle as a carrier and curcumin, a natural antibacterial agent, were simulated. The binding conformation between curcumin-chitosan was obtained using the Lamarckian Genetic Algorithm in Autodock™ software in chitosan nanoparticle. The interaction stability was examined in the molecular dynamic stages, with isothermal-isobaric ensemble in the CHARMM Force Field. The results showed the root mean square deviation (RMSD) and the root mean square fluctuations (RMSF) for all complex's atoms were relaxed after 4ns (RMSD for the all-atoms was 26.81±0.1 (Å); RMSF 1.13±0.02Å). For each section, the estimation of RMSD, RMSF, radius of gyration, inter-H bond and other analysis confirmed that, during the first interval;10ns, there was a stable binding between the two sections. Although all bindings disappeared from 10 to 20ns, the curcumin was trapped inside the chitosan nanoparticles, and no release took place until 20ns, after which the curcumin began to release. This trend suggests that chitosan nanoparticle has ability to carry the curcumin. Copyright © 2018 Elsevier B.V. All rights reserved.

Computational screening of disease-associated mutations in OCA2 gene.

PubMed

Kamaraj, Balu; Purohit, Rituraj

2014-01-01

Oculocutaneous albinism type 2 (OCA2), caused by mutations of OCA2 gene, is an autosomal recessive disorder characterized by reduced biosynthesis of melanin pigment in the skin, hair, and eyes. The OCA2 gene encodes instructions for making a protein called the P protein. This protein plays a crucial role in melanosome biogenesis, and controls the eumelanin content in melanocytes in part via the processing and trafficking of tyrosinase which is the rate-limiting enzyme in melanin synthesis. In this study we analyzed the pathogenic effect of 95 non-synonymous single nucleotide polymorphisms reported in OCA2 gene using computational methods. We found R305W mutation as most deleterious and disease associated using SIFT, PolyPhen, PANTHER, PhD-SNP, Pmut, and MutPred tools. To understand the atomic arrangement in 3D space, the native and mutant (R305W) structures were modeled. Molecular dynamics simulation was conducted to observe the structural significance of computationally prioritized disease-associated mutation (R305W). Root-mean-square deviation, root-mean-square fluctuation, radius of gyration, solvent accessibility surface area, hydrogen bond (NH bond), trace of covariance matrix, eigenvector projection analysis, and density analysis results showed prominent loss of stability and rise in mutant flexibility values in 3D space. This study presents a well designed computational methodology to examine the albinism-associated SNPs.

Effects of different force fields on the structural character of α synuclein β-hairpin peptide (35-56) in aqueous environment.

PubMed

Kundu, Sangeeta

2018-02-01

The hallmark of Parkinson's disease (PD) is the intracellular protein aggregation forming Lewy Bodies (LB) and Lewy neuritis which comprise mostly of a protein, alpha synuclein (α-syn). Molecular dynamics (MD) simulation methods can augment experimental techniques to understand misfolding and aggregation pathways with atomistic resolution. The quality of MD simulations for proteins and peptides depends greatly on the accuracy of empirical force fields. The aim of this work is to investigate the effects of different force fields on the structural character of β hairpin fragment of α-syn (residues 35-56) peptide in aqueous solution. Six independent MD simulations are done in explicit solvent using, AMBER03, AMBER99SB, GROMOS96 43A1, GROMOS96 53A6, OPLS-AA, and CHARMM27 force fields with CMAP corrections. The performance of each force field is assessed from several structural parameters such as root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), formation of β-turn, the stability of folded β-hairpin structure, and the favourable conformations obtained for different force fields. In this study, CMAP correction of CHARMM27 force field is found to overestimate the helical conformation, while GROMOS96 53A6 is found to most successfully capture the conformational dynamics of α-syn β-hairpin fragment as elicited from NMR.

Automatic identification of mobile and rigid substructures in molecular dynamics simulations and fractional structural fluctuation analysis.

PubMed

Martínez, Leandro

2015-01-01

The analysis of structural mobility in molecular dynamics plays a key role in data interpretation, particularly in the simulation of biomolecules. The most common mobility measures computed from simulations are the Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuations (RMSF) of the structures. These are computed after the alignment of atomic coordinates in each trajectory step to a reference structure. This rigid-body alignment is not robust, in the sense that if a small portion of the structure is highly mobile, the RMSD and RMSF increase for all atoms, resulting possibly in poor quantification of the structural fluctuations and, often, to overlooking important fluctuations associated to biological function. The motivation of this work is to provide a robust measure of structural mobility that is practical, and easy to interpret. We propose a Low-Order-Value-Optimization (LOVO) strategy for the robust alignment of the least mobile substructures in a simulation. These substructures are automatically identified by the method. The algorithm consists of the iterative superposition of the fraction of structure displaying the smallest displacements. Therefore, the least mobile substructures are identified, providing a clearer picture of the overall structural fluctuations. Examples are given to illustrate the interpretative advantages of this strategy. The software for performing the alignments was named MDLovoFit and it is available as free-software at: http://leandro.iqm.unicamp.br/mdlovofit.

Exploration of structural stability in deleterious nsSNPs of the XPA gene: A molecular dynamics approach

PubMed Central

NagaSundaram, N; Priya Doss, C George

2011-01-01

Background: Distinguishing the deleterious from the massive number of non-functional nsSNPs that occur within a single genome is a considerable challenge in mutation research. In this approach, we have used the existing in silico methods to explore the mutation-structure-function relationship in the XPAgene. Materials and Methods: We used the Sorting Intolerant From Tolerant (SIFT), Polymorphism Phenotyping (PolyPhen), I-Mutant 2.0, and the Protein Analysis THrough Evolutionary Relationships methods to predict the effects of deleterious nsSNPs on protein function and evaluated the impact of mutation on protein stability by Molecular Dynamics simulations. Results: By comparing the scores of all the four in silico methods, nsSNP with an ID rs104894131 at position C108F was predicted to be highly deleterious. We extended our Molecular dynamics approach to gain insight into the impact of this non-synonymous polymorphism on structural changes that may affect the activity of the XPAgene. Conclusion: Based on the in silico methods score, potential energy, root-mean-square deviation, and root-mean-square fluctuation, we predict that deleterious nsSNP at position C108F would play a significant role in causing disease by the XPA gene. Our approach would present the application of in silicotools in understanding the functional variation from the perspective of structure, evolution, and phenotype. PMID:22190868

Determination of subthalamic nucleus location by quantitative analysis of despiked background neural activity from microelectrode recordings obtained during deep brain stimulation surgery.

PubMed

Danish, Shabbar F; Baltuch, Gordon H; Jaggi, Jurg L; Wong, Stephen

2008-04-01

Microelectrode recording during deep brain stimulation surgery is a useful adjunct for subthalamic nucleus (STN) localization. We hypothesize that information in the nonspike background activity can help identify STN boundaries. We present results from a novel quantitative analysis that accomplishes this goal. Thirteen consecutive microelectrode recordings were retrospectively analyzed. Spikes were removed from the recordings with an automated algorithm. The remaining "despiked" signals were converted via root mean square amplitude and curve length calculations into "feature profile" time series. Subthalamic nucleus boundaries determined by inspection, based on sustained deviations from baseline for each feature profile, were compared against those determined intraoperatively by the clinical neurophysiologist. Feature profile activity within STN exhibited a sustained rise in 10 of 13 tracks (77%). The sensitivity of STN entry was 60% and 90% for curve length and root mean square amplitude, respectively, when agreement within 0.5 mm of the neurophysiologist's prediction was used. Sensitivities were 70% and 100% for 1 mm accuracy. Exit point sensitivities were 80% and 90% for both features within 0.5 mm and 1.0 mm, respectively. Reproducible activity patterns in deep brain stimulation microelectrode recordings can allow accurate identification of STN boundaries. Quantitative analyses of this type may provide useful adjunctive information for electrode placement in deep brain stimulation surgery.

Automatic Identification of Mobile and Rigid Substructures in Molecular Dynamics Simulations and Fractional Structural Fluctuation Analysis

PubMed Central

Martínez, Leandro

2015-01-01

The analysis of structural mobility in molecular dynamics plays a key role in data interpretation, particularly in the simulation of biomolecules. The most common mobility measures computed from simulations are the Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuations (RMSF) of the structures. These are computed after the alignment of atomic coordinates in each trajectory step to a reference structure. This rigid-body alignment is not robust, in the sense that if a small portion of the structure is highly mobile, the RMSD and RMSF increase for all atoms, resulting possibly in poor quantification of the structural fluctuations and, often, to overlooking important fluctuations associated to biological function. The motivation of this work is to provide a robust measure of structural mobility that is practical, and easy to interpret. We propose a Low-Order-Value-Optimization (LOVO) strategy for the robust alignment of the least mobile substructures in a simulation. These substructures are automatically identified by the method. The algorithm consists of the iterative superposition of the fraction of structure displaying the smallest displacements. Therefore, the least mobile substructures are identified, providing a clearer picture of the overall structural fluctuations. Examples are given to illustrate the interpretative advantages of this strategy. The software for performing the alignments was named MDLovoFit and it is available as free-software at: http://leandro.iqm.unicamp.br/mdlovofit PMID:25816325

MDplot: Visualise Molecular Dynamics

PubMed Central

Margreitter, Christian; Oostenbrink, Chris

2017-01-01

The MDplot package provides plotting functions to allow for automated visualisation of molecular dynamics simulation output. It is especially useful in cases where the plot generation is rather tedious due to complex file formats or when a large number of plots are generated. The graphs that are supported range from those which are standard, such as RMsD/RMsF (root-mean-square deviation and root-mean-square fluctuation, respectively) to less standard, such as thermodynamic integration analysis and hydrogen bond monitoring over time. All told, they address many commonly used analyses. In this article, we set out the MDplot package′s functions, give examples of the function calls, and show the associated plots. Plotting and data parsing is separated in all cases, i.e. the respective functions can be used independently. Thus, data manipulation and the integration of additional file formats is fairly easy. Currently, the loading functions support GROMOS, GROMACS, and AMBER file formats. Moreover, we also provide a Bash interface that allows simple embedding of MDplot into Bash scripts as the final analysis step. Availability The package can be obtained in the latest major version from CRAN (https://cran.r-project.org/package=MDplot) or in the most recent version from the project′s GitHub page at https://github.com/MDplot/MDplot, where feedback is also most welcome. MDplot is published under the GPL-3 license. PMID:28845302

Exploring Protein Stability by Comparative Molecular Dynamics Simulations of Homologous Hyperthermophilic, Mesophilic, and Psychrophilic Proteins.

PubMed

Khan, Sara; Farooq, Umar; Kurnikova, Maria

2016-11-28

In the present studies, we analyzed the influence of temperature on the stability and dynamics of the α subunit of tryptophan synthase (TRPS) from hyperthermophilic, mesophilic, and psychrophilic homologues at different temperatures by molecular dynamics simulations. Employing different indicators such as root-mean-square deviations, root-mean-square fluctuations, principal component analysis, and free energy landscapes, this study manifests the diverse behavior of these homologues with changes in temperature. Especially, an enhancement in the collective motions, classified as representative motions, is observed at high temperature. Similarly, the criterion for the selection of electrostatic interactions in terms of their life span (duty cycle) has indeed helped in identifying the short- and long-lived electrostatic interactions and how they affect the protein's overall stability at different temperatures. Rigidity and flexibility patterns of the homologous proteins are examined using FIRST software along with the calculation of duty cycles with various threshold limits at different temperatures. Rigid cluster decomposition in TRPS of psychrophilic, mesophilic, and hyperthermophilic origin identifies the flexible and rigid regions in the protein. Early loss of rigidity is observed in mesophilic TRPS via loss of contact between the major fragments of the protein compared with the other homologues. In spite of the high similarity of their three-dimensional structures, the overall responses of the three proteins to varying temperatures are significantly different.

Finger muscle attachments for an OpenSim upper-extremity model.

PubMed

Lee, Jong Hwa; Asakawa, Deanna S; Dennerlein, Jack T; Jindrich, Devin L

2015-01-01

We determined muscle attachment points for the index, middle, ring and little fingers in an OpenSim upper-extremity model. Attachment points were selected to match both experimentally measured locations and mechanical function (moment arms). Although experimental measurements of finger muscle attachments have been made, models differ from specimens in many respects such as bone segment ratio, joint kinematics and coordinate system. Likewise, moment arms are not available for all intrinsic finger muscles. Therefore, it was necessary to scale and translate muscle attachments from one experimental or model environment to another while preserving mechanical function. We used a two-step process. First, we estimated muscle function by calculating moment arms for all intrinsic and extrinsic muscles using the partial velocity method. Second, optimization using Simulated Annealing and Hooke-Jeeves algorithms found muscle-tendon paths that minimized root mean square (RMS) differences between experimental and modeled moment arms. The partial velocity method resulted in variance accounted for (VAF) between measured and calculated moment arms of 75.5% on average (range from 48.5% to 99.5%) for intrinsic and extrinsic index finger muscles where measured data were available. RMS error between experimental and optimized values was within one standard deviation (S.D) of measured moment arm (mean RMS error = 1.5 mm < measured S.D = 2.5 mm). Validation of both steps of the technique allowed for estimation of muscle attachment points for muscles whose moment arms have not been measured. Differences between modeled and experimentally measured muscle attachments, averaged over all finger joints, were less than 4.9 mm (within 7.1% of the average length of the muscle-tendon paths). The resulting non-proprietary musculoskeletal model of the human fingers could be useful for many applications, including better understanding of complex multi-touch and gestural movements.

Finger Muscle Attachments for an OpenSim Upper-Extremity Model

PubMed Central

Lee, Jong Hwa; Asakawa, Deanna S.; Dennerlein, Jack T.; Jindrich, Devin L.

2015-01-01

We determined muscle attachment points for the index, middle, ring and little fingers in an OpenSim upper-extremity model. Attachment points were selected to match both experimentally measured locations and mechanical function (moment arms). Although experimental measurements of finger muscle attachments have been made, models differ from specimens in many respects such as bone segment ratio, joint kinematics and coordinate system. Likewise, moment arms are not available for all intrinsic finger muscles. Therefore, it was necessary to scale and translate muscle attachments from one experimental or model environment to another while preserving mechanical function. We used a two-step process. First, we estimated muscle function by calculating moment arms for all intrinsic and extrinsic muscles using the partial velocity method. Second, optimization using Simulated Annealing and Hooke-Jeeves algorithms found muscle-tendon paths that minimized root mean square (RMS) differences between experimental and modeled moment arms. The partial velocity method resulted in variance accounted for (VAF) between measured and calculated moment arms of 75.5% on average (range from 48.5% to 99.5%) for intrinsic and extrinsic index finger muscles where measured data were available. RMS error between experimental and optimized values was within one standard deviation (S.D) of measured moment arm (mean RMS error = 1.5 mm < measured S.D = 2.5 mm). Validation of both steps of the technique allowed for estimation of muscle attachment points for muscles whose moment arms have not been measured. Differences between modeled and experimentally measured muscle attachments, averaged over all finger joints, were less than 4.9 mm (within 7.1% of the average length of the muscle-tendon paths). The resulting non-proprietary musculoskeletal model of the human fingers could be useful for many applications, including better understanding of complex multi-touch and gestural movements. PMID:25853869

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.

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…

Dependence of average inter-particle distance upon the temperature of neutrals in dusty plasma crystals

NASA Astrophysics Data System (ADS)

Nikolaev, V. S.; Timofeev, A. V.

2018-01-01

It is often suggested that inter-particle distance in stable dusty plasma structures decreases with cooling as a square root of neutral gas temperature. Deviations from this dependence (up to the increase at cryogenic temperatures) found in the experimental results for the pressures range 0.1-8.0 mbar and for the currents range 0.1-1.0 mA are given. Inter-particle distance dependences on the charge of particles, parameter of the trap and the screening length in surrounding plasma are obtained for different conditions from molecular dynamics simulations. They are well approximated by power functions in the mentioned range of parameters. It is found that under certain assumptions thermophoretical force is responsible for inter-particle distance increase at cryogenic temperatures.

Estimating patient-specific soft-tissue properties in a TKA knee.

PubMed

Ewing, Joseph A; Kaufman, Michelle K; Hutter, Erin E; Granger, Jeffrey F; Beal, Matthew D; Piazza, Stephen J; Siston, Robert A

2016-03-01

Surgical technique is one factor that has been identified as critical to success of total knee arthroplasty. Researchers have shown that computer simulations can aid in determining how decisions in the operating room generally affect post-operative outcomes. However, to use simulations to make clinically relevant predictions about knee forces and motions for a specific total knee patient, patient-specific models are needed. This study introduces a methodology for estimating knee soft-tissue properties of an individual total knee patient. A custom surgical navigation system and stability device were used to measure the force-displacement relationship of the knee. Soft-tissue properties were estimated using a parameter optimization that matched simulated tibiofemoral kinematics with experimental tibiofemoral kinematics. Simulations using optimized ligament properties had an average root mean square error of 3.5° across all tests while simulations using generic ligament properties taken from literature had an average root mean square error of 8.4°. Specimens showed large variability among ligament properties regardless of similarities in prosthetic component alignment and measured knee laxity. These results demonstrate the importance of soft-tissue properties in determining knee stability, and suggest that to make clinically relevant predictions of post-operative knee motions and forces using computer simulations, patient-specific soft-tissue properties are needed. © 2015 Orthopaedic Research Society. Published by Wiley Periodicals, Inc.

Determination of suitable drying curve model for bread moisture loss during baking

NASA Astrophysics Data System (ADS)

Soleimani Pour-Damanab, A. R.; Jafary, A.; Rafiee, S.

2013-03-01

This study presents mathematical modelling of bread moisture loss or drying during baking in a conventional bread baking process. In order to estimate and select the appropriate moisture loss curve equation, 11 different models, semi-theoretical and empirical, were applied to the experimental data and compared according to their correlation coefficients, chi-squared test and root mean square error which were predicted by nonlinear regression analysis. Consequently, of all the drying models, a Page model was selected as the best one, according to the correlation coefficients, chi-squared test, and root mean square error values and its simplicity. Mean absolute estimation error of the proposed model by linear regression analysis for natural and forced convection modes was 2.43, 4.74%, respectively.

Parameter estimation method and updating of regional prediction equations for ungaged sites in the desert region of California

USGS Publications Warehouse

Barth, Nancy A.; Veilleux, Andrea G.

2012-01-01

The U.S. Geological Survey (USGS) is currently updating at-site flood frequency estimates for USGS streamflow-gaging stations in the desert region of California. The at-site flood-frequency analysis is complicated by short record lengths (less than 20 years is common) and numerous zero flows/low outliers at many sites. Estimates of the three parameters (mean, standard deviation, and skew) required for fitting the log Pearson Type 3 (LP3) distribution are likely to be highly unreliable based on the limited and heavily censored at-site data. In a generalization of the recommendations in Bulletin 17B, a regional analysis was used to develop regional estimates of all three parameters (mean, standard deviation, and skew) of the LP3 distribution. A regional skew value of zero from a previously published report was used with a new estimated mean squared error (MSE) of 0.20. A weighted least squares (WLS) regression method was used to develop both a regional standard deviation and a mean model based on annual peak-discharge data for 33 USGS stations throughout California’s desert region. At-site standard deviation and mean values were determined by using an expected moments algorithm (EMA) method for fitting the LP3 distribution to the logarithms of annual peak-discharge data. Additionally, a multiple Grubbs-Beck (MGB) test, a generalization of the test recommended in Bulletin 17B, was used for detecting multiple potentially influential low outliers in a flood series. The WLS regression found that no basin characteristics could explain the variability of standard deviation. Consequently, a constant regional standard deviation model was selected, resulting in a log-space value of 0.91 with a MSE of 0.03 log units. Yet drainage area was found to be statistically significant at explaining the site-to-site variability in mean. The linear WLS regional mean model based on drainage area had a Pseudo- 2 R of 51 percent and a MSE of 0.32 log units. The regional parameter estimates were then used to develop a set of equations for estimating flows with 50-, 20-, 10-, 4-, 2-, 1-, 0.5-, and 0.2-percent annual exceedance probabilities for ungaged basins. The final equations are functions of drainage area.Average standard errors of prediction for these regression equations range from 214.2 to 856.2 percent.

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.

The efficacy of calibrating hydrologic model using remotely sensed evapotranspiration and soil moisture for streamflow prediction

NASA Astrophysics Data System (ADS)

Kunnath-Poovakka, A.; Ryu, D.; Renzullo, L. J.; George, B.

2016-04-01

Calibration of spatially distributed hydrologic models is frequently limited by the availability of ground observations. Remotely sensed (RS) hydrologic information provides an alternative source of observations to inform models and extend modelling capability beyond the limits of ground observations. This study examines the capability of RS evapotranspiration (ET) and soil moisture (SM) in calibrating a hydrologic model and its efficacy to improve streamflow predictions. SM retrievals from the Advanced Microwave Scanning Radiometer-EOS (AMSR-E) and daily ET estimates from the CSIRO MODIS ReScaled potential ET (CMRSET) are used to calibrate a simplified Australian Water Resource Assessment - Landscape model (AWRA-L) for a selection of parameters. The Shuffled Complex Evolution Uncertainty Algorithm (SCE-UA) is employed for parameter estimation at eleven catchments in eastern Australia. A subset of parameters for calibration is selected based on the variance-based Sobol' sensitivity analysis. The efficacy of 15 objective functions for calibration is assessed based on streamflow predictions relative to control cases, and relative merits of each are discussed. Synthetic experiments were conducted to examine the effect of bias in RS ET observations on calibration. The objective function containing the root mean square deviation (RMSD) of ET result in best streamflow predictions and the efficacy is superior for catchments with medium to high average runoff. Synthetic experiments revealed that accurate ET product can improve the streamflow predictions in catchments with low average runoff.

Autonomic regulation in fetuses with Congenital Heart Disease

PubMed Central

Siddiqui, Saira; Wilpers, Abigail; Myers, Michael; Nugent, J. David; Fifer, William P.; Williams, Ismée A.

2015-01-01

Background Exposure to antenatal stressors affects autonomic regulation in fetuses. Whether the presence of congenital heart disease (CHD) alters the developmental trajectory of autonomic regulation is not known. Aims/Study Design This prospective observational cohort study aimed to further characterize autonomic regulation in fetuses with CHD; specifically hypoplastic left heart syndrome (HLHS), transposition of the great arteries (TGA), and tetralogy of Fallot (TOF). Subjects From 11/2010 – 11/2012, 92 fetuses were enrolled: 41 controls and 51 with CHD consisting of 19 with HLHS, 12 with TGA, and 20 with TOF. Maternal abdominal fetal electrocardiogram (ECG) recordings were obtained at 3 gestational ages: 19-27 weeks (F1), 28-33 weeks (F2), and 34-38 weeks (F3). Outcome measures Fetal ECG was analyzed for mean heart rate along with 3 measures of autonomic variability of the fetal heart rate: interquartile range, standard deviation, and root mean square of the standard deviation of the heart rate (RMSSD), a measure of parasympathetic activity. Results During F1 and F2 periods, HLHS fetuses demonstrated significantly lower mean HR than controls (p<0.05). Heart rate variability at F3, as measured by standard deviation, interquartile range, and RMSSD was lower in HLHS than controls (p<0.05). Other CHD subgroups showed a similar, though non-significant trend towards lower variability. Conclusions Autonomic regulation in CHD fetuses differs from controls with HLHS fetuses most markedly affected. PMID:25662702

Autonomic regulation in fetuses with congenital heart disease.

PubMed

Siddiqui, Saira; Wilpers, Abigail; Myers, Michael; Nugent, J David; Fifer, William P; Williams, Ismée A

2015-03-01

Exposure to antenatal stressors affects autonomic regulation in fetuses. Whether the presence of congenital heart disease (CHD) alters the developmental trajectory of autonomic regulation is not known. This prospective observational cohort study aimed to further characterize autonomic regulation in fetuses with CHD; specifically hypoplastic left heart syndrome (HLHS), transposition of the great arteries (TGA), and tetralogy of Fallot (TOF). From 11/2010 to 11/2012, 92 fetuses were enrolled: 41 controls and 51 with CHD consisting of 19 with HLHS, 12 with TGA, and 20 with TOF. Maternal abdominal fetal electrocardiogram (ECG) recordings were obtained at 3 gestational ages: 19-27 weeks (F1), 28-33 weeks (F2), and 34-38 weeks (F3). Fetal ECG was analyzed for mean heart rate along with 3 measures of autonomic variability of the fetal heart rate: interquartile range, standard deviation, and root mean square of the standard deviation of the heart rate (RMSSD), a measure of parasympathetic activity. During F1 and F2 periods, HLHS fetuses demonstrated significantly lower mean HR than controls (p<0.05). Heart rate variability at F3, as measured by standard deviation, interquartile range, and RMSSD was lower in HLHS than controls (p<0.05). Other CHD subgroups showed a similar, though non-significant trend towards lower variability. Autonomic regulation in CHD fetuses differs from controls, with HLHS fetuses most markedly affected. Copyright © 2015 Elsevier Ltd. All rights reserved.

Inferences on hydrogen bond networks in water from isopermitive frequency investigations.

PubMed

Geethu, P M; Ranganathan, Venketesh T; Satapathy, Dillip K Kumar

2018-06-26

Intermolecular hydrogen bonds play a crucial role in determining the unique characteristics of liquid water. We present low-frequency (1 Hz - 40 MHz) dielectric spectroscopic investigations on water in the presence and absence of added solutes at different temperatures from 10°C to 60°C. The intersection points of temperature dependent permittivity contours at the vicinity of isopermitive frequency (IPF) in water are recorded and its properties are presumed to be related to the extent of hydrogen bond networks in water. IPF is defined as the frequency at which the relative permittivity of water is almost independent of temperature. The set of intersection points of temperature dependent permittivity contours at the vicinity of IPF are characterized by the mean (M_IPF) and root-mean-square deviation/standard deviation (σ_IPF ) associated with IPF. The tunability of M_IPF by the addition of NaCl salt emphasizes the strong correlation between the concentration of ions in water and the M_IPF . The σ_IPF is surmised to be related to the orientational correlations of water dipoles as well as to the intermolecular hydrogen bond networks in water. Further, alterations in σ_IPF is observed with the addition of kosmotropic and chaotropic solutes into water and are thought to arise due to the restructuring of hydrogen bond networks in water in presence of added solutes. Notably, the solute induced reconfiguration of hydrogen bond networks in water or often-discussed structure making/breaking effects of the added solutes in water can be inferred, albeit qualitatively, by examining the M_IPF and σ_IPF. Further, the Gaussian deconvoluted OH-stretching modes present in the Raman Spectra of water and aqueous solutions of IPA and DMF strongly endorses the structural rearrangements occurring in water in presence of kosmotropes and chaotropes and are in-line with the results derived from the root-mean-square deviation in IPF. . © 2018 IOP Publishing Ltd.

a New Phenomenological Formula for Ground-State Binding Energies

NASA Astrophysics Data System (ADS)

Gangopadhyay, G.

A phenomenological formula based on liquid drop model has been proposed for ground-state binding energies of nuclei. The effect due to bunching of single particle levels has been incorporated through a term resembling the one-body Hamiltonian. The effect of n-p interaction has been included through a function of valence nucleons. A total of 50 parameters has been used in the present calculation. The root mean square (r.m.s.) deviation for the binding energy values for 2140 nuclei comes out to be 0.376 MeV, and that for 1091 alpha decay energies is 0.284 MeV. The correspondence with the conventional liquid drop model is discussed.

Monodisperse core-shell particles composed of magnetite and dye-functionalized mesoporous silica

NASA Astrophysics Data System (ADS)

Eurov, D. A.; Kurdyukov, D. A.; Medvedev, A. V.; Kirilenko, D. A.; Yakovlev, D. R.; Golubev, V. G.

2017-08-01

Hybrid particles with a core-shell structure have been obtained in the form of monodisperse spherical mesoporous silica particles filled with magnetite and covered with a mesoporous silica shell functionalized with a luminescent dye. The particles have a small root-mean-square size deviation (at most 10%), possess a specific surface area and specific pore volume of up to 250 m2/g and 0.15 cm3/g, respectively, and exhibit visible luminescence peaked at a wavelength of 530 nm. The particles can be used in diagnostics of cancerous diseases, serving simultaneously for therapeutic (magnetic hyperthermia and targeted drug delivery) and diagnostic (contrast agent for magnetic-resonance tomography and luminescent marker) purposes.

Foveal Curvature and Asymmetry Assessed Using Optical Coherence Tomography.

PubMed

VanNasdale, Dean A; Eilerman, Amanda; Zimmerman, Aaron; Lai, Nicky; Ramsey, Keith; Sinnott, Loraine T

2017-06-01

The aims of this study were to use cross-sectional optical coherence tomography imaging and custom curve fitting software to evaluate and model the foveal curvature as a spherical surface and to compare the radius of curvature in the horizontal and vertical meridians and test the sensitivity of this technique to anticipated meridional differences. Six 30-degree foveal-centered radial optical coherence tomography cross-section scans were acquired in the right eye of 20 clinically normal subjects. Cross sections were manually segmented, and custom curve fitting software was used to determine foveal pit radius of curvature using the central 500, 1000, and 1500 μm of the foveal contour. Radius of curvature was compared across different fitting distances. Root mean square error was used to determine goodness of fit. The radius of curvature was compared between the horizontal and vertical meridians for each fitting distance. There radius of curvature was significantly different when comparing each of the three fitting distances (P < .01 for each comparison). The average radii of curvature were 970 μm (95% confidence interval [CI], 913 to 1028 μm), 1386 μm (95% CI, 1339 to 1439 μm), and 2121 μm (95% CI, 2066 to 2183) for the 500-, 1000-, and 1500-μm fitting distances, respectively. Root mean square error was also significantly different when comparing each fitting distance (P < .01 for each comparison). The average root mean square errors were 2.48 μm (95% CI, 2.41 to 2.53 μm), 6.22 μm (95% CI, 5.77 to 6.60 μm), and 13.82 μm (95% CI, 12.93 to 14.58 μm) for the 500-, 1000-, and 1500-μm fitting distances, respectively. The radius of curvature between the horizontal and vertical meridian radii was statistically different only in the 1000- and 1500-μm fitting distances (P < .01 for each), with the horizontal meridian being flatter than the vertical. The foveal contour can be modeled as a sphere with low curve fitting error over a limited distance and capable of detecting subtle foveal contour differences between meridians.

BCL::MP-Fold: membrane protein structure prediction guided by EPR restraints

PubMed Central

Fischer, Axel W.; Alexander, Nathan S.; Woetzel, Nils; Karakaş, Mert; Weiner, Brian E.; Meiler, Jens

2016-01-01

For many membrane proteins, the determination of their topology remains a challenge for methods like X-ray crystallography and nuclear magnetic resonance (NMR) spectroscopy. Electron paramagnetic resonance (EPR) spectroscopy has evolved as an alternative technique to study structure and dynamics of membrane proteins. The present study demonstrates the feasibility of membrane protein topology determination using limited EPR distance and accessibility measurements. The BCL::MP-Fold algorithm assembles secondary structure elements (SSEs) in the membrane using a Monte Carlo Metropolis (MCM) approach. Sampled models are evaluated using knowledge-based potential functions and agreement with the EPR data and a knowledge-based energy function. Twenty-nine membrane proteins of up to 696 residues are used to test the algorithm. The protein-size-normalized root-mean-square-deviation (RMSD100) value of the most accurate model is better than 8 Å for twenty-seven, better than 6 Å for twenty-two, and better than 4 Å for fifteen out of twenty-nine proteins, demonstrating the algorithm’s ability to sample the native topology. The average enrichment could be improved from 1.3 to 2.5, showing the improved discrimination power by using EPR data. PMID:25820805

Predicting activation energy of thermolysis of polynitro arenes through molecular structure.

PubMed

Keshavarz, Mohammad Hossein; Pouretedal, Hamid Reza; Shokrolahi, Arash; Zali, Abbas; Semnani, Abolfazl

2008-12-15

The paper presents a new method for activation energy or the Arrhenius parameter E(a) of the thermolysis in the condensed state for different polynitro arenes as an important class of energetic molecules. The methodology assumes that E(a) of a polynitro arene with general formula C(a)H(b)N(c)O(d) can be expressed as a function of optimized elemental composition as well as the contribution of specific molecular structural parameters. The new method can predict E(a) of the thermolysis under conditions of Soviet Manometric Method (SMM), which can be related to the other convenient methods. The new correlation has the root mean square (rms) and the average deviations of 13.79 and 11.94kJ/mol, respectively, for 20 polynitro arenes with different molecular structures. The proposed new method can also be used to predict E(a) of three polynitro arenes, i.e. 2,2',2'',4,4',4'',6,6',6''-nonanitro-1,1':3',1''-terphenyl (NONA), 3,3'-diamino-2,2',4,4',6,6'-hexanitro-1,1'-biphenyl-3,3'-diamine (DIPAM) and N,N-bis(2,4-dinitrophenyl)-2,4,6-trinitroaniline (NTFA), which have complex molecular structures.

Time and frequency domain characteristics of detrending-operation-based scaling analysis: Exact DFA and DMA frequency responses

NASA Astrophysics Data System (ADS)

Kiyono, Ken; Tsujimoto, Yutaka

2016-07-01

We develop a general framework to study the time and frequency domain characteristics of detrending-operation-based scaling analysis methods, such as detrended fluctuation analysis (DFA) and detrending moving average (DMA) analysis. In this framework, using either the time or frequency domain approach, the frequency responses of detrending operations are calculated analytically. Although the frequency domain approach based on conventional linear analysis techniques is only applicable to linear detrending operations, the time domain approach presented here is applicable to both linear and nonlinear detrending operations. Furthermore, using the relationship between the time and frequency domain representations of the frequency responses, the frequency domain characteristics of nonlinear detrending operations can be obtained. Based on the calculated frequency responses, it is possible to establish a direct connection between the root-mean-square deviation of the detrending-operation-based scaling analysis and the power spectrum for linear stochastic processes. Here, by applying our methods to DFA and DMA, including higher-order cases, exact frequency responses are calculated. In addition, we analytically investigate the cutoff frequencies of DFA and DMA detrending operations and show that these frequencies are not optimally adjusted to coincide with the corresponding time scale.

Time and frequency domain characteristics of detrending-operation-based scaling analysis: Exact DFA and DMA frequency responses.

PubMed

Kiyono, Ken; Tsujimoto, Yutaka

2016-07-01

We develop a general framework to study the time and frequency domain characteristics of detrending-operation-based scaling analysis methods, such as detrended fluctuation analysis (DFA) and detrending moving average (DMA) analysis. In this framework, using either the time or frequency domain approach, the frequency responses of detrending operations are calculated analytically. Although the frequency domain approach based on conventional linear analysis techniques is only applicable to linear detrending operations, the time domain approach presented here is applicable to both linear and nonlinear detrending operations. Furthermore, using the relationship between the time and frequency domain representations of the frequency responses, the frequency domain characteristics of nonlinear detrending operations can be obtained. Based on the calculated frequency responses, it is possible to establish a direct connection between the root-mean-square deviation of the detrending-operation-based scaling analysis and the power spectrum for linear stochastic processes. Here, by applying our methods to DFA and DMA, including higher-order cases, exact frequency responses are calculated. In addition, we analytically investigate the cutoff frequencies of DFA and DMA detrending operations and show that these frequencies are not optimally adjusted to coincide with the corresponding time scale.

Positioning performance of the NTCM model driven by GPS Klobuchar model parameters

NASA Astrophysics Data System (ADS)

Hoque, Mohammed Mainul; Jakowski, Norbert; Berdermann, Jens

2018-03-01

Users of the Global Positioning System (GPS) utilize the Ionospheric Correction Algorithm (ICA) also known as Klobuchar model for correcting ionospheric signal delay or range error. Recently, we developed an ionosphere correction algorithm called NTCM-Klobpar model for single frequency GNSS applications. The model is driven by a parameter computed from GPS Klobuchar model and consecutively can be used instead of the GPS Klobuchar model for ionospheric corrections. In the presented work we compare the positioning solutions obtained using NTCM-Klobpar with those using the Klobuchar model. Our investigation using worldwide ground GPS data from a quiet and a perturbed ionospheric and geomagnetic activity period of 17 days each shows that the 24-hour prediction performance of the NTCM-Klobpar is better than the GPS Klobuchar model in global average. The root mean squared deviation of the 3D position errors are found to be about 0.24 and 0.45 m less for the NTCM-Klobpar compared to the GPS Klobuchar model during quiet and perturbed condition, respectively. The presented algorithm has the potential to continuously improve the accuracy of GPS single frequency mass market devices with only little software modification.

Examining a Thermodynamic Order Parameter of Protein Folding.

PubMed

Chong, Song-Ho; Ham, Sihyun

2018-05-08

Dimensionality reduction with a suitable choice of order parameters or reaction coordinates is commonly used for analyzing high-dimensional time-series data generated by atomistic biomolecular simulations. So far, geometric order parameters, such as the root mean square deviation, fraction of native amino acid contacts, and collective coordinates that best characterize rare or large conformational transitions, have been prevailing in protein folding studies. Here, we show that the solvent-averaged effective energy, which is a thermodynamic quantity but unambiguously defined for individual protein conformations, serves as a good order parameter of protein folding. This is illustrated through the application to the folding-unfolding simulation trajectory of villin headpiece subdomain. We rationalize the suitability of the effective energy as an order parameter by the funneledness of the underlying protein free energy landscape. We also demonstrate that an improved conformational space discretization is achieved by incorporating the effective energy. The most distinctive feature of this thermodynamic order parameter is that it works in pointing to near-native folded structures even when the knowledge of the native structure is lacking, and the use of the effective energy will also find applications in combination with methods of protein structure prediction.

A statistical evaluation and comparison of VISSR Atmospheric Sounder (VAS) data

NASA Technical Reports Server (NTRS)

Jedlovec, G. J.

1984-01-01

In order to account for the temporal and spatial discrepancies between the VAS and rawinsonde soundings, the rawinsonde data were adjusted to a common hour of release where the new observation time corresponded to the satellite scan time. Both the satellite and rawinsonde observations of the basic atmospheric parameters (T Td, and Z) were objectively analyzed to a uniform grid maintaining the same mesoscale structure in each data set. The performance of each retrieval algorithm in producing accurate and representative soundings was evaluated using statistical parameters such as the mean, standard deviation, and root mean square of the difference fields for each parameter and grid level. Horizontal structure was also qualitatively evaluated by examining atmospheric features on constant pressure surfaces. An analysis of the vertical structure of the atmosphere were also performed by looking at colocated and grid mean vertical profiles of both the satellite and rawinsonde data sets. Highlights of these results are presented.

A method for removing arm backscatter from EPID images

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

King, Brian W.; Greer, Peter B.; School of Mathematical and Physical Sciences, University of Newcastle, Newcastle, New South Wales 2308

2013-07-15

Purpose: To develop a method for removing the support arm backscatter from images acquired using current Varian electronic portal imaging devices (EPIDs).Methods: The effect of arm backscatter on EPID images was modeled using a kernel convolution method. The parameters of the model were optimized by comparing on-arm images to off-arm images. The model was used to develop a method to remove the effect of backscatter from measured EPID images. The performance of the backscatter removal method was tested by comparing backscatter corrected on-arm images to measured off-arm images for 17 rectangular fields of different sizes and locations on the imager.more » The method was also tested using on- and off-arm images from 42 intensity modulated radiotherapy (IMRT) fields.Results: Images generated by the backscatter removal method gave consistently better agreement with off-arm images than images without backscatter correction. For the 17 rectangular fields studied, the root mean square difference of in-plane profiles compared to off-arm profiles was reduced from 1.19% (standard deviation 0.59%) on average without backscatter removal to 0.38% (standard deviation 0.18%) when using the backscatter removal method. When comparing to the off-arm images from the 42 IMRT fields, the mean {gamma} and percentage of pixels with {gamma} < 1 were improved by the backscatter removal method in all but one of the images studied. The mean {gamma} value (1%, 1 mm) for the IMRT fields studied was reduced from 0.80 to 0.57 by using the backscatter removal method, while the mean {gamma} pass rate was increased from 72.2% to 84.6%.Conclusions: A backscatter removal method has been developed to estimate the image acquired by the EPID without any arm backscatter from an image acquired in the presence of arm backscatter. The method has been shown to produce consistently reliable results for a wide range of field sizes and jaw configurations.« less

Depression and anxiety as predictors of heart rate variability after myocardial infarction.

PubMed

Martens, E J; Nyklícek, I; Szabó, B M; Kupper, N

2008-03-01

Reduced heart rate variability (HRV) is a prognostic factor for cardiac mortality. Both depression and anxiety have been associated with increased risk for mortality in cardiac patients. Low HRV may act as an intermediary in this association. The present study examined to what extent depression and anxiety differently predict 24-h HRV indices recorded post-myocardial infarction (MI). Ninety-three patients were recruited during hospitalization for MI and assessed on self-reported symptoms of depression and anxiety. Two months post-MI, patients were assessed on clinical diagnoses of lifetime depressive and anxiety disorder. Adequate 24-h ambulatory electrocardiography data were obtained from 82 patients on average 78 days post-MI. In unadjusted analyses, lifetime diagnoses of major depressive disorder was predictive of lower SDNN [standard deviation of all normal-to-normal (NN) intervals; beta=-0.26, p=0.022] and SDANN (standard deviation of all 5-min mean NN intervals; beta=0.25, p=0.023), and lifetime anxiety disorder of lower RMSSD (root mean square of successive differences; beta=-0.23, p=0.039). Depression and anxiety symptoms did not significantly predict HRV. After adjustment for age, sex, cardiac history and multi-vessel disease, lifetime depressive disorder was no longer predictive of HRV. Lifetime anxiety disorder predicted reduced high-frequency spectral power (beta=-0.22, p=0.039) and RMSSD (beta=-0.25, p=0.019), even after additional adjustment of anxiety symptoms. Clinical anxiety, but not depression, negatively influenced parasympathetic modulation of heart rate in post-MI patients. These findings elucidate the physiological mechanisms underlying anxiety as a risk factor for adverse outcomes, but also raise questions about the potential role of HRV as an intermediary between depression and post-MI prognosis.

Cloud Droplet Size and Liquid Water Path Retrievals From Zenith Radiance Measurements: Examples From the Atmospheric Radiation Measurement Program and the Aerosol Robotic Network

NASA Technical Reports Server (NTRS)

Chiu, J. C.; Marshak, A.; Huang, C.-H.; Varnai, T.; Hogan, R. J.; Giles, D. M.; Holben, B. N.; Knyazikhin, Y.; O'Connor, E. J.; Wiscombe, W. J.

2012-01-01

The ground-based Atmospheric Radiation Measurement Program (ARM) and NASA Aerosol Robotic Network (AERONET) routinely monitor clouds using zenith radiances at visible and near-infrared wavelengths. Using the transmittance calculated from such measurements, we have developed a new retrieval method for cloud effective droplet size and conducted extensive tests for non-precipitating liquid water clouds. The underlying principle is to combine a water-absorbing wavelength (i.e. 1640 nm) with a nonwater-absorbing wavelength for acquiring information on cloud droplet size and optical depth. For simulated stratocumulus clouds with liquid water path less than 300 g/sq m and horizontal resolution of 201m, the retrieval method underestimates the mean effective radius by 0.8 m, with a root-mean-squared error of 1.7 m and a relative deviation of 13 %. For actual observations with a liquid water path less than 450 gm.2 at the ARM Oklahoma site during 2007-2008, our 1.5 min-averaged retrievals are generally larger by around 1 m than those from combined ground-based cloud radar and microwave radiometer at a 5min temporal resolution. We also compared our retrievals to those from combined shortwave flux and microwave observations for relatively homogeneous clouds, showing that the bias between these two retrieval sets is negligible, but the error of 2.6 m and the relative deviation of 22% are larger than those found in our simulation case. Finally, the transmittance-based cloud effective droplet radii agree to better than 11% with satellite observations and have a negative bias of 1 m. Overall, the retrieval method provides reasonable cloud effective radius estimates, which can enhance the cloud products of both ARM and AERONET.

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.

Improvement of near infrared spectroscopic (NIRS) analysis of caffeine in roasted Arabica coffee by variable selection method of stability competitive adaptive reweighted sampling (SCARS).

PubMed

Zhang, Xuan; Li, Wei; Yin, Bin; Chen, Weizhong; Kelly, Declan P; Wang, Xiaoxin; Zheng, Kaiyi; Du, Yiping

2013-10-01

Coffee is the most heavily consumed beverage in the world after water, for which quality is a key consideration in commercial trade. Therefore, caffeine content which has a significant effect on the final quality of the coffee products requires to be determined fast and reliably by new analytical techniques. The main purpose of this work was to establish a powerful and practical analytical method based on near infrared spectroscopy (NIRS) and chemometrics for quantitative determination of caffeine content in roasted Arabica coffees. Ground coffee samples within a wide range of roasted levels were analyzed by NIR, meanwhile, in which the caffeine contents were quantitative determined by the most commonly used HPLC-UV method as the reference values. Then calibration models based on chemometric analyses of the NIR spectral data and reference concentrations of coffee samples were developed. Partial least squares (PLS) regression was used to construct the models. Furthermore, diverse spectra pretreatment and variable selection techniques were applied in order to obtain robust and reliable reduced-spectrum regression models. Comparing the respective quality of the different models constructed, the application of second derivative pretreatment and stability competitive adaptive reweighted sampling (SCARS) variable selection provided a notably improved regression model, with root mean square error of cross validation (RMSECV) of 0.375 mg/g and correlation coefficient (R) of 0.918 at PLS factor of 7. An independent test set was used to assess the model, with the root mean square error of prediction (RMSEP) of 0.378 mg/g, mean relative error of 1.976% and mean relative standard deviation (RSD) of 1.707%. Thus, the results provided by the high-quality calibration model revealed the feasibility of NIR spectroscopy for at-line application to predict the caffeine content of unknown roasted coffee samples, thanks to the short analysis time of a few seconds and non-destructive advantages of NIRS. Copyright © 2013 Elsevier B.V. All rights reserved.

Improvement of near infrared spectroscopic (NIRS) analysis of caffeine in roasted Arabica coffee by variable selection method of stability competitive adaptive reweighted sampling (SCARS)

NASA Astrophysics Data System (ADS)

Zhang, Xuan; Li, Wei; Yin, Bin; Chen, Weizhong; Kelly, Declan P.; Wang, Xiaoxin; Zheng, Kaiyi; Du, Yiping

2013-10-01

Coffee is the most heavily consumed beverage in the world after water, for which quality is a key consideration in commercial trade. Therefore, caffeine content which has a significant effect on the final quality of the coffee products requires to be determined fast and reliably by new analytical techniques. The main purpose of this work was to establish a powerful and practical analytical method based on near infrared spectroscopy (NIRS) and chemometrics for quantitative determination of caffeine content in roasted Arabica coffees. Ground coffee samples within a wide range of roasted levels were analyzed by NIR, meanwhile, in which the caffeine contents were quantitative determined by the most commonly used HPLC-UV method as the reference values. Then calibration models based on chemometric analyses of the NIR spectral data and reference concentrations of coffee samples were developed. Partial least squares (PLS) regression was used to construct the models. Furthermore, diverse spectra pretreatment and variable selection techniques were applied in order to obtain robust and reliable reduced-spectrum regression models. Comparing the respective quality of the different models constructed, the application of second derivative pretreatment and stability competitive adaptive reweighted sampling (SCARS) variable selection provided a notably improved regression model, with root mean square error of cross validation (RMSECV) of 0.375 mg/g and correlation coefficient (R) of 0.918 at PLS factor of 7. An independent test set was used to assess the model, with the root mean square error of prediction (RMSEP) of 0.378 mg/g, mean relative error of 1.976% and mean relative standard deviation (RSD) of 1.707%. Thus, the results provided by the high-quality calibration model revealed the feasibility of NIR spectroscopy for at-line application to predict the caffeine content of unknown roasted coffee samples, thanks to the short analysis time of a few seconds and non-destructive advantages of NIRS.

Percentage depth dose calculation accuracy of model based algorithms in high energy photon small fields through heterogeneous media and comparison with plastic scintillator dosimetry.

PubMed

Alagar, Ananda Giri Babu; Mani, Ganesh Kadirampatti; Karunakaran, Kaviarasu

2016-01-08

Small fields smaller than 4 × 4 cm2 are used in stereotactic and conformal treatments where heterogeneity is normally present. Since dose calculation accuracy in both small fields and heterogeneity often involves more discrepancy, algorithms used by treatment planning systems (TPS) should be evaluated for achieving better treatment results. This report aims at evaluating accuracy of four model-based algorithms, X-ray Voxel Monte Carlo (XVMC) from Monaco, Superposition (SP) from CMS-Xio, AcurosXB (AXB) and analytical anisotropic algorithm (AAA) from Eclipse are tested against the measurement. Measurements are done using Exradin W1 plastic scintillator in Solid Water phantom with heterogeneities like air, lung, bone, and aluminum, irradiated with 6 and 15 MV photons of square field size ranging from 1 to 4 cm2. Each heterogeneity is introduced individually at two different depths from depth-of-dose maximum (Dmax), one setup being nearer and another farther from the Dmax. The central axis percentage depth-dose (CADD) curve for each setup is measured separately and compared with the TPS algorithm calculated for the same setup. The percentage normalized root mean squared deviation (%NRMSD) is calculated, which represents the whole CADD curve's deviation against the measured. It is found that for air and lung heterogeneity, for both 6 and 15 MV, all algorithms show maximum deviation for field size 1 × 1 cm2 and gradually reduce when field size increases, except for AAA. For aluminum and bone, all algorithms' deviations are less for 15 MV irrespective of setup. In all heterogeneity setups, 1 × 1 cm2 field showed maximum deviation, except in 6MV bone setup. All algorithms in the study, irrespective of energy and field size, when any heterogeneity is nearer to Dmax, the dose deviation is higher compared to the same heterogeneity far from the Dmax. Also, all algorithms show maximum deviation in lower-density materials compared to high-density materials.

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.

Arm-eye coordination test to objectively quantify motor performance and muscles activation in persons after stroke undergoing robot-aided rehabilitation training: a pilot study.

PubMed

Song, Rong; Tong, Kai-Yu; Hu, Xiaoling; Li, Le; Sun, Rui

2013-09-01

This study designed an arm-eye coordination test to investigate the effectiveness of the robot-aided rehabilitation for persons after stroke. Six chronic poststroke subjects were recruited to attend a 20-session robot-aided rehabilitation training of elbow joint. Before and after the training program, subjects were asked to perform voluntary movements of elbow flection and extension by following sinusoidal trajectories at different velocities with visual feedback on their joint positions. The elbow angle and the electromyographic signal of biceps and triceps as well as clinical scores were evaluated together with the parameters. Performance was objectively quantified by root mean square error (RMSE), root mean square jerk (RMSJ), range of motion (ROM), and co-contraction index (CI). After 20 sessions, RMSE and ROM improved significantly in both the affected and the unaffected side based on two-way ANOVA (P < 0.05). There was significant lower RMSJ in the affected side at higher velocities (P < 0.05). There was significant negative correlation between average RMSE with different tracking velocities and Fugl-Meyer shoulder-elbow score (P < 0.05). There was also significant negative correlation between average RMSE and average ROM (P < 0.05), and moderate nonsignificant negative correlation with RMSJ, and CI. The characterization of velocity-dependent deficiencies, monitoring of training-induced improvement, and the correlation between quantitative parameters and clinical scales could enable the exploration of effects of different types of treatment and design progress-based training method to accelerate the processes of recovery.

A comparative study of optimum and suboptimum direct-detection laser ranging receivers

NASA Technical Reports Server (NTRS)

Abshire, J. B.

1978-01-01

A summary of previously proposed receiver strategies for direct-detection laser ranging receivers is presented. Computer simulations are used to compare performance of candidate implementation strategies in the 1- to 100-photoelectron region. Under the condition of no background radiation, the maximum-likelihood and minimum mean-square error estimators were found to give the same performance for both bell-shaped and rectangular optical-pulse shapes. For signal energies greater than 100 photoelectrons, the root-mean-square range error is shown to decrease as Q to the -1/2 power for bell-shaped pulses and Q to the -1 power for rectangular pulses, where Q represents the average pulse energy. Of several receiver implementations presented, the matched-filter peak detector was found to be preferable. A similar configuration, using a constant-fraction discriminator, exhibited a signal-level dependent time bias.

Cardiac autonomic regulation is disturbed in children with euthyroid Hashimoto thyroiditis.

PubMed

Kilic, Ayhan; Gulgun, Mustafa; Tascilar, Mehmet Emre; Sari, Erkan; Yokusoglu, Mehmet

2012-03-01

Hashimoto thyroiditis (chronic autoimmune thyroiditis) is the most common form of thyroiditis in childhood. Previous studies have found autonomic dysfunction of varying magnitude in patients with autoimmune diseases, which is considered a cardiovascular risk factor. We aimed to evaluate the heart rate variability (HRV), a measure of cardiac autonomic modulation, in children with euthyroid Hashimoto thyroiditis (eHT). The study included 32 patients with eHT (27 girls and 5 boys; mean age 11 ± 4.1 years, range 8-16; body mass index 0.47 ± 0.69 kg/m(2)), as judged by normal or minimally elevated serum TSH levels (normal range: 0.34-5.6 mIU/l) and normal levels of free thyroid hormones (FT4 and FT3) and 38 euthyroid age-matched controls. Patients with eHT and control subjects underwent physical examination and 24-hour ambulatory ECG monitoring. Time-domain parameters of HRV were evaluated for cardiac autonomic functions. Children with eHT displayed significantly lower values of time-domain parameters of SDANN (standard deviation of the averages of NN intervals), RMSSD (square root of the mean of the sum of the squares of differences between adjacent NN intervals), NN50 counts (number of pairs of adjacent NN intervals differing by more than 50 ms) and PNN50 (NN50 count divided by the total number of all NN intervals) for each 5-min interval, compared to healthy controls (p < 0.05 for each), indicating the decreased beat-to-beat variation of heart rate. In conclusion, eHT is associated with disturbed autonomic regulation of heart rate. Hence, the children with eHT are at higher risk for developing cardiovascular diseases.

A new approach to measure visual field progression in glaucoma patients using variational bayes linear regression.

PubMed

Murata, Hiroshi; Araie, Makoto; Asaoka, Ryo

2014-11-20

We generated a variational Bayes model to predict visual field (VF) progression in glaucoma patients. This retrospective study included VF series from 911 eyes of 547 glaucoma patients as test data, and VF series from 5049 eyes of 2858 glaucoma patients as training data. Using training data, variational Bayes linear regression (VBLR) was created to predict VF progression. The performance of VBLR was compared against ordinary least-squares linear regression (OLSLR) by predicting VFs in the test dataset. The total deviation (TD) values of test patients' 11th VFs were predicted using TD values from their second to 10th VFs (VF2-10), the root mean squared error (RMSE) associated with each approach then was calculated. Similarly, mean TD (mTD) of test patients' 11th VFs was predicted using VBLR and OLSLR, and the absolute prediction errors compared. The RMSE resulting from VBLR averaged 3.9 ± 2.1 (SD) and 4.9 ± 2.6 dB for prediction based on the second to 10th VFs (VF2-10) and the second to fourth VFs (VF2-4), respectively. The RMSE resulting from OLSLR was 4.1 ± 2.0 (VF2-10) and 19.9 ± 12.0 (VF2-4) dB. The absolute prediction error (SD) for mTD using VBLR was 1.2 ± 1.3 (VF2-10) and 1.9 ± 2.0 (VF2-4) dB, while the prediction error resulting from OLSLR was 1.2 ± 1.3 (VF2-10) and 6.2 ± 6.6 (VF2-4) dB. The VBLR more accurately predicts future VF progression in glaucoma patients compared to conventional OLSLR, especially in short VF series. © ARVO.

Scaling and entropy in p-median facility location along a line

NASA Astrophysics Data System (ADS)

Gastner, Michael T.

2011-09-01

The p-median problem is a common model for optimal facility location. The task is to place p facilities (e.g., warehouses or schools) in a heterogeneously populated space such that the average distance from a person's home to the nearest facility is minimized. Here we study the special case where the population lives along a line (e.g., a road or a river). If facilities are optimally placed, the length of the line segment served by a facility is inversely proportional to the square root of the population density. This scaling law is derived analytically and confirmed for concrete numerical examples of three US interstate highways and the Mississippi River. If facility locations are permitted to deviate from the optimum, the number of possible solutions increases dramatically. Using Monte Carlo simulations, we compute how scaling is affected by an increase in the average distance to the nearest facility. We find that the scaling exponents change and are most sensitive near the optimum facility distribution.

Movable-Bed Laboratory Experiments Comparing Radiation Stress and Energy Flux Factor as Predictors of Longshore Transport Rate.

DTIC Science & Technology

1981-04-01

acceleration of gravity H wave height H average wave height Hrms root-mean-square wave height Hs significant wave height IX longshore transport rate in...wave height, H, measured during the tests (and discussed later in Section IV) is equal to Hrms . By rewriting equation (4), S ( Cg cos.) C (7) xy 8 Cg...only for conditions where H equals Hrms * 2. Energy Flux. In literature, the longshore transport rate has been empirically related most frequently to a

Spiral tracing on a touchscreen is influenced by age, hand, implement, and friction.

PubMed

Heintz, Brittany D; Keenan, Kevin G

2018-01-01

Dexterity impairments are well documented in older adults, though it is unclear how these influence touchscreen manipulation. This study examined age-related differences while tracing on high- and low-friction touchscreens using the finger or stylus. 26 young and 24 older adults completed an Archimedes spiral tracing task on a touchscreen mounted on a force sensor. Root mean square error was calculated to quantify performance. Root mean square error increased by 29.9% for older vs. young adults using the fingertip, but was similar to young adults when using the stylus. Although other variables (e.g., touchscreen usage, sensation, and reaction time) differed between age groups, these variables were not related to increased error in older adults while using their fingertip. Root mean square error also increased on the low-friction surface for all subjects. These findings suggest that utilizing a stylus and increasing surface friction may improve touchscreen use in older adults.

Influence of Axial Load on Electromechanical Impedance (EMI) of Embedded Piezoceramic Transducers in Steel Fiber Concrete.

PubMed

Wang, Zhijie; Chen, Dongdong; Zheng, Liqiong; Huo, Linsheng; Song, Gangbing

2018-06-01

With the advantages of high tensile, bending, and shear strength, steel fiber concrete structures have been widely used in civil engineering. The health monitoring of concrete structures, including steel fiber concrete structures, receives increasing attention, and the Electromechanical Impedance (EMI)-based method is commonly used. Structures are often subject to changing axial load and ignoring the effect of axial forces may introduce error to Structural Health Monitoring (SHM), including the EMI-based method. However, many of the concrete structure monitoring algorithms do not consider the effects of axial loading. To investigate the influence of axial load on the EMI of a steel fiber concrete structure, concrete specimens with different steel fiber content (0, 30, 60, 90, 120) (kg/m³) were casted and the Lead Zirconate Titanate (PZT)-based Smart Aggregate (SA) was used as the EMI sensor. During tests, the step-by-step loading procedure was applied on different steel fiber content specimens, and the electromechanical impedance values were measured. The Normalized root-mean-square deviation Index (NI) was developed to analyze the EMI information and evaluate the test results. The results show that the normalized root-mean-square deviation index increases with the increase of the axial load, which clearly demonstrates the influence of axial load on the EMI values for steel fiber concrete and this influence should be considered during a monitoring or damage detection procedure if the axial load changes. In addition, testing results clearly reveal that the steel fiber content, often at low mass and volume percentage, has no obvious influence on the PZT's EMI values. Furthermore, experiments to test the repeatability of the proposed method were conducted. The repeating test results show that the EMI-based indices are repeatable and there is a great linearity between the NI and the applied loading.

Analysis of Twenty-Two Performance Properties of Diesel, Gasoline, and Jet Fuels Using a Field-Portable Near-Infrared (NIR) Analyzer.

PubMed

Brouillette, Carl; Smith, Wayne; Shende, Chetan; Gladding, Zack; Farquharson, Stuart; Morris, Robert E; Cramer, Jeffrey A; Schmitigal, Joel

2016-05-01

The change in custody of fuel shipments at depots, pipelines, and ports could benefit from an analyzer that could rapidly verify that properties are within specifications. To meet this need, the design requirements for a fuel analyzer based on near-infrared (NIR) spectroscopy, such as spectral region and resolution, were examined. It was found that the 1000 to 1600 nm region, containing the second CH overtone and combination vibrational modes of hydrocarbons, provided the best near-infrared to fuel property correlations when path length was taken into account, whereas 4 cm(-1) resolution provided only a modest improvement compared to 16 cm(-1) resolution when four or more latent variables were used. Based on these results, a field-portable near-infrared fuel analyzer was built that employed an incandescent light source, sample compartment optics to hold 2 mL glass sample vials with ∼1 cm path length, a transmission grating, and a 256 channel InGaAs detector that measured the above stated wavelength range with 5-6 nm (∼32 cm(-1)) resolution. The analyzer produced high signal-to-noise ratio (SNR) spectra of samples in 5 s. Twenty-two property correlation models were developed for diesel, gasoline, and jet fuels with root mean squared error of correlation - cross-validated values that compared favorably to corresponding ASTM reproducibility values. The standard deviations of predicted properties for repeat measurements at 4, 24, and 38℃ were often better than ASTM documented repeatability values. The analyzer and diesel property models were tested by measuring seven diesel samples at a local ASTM certification laboratory. The standard deviations between the analyzer determined values and the ASTM measured values for these samples were generally better than the model root mean squared error of correlation-cross-validated values for each property. © The Author(s) 2016.

Three-dimensional (3D) structure prediction of the American and African oil-palms β-ketoacyl-[ACP] synthase-II protein by comparative modelling

PubMed Central

Wang, Edina; Chinni, Suresh; Bhore, Subhash Janardhan

2014-01-01

Background: The fatty-acid profile of the vegetable oils determines its properties and nutritional value. Palm-oil obtained from the African oil-palm [Elaeis guineensis Jacq. (Tenera)] contains 44% palmitic acid (C16:0), but, palm-oil obtained from the American oilpalm [Elaeis oleifera] contains only 25% C16:0. In part, the b-ketoacyl-[ACP] synthase II (KASII) [EC: 2.3.1.179] protein is responsible for the high level of C16:0 in palm-oil derived from the African oil-palm. To understand more about E. guineensis KASII (EgKASII) and E. oleifera KASII (EoKASII) proteins, it is essential to know its structures. Hence, this study was undertaken. Objective: The objective of this study was to predict three-dimensional (3D) structure of EgKASII and EoKASII proteins using molecular modelling tools. Materials and Methods: The amino-acid sequences for KASII proteins were retrieved from the protein database of National Center for Biotechnology Information (NCBI), USA. The 3D structures were predicted for both proteins using homology modelling and ab-initio technique approach of protein structure prediction. The molecular dynamics (MD) simulation was performed to refine the predicted structures. The predicted structure models were evaluated and root mean square deviation (RMSD) and root mean square fluctuation (RMSF) values were calculated. Results: The homology modelling showed that EgKASII and EoKASII proteins are 78% and 74% similar with Streptococcus pneumonia KASII and Brucella melitensis KASII, respectively. The EgKASII and EoKASII structures predicted by using ab-initio technique approach shows 6% and 9% deviation to its structures predicted by homology modelling, respectively. The structure refinement and validation confirmed that the predicted structures are accurate. Conclusion: The 3D structures for EgKASII and EoKASII proteins were predicted. However, further research is essential to understand the interaction of EgKASII and EoKASII proteins with its substrates. PMID:24748752

Molecular Modeling and Structural Stability of Wild-Type and Mutant CYP51 from Leishmania major: In Vitro and In Silico Analysis of a Laboratory Strain.

PubMed

Keighobadi, Masoud; Emami, Saeed; Lagzian, Milad; Fakhar, Mahdi; Rafiei, Alireza; Valadan, Reza

2018-03-19

Cutaneous leishmaniasis is a neglected tropical disease and a major public health in the most countries. Leishmania major is the most common cause of cutaneous leishmaniasis. In the Leishmania parasites, sterol 14α-demethylase (CYP51), which is involved in the biosynthesis of sterols, has been identified as an attractive target for development of new therapeutic agents. In this study, the sequence and structure of CYP51 in a laboratory strain (MRHO/IR/75/ER) of L. major were determined and compared to the wild-type strain. The results showed 19 mutations including seven non-synonymous and 12 synonymous ones in the CYP51 sequence of strain MRHO/IR/75/ER. Importantly, an arginine to lysine substitution at position of 474 resulted in destabilization of CYP51 (ΔΔG = 1.17 kcal/mol) in the laboratory strain; however, when the overall effects of all substitutions were evaluated by 100 ns molecular dynamics simulation, the final structure did not show any significant changes ( p -value < 0.05) in stability parameter of the strain MRHO/IR/75/ER compared to the wild-type protein. The energy level for the CYP51 of wild-type and MRHO/IR/75/ER strain were -40,027.1 and -39,706.48 Kcal/mol respectively. The overall Root-mean-square deviation (RMSD) deviation between two proteins was less than 1 Å throughout the simulation and Root-mean-square fluctuation (RMSF) plot also showed no substantial differences between amino acids fluctuation of the both protein. The results also showed that, these mutations were located on the protein periphery that neither interferes with protein folding nor with substrate/inhibitor binding. Therefore, L. major strain MRHO/IR/75/ER is suggested as a suitable laboratory model for studying biological role of CYP51 and inhibitory effects of sterol 14α-demethylase inhibitors.

Three-dimensional (3D) structure prediction of the American and African oil-palms β-ketoacyl-[ACP] synthase-II protein by comparative modelling.

PubMed

Wang, Edina; Chinni, Suresh; Bhore, Subhash Janardhan

2014-01-01

The fatty-acid profile of the vegetable oils determines its properties and nutritional value. Palm-oil obtained from the African oil-palm [Elaeis guineensis Jacq. (Tenera)] contains 44% palmitic acid (C16:0), but, palm-oil obtained from the American oilpalm [Elaeis oleifera] contains only 25% C16:0. In part, the b-ketoacyl-[ACP] synthase II (KASII) [EC: 2.3.1.179] protein is responsible for the high level of C16:0 in palm-oil derived from the African oil-palm. To understand more about E. guineensis KASII (EgKASII) and E. oleifera KASII (EoKASII) proteins, it is essential to know its structures. Hence, this study was undertaken. The objective of this study was to predict three-dimensional (3D) structure of EgKASII and EoKASII proteins using molecular modelling tools. The amino-acid sequences for KASII proteins were retrieved from the protein database of National Center for Biotechnology Information (NCBI), USA. The 3D structures were predicted for both proteins using homology modelling and ab-initio technique approach of protein structure prediction. The molecular dynamics (MD) simulation was performed to refine the predicted structures. The predicted structure models were evaluated and root mean square deviation (RMSD) and root mean square fluctuation (RMSF) values were calculated. The homology modelling showed that EgKASII and EoKASII proteins are 78% and 74% similar with Streptococcus pneumonia KASII and Brucella melitensis KASII, respectively. The EgKASII and EoKASII structures predicted by using ab-initio technique approach shows 6% and 9% deviation to its structures predicted by homology modelling, respectively. The structure refinement and validation confirmed that the predicted structures are accurate. The 3D structures for EgKASII and EoKASII proteins were predicted. However, further research is essential to understand the interaction of EgKASII and EoKASII proteins with its substrates.

[Exploration on Electroencephalogram Mechanism Differences of Negative Emotions Induced by Disgusted and Sad Situation Images].

PubMed

Wang, Xin; Jin, Jingna; Li, Song; Liu, Zhipeng; Yin, Tao

2015-12-01

Evolutionary psychology holds such an opinion that negative situation may threaten survival, trigger avoidance motive and have poor effects on the human-body function and the psychological quality. Both disgusted and sad situations can induce negative emotions. However, differences between the two situations on attention capture and emotion cognition during the emotion induction are still not well known. Typical disgusted and sad situation images were used in the present study to induce two negative emotions, and 15 young students (7 males and 8 females, aged 27 ± 3) were recruited in the experiments. Electroencephalogram of 32 leads was recorded when the subjects were viewing situation images, and event-related potentials (ERP) of all leads were obtained for future analysis. Paired sample t tests were carried out on two ERP signals separately induced by disgusted and sad situation images to get time quantum with significant statistical differences between the two ERP signals. Root-mean-square deviations of two ERP signals during each time quantum were calculated and the brain topographic map based on root-mean-square deviations was drawn to display differences of two ERP signals in spatial. Results showed that differences of ERP signals induced by disgusted and sad situation images were mainly manifested in T1 (120-450 ms) early and T2 (800-1,000 ms) later. During the period of T1, the occipital lobe reflecting attention capture was activated by both disgusted and sad situation images, but the prefrontal cortex reflecting emotion sense was activated only by disgusted situation images. During the period of T2, the prefrontal cortex was activated by both disgusted and sad situation images. However, the parietal lobe was activated only by disgusted situation images, which showed stronger emotional perception. The research results would have enlightenment to deepen understanding of negative emotion and to exploredeep cognitive neuroscience mechanisms of negative emotion induction.

Robust scoring functions for protein-ligand interactions with quantum chemical charge models.

PubMed

Wang, Jui-Chih; Lin, Jung-Hsin; Chen, Chung-Ming; Perryman, Alex L; Olson, Arthur J

2011-10-24

Ordinary least-squares (OLS) regression has been used widely for constructing the scoring functions for protein-ligand interactions. However, OLS is very sensitive to the existence of outliers, and models constructed using it are easily affected by the outliers or even the choice of the data set. On the other hand, determination of atomic charges is regarded as of central importance, because the electrostatic interaction is known to be a key contributing factor for biomolecular association. In the development of the AutoDock4 scoring function, only OLS was conducted, and the simple Gasteiger method was adopted. It is therefore of considerable interest to see whether more rigorous charge models could improve the statistical performance of the AutoDock4 scoring function. In this study, we have employed two well-established quantum chemical approaches, namely the restrained electrostatic potential (RESP) and the Austin-model 1-bond charge correction (AM1-BCC) methods, to obtain atomic partial charges, and we have compared how different charge models affect the performance of AutoDock4 scoring functions. In combination with robust regression analysis and outlier exclusion, our new protein-ligand free energy regression model with AM1-BCC charges for ligands and Amber99SB charges for proteins achieve lowest root-mean-squared error of 1.637 kcal/mol for the training set of 147 complexes and 2.176 kcal/mol for the external test set of 1427 complexes. The assessment for binding pose prediction with the 100 external decoy sets indicates very high success rate of 87% with the criteria of predicted root-mean-squared deviation of less than 2 Å. The success rates and statistical performance of our robust scoring functions are only weakly class-dependent (hydrophobic, hydrophilic, or mixed).

Quantitative analysis of essential oils in perfume using multivariate curve resolution combined with comprehensive two-dimensional gas chromatography.

PubMed

de Godoy, Luiz Antonio Fonseca; Hantao, Leandro Wang; Pedroso, Marcio Pozzobon; Poppi, Ronei Jesus; Augusto, Fabio

2011-08-05

The use of multivariate curve resolution (MCR) to build multivariate quantitative models using data obtained from comprehensive two-dimensional gas chromatography with flame ionization detection (GC×GC-FID) is presented and evaluated. The MCR algorithm presents some important features, such as second order advantage and the recovery of the instrumental response for each pure component after optimization by an alternating least squares (ALS) procedure. A model to quantify the essential oil of rosemary was built using a calibration set containing only known concentrations of the essential oil and cereal alcohol as solvent. A calibration curve correlating the concentration of the essential oil of rosemary and the instrumental response obtained from the MCR-ALS algorithm was obtained, and this calibration model was applied to predict the concentration of the oil in complex samples (mixtures of the essential oil, pineapple essence and commercial perfume). The values of the root mean square error of prediction (RMSEP) and of the root mean square error of the percentage deviation (RMSPD) obtained were 0.4% (v/v) and 7.2%, respectively. Additionally, a second model was built and used to evaluate the accuracy of the method. A model to quantify the essential oil of lemon grass was built and its concentration was predicted in the validation set and real perfume samples. The RMSEP and RMSPD obtained were 0.5% (v/v) and 6.9%, respectively, and the concentration of the essential oil of lemon grass in perfume agreed to the value informed by the manufacturer. The result indicates that the MCR algorithm is adequate to resolve the target chromatogram from the complex sample and to build multivariate models of GC×GC-FID data. Copyright © 2011 Elsevier B.V. All rights reserved.

Desert soil clay content estimation using reflectance spectroscopy preprocessed by fractional derivative

PubMed Central

Tiyip, Tashpolat; Ding, Jianli; Zhang, Dong; Liu, Wei; Wang, Fei; Tashpolat, Nigara

2017-01-01

Effective pretreatment of spectral reflectance is vital to model accuracy in soil parameter estimation. However, the classic integer derivative has some disadvantages, including spectral information loss and the introduction of high-frequency noise. In this paper, the fractional order derivative algorithm was applied to the pretreatment and partial least squares regression (PLSR) was used to assess the clay content of desert soils. Overall, 103 soil samples were collected from the Ebinur Lake basin in the Xinjiang Uighur Autonomous Region of China, and used as data sets for calibration and validation. Following laboratory measurements of spectral reflectance and clay content, the raw spectral reflectance and absorbance data were treated using the fractional derivative order from the 0.0 to the 2.0 order (order interval: 0.2). The ratio of performance to deviation (RPD), determinant coefficients of calibration (Rc2), root mean square errors of calibration (RMSEC), determinant coefficients of prediction (Rp2), and root mean square errors of prediction (RMSEP) were applied to assess the performance of predicting models. The results showed that models built on the fractional derivative order performed better than when using the classic integer derivative. Comparison of the predictive effects of 22 models for estimating clay content, calibrated by PLSR, showed that those models based on the fractional derivative 1.8 order of spectral reflectance (Rc2 = 0.907, RMSEC = 0.425%, Rp2 = 0.916, RMSEP = 0.364%, and RPD = 2.484 ≥ 2.000) and absorbance (Rc2 = 0.888, RMSEC = 0.446%, Rp2 = 0.918, RMSEP = 0.383% and RPD = 2.511 ≥ 2.000) were most effective. Furthermore, they performed well in quantitative estimations of the clay content of soils in the study area. PMID:28934274

Evaluation of the coracoid and coracoacromial arch geometry on Thiel-embalmed cadavers using the three-dimensional MicroScribe digitizer.

PubMed

Alobaidy, Mohammad A; Soames, Roger W

2016-01-01

Understanding the geometry of the coracoid and coracoacromial arch will improve surgical intervention in shoulder surgery. Thirty pairs of scapulae from 20 female and 10 male deceased donors, average age of 82 years (range, 62-101 years), were scanned and measurements taken using the 3-dimensional (3D) MicroScribe digitizer (Immersion Corp, San Jose CA, USA) and Rhino software (McNeel North America, Seattle, WA, USA). The following mean angles were determined: coracoid slope, 44° ± 11°; coracoid deviation, 35° ± 6°; coracoid root to glenoid, 115° ± 14°; coracoid head to glenoid, 110° ± 11°; scapular spine angle, 35° ± 6°; and coracoacromial angle, 63° ± 9°. The following mean distances were also determined: coracoid height, 10 ± 3 mm; coracoacromial distance, 42 ± 7 mm; coracoacromial arch height, 20 ± 5 mm; and coracoid (anterior, 29 ± 6 mm; middle, 20 ± 4 mm; posterior tip, 18 ± 6 mm) to the glenoid fossa. The coracoid root-to-glenoid angle was significantly correlated with the coracoacromial angle. In addition, coracoid slope was significantly correlated with coracoid root-to-glenoid angle and also with coracoid deviation. Left shoulders had a significantly higher coracoid-to-glenoid angle (P < .029) than right shoulders. Women had a significantly higher coracoid root-to-glenoid angle than men (P < .042), and men had a significantly higher coracoid deviation (P < .011), anterior (P < .006) and posterior coracoid-to-glenoid distances (P < .03), and coracoacromial arch height (P < .07) than women. This is the first time that the 3D MicroScribe digitizer has been used to evaluate the geometry of the coracoacromial arch and coracoid process. Copyright © 2016 Journal of Shoulder and Elbow Surgery Board of Trustees. Published by Elsevier Inc. 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

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

Devising a method towards development of early warning tool for detection of malaria outbreak.

PubMed

Verma, Preeti; Sarkar, Soma; Singh, Poonam; Dhiman, Ramesh C

2017-11-01

Uncertainty often arises in differentiating seasonal variation from outbreaks of malaria. The present study was aimed to generalize the theoretical structure of sine curve for detecting an outbreak so that a tool for early warning of malaria may be developed. A 'case/mean-ratio scale' system was devised for labelling the outbreak in respect of two diverse districts of Assam and Rajasthan. A curve-based method of analysis was developed for determining outbreak and using the properties of sine curve. It could be used as an early warning tool for Plasmodium falciparum malaria outbreaks. In the present method of analysis, the critical C max (peak value of sine curve) value of seasonally adjusted curve for P. falciparum malaria outbreak was 2.3 for Karbi Anglong and 2.2 for Jaisalmer districts. On case/mean-ratio scale, the C max value of malaria curve between C max and 3.5, the outbreak could be labelled as minor while >3.5 may be labelled as major. In epidemic years, with mean of case/mean ratio of ≥1.00 and root mean square (RMS) ≥1.504 of case/mean ratio, outbreaks can be predicted 1-2 months in advance. The present study showed that in P. falciparum cases in Karbi Anglong (Assam) and Jaisalmer (Rajasthan) districts, the rise in C max value of curve was always followed by rise in average/RMS or both and hence could be used as an early warning tool. The present method provides better detection of outbreaks than the conventional method of mean plus two standard deviation (mean+2 SD). The identified tools are simple and may be adopted for preparedness of malaria outbreaks.

Mass predictions of atomic nuclei in the infinite nuclear matter model

NASA Astrophysics Data System (ADS)

Nayak, R. C.; Satpathy, L.

2012-07-01

We present here the mass excesses, binding energies, one- and two-neutron, one- and two-proton and α-particle separation energies of 6727 nuclei in the ranges 4≤Z≤120 and 8≤A≤303 calculated in the infinite nuclear matter model. Compared to our predictions of 1999 mass table, the present ones are obtained using larger data base of 2003 mass table of Wapstra and Audi and resorting to higher accuracy in the solutions of the η-differential equations of the INM model. The local energy η's supposed to carry signature of the characteristic properties of nuclei are found to possess the predictive capability. In fact η-systematics reveal new magic numbers in the drip-line regions giving rise to new islands of stability supported by relativistic mean field theoretic calculations. This is a manifestation of a new phenomenon where shell-effect overcomes the instability due to repulsive components of the nucleon-nucleon force broadening the stability peninsula. The two-neutron separation energy-systematics derived from the present mass predictions reveal a general new feature for the existence of islands of inversion in the exotic neutron-rich regions of nuclear landscape, apart from supporting the presently known islands around 31Na and 62Ti. The five global parameters representing the properties of infinite nuclear matter, the surface, the Coulomb and the pairing terms are retained as per our 1999 mass table. The root-mean-square deviation of the present mass-fit to 2198 known masses is 342 keV, while the mean deviation is 1.3 keV, reminiscent of no left-over systematic effects. This is a substantive improvement over our 1999 mass table having rms deviation of 401 keV and mean deviation of 9 keV for 1884 data nuclei.

Extracting the regional common-mode component of GPS station position time series from dense continuous network

NASA Astrophysics Data System (ADS)

Tian, Yunfeng; Shen, Zheng-Kang

2016-02-01

We develop a spatial filtering method to remove random noise and extract the spatially correlated transients (i.e., common-mode component (CMC)) that deviate from zero mean over the span of detrended position time series of a continuous Global Positioning System (CGPS) network. The technique utilizes a weighting scheme that incorporates two factors—distances between neighboring sites and their correlations of long-term residual position time series. We use a grid search algorithm to find the optimal thresholds for deriving the CMC that minimizes the root-mean-square (RMS) of the filtered residual position time series. Comparing to the principal component analysis technique, our method achieves better (>13% on average) reduction of residual position scatters for the CGPS stations in western North America, eliminating regional transients of all spatial scales. It also has advantages in data manipulation: less intervention and applicable to a dense network of any spatial extent. Our method can also be used to detect CMC irrespective of its origins (i.e., tectonic or nontectonic), if such signals are of particular interests for further study. By varying the filtering distance range, the long-range CMC related to atmospheric disturbance can be filtered out, uncovering CMC associated with transient tectonic deformation. A correlation-based clustering algorithm is adopted to identify stations cluster that share the common regional transient characteristics.

Sweat loss prediction using a multi-model approach

NASA Astrophysics Data System (ADS)

Xu, Xiaojiang; Santee, William R.

2011-07-01

A new multi-model approach (MMA) for sweat loss prediction is proposed to improve prediction accuracy. MMA was computed as the average of sweat loss predicted by two existing thermoregulation models: i.e., the rational model SCENARIO and the empirical model Heat Strain Decision Aid (HSDA). Three independent physiological datasets, a total of 44 trials, were used to compare predictions by MMA, SCENARIO, and HSDA. The observed sweat losses were collected under different combinations of uniform ensembles, environmental conditions (15-40°C, RH 25-75%), and exercise intensities (250-600 W). Root mean square deviation (RMSD), residual plots, and paired t tests were used to compare predictions with observations. Overall, MMA reduced RMSD by 30-39% in comparison with either SCENARIO or HSDA, and increased the prediction accuracy to 66% from 34% or 55%. Of the MMA predictions, 70% fell within the range of mean observed value ± SD, while only 43% of SCENARIO and 50% of HSDA predictions fell within the same range. Paired t tests showed that differences between observations and MMA predictions were not significant, but differences between observations and SCENARIO or HSDA predictions were significantly different for two datasets. Thus, MMA predicted sweat loss more accurately than either of the two single models for the three datasets used. Future work will be to evaluate MMA using additional physiological data to expand the scope of populations and conditions.

Quantum mechanics of hyperbolic orbits in the Kepler problem

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

Rauh, Alexander; Parisi, Juergen

2011-04-15

The problem of deriving macroscopic properties from the Hamiltonian of the hydrogen atom is resumed by extending previous results in the literature, which predicted elliptic orbits, into the region of hyperbolic orbits. As a main tool, coherent states of the harmonic oscillator are used which are continued to imaginary frequencies. The Kustaanheimo-Stiefel (KS) map is applied to transform the original configuration space into the product space of four harmonic oscillators with a constraint. The relation derived between real time and oscillator (pseudo) time includes quantum corrections. In the limit ({h_bar}/2{pi}){yields}0, the time-dependent mean values of position and velocity describe themore » classical motion on a hyperbola and a circular hodograph, respectively. Moreover, the connection between pseudotime and real time comes out in analogy to Kepler's equation for elliptic orbits. The mean-square-root deviations of position and velocity components behave similarly in time to the corresponding ones of a spreading Gaussian wave packet in free space. To check the approximate treatment of the constraint, its contribution to the mean energy is determined with the result that it is negligible except for energy values close to the parabolic orbit with eccentricity equal to 1. It is inevitable to introduce a suitable scalar product in R{sup 4} which makes both the transformed Hamiltonian and the velocity operators Hermitian. An elementary necessary criterion is given for the energy interval where the constraint can be approximated by averaging.« less

Comparison of direct numerical simulation databases of turbulent channel flow at Reτ = 180

NASA Astrophysics Data System (ADS)

Vreman, A. W.; Kuerten, J. G. M.

2014-01-01

Direct numerical simulation (DNS) databases are compared to assess the accuracy and reproducibility of standard and non-standard turbulence statistics of incompressible plane channel flow at Reτ = 180. Two fundamentally different DNS codes are shown to produce maximum relative deviations below 0.2% for the mean flow, below 1% for the root-mean-square velocity and pressure fluctuations, and below 2% for the three components of the turbulent dissipation. Relatively fine grids and long statistical averaging times are required. An analysis of dissipation spectra demonstrates that the enhanced resolution is necessary for an accurate representation of the smallest physical scales in the turbulent dissipation. The results are related to the physics of turbulent channel flow in several ways. First, the reproducibility supports the hitherto unproven theoretical hypothesis that the statistically stationary state of turbulent channel flow is unique. Second, the peaks of dissipation spectra provide information on length scales of the small-scale turbulence. Third, the computed means and fluctuations of the convective, pressure, and viscous terms in the momentum equation show the importance of the different forces in the momentum equation relative to each other. The Galilean transformation that leads to minimum peak fluctuation of the convective term is determined. Fourth, an analysis of higher-order statistics is performed. The skewness of the longitudinal derivative of the streamwise velocity is stronger than expected (-1.5 at y+ = 30). This skewness and also the strong near-wall intermittency of the normal velocity are related to coherent structures.

Measurements of scalar released from point sources in a turbulent boundary layer

NASA Astrophysics Data System (ADS)

Talluru, K. M.; Hernandez-Silva, C.; Philip, J.; Chauhan, K. A.

2017-04-01

Measurements of velocity and concentration fluctuations for a horizontal plume released at several wall-normal locations in a turbulent boundary layer (TBL) are discussed in this paper. The primary objective of this study is to establish a systematic procedure to acquire accurate single-point concentration measurements for a substantially long time so as to obtain converged statistics of long tails of probability density functions of concentration. Details of the calibration procedure implemented for long measurements are presented, which include sensor drift compensation to eliminate the increase in average background concentration with time. While most previous studies reported measurements where the source height is limited to, {{s}z}/δ ≤slant 0.2 , where s z is the wall-normal source height and δ is the boundary layer thickness, here results of concentration fluctuations when the plume is released in the outer layer are emphasised. Results of mean and root-mean-square (r.m.s.) profiles of concentration for elevated sources agree with the well-accepted reflected Gaussian model (Fackrell and Robins 1982 J. Fluid. Mech. 117). However, there is clear deviation from the reflected Gaussian model for source in the intermittent region of TBL particularly at locations higher than the source itself. Further, we find that the plume half-widths are different for the mean and r.m.s. concentration profiles. Long sampling times enabled us to calculate converged probability density functions at high concentrations and these are found to exhibit exponential distribution.

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.

On roots and squares - estimation, intuition and creativity

NASA Astrophysics Data System (ADS)

Patkin, Dorit; Gazit, Avikam

2013-12-01

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 order to obtain a certain units digit as a result. They were also asked to formulate a rule - an algorithm for calculating the square of a 2-digit number which is a multiple of 5. Based on this knowledge and estimation capability, they were required to find, without using calculators, the square roots of given natural numbers. The findings show that most of the participants had only partial intuition regarding the units' digit of a number which is squared when the units' digit of the square is known. At the same time, the participants manifested some evidence of creativity and flow of ideas in identifying the rule for calculating the square of a natural number whose units digit is 5. However, when asked to identify, by means of estimation and based on knowledge from previous items, the square roots of three natural numbers, only few of them managed to find the three roots by estimation.

Solar Irradiance from GOES Albedo performance in a Hydrologic Model Simulation of Snowmelt Runoff

NASA Astrophysics Data System (ADS)

Sumargo, E.; Cayan, D. R.; McGurk, B. J.

2015-12-01

In many hydrologic modeling applications, solar radiation has been parameterized using commonly available measures, such as the daily temperature range, due to scarce in situ solar radiation measurement network. However, these parameterized estimates often produce significant biases. Here we test hourly solar irradiance derived from the Geostationary Operational Environmental Satellite (GOES) visible albedo product, using several established algorithms. Focusing on the Sierra Nevada and White Mountain in California, we compared the GOES irradiance and that from a traditional temperature-based algorithm with incoming irradiance from pyranometers at 19 stations. The GOES based estimates yielded 21-27% reduction in root-mean-squared error (average over 19 sites). The derived irradiance is then prescribed as an input to Precipitation-Runoff Modeling System (PRMS). We constrain our experiment to the Tuolumne River watershed and focus our attention on the winter and spring of 1996-2014. A root-mean-squared error reduction of 2-6% in daily inflow to Hetch Hetchy at the lower end of the Tuolumne catchment was achieved by incorporating the insolation estimates at only 8 out of 280 Hydrologic Response Units (HRUs) within the basin. Our ongoing work endeavors to apply satellite-derived irradiance at each individual HRU.

Highly Efficient Compression Algorithms for Multichannel EEG.

PubMed

Shaw, Laxmi; Rahman, Daleef; Routray, Aurobinda

2018-05-01

The difficulty associated with processing and understanding the high dimensionality of electroencephalogram (EEG) data requires developing efficient and robust compression algorithms. In this paper, different lossless compression techniques of single and multichannel EEG data, including Huffman coding, arithmetic coding, Markov predictor, linear predictor, context-based error modeling, multivariate autoregression (MVAR), and a low complexity bivariate model have been examined and their performances have been compared. Furthermore, a high compression algorithm named general MVAR and a modified context-based error modeling for multichannel EEG have been proposed. The resulting compression algorithm produces a higher relative compression ratio of 70.64% on average compared with the existing methods, and in some cases, it goes up to 83.06%. The proposed methods are designed to compress a large amount of multichannel EEG data efficiently so that the data storage and transmission bandwidth can be effectively used. These methods have been validated using several experimental multichannel EEG recordings of different subjects and publicly available standard databases. The satisfactory parametric measures of these methods, namely percent-root-mean square distortion, peak signal-to-noise ratio, root-mean-square error, and cross correlation, show their superiority over the state-of-the-art compression methods.

A root-mean-square pressure fluctuations model for internal flow applications

NASA Technical Reports Server (NTRS)

Chen, Y. S.

1985-01-01

A transport equation for the root-mean-square pressure fluctuations of turbulent flow is derived from the time-dependent momentum equation for incompressible flow. Approximate modeling of this transport equation is included to relate terms with higher order correlations to the mean quantities of turbulent flow. Three empirical constants are introduced in the model. Two of the empirical constants are estimated from homogeneous turbulence data and wall pressure fluctuations measurements. The third constant is determined by comparing the results of large eddy simulations for a plane channel flow and an annulus flow.

Cross-Shore Exchange on Natural Beaches

DTIC Science & Technology

2014-09-01

87   Figure 2.   Wave conditions measured by the ADCP in 13 m water depth of (a) root- mean-square wave height Hrms...horizontal velocity, Umean, measured in the reference level, ∑Tsig,pulse T3−hour ∑Tsig,pulse T3−hour xi (e) local water depth, h, and (f) local root...mean-square wave height normalized by the local water depth, Hrms/h, measured by ADCPin (blue) and ADCPout (red) during the 3HRLTs. Colored lines

Assessing and calibrating the ATR-FTIR approach as a carbonate rock characterization tool

NASA Astrophysics Data System (ADS)

Henry, Delano G.; Watson, Jonathan S.; John, Cédric M.

2017-01-01

ATR-FTIR (attenuated total reflectance Fourier transform infrared) spectroscopy can be used as a rapid and economical tool for qualitative identification of carbonates, calcium sulphates, oxides and silicates, as well as quantitatively estimating the concentration of minerals. Over 200 powdered samples with known concentrations of two, three, four and five phase mixtures were made, then a suite of calibration curves were derived that can be used to quantify the minerals. The calibration curves in this study have an R2 that range from 0.93-0.99, a RMSE (root mean square error) of 1-5 wt.% and a maximum error of 3-10 wt.%. The calibration curves were used on 35 geological samples that have previously been studied using XRD (X-ray diffraction). The identification of the minerals using ATR-FTIR is comparable with XRD and the quantitative results have a RMSD (root mean square deviation) of 14% and 12% for calcite and dolomite respectively when compared to XRD results. ATR-FTIR is a rapid technique (identification and quantification takes < 5 min) that involves virtually no cost if the machine is available. It is a common tool in most analytical laboratories, but it also has the potential to be deployed on a rig for real-time data acquisition of the mineralogy of cores and rock chips at the surface as there is no need for special sample preparation, rapid data collection and easy analysis.

Quantitative comparison of the application accuracy between NDI and IGT tracking systems

NASA Astrophysics Data System (ADS)

Li, Qinghang; Zamorano, Lucia J.; Jiang, Charlie Z. W.; Gong, JianXing; Diaz, Fernando

1999-07-01

The application accuracy is a crucial factor for the stereotactic surgical localization system in which space digitization system is one of the most important part of equipment. In this study we compared the application accuracy of using the OPTOTRAK space digitization system (OPTOTRAK 3020, Northern Digital, Waterloo, CAN) and FlashPoint Model 3000 and 5000 3-D digitizer systems (FlashPoint Model 3000 and 5000, Image Guided Surgery Technology Inc., Boulder, CO 80301, USA) for interactive localization of intracranial lesions. A phantom was mounted with the implantable frameless marker system (Fischer- Leibinger, Freiburg, Germany) which randomly distributed markers on the surface of the phantom. The target point was digitized and the coordinates were recorded and compared with reference points. The differences from the reference points were used as the deviation from the `true point'. The mean square root was calculated to show the sum of vectors. A paired t-test was used to analyze results. The results of the phantom showed that the mean square roots were 0.76 +/- 0.54 mm for the OPTOTRAK system and 1.23 +/- 0.53 mm for FlashPoint Model 3000 3-D digitizer system and 1.00 +/- 0.42 mm for FlashPoint Model 3000 3-D digitizer system in the 1 mm sections of CT scan. This preliminary results showed that there is no significant difference between two tracking systems. Both of them can be used for image guided surgery procedure.

Exploring the structural insights on human laforin mutation K87A in Lafora disease--a molecular dynamics study.

PubMed

Srikumar, P S; Rohini, K

2013-10-01

Lafora disease (LD) is an autosomal recessive, progressive form of myoclonus epilepsy which affects worldwide. LD occurs mainly in countries like southern Europe, northern Africa, South India, and in the Middle East. LD occurs with its onset mainly in teenagers and leads to decline and death within 2 to 10 years. The genes EPM2A and EPM2B are commonly involved in 90 % of LD cases. EPM2A codes for protein laforin which contains an amino terminal carbohydrate binding module (CBM) belonging to the CBM20 family and a carboxy terminal dual specificity phosphatase domain. Mutations in laforin are found to abolish glycogen binding and have been reported in wet lab methods. In order to investigate on structural insights on laforin mutation K81A, we performed molecular dynamics (MD) simulation studies for native and mutant protein. MD simulation results showed loss of stability due to mutation K87A which confirmed the structural reason for conformational changes observed in laforin. The conformational change of mutant laforin was confirmed by analysis using root mean square deviation, root mean square fluctuation, solvent accessibility surface area, radius of gyration, hydrogen bond, and principle component analysis. Our results identified that the flexibility of K87A mutated laforin structure, with replacement of acidic amino acid to aliphatic amino acid in functional CBM domain, have more impact in abolishing glycogen binding that favors LD.

Role of ELA region in auto-activation of mutant KIT receptor: a molecular dynamics simulation insight.

PubMed

Purohit, Rituraj

2014-01-01

KIT receptor is the prime target in gastrointestinal stromal tumor (GISTs) therapy. Second generation inhibitor, Sunitinib, binds to an inactivated conformation of KIT receptor and stabilizes it in order to prevent tumor formation. Here, we investigated the dynamic behavior of wild type and mutant D816H KIT receptor, and emphasized the extended A-loop (EAL) region (805-850) by conducting molecular dynamics simulation (∼100 ns). We analyzed different properties such as root mean square cutoff or deviation, root mean square fluctuation, radius of gyration, solvent-accessible surface area, hydrogen bonding network analysis, and essential dynamics. Apart from this, clustering and cross-correlation matrix approach was used to explore the conformational space of the wild type and mutant EAL region of KIT receptor. Molecular dynamics analysis indicated that mutation (D816H) was able to alter intramolecular hydrogen bonding pattern and affected the structural flexibility of EAL region. Moreover, flexible secondary elements, specially, coil and turns were dominated in EAL region of mutant KIT receptor during simulation. This phenomenon increased the movement of EAL region which in turn helped in shifting the equilibrium towards the active kinase conformation. Our atomic investigation of mutant KIT receptor which emphasized on EAL region provided a better insight into the understanding of Sunitinib resistance mechanism of KIT receptor and would help to discover new therapeutics for KIT-based resistant tumor cells in GIST therapy.

In Silico Molecular Modeling and Docking Studies on Novel Mutants (E229V, H225P and D230C) of the Nucleotide-Binding Domain of Homo sapiens Hsp70.

PubMed

Elengoe, Asita; Hamdan, Salehhuddin

2017-12-01

In this study, we explored the possibility of determining the synergistic interactions between nucleotide-binding domain (NBD) of Homo sapiens heat-shock 70 kDa protein (Hsp70) and E1A 32 kDa of adenovirus serotype 5 motif (PNLVP) in the efficiency of killing of tumor cells in cancer treatment. At present, the protein interaction between NBD and PNLVP motif is still unknown, but believed to enhance the rate of virus replication in tumor cells. Three mutant models (E229V, H225P and D230C) were built and simulated, and their interactions with PNLVP motif were studied. The PNLVP motif showed the binding energy and intermolecular energy values with the novel E229V mutant at -7.32 and -11.2 kcal/mol. The E229V mutant had the highest number of hydrogen bonds (7). Based on the root mean square deviation, root mean square fluctuation, hydrogen bonds, salt bridge, secondary structure, surface-accessible solvent area, potential energy and distance matrices analyses, it was proved that the E229V had the strongest and most stable interaction with the PNLVP motif among all the four protein-ligand complex structures. The knowledge of this protein-ligand complex model would help in designing Hsp70 structure-based drug for cancer therapy.

Dynamic characterization of HLA-B*44 Alleles: A comparative molecular dynamics simulation study.

PubMed

Ozbek, Pemra

2016-06-01

Human Leukocyte Antigens (HLA) are highly polymorphic proteins that play a key role in the immune system. HLA molecule is present on the cell membrane of antigen-presenting cells of the immune system and presents short peptides, originating from the proteins of invading pathogens or self-proteins, to the T-cell Receptor (TCR) molecule of the T-cells. In this study, peptide-binding characteristics of HLA-B*44:02, 44:03, 44:05 alleles bound to three nonameric peptides were studied using molecular dynamics simulations. Polymorphisms among these alleles (Asp116Tyr and Asp156Leu) result in major differences in the allele characteristics. While HLA-B*44:02 (Asp116, Asp156) and HLA-B*44:03 (Asp116, Leu156) depend on tapasin for efficient peptide loading, HLA-B*44:05 (Tyr116, Asp156) is tapasin independent. On the other hand, HLA-B*44:02 and HLA-B*44:03 mismatch is closely related to transplant rejection and acute-graft-versus-host disease. In order to understand the dynamic characteristics, the simulation trajectories were analyzed by applying Root Mean Square Deviation (RMSD) and Root Mean Square Fluctuation (RMSF) calculations and hydrogen bonding analysis. Binding dynamics of the three HLA-B*44 alleles and peptide sequences are comparatively discussed. In general, peptide binding stability is found to depend on the peptide rather than the allele type for HLA-B*44 alleles. Copyright © 2016 Elsevier Ltd. All rights reserved.

The effect of pressure on spontaneous Rayleigh-Brillouin scattering spectrum in nitrogen

NASA Astrophysics Data System (ADS)

Yang, Chuanyin; Wu, Tao; Shang, Jingcheng; Zhang, Xinyi; Hu, Rongjing; He, XingDao

2018-05-01

In order to study the effect of gas pressure on spontaneous Rayleigh-Brillouin scattering spectrum and verify the validity of Tenti S6 model at pressures up to 8 atm, the spontaneous Rayleigh-Brillouin scattering experiment in nitrogen was performed for a wavelength of 532 nm at the constant room temperature of 296 K and a 90° scattering angle. By comparing the experimental spectrum with the theoretical spectrum, the normalized root mean square deviation was calculated and found less than 2.2%. It is verified that Tenti S6 model can be applied to the spontaneous Rayleigh-Brillion scattering of nitrogen under higher pressures. The results of the experimental data analysis demonstrate that pressure has more effect on Brillouin peak intensity and has negligible effect on Brillouin frequency shift, and pressure retrieval based on spontaneous Rayleigh-Brillouin scattering profile is a promising method for remote of pressure, such as harsh environment applications. Some factors that caused experiment deviations are also discussed.

Statistical Characteristics of the Gaussian-Noise Spikes Exceeding the Specified Threshold as Applied to Discharges in a Thundercloud

NASA Astrophysics Data System (ADS)

Klimenko, V. V.

2017-12-01

We obtain expressions for the probabilities of the normal-noise spikes with the Gaussian correlation function and for the probability density of the inter-spike intervals. As distinct from the delta-correlated noise, in which the intervals are distributed by the exponential law, the probability of the subsequent spike depends on the previous spike and the interval-distribution law deviates from the exponential one for a finite noise-correlation time (frequency-bandwidth restriction). This deviation is the most pronounced for a low detection threshold. Similarity of the behaviors of the distributions of the inter-discharge intervals in a thundercloud and the noise spikes for the varying repetition rate of the discharges/spikes, which is determined by the ratio of the detection threshold to the root-mean-square value of noise, is observed. The results of this work can be useful for the quantitative description of the statistical characteristics of the noise spikes and studying the role of fluctuations for the discharge emergence in a thundercloud.

An Ab Initio Based Potential Energy Surface for Water

NASA Technical Reports Server (NTRS)

Partridge, Harry; Schwenke, David W.; Langhoff, Stephen R. (Technical Monitor)

1996-01-01

We report a new determination of the water potential energy surface. A high quality ab initio potential energy surface (PES) and dipole moment function of water have been computed. This PES is empirically adjusted to improve the agreement between the computed line positions and those from the HITRAN 92 data base. The adjustment is small, nonetheless including an estimate of core (oxygen 1s) electron correlation greatly improves the agreement with experiment. Of the 27,245 assigned transitions in the HITRAN 92 data base for H2(O-16), the overall root mean square (rms) deviation between the computed and observed line positions is 0.125/cm. However the deviations do not correspond to a normal distribution: 69% of the lines have errors less than 0.05/cm. Overall, the agreement between the line intensities computed in the present work and those contained in the data base is quite good, however there are a significant number of line strengths which differ greatly.

A simple and efficient algorithm operating with linear time for MCEEG data compression.

PubMed

Titus, Geevarghese; Sudhakar, M S

2017-09-01

Popularisation of electroencephalograph (EEG) signals in diversified fields have increased the need for devices capable of operating at lower power and storage requirements. This has led to a great deal of research in data compression, that can address (a) low latency in the coding of the signal, (b) reduced hardware and software dependencies, (c) quantify the system anomalies, and (d) effectively reconstruct the compressed signal. This paper proposes a computationally simple and novel coding scheme named spatial pseudo codec (SPC), to achieve lossy to near lossless compression of multichannel EEG (MCEEG). In the proposed system, MCEEG signals are initially normalized, followed by two parallel processes: one operating on integer part and the other, on fractional part of the normalized data. The redundancies in integer part are exploited using spatial domain encoder, and the fractional part is coded as pseudo integers. The proposed method has been tested on a wide range of databases having variable sampling rates and resolutions. Results indicate that the algorithm has a good recovery performance with an average percentage root mean square deviation (PRD) of 2.72 for an average compression ratio (CR) of 3.16. Furthermore, the algorithm has a complexity of only O(n) with an average encoding and decoding time per sample of 0.3 ms and 0.04 ms respectively. The performance of the algorithm is comparable with recent methods like fast discrete cosine transform (fDCT) and tensor decomposition methods. The results validated the feasibility of the proposed compression scheme for practical MCEEG recording, archiving and brain computer interfacing systems.

Modelling environmentally friendly fairways using Lagrangian trajectories: a case study for the Gulf of Finland, the Baltic Sea

NASA Astrophysics Data System (ADS)

Soomere, Tarmo; Berezovski, Mihhail; Quak, Ewald; Viikmäe, Bert

2011-10-01

We address possibilities of minimising environmental risks using statistical features of current-driven propagation of adverse impacts to the coast. The recently introduced method for finding the optimum locations of potentially dangerous activities (Soomere et al. in Proc Estonian Acad Sci 59:156-165, 2010) is expanded towards accounting for the spatial distributions of probabilities and times for reaching the coast for passively advecting particles released in different sea areas. These distributions are calculated using large sets of Lagrangian trajectories found from Eulerian velocity fields provided by the Rossby Centre Ocean Model with a horizontal resolution of 2 nautical miles for 1987-1991. The test area is the Gulf of Finland in the northeastern Baltic Sea. The potential gain using the optimum fairways from the Baltic Proper to the eastern part of the gulf is an up to 44% decrease in the probability of coastal pollution and a similar increase in the average time for reaching the coast. The optimum fairways are mostly located to the north of the gulf axis (by 2-8 km on average) and meander substantially in some sections. The robustness of this approach is quantified as the typical root mean square deviation (6-16 km) between the optimum fairways specified from different criteria. Drastic variations in the width of the `corridors' for almost optimal fairways (2-30 km for the average width of 15 km) signifies that the sensitivity of the results with respect to small changes in the environmental criteria largely varies in different parts of the gulf.

Rugometric and microtopographic non-invasive inspection in dental-resin composites and zirconia ceramics

NASA Astrophysics Data System (ADS)

Fernández-Oliveras, Alicia; Costa, Manuel F. M.; Pecho, Oscar E.; Rubiño, Manuel; Pérez, María. M.

2013-11-01

Surface properties are essential for a complete characterization of biomaterials. In restorative dentistry, the study of the surface properties of materials meant to replace dental tissues in an irreversibly diseased tooth is important to avoid harmful changes in future treatments. We have experimentally analyzed the surface characterization parameters of two different types of dental-resin composites and pre-sintered and sintered zirconia ceramics. We studied two shades of both composite types and two sintered zirconia ceramics: colored and uncolored. Moreover, a surface treatment was applied to one specimen of each dental-resin. All the samples were submitted to rugometric and microtopographic non-invasive inspection with the MICROTOP.06.MFC laser microtopographer in order to gather meaningful statistical parameters such as the average roughness (Ra), the root-mean-square deviation (Rq), the skewness (Rsk), and the kurtosis of the surface height distribution (Rku). For a comparison of the different biomaterials, the uncertainties associated to the surface parameters were also determined. With respect to Ra and Rq, significant differences between the composite shades were found. Among the dental resins, the nanocomposite presented the highest values and, for the zirconia ceramics, the pre-sintered sample registered the lowest ones. The composite performance may have been due to cluster-formation variations. Except for the composites with the surface treatment, the sample surfaces had approximately a normal distribution of heights. The surface treatment applied to the composites increased the average roughness and moved the height distribution farther away from the normal distribution. The zirconia-sintering process resulted in higher average roughness without affecting the height distribution.

Estimating current and future streamflow characteristics at ungaged sites, central and eastern Montana, with application to evaluating effects of climate change on fish populations

USGS Publications Warehouse

Sando, Roy; Chase, Katherine J.

2017-03-23

A common statistical procedure for estimating streamflow statistics at ungaged locations is to develop a relational model between streamflow and drainage basin characteristics at gaged locations using least squares regression analysis; however, least squares regression methods are parametric and make constraining assumptions about the data distribution. The random forest regression method provides an alternative nonparametric method for estimating streamflow characteristics at ungaged sites and requires that the data meet fewer statistical conditions than least squares regression methods.Random forest regression analysis was used to develop predictive models for 89 streamflow characteristics using Precipitation-Runoff Modeling System simulated streamflow data and drainage basin characteristics at 179 sites in central and eastern Montana. The predictive models were developed from streamflow data simulated for current (baseline, water years 1982–99) conditions and three future periods (water years 2021–38, 2046–63, and 2071–88) under three different climate-change scenarios. These predictive models were then used to predict streamflow characteristics for baseline conditions and three future periods at 1,707 fish sampling sites in central and eastern Montana. The average root mean square error for all predictive models was about 50 percent. When streamflow predictions at 23 fish sampling sites were compared to nearby locations with simulated data, the mean relative percent difference was about 43 percent. When predictions were compared to streamflow data recorded at 21 U.S. Geological Survey streamflow-gaging stations outside of the calibration basins, the average mean absolute percent error was about 73 percent.

HIGH-RESOLUTION FOURIER TRANSFORM INFRARED SPECTRUM OF THE ν2 + ν12 BAND OF ETHYLENE (12C2H4)

NASA Astrophysics Data System (ADS)

Lebron, G. B.; Tan, T. L.

2013-09-01

The high-resolution Fourier transform infrared absorption spectrum of the ν2 + ν12 combination band of normal ethylene (12C2H4) in the 3050-3105 cm-1 region was recorded at a resolution of 0.0063 cm-1 and at an ambient temperature of 296 K. Upper state rovibrational analysis was carried out using a standard Watson's Hamiltonian in asymmetric reduction in Ir representation. The band center, rotational constants and centrifugal distortion constants up to quartic terms of the upper ν2 + ν12 = 1 state were determined from the final fit that included 102 infrared transitions. The root-mean-square deviation of the fit was 0.000729 cm-1.

An automated exploration of the isomerization and dissociation pathways of (E)-1,2-dichloroethene cations and anions

NASA Astrophysics Data System (ADS)

Kishimoto, Naoki; Nishi, Yuito

2017-04-01

Isomerization and dissociation pathways after the photoionization or electron attachment of (E)-1,2-dichloroethene were calculated with an automated exploration method utilizing a scaled hypersphere search of the anharmonic downward distortion following algorithm at the UB3LYP/6-311G(2d,d,p) level of theory. The potential energies of transition states and dissociation channels were calculated by a composite method ((RO)CBS-QB3) and compared with the breakdown diagrams and electron attachment spectra observed in previous spectroscopic studies. The results of single point calculations with several DFT and post-SCF methods are compared using the root mean square deviations from the (RO)CBS-QB3 energies for six states of anionic dichloroethene.

Comparison of MRI segmentation techniques for measuring liver cyst volumes in autosomal dominant polycystic kidney disease.

PubMed

Farooq, Zerwa; Behzadi, Ashkan Heshmatzadeh; Blumenfeld, Jon D; Zhao, Yize; Prince, Martin R

To compare MRI segmentation methods for measuring liver cyst volumes in autosomal dominant polycystic kidney disease (ADPKD). Liver cyst volumes in 42 ADPKD patients were measured using region growing, thresholding and cyst diameter techniques. Manual segmentation was the reference standard. Root mean square deviation was 113, 155, and 500 for cyst diameter, thresholding and region growing respectively. Thresholding error for cyst volumes below 500ml was 550% vs 17% for cyst volumes above 500ml (p<0.001). For measuring volume of a small number of cysts, cyst diameter and manual segmentation methods are recommended. For severe disease with numerous, large hepatic cysts, thresholding is an acceptable alternative. Copyright © 2017 Elsevier Inc. All rights reserved.

Performance of a docking/molecular dynamics protocol for virtual screening of nutlin-class inhibitors of Mdmx.

PubMed

Bharatham, Nagakumar; Finch, Kristin E; Min, Jaeki; Mayasundari, Anand; Dyer, Michael A; Guy, R Kiplin; Bashford, Donald

2017-06-01

A virtual screening protocol involving docking and molecular dynamics has been tested against the results of fluorescence polarization assays testing the potency of a series of compounds of the nutlin class for inhibition of the interaction between p53 and Mdmx, an interaction identified as a driver of certain cancers. The protocol uses a standard docking method (AutoDock) with a cutoff based on the AutoDock score (ADscore), followed by molecular dynamics simulation with a cutoff based on root-mean-square-deviation (RMSD) from the docked pose. An analysis of the experimental and computational results shows modest performance of ADscore alone, but dramatically improved performance when RMSD is also used. Published by Elsevier Inc.

Physicochemical characterization of Lavandula spp. honey with FT-Raman spectroscopy.

PubMed

Anjos, Ofélia; Santos, António J A; Paixão, Vasco; Estevinho, Letícia M

2018-02-01

This study aimed to evaluate the potential of FT-Raman spectroscopy in the prediction of the chemical composition of Lavandula spp. monofloral honey. Partial Least Squares (PLS) regression models were performed for the quantitative estimation and the results were correlated with those obtained using reference methods. Good calibration models were obtained for electrical conductivity, ash, total acidity, pH, reducing sugars, hydroxymethylfurfural (HMF), proline, diastase index, apparent sucrose, total flavonoids content and total phenol content. On the other hand, the model was less accurate for pH determination. The calibration models had high r 2 (ranging between 92.8% and 99.9%), high residual prediction deviation - RPD (ranging between 4.2 and 26.8) and low root mean square errors. These results confirm the hypothesis that FT-Raman is a useful technique for the quality control and chemical properties' evaluation of Lavandula spp honey. Its application may allow improving the efficiency, speed and cost of the current laboratory analysis. Copyright © 2017 Elsevier B.V. All rights reserved.

Anomalous Impact in Reaction-Diffusion Financial Models

NASA Astrophysics Data System (ADS)

Mastromatteo, I.; Tóth, B.; Bouchaud, J.-P.

2014-12-01

We generalize the reaction-diffusion model A +B → /0 in order to study the impact of an excess of A (or B ) at the reaction front. We provide an exact solution of the model, which shows that the linear response breaks down: the average displacement of the reaction front grows as the square root of the imbalance. We argue that this model provides a highly simplified but generic framework to understand the square-root impact of large orders in financial markets.

Distribution of Hydroxyl Groups in Kukersite Shale Oil: Quantitative Determination Using Fourier Transform Infrared (FT-IR) Spectroscopy.

PubMed

Baird, Zachariah Steven; Oja, Vahur; Järvik, Oliver

2015-05-01

This article describes the use of Fourier transform infrared (FT-IR) spectroscopy to quantitatively measure the hydroxyl concentrations among narrow boiling shale oil cuts. Shale oil samples were from an industrial solid heat carrier retort. Reference values were measured by titration and were used to create a partial least squares regression model from FT-IR data. The model had a root mean squared error (RMSE) of 0.44 wt% OH. This method was then used to study the distribution of hydroxyl groups among more than 100 shale oil cuts, which showed that hydroxyl content increased with the average boiling point of the cut up to about 350 °C and then leveled off and decreased.

Reconstruction of regional mean temperature for East Asia since 1900s and its uncertainties

NASA Astrophysics Data System (ADS)

Hua, W.

2017-12-01

Regional average surface air temperature (SAT) is one of the key variables often used to investigate climate change. Unfortunately, because of the limited observations over East Asia, there were also some gaps in the observation data sampling for regional mean SAT analysis, which was important to estimate past climate change. In this study, the regional average temperature of East Asia since 1900s is calculated by the Empirical Orthogonal Function (EOF)-based optimal interpolation (OA) method with considering the data errors. The results show that our estimate is more precise and robust than the results from simple average, which provides a better way for past climate reconstruction. In addition to the reconstructed regional average SAT anomaly time series, we also estimated uncertainties of reconstruction. The root mean square error (RMSE) results show that the the error decreases with respect to time, and are not sufficiently large to alter the conclusions on the persist warming in East Asia during twenty-first century. Moreover, the test of influence of data error on reconstruction clearly shows the sensitivity of reconstruction to the size of the data error.

Role of dispersion corrected hybrid GGA class in accurately calculating the bond dissociation energy of carbon halogen bond: A benchmark study

NASA Astrophysics Data System (ADS)

Kosar, Naveen; Mahmood, Tariq; Ayub, Khurshid

2017-12-01

Benchmark study has been carried out to find a cost effective and accurate method for bond dissociation energy (BDE) of carbon halogen (Csbnd X) bond. BDE of C-X bond plays a vital role in chemical reactions, particularly for kinetic barrier and thermochemistry etc. The compounds (1-16, Fig. 1) with Csbnd X bond used for current benchmark study are important reactants in organic, inorganic and bioorganic chemistry. Experimental data of Csbnd X bond dissociation energy is compared with theoretical results. The statistical analysis tools such as root mean square deviation (RMSD), standard deviation (SD), Pearson's correlation (R) and mean absolute error (MAE) are used for comparison. Overall, thirty-one density functionals from eight different classes of density functional theory (DFT) along with Pople and Dunning basis sets are evaluated. Among different classes of DFT, the dispersion corrected range separated hybrid GGA class along with 6-31G(d), 6-311G(d), aug-cc-pVDZ and aug-cc-pVTZ basis sets performed best for bond dissociation energy calculation of C-X bond. ωB97XD show the best performance with less deviations (RMSD, SD), mean absolute error (MAE) and a significant Pearson's correlation (R) when compared to experimental data. ωB97XD along with Pople basis set 6-311g(d) has RMSD, SD, R and MAE of 3.14 kcal mol-1, 3.05 kcal mol-1, 0.97 and -1.07 kcal mol-1, respectively.

Wind Characteristics of Coastal and Inland Surface Flows

NASA Astrophysics Data System (ADS)

Subramanian, Chelakara; Lazarus, Steven; Jin, Tetsuya

2015-11-01

Lidar measurements of the winds in the surface layer (up to 80 m) inland and near the beach are studied to better characterize the velocity profile and the effect of roughness. Mean and root-mean-squared profiles of horizontal and vertical wind components are analyzed. The effects of variable time (18, 60 and 600 seconds) averaging on the above profiles are discussed. The validity of common surface layer wind profile models to estimate skin friction drag is assessed in light of these measurements. Other turbulence statistics such as auto- and cross- correlations in spatial and temporal domains are also presented. The help of FIT DMES field measurement crew is acknowledged.

Simple Forest Canopy Thermal Exitance Model

NASA Technical Reports Server (NTRS)

Smith J. A.; Goltz, S. M.

1999-01-01

We describe a model to calculate brightness temperature and surface energy balance for a forest canopy system. The model is an extension of an earlier vegetation only model by inclusion of a simple soil layer. The root mean square error in brightness temperature for a dense forest canopy was 2.5 C. Surface energy balance predictions were also in good agreement. The corresponding root mean square errors for net radiation, latent, and sensible heat were 38.9, 30.7, and 41.4 W/sq m respectively.

Analysis of basic clustering algorithms for numerical estimation of statistical averages in biomolecules.

PubMed

Anandakrishnan, Ramu; Onufriev, Alexey

2008-03-01

In statistical mechanics, the equilibrium properties of a physical system of particles can be calculated as the statistical average over accessible microstates of the system. In general, these calculations are computationally intractable since they involve summations over an exponentially large number of microstates. Clustering algorithms are one of the methods used to numerically approximate these sums. The most basic clustering algorithms first sub-divide the system into a set of smaller subsets (clusters). Then, interactions between particles within each cluster are treated exactly, while all interactions between different clusters are ignored. These smaller clusters have far fewer microstates, making the summation over these microstates, tractable. These algorithms have been previously used for biomolecular computations, but remain relatively unexplored in this context. Presented here, is a theoretical analysis of the error and computational complexity for the two most basic clustering algorithms that were previously applied in the context of biomolecular electrostatics. We derive a tight, computationally inexpensive, error bound for the equilibrium state of a particle computed via these clustering algorithms. For some practical applications, it is the root mean square error, which can be significantly lower than the error bound, that may be more important. We how that there is a strong empirical relationship between error bound and root mean square error, suggesting that the error bound could be used as a computationally inexpensive metric for predicting the accuracy of clustering algorithms for practical applications. An example of error analysis for such an application-computation of average charge of ionizable amino-acids in proteins-is given, demonstrating that the clustering algorithm can be accurate enough for practical purposes.

The effects of cold water immersion with different dosages (duration and temperature variations) on heart rate variability post-exercise recovery: A randomized controlled trial.

PubMed

Almeida, Aline C; Machado, Aryane F; Albuquerque, Maíra C; Netto, Lara M; Vanderlei, Franciele M; Vanderlei, Luiz Carlos M; Junior, Jayme Netto; Pastre, Carlos M

2016-08-01

The aim of the present study was to investigate the effects of cold water immersion during post-exercise recovery, with different durations and temperatures, on heart rate variability indices. Hundred participants performed a protocol of jumps and a Wingate test, and immediately afterwards were immersed in cold water, according to the characteristics of each group (CG: control; G1: 5' at 9±1°C; G2: 5' at 14±1°C; G3: 15' at 9±1°C; G4: 15' at 14±1°C). Analyses were performed at baseline, during the CWI recuperative technique (TRec) and 20, 30, 40, 50 and 60min post-exercise. The average HRV indices of all RR-intervals in each analysis period (MeanRR), standard deviation of normal RR-intervals (SDNN), square root of the mean of the sum of the squares of differences between adjacent RR-intervals (RMSSD), spectral components of very low frequency (VLF), low frequency (LF) and high frequency (HF), scatter of points perpendicular to the line of identity of the Poincaré Plot (SD1) and scatter points along the line of identity (SD2) were assessed. Mean RR, VLF and LF presented an anticipated return to baseline values at all the intervention groups, but the same was observed for SDNN and SD2 only in the immersion for 15min at 14°C group (G4). In addition, G4 presented higher values when compared to CG. These findings demonstrate that if the purpose of the recovery process is restoration of cardiac autonomic modulation, the technique is recommended, specifically for 15min at 14°C. Copyright © 2015 Sports Medicine Australia. Published by Elsevier Ltd. All rights reserved.

Resting and postexercise heart rate variability in professional handball players.

PubMed

Kayacan, Yildirim; Yildiz, Sedat

2016-03-01

The aim of this study was to evaluate heart rate variability (HRV) in professional handball players during rest and following a 5 min mild jogging exercise. For that purpose, electrocardiogram (ECG) of male handball players (N.=12, mean age 25±3.95 years) and sedentary controls (N.=14, mean age 23.5±2.95 years) were recorded for 5 min at rest and just after 5 min of mild jogging. ECGs were recorded and following HRV parameters were calculated: time-domain variables such as heart rate (HR), average normal-to-normal RR intervals, standard deviation of normal-to-normal RR intervals, square root of the mean of the squares of differences between adjacent NN intervals, percentage of differences between adjacent NN intervals that are greater than 50 milliseconds (pNN50), and frequency-domain variables such as very low frequency, low (LF) and high frequency (HF) of the power and LF/HF ratio. Unpaired t-test was used to find out differences among groups while paired t-test was used for comparison of each group for pre- and postjogging HRV. Pearson correlations were carried out to find out the relationships between the parameters. Blood pressures were not different between handball players and sedentary controls but exercise increased systolic blood pressure (P<0.01). HR was increased with exercise (P<0.001) and was slower in handball players (P<0.01). QTc was increased with exercise (P<0.001) and was higher in handball players (P<0.001). Exercise decreased pNN50 values in both groups but LF/HF ratio increased only in sedentary subjects. In conclusion, results of the HRV parameters show that sympathovagal balance does not appear to change in handball players in response to a mild, short-time (5 min) jogging exercise. However, in sedentary subjects, either the sympathetic regulation of the autonomous nervous system increased or vagal withdrawal occurred.

Influence of container shape on scaling of turbulent fluctuations in convection

NASA Astrophysics Data System (ADS)

Foroozani, Najmeh; Niemela, Joseph J.; Armenio, Vincenzo; Sreenivasan, Katepalli R.

2014-11-01

We perform large-eddy simulations of turbulent convection in a cubic enclosure for Rayleigh numbers 1 ×106 <= Ra <= 1 ×1010 and molecular Prandtl number, Pr = 0 . 7 . The simulations were carried out using a second-order-accurate finite-difference method in which subgrid-scale fluxes of momentum and heat were parametrized using a Lagrangian dynamic Smagorinsky model. The scalings of root-mean-square fluctuations of density and velocity in the cell center with Ra differ significantly from those in cylindrical containers, and are in agreement with laboratory observations by, also using a cell with square cross-section. We find that the time-averaged spatial distributions of the local heat flux and temperature fluctuations are inhomogeneous in the horizontal plane, associated with the forced orientation of the mean wind along either one or the other diagonal. Larger values of the steady-state density (temperature) gradients occur at the mid-plane corners of the diagonal opposite to that of the mean wind, due to the presence of strong counter-rotating circulations.

Distributed multi-criteria model evaluation and spatial association analysis

NASA Astrophysics Data System (ADS)

Scherer, Laura; Pfister, Stephan

2015-04-01

Model performance, if evaluated, is often communicated by a single indicator and at an aggregated level; however, it does not embrace the trade-offs between different indicators and the inherent spatial heterogeneity of model efficiency. In this study, we simulated the water balance of the Mississippi watershed using the Soil and Water Assessment Tool (SWAT). The model was calibrated against monthly river discharge at 131 measurement stations. Its time series were bisected to allow for subsequent validation at the same gauges. Furthermore, the model was validated against evapotranspiration which was available as a continuous raster based on remote sensing. The model performance was evaluated for each of the 451 sub-watersheds using four different criteria: 1) Nash-Sutcliffe efficiency (NSE), 2) percent bias (PBIAS), 3) root mean square error (RMSE) normalized to standard deviation (RSR), as well as 4) a combined indicator of the squared correlation coefficient and the linear regression slope (bR2). Conditions that might lead to a poor model performance include aridity, a very flat and steep relief, snowfall and dams, as indicated by previous research. In an attempt to explain spatial differences in model efficiency, the goodness of the model was spatially compared to these four phenomena by means of a bivariate spatial association measure which combines Pearson's correlation coefficient and Moran's index for spatial autocorrelation. In order to assess the model performance of the Mississippi watershed as a whole, three different averages of the sub-watershed results were computed by 1) applying equal weights, 2) weighting by the mean observed river discharge, 3) weighting by the upstream catchment area and the square root of the time series length. Ratings of model performance differed significantly in space and according to efficiency criterion. The model performed much better in the humid Eastern region than in the arid Western region which was confirmed by the high spatial association with the aridity index (ratio of mean annual precipitation to mean annual potential evapotranspiration). This association was still significant when controlling for slopes which manifested the second highest spatial association. In line with these findings, overall model efficiency of the entire Mississippi watershed appeared better when weighted with mean observed river discharge. Furthermore, the model received the highest rating with regards to PBIAS and was judged worst when considering NSE as the most comprehensive indicator. No universal performance indicator exists that considers all aspects of a hydrograph. Therefore, sound model evaluation must take into account multiple criteria. Since model efficiency varies in space which is masked by aggregated ratings spatially explicit model goodness should be communicated as standard praxis - at least as a measure of spatial variability of indicators. Furthermore, transparent documentation of the evaluation procedure also with regards to weighting of aggregated model performance is crucial but often lacking in published research. Finally, the high spatial association between model performance and aridity highlights the need to improve modelling schemes for arid conditions as priority over other aspects that might weaken model goodness.

Ambient Sound-Based Collaborative Localization of Indeterministic Devices

PubMed Central

Kamminga, Jacob; Le, Duc; Havinga, Paul

2016-01-01

Localization is essential in wireless sensor networks. To our knowledge, no prior work has utilized low-cost devices for collaborative localization based on only ambient sound, without the support of local infrastructure. The reason may be the fact that most low-cost devices are indeterministic and suffer from uncertain input latencies. This uncertainty makes accurate localization challenging. Therefore, we present a collaborative localization algorithm (Cooperative Localization on Android with ambient Sound Sources (CLASS)) that simultaneously localizes the position of indeterministic devices and ambient sound sources without local infrastructure. The CLASS algorithm deals with the uncertainty by splitting the devices into subsets so that outliers can be removed from the time difference of arrival values and localization results. Since Android is indeterministic, we select Android devices to evaluate our approach. The algorithm is evaluated with an outdoor experiment and achieves a mean Root Mean Square Error (RMSE) of 2.18 m with a standard deviation of 0.22 m. Estimated directions towards the sound sources have a mean RMSE of 17.5° and a standard deviation of 2.3°. These results show that it is feasible to simultaneously achieve a relative positioning of both devices and sound sources with sufficient accuracy, even when using non-deterministic devices and platforms, such as Android. PMID:27649176

Fast large-scale clustering of protein structures using Gauss integrals.

PubMed

Harder, Tim; Borg, Mikael; Boomsma, Wouter; Røgen, Peter; Hamelryck, Thomas

2012-02-15

Clustering protein structures is an important task in structural bioinformatics. De novo structure prediction, for example, often involves a clustering step for finding the best prediction. Other applications include assigning proteins to fold families and analyzing molecular dynamics trajectories. We present Pleiades, a novel approach to clustering protein structures with a rigorous mathematical underpinning. The method approximates clustering based on the root mean square deviation by first mapping structures to Gauss integral vectors--which were introduced by Røgen and co-workers--and subsequently performing K-means clustering. Compared to current methods, Pleiades dramatically improves on the time needed to perform clustering, and can cluster a significantly larger number of structures, while providing state-of-the-art results. The number of low energy structures generated in a typical folding study, which is in the order of 50,000 structures, can be clustered within seconds to minutes.

Accuracy of Digital Impressions and Fitness of Single Crowns Based on Digital Impressions

PubMed Central

Yang, Xin; Lv, Pin; Liu, Yihong; Si, Wenjie; Feng, Hailan

2015-01-01

In this study, the accuracy (precision and trueness) of digital impressions and the fitness of single crowns manufactured based on digital impressions were evaluated. #14-17 epoxy resin dentitions were made, while full-crown preparations of extracted natural teeth were embedded at #16. (1) To assess precision, deviations among repeated scan models made by intraoral scanner TRIOS and MHT and model scanner D700 and inEos were calculated through best-fit algorithm and three-dimensional (3D) comparison. Root mean square (RMS) and color-coded difference images were offered. (2) To assess trueness, micro computed tomography (micro-CT) was used to get the reference model (REF). Deviations between REF and repeated scan models (from (1)) were calculated. (3) To assess fitness, single crowns were manufactured based on TRIOS, MHT, D700 and inEos scan models. The adhesive gaps were evaluated under stereomicroscope after cross-sectioned. Digital impressions showed lower precision and better trueness. Except for MHT, the means of RMS for precision were lower than 10 μm. Digital impressions showed better internal fitness. Fitness of single crowns based on digital impressions was up to clinical standard. Digital impressions could be an alternative method for single crowns manufacturing. PMID:28793417

Using Mathematical Algorithms to Modify Glomerular Filtration Rate Estimation Equations

PubMed Central

Zhu, Bei; Wu, Jianqing; Zhu, Jin; Zhao, Weihong

2013-01-01

Background The equations provide a rapid and low-cost method of evaluating glomerular filtration rate (GFR). Previous studies indicated that the Modification of Diet in Renal Disease (MDRD), Chronic Kidney Disease-Epidemiology (CKD-EPI) and MacIsaac equations need further modification for application in Chinese population. Thus, this study was designed to modify the three equations, and compare the diagnostic accuracy of the equations modified before and after. Methodology With the use of 99 mTc-DTPA renal dynamic imaging as the reference GFR (rGFR), the MDRD, CKD-EPI and MacIsaac equations were modified by two mathematical algorithms: the hill-climbing and the simulated-annealing algorithms. Results A total of 703 Chinese subjects were recruited, with the average rGFR 77.14±25.93 ml/min. The entire modification process was based on a random sample of 80% of subjects in each GFR level as a training sample set, the rest of 20% of subjects as a validation sample set. After modification, the three equations performed significant improvement in slop, intercept, correlated coefficient, root mean square error (RMSE), total deviation index (TDI), and the proportion of estimated GFR (eGFR) within 10% and 30% deviation of rGFR (P10 and P30). Of the three modified equations, the modified CKD-EPI equation showed the best accuracy. Conclusions Mathematical algorithms could be a considerable tool to modify the GFR equations. Accuracy of all the three modified equations was significantly improved in which the modified CKD-EPI equation could be the optimal one. PMID:23472113

Density, ultrasound velocity, acoustic impedance, reflection and absorption coefficient determination of liquids via multiple reflection method.

PubMed

Hoche, S; Hussein, M A; Becker, T

2015-03-01

The accuracy of density, reflection coefficient, and acoustic impedance determination via multiple reflection method was validated experimentally. The ternary system water-maltose-ethanol was used to execute a systematic, temperature dependent study over a wide range of densities and viscosities aiming an application as inline sensor in beverage industries. The validation results of the presented method and setup show root mean square errors of: 1.201E-3 g cm(-3) (±0.12%) density, 0.515E-3 (0.15%) reflection coefficient and 1.851E+3 kg s(-1) m(-2) (0.12%) specific acoustic impedance. The results of the diffraction corrected absorption showed an average standard deviation of only 0.12%. It was found that the absorption change shows a good correlation to concentration variations and may be useful for laboratory analysis of sufficiently pure liquids. The main part of the observed errors can be explained by the observed noise, temperature variation and the low signal resolution of 50 MHz. In particular, the poor signal-to-noise ratio of the second reflector echo was found to be a main accuracy limitation. Concerning the investigation of liquids the unstable properties of the reference material PMMA, due to hygroscopicity, were identified to be an additional, unpredictable source of uncertainty. While dimensional changes can be considered by adequate methodology, the impact of the time and temperature dependent water absorption on relevant reference properties like the buffer's sound velocity and density could not be considered and may explain part of the observed deviations. Copyright © 2014 Elsevier B.V. All rights reserved.

Dynamic electronic collimation method for 3-D catheter tracking on a scanning-beam digital x-ray system

PubMed Central

Dunkerley, David A. P.; Slagowski, Jordan M.; Funk, Tobias; Speidel, Michael A.

2017-01-01

Abstract. Scanning-beam digital x-ray (SBDX) is an inverse geometry x-ray fluoroscopy system capable of tomosynthesis-based 3-D catheter tracking. This work proposes a method of dose-reduced 3-D catheter tracking using dynamic electronic collimation (DEC) of the SBDX scanning x-ray tube. This is achieved through the selective deactivation of focal spot positions not needed for the catheter tracking task. The technique was retrospectively evaluated with SBDX detector data recorded during a phantom study. DEC imaging of a catheter tip at isocenter required 340 active focal spots per frame versus 4473 spots in full field-of-view (FOV) mode. The dose-area product (DAP) and peak skin dose (PSD) for DEC versus full FOV scanning were calculated using an SBDX Monte Carlo simulation code. The average DAP was reduced to 7.8% of the full FOV value, consistent with the relative number of active focal spots (7.6%). For image sequences with a moving catheter, PSD was 33.6% to 34.8% of the full FOV value. The root-mean-squared-deviation between DEC-based 3-D tracking coordinates and full FOV 3-D tracking coordinates was less than 0.1 mm. The 3-D distance between the tracked tip and the sheath centerline averaged 0.75 mm. DEC is a feasible method for dose reduction during SBDX 3-D catheter tracking. PMID:28439521

Peculiarities of stochastic regime of Arctic ice cover time evolution over 1987-2014 from microwave satellite sounding on the basis of NASA team 2 algorithm

NASA Astrophysics Data System (ADS)

Raev, M. D.; Sharkov, E. A.; Tikhonov, V. V.; Repina, I. A.; Komarova, N. Yu.

2015-12-01

The GLOBAL-RT database (DB) is composed of long-term radio heat multichannel observation data received from DMSP F08-F17 satellites; it is permanently supplemented with new data on the Earth's exploration from the space department of the Space Research Institute, Russian Academy of Sciences. Arctic ice-cover areas for regions higher than 60° N latitude were calculated using the DB polar version and NASA Team 2 algorithm, which is widely used in foreign scientific literature. According to the analysis of variability of Arctic ice cover during 1987-2014, 2 months were selected when the Arctic ice cover was maximal (February) and minimal (September), and the average ice cover area was calculated for these months. Confidence intervals of the average values are in the 95-98% limits. Several approximations are derived for the time dependences of the ice-cover maximum and minimum over the period under study. Regression dependences were calculated for polynomials from the first degree (linear) to sextic. It was ascertained that the minimal root-mean-square error of deviation from the approximated curve sharply decreased for the biquadratic polynomial and then varied insignificantly: from 0.5593 for the polynomial of third degree to 0.4560 for the biquadratic polynomial. Hence, the commonly used strictly linear regression with a negative time gradient for the September Arctic ice cover minimum over 30 years should be considered incorrect.

A hidden markov model derived structural alphabet for proteins.

PubMed

Camproux, A C; Gautier, R; Tufféry, P

2004-06-04

Understanding and predicting protein structures depends on the complexity and the accuracy of the models used to represent them. We have set up a hidden Markov model that discretizes protein backbone conformation as series of overlapping fragments (states) of four residues length. This approach learns simultaneously the geometry of the states and their connections. We obtain, using a statistical criterion, an optimal systematic decomposition of the conformational variability of the protein peptidic chain in 27 states with strong connection logic. This result is stable over different protein sets. Our model fits well the previous knowledge related to protein architecture organisation and seems able to grab some subtle details of protein organisation, such as helix sub-level organisation schemes. Taking into account the dependence between the states results in a description of local protein structure of low complexity. On an average, the model makes use of only 8.3 states among 27 to describe each position of a protein structure. Although we use short fragments, the learning process on entire protein conformations captures the logic of the assembly on a larger scale. Using such a model, the structure of proteins can be reconstructed with an average accuracy close to 1.1A root-mean-square deviation and for a complexity of only 3. Finally, we also observe that sequence specificity increases with the number of states of the structural alphabet. Such models can constitute a very relevant approach to the analysis of protein architecture in particular for protein structure prediction.

Missing value imputation in DNA microarrays based on conjugate gradient method.

PubMed

Dorri, Fatemeh; Azmi, Paeiz; Dorri, Faezeh

2012-02-01

Analysis of gene expression profiles needs a complete matrix of gene array values; consequently, imputation methods have been suggested. In this paper, an algorithm that is based on conjugate gradient (CG) method is proposed to estimate missing values. k-nearest neighbors of the missed entry are first selected based on absolute values of their Pearson correlation coefficient. Then a subset of genes among the k-nearest neighbors is labeled as the best similar ones. CG algorithm with this subset as its input is then used to estimate the missing values. Our proposed CG based algorithm (CGimpute) is evaluated on different data sets. The results are compared with sequential local least squares (SLLSimpute), Bayesian principle component analysis (BPCAimpute), local least squares imputation (LLSimpute), iterated local least squares imputation (ILLSimpute) and adaptive k-nearest neighbors imputation (KNNKimpute) methods. The average of normalized root mean squares error (NRMSE) and relative NRMSE in different data sets with various missing rates shows CGimpute outperforms other methods. Copyright © 2011 Elsevier Ltd. All rights reserved.

Performance of statistical models to predict mental health and substance abuse cost.

PubMed

Montez-Rath, Maria; Christiansen, Cindy L; Ettner, Susan L; Loveland, Susan; Rosen, Amy K

2006-10-26

Providers use risk-adjustment systems to help manage healthcare costs. Typically, ordinary least squares (OLS) models on either untransformed or log-transformed cost are used. We examine the predictive ability of several statistical models, demonstrate how model choice depends on the goal for the predictive model, and examine whether building models on samples of the data affects model choice. Our sample consisted of 525,620 Veterans Health Administration patients with mental health (MH) or substance abuse (SA) diagnoses who incurred costs during fiscal year 1999. We tested two models on a transformation of cost: a Log Normal model and a Square-root Normal model, and three generalized linear models on untransformed cost, defined by distributional assumption and link function: Normal with identity link (OLS); Gamma with log link; and Gamma with square-root link. Risk-adjusters included age, sex, and 12 MH/SA categories. To determine the best model among the entire dataset, predictive ability was evaluated using root mean square error (RMSE), mean absolute prediction error (MAPE), and predictive ratios of predicted to observed cost (PR) among deciles of predicted cost, by comparing point estimates and 95% bias-corrected bootstrap confidence intervals. To study the effect of analyzing a random sample of the population on model choice, we re-computed these statistics using random samples beginning with 5,000 patients and ending with the entire sample. The Square-root Normal model had the lowest estimates of the RMSE and MAPE, with bootstrap confidence intervals that were always lower than those for the other models. The Gamma with square-root link was best as measured by the PRs. The choice of best model could vary if smaller samples were used and the Gamma with square-root link model had convergence problems with small samples. Models with square-root transformation or link fit the data best. This function (whether used as transformation or as a link) seems to help deal with the high comorbidity of this population by introducing a form of interaction. The Gamma distribution helps with the long tail of the distribution. However, the Normal distribution is suitable if the correct transformation of the outcome is used.

Electrocardiogram signal denoising based on a new improved wavelet thresholding

NASA Astrophysics Data System (ADS)

Han, Guoqiang; Xu, Zhijun

2016-08-01

Good quality electrocardiogram (ECG) is utilized by physicians for the interpretation and identification of physiological and pathological phenomena. In general, ECG signals may mix various noises such as baseline wander, power line interference, and electromagnetic interference in gathering and recording process. As ECG signals are non-stationary physiological signals, wavelet transform is investigated to be an effective tool to discard noises from corrupted signals. A new compromising threshold function called sigmoid function-based thresholding scheme is adopted in processing ECG signals. Compared with other methods such as hard/soft thresholding or other existing thresholding functions, the new algorithm has many advantages in the noise reduction of ECG signals. It perfectly overcomes the discontinuity at ±T of hard thresholding and reduces the fixed deviation of soft thresholding. The improved wavelet thresholding denoising can be proved to be more efficient than existing algorithms in ECG signal denoising. The signal to noise ratio, mean square error, and percent root mean square difference are calculated to verify the denoising performance as quantitative tools. The experimental results reveal that the waves including P, Q, R, and S waves of ECG signals after denoising coincide with the original ECG signals by employing the new proposed method.

High-precision multi-node clock network distribution.

PubMed

Chen, Xing; Cui, Yifan; Lu, Xing; Ci, Cheng; Zhang, Xuesong; Liu, Bo; Wu, Hong; Tang, Tingsong; Shi, Kebin; Zhang, Zhigang

2017-10-01

A high precision multi-node clock network for multiple users was built following the precise frequency transmission and time synchronization of 120 km fiber. The network topology adopts a simple star-shaped network structure. The clock signal of a hydrogen maser (synchronized with UTC) was recovered from a 120 km telecommunication fiber link and then was distributed to 4 sub-stations. The fractional frequency instability of all substations is in the level of 10 -15 in a second and the clock offset instability is in sub-ps in root-mean-square average.

Evaluation of Satellite and Model Precipitation Products Over Turkey

NASA Astrophysics Data System (ADS)

Yilmaz, M. T.; Amjad, M.

2017-12-01

Satellite-based remote sensing, gauge stations, and models are the three major platforms to acquire precipitation dataset. Among them satellites and models have the advantage of retrieving spatially and temporally continuous and consistent datasets, while the uncertainty estimates of these retrievals are often required for many hydrological studies to understand the source and the magnitude of the uncertainty in hydrological response parameters. In this study, satellite and model precipitation data products are validated over various temporal scales (daily, 3-daily, 7-daily, 10-daily and monthly) using in-situ measured precipitation observations from a network of 733 gauges from all over the Turkey. Tropical Rainfall Measurement Mission (TRMM) Multi-satellite Precipitation Analysis (TMPA) 3B42 version 7 and European Center of Medium-Range Weather Forecast (ECMWF) model estimates (daily, 3-daily, 7-daily and 10-daily accumulated forecast) are used in this study. Retrievals are evaluated for their mean and standard deviation and their accuracies are evaluated via bias, root mean square error, error standard deviation and correlation coefficient statistics. Intensity vs frequency analysis and some contingency table statistics like percent correct, probability of detection, false alarm ratio and critical success index are determined using daily time-series. Both ECMWF forecasts and TRMM observations, on average, overestimate the precipitation compared to gauge estimates; wet biases are 10.26 mm/month and 8.65 mm/month, respectively for ECMWF and TRMM. RMSE values of ECMWF forecasts and TRMM estimates are 39.69 mm/month and 41.55 mm/month, respectively. Monthly correlations between Gauges-ECMWF, Gauges-TRMM and ECMWF-TRMM are 0.76, 0.73 and 0.81, respectively. The model and the satellite error statistics are further compared against the gauges error statistics based on inverse distance weighting (IWD) analysis. Both the model and satellite data have less IWD errors (14.72 mm/month and 10.75 mm/month, respectively) compared to gauges IWD error (21.58 mm/month). These results show that, on average, ECMWF forecast data have higher skill than TRMM observations. Overall, both ECMWF forecast data and TRMM observations show good potential for catchment scale hydrological analysis.

Long-term cliff retreat and erosion hotspots along the central shores of the Monterey Bay National Marine Sanctuary

USGS Publications Warehouse

Moore, Laura J.; Griggs, Gary B.

2002-01-01

Quantification of cliff retreat rates for the southern half of Santa Cruz County, CA, USA, located within the Monterey Bay National Marine Sanctuary, using the softcopy/geographic information system (GIS) methodology results in average cliff retreat rates of 7–15 cm/yr between 1953 and 1994. The coastal dunes at the southern end of Santa Cruz County migrate seaward and landward through time and display net accretion between 1953 and 1994, which is partially due to development. In addition, three critically eroding segments of coastline with high average erosion rates ranging from 20 to 63 cm/yr are identified as erosion ‘hotspots’. These locations include: Opal Cliffs, Depot Hill and Manresa. Although cliff retreat is episodic, spatially variable at the scale of meters, and the factors affecting cliff retreat vary along the Santa Cruz County coastline, there is a compensation between factors affecting retreat such that over the long-term the coastline maintains a relatively smooth configuration. The softcopy/GIS methodology significantly reduces errors inherent in the calculation of retreat rates in high-relief areas (e.g. erosion rates generated in this study are generally correct to within 10 cm) by removing errors due to relief displacement. Although the resulting root mean squared error for erosion rates is relatively small, simple projections of past erosion rates are inadequate to provide predictions of future cliff position. Improved predictions can be made for individual coastal segments by using a mean erosion rate and the standard deviation as guides to future cliff behavior in combination with an understanding of processes acting along the coastal segments in question. This methodology can be applied on any high-relief coast where retreat rates can be measured.

A Bayesian Approach for Summarizing and Modeling Time-Series Exposure Data with Left Censoring.

PubMed

Houseman, E Andres; Virji, M Abbas

2017-08-01

Direct reading instruments are valuable tools for measuring exposure as they provide real-time measurements for rapid decision making. However, their use is limited to general survey applications in part due to issues related to their performance. Moreover, statistical analysis of real-time data is complicated by autocorrelation among successive measurements, non-stationary time series, and the presence of left-censoring due to limit-of-detection (LOD). A Bayesian framework is proposed that accounts for non-stationary autocorrelation and LOD issues in exposure time-series data in order to model workplace factors that affect exposure and estimate summary statistics for tasks or other covariates of interest. A spline-based approach is used to model non-stationary autocorrelation with relatively few assumptions about autocorrelation structure. Left-censoring is addressed by integrating over the left tail of the distribution. The model is fit using Markov-Chain Monte Carlo within a Bayesian paradigm. The method can flexibly account for hierarchical relationships, random effects and fixed effects of covariates. The method is implemented using the rjags package in R, and is illustrated by applying it to real-time exposure data. Estimates for task means and covariates from the Bayesian model are compared to those from conventional frequentist models including linear regression, mixed-effects, and time-series models with different autocorrelation structures. Simulations studies are also conducted to evaluate method performance. Simulation studies with percent of measurements below the LOD ranging from 0 to 50% showed lowest root mean squared errors for task means and the least biased standard deviations from the Bayesian model compared to the frequentist models across all levels of LOD. In the application, task means from the Bayesian model were similar to means from the frequentist models, while the standard deviations were different. Parameter estimates for covariates were significant in some frequentist models, but in the Bayesian model their credible intervals contained zero; such discrepancies were observed in multiple datasets. Variance components from the Bayesian model reflected substantial autocorrelation, consistent with the frequentist models, except for the auto-regressive moving average model. Plots of means from the Bayesian model showed good fit to the observed data. The proposed Bayesian model provides an approach for modeling non-stationary autocorrelation in a hierarchical modeling framework to estimate task means, standard deviations, quantiles, and parameter estimates for covariates that are less biased and have better performance characteristics than some of the contemporary methods. Published by Oxford University Press on behalf of the British Occupational Hygiene Society 2017.

Wavelet-based multiscale performance analysis: An approach to assess and improve hydrological models

NASA Astrophysics Data System (ADS)

Rathinasamy, Maheswaran; Khosa, Rakesh; Adamowski, Jan; ch, Sudheer; Partheepan, G.; Anand, Jatin; Narsimlu, Boini

2014-12-01

The temporal dynamics of hydrological processes are spread across different time scales and, as such, the performance of hydrological models cannot be estimated reliably from global performance measures that assign a single number to the fit of a simulated time series to an observed reference series. Accordingly, it is important to analyze model performance at different time scales. Wavelets have been used extensively in the area of hydrological modeling for multiscale analysis, and have been shown to be very reliable and useful in understanding dynamics across time scales and as these evolve in time. In this paper, a wavelet-based multiscale performance measure for hydrological models is proposed and tested (i.e., Multiscale Nash-Sutcliffe Criteria and Multiscale Normalized Root Mean Square Error). The main advantage of this method is that it provides a quantitative measure of model performance across different time scales. In the proposed approach, model and observed time series are decomposed using the Discrete Wavelet Transform (known as the à trous wavelet transform), and performance measures of the model are obtained at each time scale. The applicability of the proposed method was explored using various case studies-both real as well as synthetic. The synthetic case studies included various kinds of errors (e.g., timing error, under and over prediction of high and low flows) in outputs from a hydrologic model. The real time case studies investigated in this study included simulation results of both the process-based Soil Water Assessment Tool (SWAT) model, as well as statistical models, namely the Coupled Wavelet-Volterra (WVC), Artificial Neural Network (ANN), and Auto Regressive Moving Average (ARMA) methods. For the SWAT model, data from Wainganga and Sind Basin (India) were used, while for the Wavelet Volterra, ANN and ARMA models, data from the Cauvery River Basin (India) and Fraser River (Canada) were used. The study also explored the effect of the choice of the wavelets in multiscale model evaluation. It was found that the proposed wavelet-based performance measures, namely the MNSC (Multiscale Nash-Sutcliffe Criteria) and MNRMSE (Multiscale Normalized Root Mean Square Error), are a more reliable measure than traditional performance measures such as the Nash-Sutcliffe Criteria (NSC), Root Mean Square Error (RMSE), and Normalized Root Mean Square Error (NRMSE). Further, the proposed methodology can be used to: i) compare different hydrological models (both physical and statistical models), and ii) help in model calibration.

Numerical investigation of airflow in an idealised human extra-thoracic airway: a comparison study

PubMed Central

Chen, Jie; Gutmark, Ephraim

2013-01-01

Large eddy simulation (LES) technique is employed to numerically investigate the airflow through an idealised human extra-thoracic airway under different breathing conditions, 10 l/min, 30 l/min, and 120 l/min. The computational results are compared with single and cross hot-wire measurements, and with time-averaged flow field computed by standard k-ω and k-ω-SST Reynolds averaged Navier-Stokes (RANS) models and the Lattice-Boltzmann method (LBM). The LES results are also compared to root-mean-square (RMS) flow field computed by the Reynolds stress model (RSM) and LBM. LES generally gives better prediction of the time-averaged flow field than RANS models and LBM. LES also provides better estimation of the RMS flow field than both the RSM and the LBM. PMID:23619907

Predictive ability of mid-infrared spectroscopy for major mineral composition and coagulation traits of bovine milk by using the uninformative variable selection algorithm.

PubMed

Visentin, G; Penasa, M; Gottardo, P; Cassandro, M; De Marchi, M

2016-10-01

Milk minerals and coagulation properties are important for both consumers and processors, and they can aid in increasing milk added value. However, large-scale monitoring of these traits is hampered by expensive and time-consuming reference analyses. The objective of the present study was to develop prediction models for major mineral contents (Ca, K, Mg, Na, and P) and milk coagulation properties (MCP: rennet coagulation time, curd-firming time, and curd firmness) using mid-infrared spectroscopy. Individual milk samples (n=923) of Holstein-Friesian, Brown Swiss, Alpine Grey, and Simmental cows were collected from single-breed herds between January and December 2014. Reference analysis for the determination of both mineral contents and MCP was undertaken with standardized methods. For each milk sample, the mid-infrared spectrum in the range from 900 to 5,000cm(-1) was stored. Prediction models were calibrated using partial least squares regression coupled with a wavenumber selection technique called uninformative variable elimination, to improve model accuracy, and validated both internally and externally. The average reduction of wavenumbers used in partial least squares regression was 80%, which was accompanied by an average increment of 20% of the explained variance in external validation. The proportion of explained variance in external validation was about 70% for P, K, Ca, and Mg, and it was lower (40%) for Na. Milk coagulation properties prediction models explained between 54% (rennet coagulation time) and 56% (curd-firming time) of the total variance in external validation. The ratio of standard deviation of each trait to the respective root mean square error of prediction, which is an indicator of the predictive ability of an equation, suggested that the developed models might be effective for screening and collection of milk minerals and coagulation properties at the population level. Although prediction equations were not accurate enough to be proposed for analytic purposes, mid-infrared spectroscopy predictions could be evaluated as phenotypic information to genetically improve milk minerals and MCP on a large scale. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

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

D2N: Distance to the native.

PubMed

Mishra, Avinash; Rana, Prashant Singh; Mittal, Aditya; Jayaram, B

2014-10-01

Root-mean-square-deviation (RMSD), of computationally-derived protein structures from experimentally determined structures, is a critical index to assessing protein-structure-prediction-algorithms (PSPAs). The development of PSPAs to obtain 0Å RMSD from native structures is considered central to computational biology. However, till date it has been quite challenging to measure how far a predicted protein structure is from its native - in the absence of a known experimental/native structure. In this work, we report the development of a metric "D2N" (distance to the native) - that predicts the "RMSD" of any structure without actually knowing the native structure. By combining physico-chemical properties and known universalities in spatial organization of soluble proteins to develop D2N, we demonstrate the ability to predict the distance of a proposed structure to within ±1.5Ǻ error with a remarkable average accuracy of 93.6% for structures below 5Ǻ from the native. We believe that this work opens up a completely new avenue towards assigning reliable structures to whole proteomes even in the absence of experimentally determined native structures. The D2N tool is freely available at http://www.scfbio-iitd.res.in/software/d2n.jsp. Copyright © 2014 Elsevier B.V. All rights reserved.

Molecular dynamics of individual alpha-helices of bacteriorhodopsin in dimyristol phosphatidylocholine. I. Structure and dynamics.

PubMed

Woolf, T B

1997-11-01

Understanding the role of the lipid bilayer in membrane protein structure and dynamics is needed for tertiary structure determination methods. However, the molecular details are not well understood. Molecular dynamics computer calculations can provide insight into these molecular details of protein:lipid interactions. This paper reports on 10 simulations of individual alpha-helices in explicit lipid bilayers. The 10 helices were selected from the bacteriorhodopsin structure as representative alpha-helical membrane folding components. The bilayer is constructed of dimyristoyl phosphatidylcholine molecules. The only major difference between simulations is the primary sequence of the alpha-helix. The results show dramatic differences in motional behavior between alpha-helices. For example, helix A has much smaller root-mean-squared deviations than does helix D. This can be understood in terms of the presence of aromatic residues at the interface for helix A that are not present in helix D. Additional motions are possible for the helices that contain proline side chains relative to other amino acids. The results thus provide insight into the types of motion and the average structures possible for helices within the bilayer setting and demonstrate the strength of molecular simulations in providing molecular details that are not directly visualized in experiments.

Automatic cable artifact removal for cardiac C-arm CT imaging

NASA Astrophysics Data System (ADS)

Haase, C.; Schäfer, D.; Kim, M.; Chen, S. J.; Carroll, J.; Eshuis, P.; Dössel, O.; Grass, M.

2014-03-01

Cardiac C-arm computed tomography (CT) imaging using interventional C-arm systems can be applied in various areas of interventional cardiology ranging from structural heart disease and electrophysiology interventions to valve procedures in hybrid operating rooms. In contrast to conventional CT systems, the reconstruction field of view (FOV) of C-arm systems is limited to a region of interest in cone-beam (along the patient axis) and fan-beam (in the transaxial plane) direction. Hence, highly X-ray opaque objects (e.g. cables from the interventional setup) outside the reconstruction field of view, yield streak artifacts in the reconstruction volume. To decrease the impact of these streaks a cable tracking approach on the 2D projection sequences with subsequent interpolation is applied. The proposed approach uses the fact that the projected position of objects outside the reconstruction volume depends strongly on the projection perspective. By tracking candidate points over multiple projections only objects outside the reconstruction volume are segmented in the projections. The method is quantitatively evaluated based on 30 simulated CT data sets. The 3D root mean square deviation to a reference image could be reduced for all cases by an average of 50 % (min 16 %, max 76 %). Image quality improvement is shown for clinical whole heart data sets acquired on an interventional C-arm system.

In silico study of the human rhodopsin and meta rhodopsin II/S-arrestin complexes: impact of single point mutations related to retina degenerative diseases.

PubMed

Mokarzel-Falcón, Leonardo; Padrón-García, Juan Alexander; Carrasco-Velar, Ramón; Berry, Colin; Montero-Cabrera, Luis A

2008-03-01

We propose two models of the human S-arrestin/rhodopsin complex in the inactive dark adapted rhodopsin and meta rhodopsin II form, obtained by homology modeling and knowledge based docking. First, a homology model for the human S-arrestin was built and validated by molecular dynamics, showing an average root mean square deviation difference from the pattern behavior of 0.76 A. Then, combining the human S-arrestin model and the modeled structure of the two human rhodopsin forms, we propose two models of interaction for the human S-arrestin/rhodopsin complex. The models involve two S-arrestin regions related to the N domain (residues 68-78; 170-182) and a third constituent of the C domain (248-253), with the rhodopsin C terminus (330-348). Of the 22 single point mutations related to retinitis pigmentosa and congenital night blindness located in the cytoplasmatic portion of rhodopsin or in S-arrestin, our models locate 16 in the interaction region and relate two others to possible dimer formation. Our calculations also predict that the light activated complex is more stable than the dark adapted rhodopsin and, therefore, of higher affinity to S-arrestin. 2008 Wiley-Liss, Inc.

Comparison of GPS receiver DCB estimation methods using a GPS network

NASA Astrophysics Data System (ADS)

Choi, Byung-Kyu; Park, Jong-Uk; Min Roh, Kyoung; Lee, Sang-Jeong

2013-07-01

Two approaches for receiver differential code biases (DCB) estimation using the GPS data obtained from the Korean GPS network (KGN) in South Korea are suggested: the relative and single (absolute) methods. The relative method uses a GPS network, while the single method determines DCBs from a single station only. Their performance was assessed by comparing the receiver DCB values obtained from the relative method with those estimated by the single method. The daily averaged receiver DCBs obtained from the two different approaches showed good agreement for 7 days. The root mean square (RMS) value of those differences is 0.83 nanoseconds (ns). The standard deviation of the receiver DCBs estimated by the relative method was smaller than that of the single method. From these results, it is clear that the relative method can obtain more stable receiver DCBs compared with the single method over a short-term period. Additionally, the comparison between the receiver DCBs obtained by the Korea Astronomy and Space Science Institute (KASI) and those of the IGS Global Ionosphere Maps (GIM) showed a good agreement at 0.3 ns. As the accuracy of DCB values significantly affects the accuracy of ionospheric total electron content (TEC), more studies are needed to ensure the reliability and stability of the estimated receiver DCBs.

Flight Measurement of Wall-Pressure Fluctuations and Boundary-Layer Turbulence

NASA Technical Reports Server (NTRS)

Mull, Harold R.; Algranti, Joseph S.

1960-01-01

The results are presented for a flight test program using a fighter type jet aircraft flying at pressure altitudes of 10,000, 20,000, and 30,000 feet at Mach numbers from 0.3 to 0.8. Specially designed apparatus was used to measure and record the output of microphones and hot-wire anemometers mounted on the forward-fuselage section and wing of the airplane. Mean-velocity profiles in the boundary layers were obtained from total-pressure measurements. The ratio of the root-mean-square fluctuating wall pressure to the free-stream dynamic pressure is presented as a function of Reynolds number and Mach number. The longitudinal component of the turbulent-velocity fluctuations was measured, and the turbulence-intensity profiles are presented for the wing and forward-fuselage section. In general, the results are in agreement with wind-tunnel measurements which have been-reported in the literature. For example, the variation the square root of p(sup 2)/q times the square root of p(sup 2) is the root mean square of the wall-pressure fluctuation, and q is the free-stream dynamic pressure) with Reynolds number was found to be essentially constant for the forward-fuselage-section boundary layer, while variations at the wing station were probably unduly affected by the microphone diameter (5/8 in.), which was large compared with the boundary-layer thickness.

Analytical probabilistic proton dose calculation and range uncertainties

NASA Astrophysics Data System (ADS)

Bangert, M.; Hennig, P.; Oelfke, U.

2014-03-01

We introduce the concept of analytical probabilistic modeling (APM) to calculate the mean and the standard deviation of intensity-modulated proton dose distributions under the influence of range uncertainties in closed form. For APM, range uncertainties are modeled with a multivariate Normal distribution p(z) over the radiological depths z. A pencil beam algorithm that parameterizes the proton depth dose d(z) with a weighted superposition of ten Gaussians is used. Hence, the integrals ∫ dz p(z) d(z) and ∫ dz p(z) d(z)2 required for the calculation of the expected value and standard deviation of the dose remain analytically tractable and can be efficiently evaluated. The means μk, widths δk, and weights ωk of the Gaussian components parameterizing the depth dose curves are found with least squares fits for all available proton ranges. We observe less than 0.3% average deviation of the Gaussian parameterizations from the original proton depth dose curves. Consequently, APM yields high accuracy estimates for the expected value and standard deviation of intensity-modulated proton dose distributions for two dimensional test cases. APM can accommodate arbitrary correlation models and account for the different nature of random and systematic errors in fractionated radiation therapy. Beneficial applications of APM in robust planning are feasible.

Quick method (FT-NIR) for the determination of oil and major fatty acids content in whole achenes of milk thistle (Silybum marianum (L.) Gaertn.).

PubMed

Koláčková, Pavla; Růžičková, Gabriela; Gregor, Tomáš; Šišperová, Eliška

2015-08-30

Calibration models for the Fourier transform-near infrared (FT-NIR) instrument were developed for quick and non-destructive determination of oil and fatty acids in whole achenes of milk thistle. Samples with a range of oil and fatty acid levels were collected and their transmittance spectra were obtained by the FT-NIR instrument. Based on these spectra and data gained by the means of the reference method - Soxhlet extraction and gas chromatography (GC) - calibration models were created by means of partial least square (PLS) regression analysis. Precision and accuracy of the calibration models was verified via the cross-validation of validation samples whose spectra were not part of the calibration model and also according to the root mean square error of prediction (RMSEP), root mean square error of calibration (RMSEC), root mean square error of cross-validation (RMSECV) and the validation coefficient of determination (R(2) ). R(2) for whole seeds were 0.96, 0.96, 0.83 and 0.67 and the RMSEP values were 0.76, 1.68, 1.24, 0.54 for oil, linoleic (C18:2), oleic (C18:1) and palmitic (C16:0) acids, respectively. The calibration models are appropriate for the non-destructive determination of oil and fatty acids levels in whole seeds of milk thistle. © 2014 Society of Chemical Industry.

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

Wulff, J; Huggins, A

Purpose: The shape of a single beam in proton PBS influences the resulting dose distribution. Spot profiles are modelled as two-dimensional Gaussian (single/ double) distributions in treatment planning systems (TPS). Impact of slight deviations from an ideal Gaussian on resulting dose distributions is typically assumed to be small due to alleviation by multiple Coulomb scattering (MCS) in tissue and superposition of many spots. Quantitative limits are however not clear per se. Methods: A set of 1250 deliberately deformed profiles with sigma=4 mm for a Gaussian fit were constructed. Profiles and fit were normalized to the same area, resembling output calibrationmore » in the TPS. Depth-dependent MCS was considered. The deviation between deformed and ideal profiles was characterized by root-mean-squared deviation (RMSD), skewness/ kurtosis (SK) and full-width at different percentage of maximum (FWxM). The profiles were convolved with different fluence patterns (regular/ random) resulting in hypothetical dose distributions. The resulting deviations were analyzed by applying a gamma-test. Results were compared to measured spot profiles. Results: A clear correlation between pass-rate and profile metrics could be determined. The largest impact occurred for a regular fluence-pattern with increasing distance between single spots, followed by a random distribution of spot weights. The results are strongly dependent on gamma-analysis dose and distance levels. Pass-rates of >95% at 2%/2 mm and 40 mm depth (=70 MeV) could only be achieved for RMSD<10%, deviation in FWxM at 20% and root of quadratic sum of SK <0.8. As expected the results improve for larger depths. The trends were well resembled for measured spot profiles. Conclusion: All measured profiles from ProBeam sites passed the criteria. Given the fact, that beam-line tuning can result shape distortions, the derived criteria represent a useful QA tool for commissioning and design of future beam-line optics.« less

SPA- STATISTICAL PACKAGE FOR TIME AND FREQUENCY DOMAIN ANALYSIS

NASA Technical Reports Server (NTRS)

Brownlow, J. D.

1994-01-01

The need for statistical analysis often arises when data is in the form of a time series. This type of data is usually a collection of numerical observations made at specified time intervals. Two kinds of analysis may be performed on the data. First, the time series may be treated as a set of independent observations using a time domain analysis to derive the usual statistical properties including the mean, variance, and distribution form. Secondly, the order and time intervals of the observations may be used in a frequency domain analysis to examine the time series for periodicities. In almost all practical applications, the collected data is actually a mixture of the desired signal and a noise signal which is collected over a finite time period with a finite precision. Therefore, any statistical calculations and analyses are actually estimates. The Spectrum Analysis (SPA) program was developed to perform a wide range of statistical estimation functions. SPA can provide the data analyst with a rigorous tool for performing time and frequency domain studies. In a time domain statistical analysis the SPA program will compute the mean variance, standard deviation, mean square, and root mean square. It also lists the data maximum, data minimum, and the number of observations included in the sample. In addition, a histogram of the time domain data is generated, a normal curve is fit to the histogram, and a goodness-of-fit test is performed. These time domain calculations may be performed on both raw and filtered data. For a frequency domain statistical analysis the SPA program computes the power spectrum, cross spectrum, coherence, phase angle, amplitude ratio, and transfer function. The estimates of the frequency domain parameters may be smoothed with the use of Hann-Tukey, Hamming, Barlett, or moving average windows. Various digital filters are available to isolate data frequency components. Frequency components with periods longer than the data collection interval are removed by least-squares detrending. As many as ten channels of data may be analyzed at one time. Both tabular and plotted output may be generated by the SPA program. This program is written in FORTRAN IV and has been implemented on a CDC 6000 series computer with a central memory requirement of approximately 142K (octal) of 60 bit words. This core requirement can be reduced by segmentation of the program. The SPA program was developed in 1978.

Descriptive Statistics and Cluster Analysis for Extreme Rainfall in Java Island

NASA Astrophysics Data System (ADS)

E Komalasari, K.; Pawitan, H.; Faqih, A.

2017-03-01

This study aims to describe regional pattern of extreme rainfall based on maximum daily rainfall for period 1983 to 2012 in Java Island. Descriptive statistics analysis was performed to obtain centralization, variation and distribution of maximum precipitation data. Mean and median are utilized to measure central tendency data while Inter Quartile Range (IQR) and standard deviation are utilized to measure variation of data. In addition, skewness and kurtosis used to obtain shape the distribution of rainfall data. Cluster analysis using squared euclidean distance and ward method is applied to perform regional grouping. Result of this study show that mean (average) of maximum daily rainfall in Java Region during period 1983-2012 is around 80-181mm with median between 75-160mm and standard deviation between 17 to 82. Cluster analysis produces four clusters and show that western area of Java tent to have a higher annual maxima of daily rainfall than northern area, and have more variety of annual maximum value.

Finite Element Model of the Knee for Investigation of Injury Mechanisms: Development and Validation

PubMed Central

Kiapour, Ali; Kiapour, Ata M.; Kaul, Vikas; Quatman, Carmen E.; Wordeman, Samuel C.; Hewett, Timothy E.; Demetropoulos, Constantine K.; Goel, Vijay K.

2014-01-01

Multiple computational models have been developed to study knee biomechanics. However, the majority of these models are mainly validated against a limited range of loading conditions and/or do not include sufficient details of the critical anatomical structures within the joint. Due to the multifactorial dynamic nature of knee injuries, anatomic finite element (FE) models validated against multiple factors under a broad range of loading conditions are necessary. This study presents a validated FE model of the lower extremity with an anatomically accurate representation of the knee joint. The model was validated against tibiofemoral kinematics, ligaments strain/force, and articular cartilage pressure data measured directly from static, quasi-static, and dynamic cadaveric experiments. Strong correlations were observed between model predictions and experimental data (r > 0.8 and p < 0.0005 for all comparisons). FE predictions showed low deviations (root-mean-square (RMS) error) from average experimental data under all modes of static and quasi-static loading, falling within 2.5 deg of tibiofemoral rotation, 1% of anterior cruciate ligament (ACL) and medial collateral ligament (MCL) strains, 17 N of ACL load, and 1 mm of tibiofemoral center of pressure. Similarly, the FE model was able to accurately predict tibiofemoral kinematics and ACL and MCL strains during simulated bipedal landings (dynamic loading). In addition to minimal deviation from direct cadaveric measurements, all model predictions fell within 95% confidence intervals of the average experimental data. Agreement between model predictions and experimental data demonstrates the ability of the developed model to predict the kinematics of the human knee joint as well as the complex, nonuniform stress and strain fields that occur in biological soft tissue. Such a model will facilitate the in-depth understanding of a multitude of potential knee injury mechanisms with special emphasis on ACL injury. PMID:24763546

Percentage depth dose calculation accuracy of model based algorithms in high energy photon small fields through heterogeneous media and comparison with plastic scintillator dosimetry

PubMed Central

Mani, Ganesh Kadirampatti; Karunakaran, Kaviarasu

2016-01-01

Small fields smaller than 4×4 cm2 are used in stereotactic and conformal treatments where heterogeneity is normally present. Since dose calculation accuracy in both small fields and heterogeneity often involves more discrepancy, algorithms used by treatment planning systems (TPS) should be evaluated for achieving better treatment results. This report aims at evaluating accuracy of four model‐based algorithms, X‐ray Voxel Monte Carlo (XVMC) from Monaco, Superposition (SP) from CMS‐Xio, AcurosXB (AXB) and analytical anisotropic algorithm (AAA) from Eclipse are tested against the measurement. Measurements are done using Exradin W1 plastic scintillator in Solid Water phantom with heterogeneities like air, lung, bone, and aluminum, irradiated with 6 and 15 MV photons of square field size ranging from 1 to 4 cm2. Each heterogeneity is introduced individually at two different depths from depth‐of‐dose maximum (Dmax), one setup being nearer and another farther from the Dmax. The central axis percentage depth‐dose (CADD) curve for each setup is measured separately and compared with the TPS algorithm calculated for the same setup. The percentage normalized root mean squared deviation (%NRMSD) is calculated, which represents the whole CADD curve's deviation against the measured. It is found that for air and lung heterogeneity, for both 6 and 15 MV, all algorithms show maximum deviation for field size 1×1 cm2 and gradually reduce when field size increases, except for AAA. For aluminum and bone, all algorithms' deviations are less for 15 MV irrespective of setup. In all heterogeneity setups, 1×1 cm2 field showed maximum deviation, except in 6 MV bone setup. All algorithms in the study, irrespective of energy and field size, when any heterogeneity is nearer to Dmax, the dose deviation is higher compared to the same heterogeneity far from the Dmax. Also, all algorithms show maximum deviation in lower‐density materials compared to high‐density materials. PACS numbers: 87.53.Bn, 87.53.kn, 87.56.bd, 87.55.Kd, 87.56.jf PMID:26894345

Atlas of interoccurrence intervals for selected thresholds of daily precipitation in Texas

USGS Publications Warehouse

Asquith, William H.; Roussel, Meghan C.

2003-01-01

A Poisson process model is used to define the distribution of interoccurrence intervals of daily precipitation in Texas. A precipitation interoccurrence interval is the time period between two successive rainfall events. Rainfall events are defined as daily precipitation equaling or exceeding a specified depth threshold. Ten precipitation thresholds are considered: 0.05, 0.10, 0.25, 0.50, 0.75, 1.0, 1.5, 2.0, 2.5, and 3.0 inches. Site-specific mean interoccurrence interval and ancillary statistics are presented for each threshold and for each of 1,306 National Weather Service daily precipitation gages. Maps depicting the spatial variation across Texas of the mean interoccurrence interval for each threshold are presented. The percent change from the statewide standard deviation of the interoccurrence intervals to the root-mean-square error ranges from a magnitude minimum of (negative) -24 to a magnitude maximum of -60 percent for the 0.05- and 2.0-inch thresholds, respectively. Because of the substantial negative percent change, the maps are considered more reliable estimators of the mean interoccurrence interval for most locations in Texas than the statewide mean values.

Prediction of Moisture Content for Congou Black Tea Withering Leaves Using Image Features and Nonlinear Method.

PubMed

Liang, Gaozhen; Dong, Chunwang; Hu, Bin; Zhu, Hongkai; Yuan, Haibo; Jiang, Yongwen; Hao, Guoshuang

2018-05-18

Withering is the first step in the processing of congou black tea. With respect to the deficiency of traditional water content detection methods, a machine vision based NDT (Non Destructive Testing) method was established to detect the moisture content of withered leaves. First, according to the time sequences using computer visual system collected visible light images of tea leaf surfaces, and color and texture characteristics are extracted through the spatial changes of colors. Then quantitative prediction models for moisture content detection of withered tea leaves was established through linear PLS (Partial Least Squares) and non-linear SVM (Support Vector Machine). The results showed correlation coefficients higher than 0.8 between the water contents and green component mean value (G), lightness component mean value (L * ) and uniformity (U), which means that the extracted characteristics have great potential to predict the water contents. The performance parameters as correlation coefficient of prediction set (Rp), root-mean-square error of prediction (RMSEP), and relative standard deviation (RPD) of the SVM prediction model are 0.9314, 0.0411 and 1.8004, respectively. The non-linear modeling method can better describe the quantitative analytical relations between the image and water content. With superior generalization and robustness, the method would provide a new train of thought and theoretical basis for the online water content monitoring technology of automated production of black tea.

Effect of laser frequency noise on fiber-optic frequency reference distribution

NASA Technical Reports Server (NTRS)

Logan, R. T., Jr.; Lutes, G. F.; Maleki, L.

1989-01-01

The effect of the linewidth of a single longitude-mode laser on the frequency stability of a frequency reference transmitted over a single-mode optical fiber is analyzed. The interaction of the random laser frequency deviations with the dispersion of the optical fiber is considered to determine theoretically the effect on the Allan deviation (square root of the Allan variance) of the transmitted frequency reference. It is shown that the magnitude of this effect may determine the limit of the ultimate stability possible for frequency reference transmission on optical fiber, but is not a serious limitation to present system performance.

Protein–DNA Interactions: The Story so Far and a New Method for Prediction

DOE PAGES

Jones, Susan; Thornton, Janet M.

2003-01-01

This review describes methods for the prediction of DNA binding function, and specifically summarizes a new method using 3D structural templates. The new method features the HTH motif that is found in approximately one-third of DNAbinding protein families. A library of 3D structural templates of HTH motifs was derived from proteins in the PDB. Templates were scanned against complete protein structures and the optimal superposition of a template on a structure calculated. Significance thresholds in terms of a minimum root mean squared deviation (rmsd) of an optimal superposition, and a minimum motif accessible surface area (ASA), have been calculated. Inmore » this way, it is possible to scan the template library against proteins of unknown function to make predictions about DNA-binding functionality.« less

Pharmacophore modeling of diverse classes of p38 MAP kinase inhibitors.

PubMed

Sarma, Rituparna; Sinha, Sharat; Ravikumar, Muttineni; Kishore Kumar, Madala; Mahmood, S K

2008-12-01

Mitogen-activated protein (MAP) p38 kinase is a serine-threonine protein kinase and its inhibitors are useful in the treatment of inflammatory diseases. Pharmacophore models were developed using HypoGen program of Catalyst with diverse classes of p38 MAP kinase inhibitors. The best pharmacophore hypothesis (Hypo1) with hydrogen-bond acceptor (HBA), hydrophobic (HY), hydrogen-bond donor (HBD), and ring aromatic (RA) as features has correlation coefficient of 0.959, root mean square deviation (RMSD) of 1.069 and configuration cost of 14.536. The model was validated using test set containing 119 compounds and had high correlation coefficient of 0.851. The results demonstrate that results obtained in this study can be considered to be useful and reliable tools in identifying structurally diverse compounds with desired biological activity.

Geometric effects resulting from the asymmetry of dipping fault: Hanging wall/ footwall effects

NASA Astrophysics Data System (ADS)

Wang, Dong; Xie, Li-Li; Hu, Jin-Jun

2008-05-01

Root-mean-square distance D rms with characteristic of weighted-average is introduced in this article firstly. D rms can be used to capture the general proximity of a site to a dipping fault plane comparing with the rupture distance D rup and the seismogenic distance D seis. Then, using D rup, D seis and D rms, the hanging wall/footwall effects on the peak ground acceleration (PGA) during the 1999 Chi-Chi earthquake are evaluated by regression analysis. The logarithm residual shows that the PGA on hanging wall is much greater than that on footwall at the same D rup or D seis when the D rup or D seis is used as site-to-source distance measure. In contrast, there is no significant difference between the PGA on hanging wall and that on footwall at the same D rms when D rms is used. This result confirms that the hanging wall/footwall effect is mainly a geometric effect caused by the asymmetry of dipping fault. Therefore, the hanging wall/footwall effect on the near-fault ground motions can be ignored in the future attenuation analysis if the root-mean-square distance D rms is used as the site-to-source distance measure.

Comparative molecular dynamics simulation studies for determining factors contributing to the thermostability of chemotaxis protein "CheY".

PubMed

Paul, Manish; Hazra, Mousumi; Barman, Arghya; Hazra, Saugata

2014-01-01

Comparative molecular dynamics simulations of chemotaxis protein "CheY" from thermophilic origin Thermotoga maritima and its mesophilic counterpart Salmonella enterica have been performed for 10 ns each at 300 and 350 K, and 20 ns each at 400 and 450 K. The trajectories were analyzed in terms of different factors like root-mean-square deviation, root-mean-square fluctuation, radius of gyration, solvent accessible surface area, H-bonds, salt bridge content, and protein-solvent interactions which indicate distinct differences between the two of them. The two proteins also follow dissimilar unfolding pathways. The overall flexibility calculated by the trace of the diagonalized covariance matrix displays similar flexibility of both the proteins near their optimum growth temperatures. However, at higher temperatures mesophilic protein shows increased overall flexibility than its thermophilic counterpart. Principal component analysis also indicates that the essential subspaces explored by the simulations of two proteins at different temperatures are nonoverlapping and they show significantly different directions of motion. However, there are significant overlaps within the trajectories and similar direction of motions are observed for both proteins at 300 K. Overall, the mesophilic protein leads to increased conformational sampling of the phase space than its thermophilic counterpart. This is the first ever study of thermostability of CheY protein homologs by using protein dynamism as a main impact. Our study might be used as a model for studying the molecular basis of thermostability of two homologous proteins from two organisms living at different temperatures with less visible differences.

Mechanism of Inhibition of Hsp90 Dimerization by Gyrase B Inhibitor Coumermycin A1 (C-A1) Revealed by Molecular Dynamics Simulations and Thermodynamic Calculations.

PubMed

Cele, Favourite N; Kumalo, Hezekiel; Soliman, Mahmoud E S

2016-09-01

Heat shock protein (Hsp) 90 an emerging and attracting target in the anti-HIV drug discovery process due to the key role it plays in the pathogenicity of HIV-1 virus. In this research study, long-range all-atom molecular dynamics simulations were engaged for the bound and the unbound proteins to enhance the understanding of the molecular mechanisms of the Hsp90 dimerization and inhibition. Results evidently showed that coumermycin A1 (C-A1), a recently discovered Hsp90 inhibitor, binds at the dimer's active site of the Hsp90 protein and leads to a substantial parting between dimeric opposed residues, which include Arg591.B, Lys594.A, Ser663.A, Thr653.B, Ala665.A, Thr649.B, Leu646.B and Asn669.A. Significant differences in magnitudes were observed in radius of gyration, root-mean-square deviation and root-mean-square fluctuation, which confirms a reasonably more flexible state in the apo conformation associated with it dimerization. In contrast, the bound conformer of Hsp90 showed less flexibility. This visibly highpoints the inhibition process resulting from the binding of the ligand. These findings were further validated by principal component analysis. We believe that the detailed dynamic analyses of Hsp90 presented in this study, would give an imperative insight and better understanding to the function and mechanisms of inhibition. Furthermore, information obtained from the binding mode of the inhibitor would be of great assistance in the design of more potent inhibitors against the HIV target Hsp90.

Allosteric effects of gold nanoparticles on human serum albumin.

PubMed

Shao, Qing; Hall, Carol K

2017-01-07

The ability of nanoparticles to alter protein structure and dynamics plays an important role in their medical and biological applications. We investigate allosteric effects of gold nanoparticles on human serum albumin protein using molecular simulations. The extent to which bound nanoparticles influence the structure and dynamics of residues distant from the binding site is analyzed. The root mean square deviation, root mean square fluctuation and variation in the secondary structure of individual residues on a human serum albumin protein are calculated for four protein-gold nanoparticle binding complexes. The complexes are identified in a brute-force search process using an implicit-solvent coarse-grained model for proteins and nanoparticles. They are then converted to atomic resolution and their structural and dynamic properties are investigated using explicit-solvent atomistic molecular dynamics simulations. The results show that even though the albumin protein remains in a folded structure, the presence of a gold nanoparticle can cause more than 50% of the residues to decrease their flexibility significantly, and approximately 10% of the residues to change their secondary structure. These affected residues are distributed on the whole protein, even on regions that are distant from the nanoparticle. We analyze the changes in structure and flexibility of amino acid residues on a variety of binding sites on albumin and confirm that nanoparticles could allosterically affect the ability of albumin to bind fatty acids, thyroxin and metals. Our simulations suggest that allosteric effects must be considered when designing and deploying nanoparticles in medical and biological applications that depend on protein-nanoparticle interactions.

In Silico Template Selection of Short Antimicrobial Peptide Viscotoxin for Improving Its Antimicrobial Efficiency in Development of Potential Therapeutic Drugs.

PubMed

Senthilkumar, B; Rajasekaran, R

2017-03-01

Rapid increase in antibiotic resistance has posed a worldwide threat, due to increased mortality, morbidity, and expenditure caused by antibiotic-resistant microbes. Recent development of the antimicrobial peptides like viscotoxin (Vt) has been successfully comprehended as a substitute for classical antibiotics. A structurally stable peptide, Vt can enhance antimicrobial property and can be used for various developmental purposes. Thus, structural stability among the antimicrobial peptides, Vt A1 (3C8P), A2 (1JMN), A3 (1ED0), B (1JMP), and C (1ORL) of Viscus album was computationally analyzed. In specific, the static confirmation of VtA3 showed high number of intramolecular interactions, along with an increase in hydrophobicity than others comparatively. Further, conformational sampling was used to analyze various geometrical parameters such as root mean square deviation, root mean square fluctuation, radius of gyration, and ovality which also revealed the structural stability of VtA3. Moreover, the statistically validated contours of surface area, lipophilicity, and distance constraints of disulfide bonds also supported the priority of VtA3 with respect to stability. Finally, the functional activity of peptides was accessed by computing their free energy of membrane association and membrane interactions, which defined VtA3 as functionally stable. Currently, peptide-based antibiotics and nanoparticles have attracted the pharmaceutical industries for their potential therapeutic applications. Thereby, it is proposed that viscotoxin A3 (1ED0) could be used as a preeminent template for scaffolding potentially efficient antimicrobial peptide-based drugs and nanomaterials in future.

Computational design of a thermostable mutant of cocaine esterase via molecular dynamics simulations.

PubMed

Huang, Xiaoqin; Gao, Daquan; Zhan, Chang-Guo

2011-06-07

Cocaine esterase (CocE) has been known as the most efficient native enzyme for metabolizing naturally occurring cocaine. A major obstacle to the clinical application of CocE is the thermoinstability of native CocE with a half-life of only ∼11 min at physiological temperature (37 °C). It is highly desirable to develop a thermostable mutant of CocE for therapeutic treatment of cocaine overdose and addiction. To establish a structure-thermostability relationship, we carried out molecular dynamics (MD) simulations at 400 K on wild-type CocE and previously known thermostable mutants, demonstrating that the thermostability of the active form of the enzyme correlates with the fluctuation (characterized as the root-mean square deviation and root-mean square fluctuation of atomic positions) of the catalytic residues (Y44, S117, Y118, H287, and D259) in the simulated enzyme. In light of the structure-thermostability correlation, further computational modelling including MD simulations at 400 K predicted that the active site structure of the L169K mutant should be more thermostable. The prediction has been confirmed by wet experimental tests showing that the active form of the L169K mutant had a half-life of 570 min at 37 °C, which is significantly longer than those of the wild-type and previously known thermostable mutants. The encouraging outcome suggests that the high-temperature MD simulations and the structure-thermostability relationship may be considered as a valuable tool for the computational design of thermostable mutants of an enzyme.

Smoking, ADHD, and Problematic Video Game Use: A Structural Modeling Approach.

PubMed

Lee, Hyo Jin; Tran, Denise D; Morrell, Holly E R

2018-05-01

Problematic video game use (PVGU), or addiction-like use of video games, is associated with physical and mental health problems and problems in social and occupational functioning. Possible correlates of PVGU include frequency of play, cigarette smoking, and attention deficit hyperactivity disorder (ADHD). The aim of the current study was to explore simultaneously the relationships among these variables as well as test whether two separate measures of PVGU measure the same construct, using a structural modeling approach. Secondary data analysis was conducted on 2,801 video game users (M age  = 22.43 years, standard deviation [SD] age  = 4.7; 93 percent male) who completed an online survey. The full model fit the data well: χ 2 (2) = 2.017, p > 0.05; root mean square error of approximation (RMSEA) = 0.002 (90% CI [0.000-0.038]); comparative fit index (CFI) = 1.000; standardized root mean square residual (SRMR) = 0.004; and all standardized residuals <|0.1|. All freely estimated paths were statistically significant. ADHD symptomatology, smoking behavior, and hours of video game use explained 41.8 percent of variance in PVGU. Tracking these variables may be useful for PVGU prevention and assessment. Young's Internet Addiction Scale, adapted for video game use, and the Problem Videogame Playing Scale both loaded strongly onto a PVGU factor, suggesting that they measure the same construct, that studies using either measure may be compared to each other, and that both measures may be used as a screener of PVGU.

Study of intermolecular contacts in the proline-rich homeodomain (PRH)-DNA complex using molecular dynamics simulations.

PubMed

Jalili, Seifollah; Karami, Leila

2012-03-01

The proline-rich homeodomain (PRH)-DNA complex consists of a protein with 60 residues and a 13-base-pair DNA. The PRH protein is a transcription factor that plays a key role in the regulation of gene expression. PRH is a significant member of the Q50 class of homeodomain proteins. The homeodomain section of PRH is essential for binding to DNA and mediates sequence-specific DNA binding. Three 20-ns molecular dynamics (MD) simulations (free protein, free DNA and protein-DNA complex) in explicit solvent water were performed to elucidate the intermolecular contacts in the PRH-DNA complex and the role of dynamics of water molecules forming water-mediated contacts. The simulation provides a detailed explanation of the trajectory of hydration water molecules. The simulations show that some water molecules in the protein-DNA interface exchange with bulk waters. The simulation identifies that most of the contacts consisted of direct interactions between the protein and DNA including specific and non-specific contacts, but several water-mediated polar contacts were also observed. The specific interaction between Gln50 and C18 and water-mediated hydrogen bond between Gln50 and T7 were found to be present during almost the entire time of the simulation. These results show good consistency with experimental and previous computational studies. Structural properties such as root-mean-square deviations (RMSD), root-mean-square fluctuations (RMSF) and secondary structure were also analyzed as a function of time. Analyses of the trajectories showed that the dynamic fluctuations of both the protein and the DNA were lowered by the complex formation.

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.

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

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.

Automatic detection of end-diastolic and end-systolic frames in 2D echocardiography.

PubMed

Zolgharni, Massoud; Negoita, Madalina; Dhutia, Niti M; Mielewczik, Michael; Manoharan, Karikaran; Sohaib, S M Afzal; Finegold, Judith A; Sacchi, Stefania; Cole, Graham D; Francis, Darrel P

2017-07-01

Correctly selecting the end-diastolic and end-systolic frames on a 2D echocardiogram is important and challenging, for both human experts and automated algorithms. Manual selection is time-consuming and subject to uncertainty, and may affect the results obtained, especially for advanced measurements such as myocardial strain. We developed and evaluated algorithms which can automatically extract global and regional cardiac velocity, and identify end-diastolic and end-systolic frames. We acquired apical four-chamber 2D echocardiographic video recordings, each at least 10 heartbeats long, acquired twice at frame rates of 52 and 79 frames/s from 19 patients, yielding 38 recordings. Five experienced echocardiographers independently marked end-systolic and end-diastolic frames for the first 10 heartbeats of each recording. The automated algorithm also did this. Using the average of time points identified by five human operators as the reference gold standard, the individual operators had a root mean square difference from that gold standard of 46.5 ms. The algorithm had a root mean square difference from the human gold standard of 40.5 ms (P<.0001). Put another way, the algorithm-identified time point was an outlier in 122/564 heartbeats (21.6%), whereas the average human operator was an outlier in 254/564 heartbeats (45%). An automated algorithm can identify the end-systolic and end-diastolic frames with performance indistinguishable from that of human experts. This saves staff time, which could therefore be invested in assessing more beats, and reduces uncertainty about the reliability of the choice of frame. © 2017, Wiley Periodicals, Inc.

In-car particles and cardiovascular health: an air conditioning-based intervention study.

PubMed

Chuang, Hsiao-Chi; Lin, Lian-Yu; Hsu, Ya-Wen; Ma, Chih-Ming; Chuang, Kai-Jen

2013-05-01

Exposure to traffic-related particulate matter (PM) is considered a potential risk for cardiovascular events. Little is known about whether improving air quality in car can modify cardiovascular effects among human subjects during commuting. We recruited a panel of 60 healthy subjects to commute for 2 h by a car equipped with an air conditioning (AC) system during the morning rush hour in Taipei. Operation modes of AC system using outside air (OA-mode), circulating inside air (IA-mode) and turning off (Off-mode) were examined. Repeated measurements of heart rate variability (HRV) indices, PM≤2.5 μm in aerodynamic diameter (PM2.5) and noise level were conducted for each participant in different modes during the commute. We used linear mixed-effects models to associate HRV indices with in-car PM2.5. We found that decreases in HRV indices were associated with increased levels of in-car PM2.5. For Off-mode, an interquartile range (IQR) increase in in-car PM2.5 with 15-min moving average was associated with 2.7% and 4.1% decreases in standard deviation of NN intervals (SDNN) and the square root of the mean of the sum of the squares of differences between adjacent NN intervals (r-MSSD), respectively. During OA and IA modes, participants showed slight decreases in SDNN (OA mode: 0.1%; IA mode: 1.3%) and r-MSSD (OA mode: 1.1%; IA mode: 1.8%) by an IQR increase in in-car PM2.5 with 15-min moving average. We concluded that in-car PM2.5 is associated with autonomic alteration. Utilization of the car's AC system can improve air quality and modify the effects of in-car PM2.5 on HRV indices among human subjects during the commute. Copyright © 2013 Elsevier B.V. All rights reserved.

Hybrid empirical mode decomposition- ARIMA for forecasting exchange rates

NASA Astrophysics Data System (ADS)

Abadan, Siti Sarah; Shabri, Ani; Ismail, Shuhaida

2015-02-01

This paper studied the forecasting of monthly Malaysian Ringgit (MYR)/ United State Dollar (USD) exchange rates using the hybrid of two methods which are the empirical model decomposition (EMD) and the autoregressive integrated moving average (ARIMA). MYR is pegged to USD during the Asian financial crisis causing the exchange rates are fixed to 3.800 from 2nd of September 1998 until 21st of July 2005. Thus, the chosen data in this paper is the post-July 2005 data, starting from August 2005 to July 2010. The comparative study using root mean square error (RMSE) and mean absolute error (MAE) showed that the EMD-ARIMA outperformed the single-ARIMA and the random walk benchmark model.

Measuring changes in the illicit cigarette market using government revenue data: the example of South Africa

PubMed Central

van Walbeek, Corné

2014-01-01

Background The tobacco industry claims that illicit trade in cigarettes has increased sharply since the 1990s and that government has lost substantial tax revenue. Objectives (1) To determine whether cigarette excise tax revenue has been below budget in recent years, compared with previous decades. (2) To determine trends in the size of the illicit market since 1995. Methods For (1), mean percentage errors and root mean square percentage errors were calculated for budget revenue deviation for three products (cigarettes, beer and spirits), for various subperiods. For (2), predicted changes in total consumption, using actual cigarette price and GDP changes and previously published price and income elasticity estimates, were calculated and compared with changes in tax-paid consumption. Results Cigarette excise revenues were 0.7% below budget for 2000–2012 on average, compared with 3.0% below budget for beer and 4.7% below budget for spirits. There is no evidence that illicit trade in cigarettes in South Africa increased between 2002 and 2009. There is a substantial increase in illicit trade in 2010, probably peaking in 2011. In 2012 tax-paid consumption of cigarettes increased 2.6%, implying that the illicit market share decreased an estimated 0.6 percentage points. Conclusions Other than in 2010, there is no evidence that illicit trade is significantly undermining government revenue. Claims that illicit trade has consistently increased over the past 15 years, and has continued its sharp increase since 2010, are not supported. PMID:24431121

Alterations in Masticatory Muscle Activation in People with Persistent Neck Pain Despite the Absence of Orofacial Pain or Temporomandibular Disorders.

PubMed

Testa, Marco; Geri, Tommaso; Gizzi, Leonardo; Petzke, Frank; Falla, Deborah

2015-01-01

To assess whether patients with persistent neck pain display evidence of altered masticatory muscle behavior during a jaw-clenching task, despite the absence of orofacial pain or temporomandibular disorders. Ten subjects with persistent, nonspecific neck pain and 10 age- and sex-matched healthy controls participated. Maximal voluntary contractions (MVCs) of unilateral jaw clenching followed by 5-second submaximal contractions at 10%, 30%, 50%, and 70% MVC were recorded by two flexible force transducers positioned between the first molar teeth. Task performance was quantified by mean distance and offset error from the reference target force as error indices, and standard deviation of force was used as an index of force steadiness. Electromyographic (EMG) activity was recorded bilaterally from the masseter muscle with 13 X 5 grids of electrodes and from the anterior temporalis with bipolar electrodes. Normalized EMG root mean square (RMS) was computed for each location of the grid to form a map of the EMG amplitude distribution, and the average normalized RMS was determined for the bipolar acquisition. Between-group differences were analyzed with the Kruskal Wallis analysis of variance. Task performance was similar in patients and controls. However, patients displayed greater masseter EMG activity bilaterally at higher force levels (P<.05). This study has provided novel evidence of altered motor control of the jaw in people with neck pain despite the absence of orofacial pain or temporomandibular disorders.

Rapid Detection of Volatile Oil in Mentha haplocalyx by Near-Infrared Spectroscopy and Chemometrics.

PubMed

Yan, Hui; Guo, Cheng; Shao, Yang; Ouyang, Zhen

2017-01-01

Near-infrared spectroscopy combined with partial least squares regression (PLSR) and support vector machine (SVM) was applied for the rapid determination of chemical component of volatile oil content in Mentha haplocalyx . The effects of data pre-processing methods on the accuracy of the PLSR calibration models were investigated. The performance of the final model was evaluated according to the correlation coefficient ( R ) and root mean square error of prediction (RMSEP). For PLSR model, the best preprocessing method combination was first-order derivative, standard normal variate transformation (SNV), and mean centering, which had of 0.8805, of 0.8719, RMSEC of 0.091, and RMSEP of 0.097, respectively. The wave number variables linking to volatile oil are from 5500 to 4000 cm-1 by analyzing the loading weights and variable importance in projection (VIP) scores. For SVM model, six LVs (less than seven LVs in PLSR model) were adopted in model, and the result was better than PLSR model. The and were 0.9232 and 0.9202, respectively, with RMSEC and RMSEP of 0.084 and 0.082, respectively, which indicated that the predicted values were accurate and reliable. This work demonstrated that near infrared reflectance spectroscopy with chemometrics could be used to rapidly detect the main content volatile oil in M. haplocalyx . The quality of medicine directly links to clinical efficacy, thus, it is important to control the quality of Mentha haplocalyx . Near-infrared spectroscopy combined with partial least squares regression (PLSR) and support vector machine (SVM) was applied for the rapid determination of chemical component of volatile oil content in Mentha haplocalyx . For SVM model, 6 LVs (less than 7 LVs in PLSR model) were adopted in model, and the result was better than PLSR model. It demonstrated that near infrared reflectance spectroscopy with chemometrics could be used to rapidly detect the main content volatile oil in Mentha haplocalyx . Abbreviations used: 1 st der: First-order derivative; 2 nd der: Second-order derivative; LOO: Leave-one-out; LVs: Latent variables; MC: Mean centering, NIR: Near-infrared; NIRS: Near infrared spectroscopy; PCR: Principal component regression, PLSR: Partial least squares regression; RBF: Radial basis function; RMSEC: Root mean square error of cross validation, RMSEC: Root mean square error of calibration; RMSEP: Root mean square error of prediction; SNV: Standard normal variate transformation; SVM: Support vector machine; VIP: Variable Importance in projection.

Modeling the effect of control on the wake of a utility-scale turbine via large-eddy simulation

NASA Astrophysics Data System (ADS)

Yang, Xiaolei; Annoni, Jennifer; Seiler, Pete; Sotiropoulos, Fotis

2014-06-01

A model of the University of Minnesota EOLOS research turbine (Clipper Liberty C96) is developed, integrating the C96 torque control law with a high fidelity actuator line large- eddy simulation (LES) model. Good agreement with the blade element momentum theory is obtained for the power coefficient curve under uniform inflow. Three different cases, fixed rotor rotational speed ω, fixed tip-speed ratio (TSR) and generator torque control, have been simulated for turbulent inflow. With approximately the same time-averaged ω, the time- averaged power is in good agreement with measurements for all three cases. Although the time-averaged aerodynamic torque is nearly the same for the three cases, the root-mean-square (rms) of the aerodynamic torque fluctuations is significantly larger for the case with fixed ω. No significant differences have been observed for the time-averaged flow fields behind the turbine for these three cases.

Autonomic cardiovascular control recovery in quadriplegics after handcycle training.

PubMed

Abreu, Elizângela Márcia de Carvalho; Alves, Rani de Souza; Borges, Ana Carolina Lacerda; Lima, Fernanda Pupio Silva; Júnior, Alderico Rodrigues de Paula; Lima, Mário Oliveira

2016-07-01

The aim of this study was to investigate the cardiovascular autonomic acute response, during recovery after handcycle training, in quadriplegics with spinal cord injury (SCI). [Subjects and Methods] Seven quadriplegics (SCIG -level C6-C7, male, age 28.00 ± 6.97 years) and eight healthy subjects (CG -male, age 25.00 ± 7.38 years) were studied. Their heart rate variability (HRV) was assessed before and after one handcycle training. [Results] After the training, the SCIG showed significantly reduced: intervals between R waves of the electrocardiogram (RR), standard deviation of the NN intervals (SDNN), square root of the mean squares differences of sucessive NN intervals (rMSSD), low frequency power (LF), high frequency power (HF), and Poincaré plot (standard deviation of short-term HRV -SD1 and standard deviation of long-term HRV -SD2). The SDNN, LF, and SD2 remained decreased during the recovery time. The CG showed significantly reduced: RR, rMSSD, number of pairs of adjacent NN intervals differing by more than 50 ms (pNN50), LF, HF, SD1, and sample entropy (SampEn). Among these parameters, only RR remained decreased during recovery time. Comparisons of the means of HRV parameters evaluated between the CG and SCIG showed that the SCIG had significantly lower pNN50, LF, HF, and SampEn before training, while immediately after training, the SCIG had significantly lower SDNN, LF, HF, and SD2. The rMSSD30s of the SCIG significantly reduced in the windows 180 and 330 seconds and between the windows 300 seconds in the CG. [Conclusion] There was a reduction of sympathetic and parasympathetic activity in the recovery period after the training in both groups; however, the CG showed a higher HRV. The parasympathetic activity also gradually increased after training, and in the SCIG, this activity remained reduced even at three minutes after the end of training, which suggests a deficiency in parasympathetic reactivation in quadriplegics after SCI.

SU-E-T-436: Fluence-Based Trajectory Optimization for Non-Coplanar VMAT

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

Smyth, G; Bamber, JC; Bedford, JL

2015-06-15

Purpose: To investigate a fluence-based trajectory optimization technique for non-coplanar VMAT for brain cancer. Methods: Single-arc non-coplanar VMAT trajectories were determined using a heuristic technique for five patients. Organ at risk (OAR) volume intersected during raytracing was minimized for two cases: absolute volume and the sum of relative volumes weighted by OAR importance. These trajectories and coplanar VMAT formed starting points for the fluence-based optimization method. Iterative least squares optimization was performed on control points 24° apart in gantry rotation. Optimization minimized the root-mean-square (RMS) deviation of PTV dose from the prescription (relative importance 100), maximum dose to the brainstemmore » (10), optic chiasm (5), globes (5) and optic nerves (5), plus mean dose to the lenses (5), hippocampi (3), temporal lobes (2), cochleae (1) and brain excluding other regions of interest (1). Control point couch rotations were varied in steps of up to 10° and accepted if the cost function improved. Final treatment plans were optimized with the same objectives in an in-house planning system and evaluated using a composite metric - the sum of optimization metrics weighted by importance. Results: The composite metric decreased with fluence-based optimization in 14 of the 15 plans. In the remaining case its overall value, and the PTV and OAR components, were unchanged but the balance of OAR sparing differed. PTV RMS deviation was improved in 13 cases and unchanged in two. The OAR component was reduced in 13 plans. In one case the OAR component increased but the composite metric decreased - a 4 Gy increase in OAR metrics was balanced by a reduction in PTV RMS deviation from 2.8% to 2.6%. Conclusion: Fluence-based trajectory optimization improved plan quality as defined by the composite metric. While dose differences were case specific, fluence-based optimization improved both PTV and OAR dosimetry in 80% of cases.« less

Method of measuring cross-flow vortices by use of an array of hot-film sensors

NASA Technical Reports Server (NTRS)

Agarwal, Aval K. (Inventor); Maddalon, Dal V. (Inventor); Mangalam, Siva M. (Inventor)

1993-01-01

The invention is a method for measuring the wavelength of cross-flow vortices of air flow having streamlines of flow traveling across a swept airfoil. The method comprises providing a plurality of hot-film sensors. Each hot-film sensor provides a signal which can be processed, and each hot-film sensor is spaced in a straight-line array such that the distance between successive hot-film sensors is less than the wavelength of the cross-flow vortices being measured. The method further comprises determining the direction of travel of the streamlines across the airfoil and positioning the straight-line array of hot film sensors perpendicular to the direction of travel of the streamlines, such that each sensor has a spanwise location. The method further comprises processing the signals provided by the sensors to provide root-mean-square values for each signal, plotting each root-mean-square value as a function of its spanwise location, and determining the wavelength of the cross-flow vortices by noting the distance between two maxima or two minima of root-mean-square values.

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…

Soil moisture retrieval by active/passive microwave remote sensing data

NASA Astrophysics Data System (ADS)

Wu, Shengli; Yang, Lijuan

2012-09-01

This study develops a new algorithm for estimating bare surface soil moisture using combined active / passive microwave remote sensing on the basis of TRMM (Tropical Rainfall Measuring Mission). Tropical Rainfall Measurement Mission was jointly launched by NASA and NASDA in 1997, whose main task was to observe the precipitation of the area in 40 ° N-40 ° S. It was equipped with active microwave radar sensors (PR) and passive sensor microwave imager (TMI). To accurately estimate bare surface soil moisture, precipitation radar (PR) and microwave imager (TMI) are simultaneously used for observation. According to the frequency and incident angle setting of PR and TMI, we first need to establish a database which includes a large range of surface conditions; and then we use Advanced Integral Equation Model (AIEM) to calculate the backscattering coefficient and emissivity. Meanwhile, under the accuracy of resolution, we use a simplified theoretical model (GO model) and the semi-empirical physical model (Qp Model) to redescribe the process of scattering and radiation. There are quite a lot of parameters effecting backscattering coefficient and emissivity, including soil moisture, surface root mean square height, correlation length, and the correlation function etc. Radar backscattering is strongly affected by the surface roughness, which includes the surface root mean square roughness height, surface correlation length and the correlation function we use. And emissivity is differently affected by the root mean square slope under different polarizations. In general, emissivity decreases with the root mean square slope increases in V polarization, and increases with the root mean square slope increases in H polarization. For the GO model, we found that the backscattering coefficient is only related to the root mean square slope and soil moisture when the incident angle is fixed. And for Qp Model, through the analysis, we found that there is a quite good relationship between Qpparameter and root mean square slope. So here, root mean square slope is a parameter that both models shared. Because of its big influence to backscattering and emissivity, we need to throw it out during the process of the combination of GO model and Qp model. The result we obtain from the combined model is the Fresnel reflection coefficient in the normal direction gama(0). It has a good relationship with the soil dielectric constant. In Dobson Model, there is a detailed description about Fresnel reflection coefficient and soil moisture. With the help of Dobson model and gama(0) that we have obtained, we can get the soil moisture that we want. The backscattering coefficient and emissivity data used in combined model is from TRMM/PR, TMI; with this data, we can obtain gama(0); further, we get the soil moisture by the relationship of the two parameters-- gama(0) and soil moisture. To validate the accuracy of the retrieval soil moisture, there is an experiment conducted in Tibet. The soil moisture data which is used to validate the retrieval algorithm is from GAME-Tibet IOP98 Soil Moisture and Temperature Measuring System (SMTMS). There are 9 observing sites in SMTMS to validate soil moisture. Meanwhile, we use the SMTMS soil moisture data obtained by Time Domain Reflectometer (TDR) to do the validation. And the result shows the comparison of retrieval and measured results is very good. Through the analysis, we can see that the retrieval and measured results in D66 is nearly close; and in MS3608, the measured result is a little higher than retrieval result; in MS3637, the retrieval result is a little higher than measured result. According to the analysis of the simulation results, we found that this combined active and passive approach to retrieve the soil moisture improves the retrieval accuracy.

Evaluation of different methods for determining growing degree-day thresholds in apricot cultivars

NASA Astrophysics Data System (ADS)

Ruml, Mirjana; Vuković, Ana; Milatović, Dragan

2010-07-01

The aim of this study was to examine different methods for determining growing degree-day (GDD) threshold temperatures for two phenological stages (full bloom and harvest) and select the optimal thresholds for a greater number of apricot ( Prunus armeniaca L.) cultivars grown in the Belgrade region. A 10-year data series were used to conduct the study. Several commonly used methods to determine the threshold temperatures from field observation were evaluated: (1) the least standard deviation in GDD; (2) the least standard deviation in days; (3) the least coefficient of variation in GDD; (4) regression coefficient; (5) the least standard deviation in days with a mean temperature above the threshold; (6) the least coefficient of variation in days with a mean temperature above the threshold; and (7) the smallest root mean square error between the observed and predicted number of days. In addition, two methods for calculating daily GDD, and two methods for calculating daily mean air temperatures were tested to emphasize the differences that can arise by different interpretations of basic GDD equation. The best agreement with observations was attained by method (7). The lower threshold temperature obtained by this method differed among cultivars from -5.6 to -1.7°C for full bloom, and from -0.5 to 6.6°C for harvest. However, the “Null” method (lower threshold set to 0°C) and “Fixed Value” method (lower threshold set to -2°C for full bloom and to 3°C for harvest) gave very good results. The limitations of the widely used method (1) and methods (5) and (6), which generally performed worst, are discussed in the paper.

Heart rate variability analysed by Poincaré plot in patients with metabolic syndrome.

PubMed

Kubičková, Alena; Kozumplík, Jiří; Nováková, Zuzana; Plachý, Martin; Jurák, Pavel; Lipoldová, Jolana

2016-01-01

The SD1 and SD2 indexes (standard deviations in two orthogonal directions of the Poincaré plot) carry similar information to the spectral density power of the high and low frequency bands but have the advantage of easier calculation and lesser stationarity dependence. ECG signals from metabolic syndrome (MetS) and control group patients during tilt table test under controlled breathing (20 breaths/minute) were obtained. SD1, SD2, SDRR (standard deviation of RR intervals) and RMSSD (root mean square of successive differences of RR intervals) were evaluated for 31 control group and 33 MetS subjects. Statistically significant lower values were observed in MetS patients in supine position (SD1: p=0.03, SD2: p=0.002, SDRR: p=0.006, RMSSD: p=0.01) and during tilt (SD2: p=0.004, SDRR: p=0.007). SD1 and SD2 combining the advantages of time and frequency domain methods, distinguish successfully between MetS and control subjects. Copyright © 2016 Elsevier Inc. All rights reserved.

Equalization of energy density in boiling water reactors (as exemplified by WB-50). Development and testing of WB -50 computational model on the basis of MCU-RR code

NASA Astrophysics Data System (ADS)

Chertkov, Yu B.; Disyuk, V. V.; Pimenov, E. Yu; Aksenova, N. V.

2017-01-01

Within the framework of research in possibility and prospects of power density equalization in boiling water reactors (as exemplified by WB-50) a work was undertaken to improve prior computational model of the WB-50 reactor implemented in MCU-RR software. Analysis of prior works showed that critical state calculations have deviation of calculated reactivity exceeding ±0.3 % (ΔKef/Kef) for minimum concentrations of boric acid in the reactor water and reaching 2 % for maximum concentration values. Axial coefficient of nonuniform burnup distribution reaches high values in the WB-50 reactor. Thus, the computational model needed refinement to take into account burnup inhomogeneity along the fuel assembly height. At this stage, computational results with mean square deviation of less than 0.7 % (ΔKef/Kef) and dispersion of design values of ±1 % (ΔK/K) shall be deemed acceptable. Further lowering of these parameters apparently requires root cause analysis of such large values and paying more attention to experimental measurement techniques.

Seismic velocity site characterization of 10 Arizona strong-motion recording stations by spectral analysis of surface wave dispersion

USGS Publications Warehouse

Kayen, Robert E.; Carkin, Brad A.; Corbett, Skye C.

2017-10-19

Vertical one-dimensional shear wave velocity (VS) profiles are presented for strong-motion sites in Arizona for a suite of stations surrounding the Palo Verde Nuclear Generating Station. The purpose of the study is to determine the detailed site velocity profile, the average velocity in the upper 30 meters of the profile (VS30), the average velocity for the entire profile (VSZ), and the National Earthquake Hazards Reduction Program (NEHRP) site classification. The VS profiles are estimated using a non-invasive continuous-sine-wave method for gathering the dispersion characteristics of surface waves. Shear wave velocity profiles were inverted from the averaged dispersion curves using three independent methods for comparison, and the root-mean-square combined coefficient of variation (COV) of the dispersion and inversion calculations are estimated for each site.

Optimal random search for a single hidden target.

PubMed

Snider, Joseph

2011-01-01

A single target is hidden at a location chosen from a predetermined probability distribution. Then, a searcher must find a second probability distribution from which random search points are sampled such that the target is found in the minimum number of trials. Here it will be shown that if the searcher must get very close to the target to find it, then the best search distribution is proportional to the square root of the target distribution regardless of dimension. For a Gaussian target distribution, the optimum search distribution is approximately a Gaussian with a standard deviation that varies inversely with how close the searcher must be to the target to find it. For a network where the searcher randomly samples nodes and looks for the fixed target along edges, the optimum is either to sample a node with probability proportional to the square root of the out-degree plus 1 or not to do so at all.

Heart rate variability parameters in horses distinguish atrial fibrillation from sinus rhythm before and after successful electrical cardioversion.

PubMed

Broux, B; De Clercq, D; Decloedt, A; Ven, S; Vera, L; van Steenkiste, G; Mitchell, K; Schwarzwald, C; van Loon, G

2017-11-01

Atrial fibrillation (AF) is the most common pathological arrhythmia in horses. After successful treatment, recurrence is common. Heart rate monitors are easily applicable in horses and some devices offer basic heart rate variability (HRV) calculations. If HRV can be used to distinguish between AF and sinus rhythm (SR), this could become a monitoring tool for horses at risk for recurrence of AF. The purpose of this study was to assess whether in horses AF (before cardioversion) and SR (after cardioversion) can be differentiated based upon HRV parameters. Cohort study with internal controls. Six HRV parameters were determined in 20 horses, both in AF and in SR, at rest (2- and 5-min and 1- and 4-h recordings) and during exercise (walk and trot, 2-min recordings). Time-domain (standard deviation of the NN intervals, root mean squared successive differences in NN intervals and triangular index), frequency domain (low/high frequency ratio) and nonlinear parameters (standard deviation of the Poincaré plot [SD]1 and SD2) were used. Statistical analysis was done using paired Wilcoxon signed rank tests and receiver operating characteristic curves. HRV was higher during AF compared to SR. Results for the detection of AF were good (area under the receiver operating characteristic curve [AUC] 0.8-1) for most HRV parameters. Root mean squared successive differences in NN intervals and SD1 yielded the best results (AUC 0.9-1). Sensitivity and specificity were high for all parameters at all recordings, but highest during exercise. Although AUCs improved with longer recordings, short recordings were also good (AUC 0.8-1) for the detection of AF. In horses with frequent second degree atrioventricular block, HRV at rest is increased and recordings at walk or trot are recommended. Animals served as their own controls and there was no long-term follow-up to identify AF recurrence. AF (before cardioversion) and SR (after cardioversion) could be distinguished with HRV. This technique has promise as a monitoring tool in horses at risk for AF development. © 2017 EVJ Ltd.

Acute Sport-Related Concussion Screening for Collegiate Athletes Using an Instrumented Balance Assessment.

PubMed

Baracks, Joshua; Casa, Douglas J; Covassin, Tracey; Sacko, Ryan; Scarneo, Samantha E; Schnyer, David; Yeargin, Susan W; Neville, Christopher

2018-06-13

  Without a true criterion standard assessment, the sport-related concussion (SRC) diagnosis remains subjective. Inertial balance sensors have been proposed to improve acute SRC assessment, but few researchers have studied their clinical utility.   To determine if group differences exist when using objective measures of balance in a sample of collegiate athletes with recent SRCs and participants serving as the control group and to calculate sensitivity and specificity to determine the diagnostic utility of the inertial balance sensor for acute SRC injuries.   Cohort study.   Multicenter clinical trial.   We enrolled 48 participants with SRC (age = 20.62 ± 1.52 years, height = 179.76 ± 10.00 cm, mass = 83.92 ± 23.22 kg) and 45 control participants (age = 20.85 ± 1.42 years, height = 177.02 ± 9.59 cm, mass = 74.61 ± 14.92 kg) at 7 clinical sites in the United States. All were varsity or club collegiate athletes, and all participants with SRC were tested within 72 hours of SRC.   Balance performance was assessed using an inertial balance sensor. Two measures (root mean square [RMS] sway and 95% ellipse sway area) were analyzed to represent a range of general balance measures. Balance assessments were conducted in double-legged, single-legged, and tandem stances.   A main effect for group was associated with the root mean square sway measure ( F 1,91 = 11.75, P = .001), with the SRC group demonstrating balance deficits compared with the control group. We observed group differences in the 95% ellipse sway area measure for the double-legged ( F 1,91 = 11.59, P = .001), single-legged ( F 1,91 = 6.91, P = .01), and tandem ( F 1,91 = 7.54, P = .007) stances. Sensitivity was greatest using a cutoff value of 0.5 standard deviations (54% [specificity = 71%]), whereas specificity was greatest using a cutoff value of 2 standard deviations (98% [sensitivity = 33%]).   Inertial balance sensors may be useful tools for objectively measuring balance during acute SRC evaluation. However, low sensitivity suggests that they may be best used in conjunction with other assessments to form a comprehensive screening that may improve sensitivity.

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®

Uncertainty Analysis of Downscaled CMIP5 Precipitation Data for Louisiana, USA

NASA Astrophysics Data System (ADS)

Sumi, S. J.; Tamanna, M.; Chivoiu, B.; Habib, E. H.

2014-12-01

The downscaled CMIP3 and CMIP5 Climate and Hydrology Projections dataset contains fine spatial resolution translations of climate projections over the contiguous United States developed using two downscaling techniques (monthly Bias Correction Spatial Disaggregation (BCSD) and daily Bias Correction Constructed Analogs (BCCA)). The objective of this study is to assess the uncertainty of the CMIP5 downscaled general circulation models (GCM). We performed an analysis of the daily, monthly, seasonal and annual variability of precipitation downloaded from the Downscaled CMIP3 and CMIP5 Climate and Hydrology Projections website for the state of Louisiana, USA at 0.125° x 0.125° resolution. A data set of daily gridded observations of precipitation of a rectangular boundary covering Louisiana is used to assess the validity of 21 downscaled GCMs for the 1950-1999 period. The following statistics are computed using the CMIP5 observed dataset with respect to the 21 models: the correlation coefficient, the bias, the normalized bias, the mean absolute error (MAE), the mean absolute percentage error (MAPE), and the root mean square error (RMSE). A measure of variability simulated by each model is computed as the ratio of its standard deviation, in both space and time, to the corresponding standard deviation of the observation. The correlation and MAPE statistics are also computed for each of the nine climate divisions of Louisiana. Some of the patterns that we observed are: 1) Average annual precipitation rate shows similar spatial distribution for all the models within a range of 3.27 to 4.75 mm/day from Northwest to Southeast. 2) Standard deviation of summer (JJA) precipitation (mm/day) for the models maintains lower value than the observation whereas they have similar spatial patterns and range of values in winter (NDJ). 3) Correlation coefficients of annual precipitation of models against observation have a range of -0.48 to 0.36 with variable spatial distribution by model. 4) Most of the models show negative correlation coefficients in summer and positive in winter. 5) MAE shows similar spatial distribution for all the models within a range of 5.20 to 7.43 mm/day from Northwest to Southeast of Louisiana. 6) Highest values of correlation coefficients are found at seasonal scale within a range of 0.36 to 0.46.

Mass predictions of atomic nuclei in the infinite nuclear matter model

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

Nayak, R.C., E-mail: rcnayak00@yahoo.com; Satpathy, L., E-mail: satpathy@iopb.res.in

We present here the mass excesses, binding energies, one- and two-neutron, one- and two-proton and {alpha}-particle separation energies of 6727 nuclei in the ranges 4{<=}Z{<=}120 and 8{<=}A{<=}303 calculated in the infinite nuclear matter model. Compared to our predictions of 1999 mass table, the present ones are obtained using larger data base of 2003 mass table of Wapstra and Audi and resorting to higher accuracy in the solutions of the {eta}-differential equations of the INM model. The local energy {eta}'s supposed to carry signature of the characteristic properties of nuclei are found to possess the predictive capability. In fact {eta}-systematics revealmore » new magic numbers in the drip-line regions giving rise to new islands of stability supported by relativistic mean field theoretic calculations. This is a manifestation of a new phenomenon where shell-effect overcomes the instability due to repulsive components of the nucleon-nucleon force broadening the stability peninsula. The two-neutron separation energy-systematics derived from the present mass predictions reveal a general new feature for the existence of islands of inversion in the exotic neutron-rich regions of nuclear landscape, apart from supporting the presently known islands around {sup 31}Na and {sup 62}Ti. The five global parameters representing the properties of infinite nuclear matter, the surface, the Coulomb and the pairing terms are retained as per our 1999 mass table. The root-mean-square deviation of the present mass-fit to 2198 known masses is 342 keV, while the mean deviation is 1.3 keV, reminiscent of no left-over systematic effects. This is a substantive improvement over our 1999 mass table having rms deviation of 401 keV and mean deviation of 9 keV for 1884 data nuclei.« less

ROBUST: an interactive FORTRAN-77 package for exploratory data analysis using parametric, ROBUST and nonparametric location and scale estimates, data transformations, normality tests, and outlier assessment

NASA Astrophysics Data System (ADS)

Rock, N. M. S.

ROBUST calculates 53 statistics, plus significance levels for 6 hypothesis tests, on each of up to 52 variables. These together allow the following properties of the data distribution for each variable to be examined in detail: (1) Location. Three means (arithmetic, geometric, harmonic) are calculated, together with the midrange and 19 high-performance robust L-, M-, and W-estimates of location (combined, adaptive, trimmed estimates, etc.) (2) Scale. The standard deviation is calculated along with the H-spread/2 (≈ semi-interquartile range), the mean and median absolute deviations from both mean and median, and a biweight scale estimator. The 23 location and 6 scale estimators programmed cover all possible degrees of robustness. (3) Normality: Distributions are tested against the null hypothesis that they are normal, using the 3rd (√ h1) and 4th ( b 2) moments, Geary's ratio (mean deviation/standard deviation), Filliben's probability plot correlation coefficient, and a more robust test based on the biweight scale estimator. These statistics collectively are sensitive to most usual departures from normality. (4) Presence of outliers. The maximum and minimum values are assessed individually or jointly using Grubbs' maximum Studentized residuals, Harvey's and Dixon's criteria, and the Studentized range. For a single input variable, outliers can be either winsorized or eliminated and all estimates recalculated iteratively as desired. The following data-transformations also can be applied: linear, log 10, generalized Box Cox power (including log, reciprocal, and square root), exponentiation, and standardization. For more than one variable, all results are tabulated in a single run of ROBUST. Further options are incorporated to assess ratios (of two variables) as well as discrete variables, and be concerned with missing data. Cumulative S-plots (for assessing normality graphically) also can be generated. The mutual consistency or inconsistency of all these measures helps to detect errors in data as well as to assess data-distributions themselves.

Modelling Transcapillary Transport of Fluid and Proteins in Hemodialysis Patients

PubMed Central

Pietribiasi, Mauro; Waniewski, Jacek; Załuska, Alicja; Załuska, Wojciech; Lindholm, Bengt

2016-01-01

Background The kinetics of protein transport to and from the vascular compartment play a major role in the determination of fluid balance and plasma refilling during hemodialysis (HD) sessions. In this study we propose a whole-body mathematical model describing water and protein shifts across the capillary membrane during HD and compare its output to clinical data while evaluating the impact of choosing specific values for selected parameters. Methods The model follows a two-compartment structure (vascular and interstitial space) and is based on balance equations of protein mass and water volume in each compartment. The capillary membrane was described according to the three-pore theory. Two transport parameters, the fractional contribution of large pores (αLP) and the total hydraulic conductivity (LpS) of the capillary membrane, were estimated from patient data. Changes in the intensity and direction of individual fluid and solute flows through each part of the transport system were analyzed in relation to the choice of different values of small pores radius and fractional conductivity, lymphatic sensitivity to hydraulic pressure, and steady-state interstitial-to-plasma protein concentration ratio. Results The estimated values of LpS and αLP were respectively 10.0 ± 8.4 mL/min/mmHg (mean ± standard deviation) and 0.062 ± 0.041. The model was able to predict with good accuracy the profiles of plasma volume and serum total protein concentration in most of the patients (average root-mean-square deviation < 2% of the measured value). Conclusions The applied model provides a mechanistic interpretation of fluid transport processes induced by ultrafiltration during HD, using a minimum of tuned parameters and assumptions. The simulated values of individual flows through each kind of pore and lymphatic absorption rate yielded by the model may suggest answers to unsolved questions on the relative impact of these not-measurable quantities on total vascular refilling and fluid balance. PMID:27483369

Evaluation of a musculoskeletal model with prosthetic knee through six experimental gait trials.

PubMed

Kia, Mohammad; Stylianou, Antonis P; Guess, Trent M

2014-03-01

Knowledge of the forces acting on musculoskeletal joint tissues during movement benefits tissue engineering, artificial joint replacement, and our understanding of ligament and cartilage injury. Computational models can be used to predict these internal forces, but musculoskeletal models that simultaneously calculate muscle force and the resulting loading on joint structures are rare. This study used publicly available gait, skeletal geometry, and instrumented prosthetic knee loading data [1] to evaluate muscle driven forward dynamics simulations of walking. Inputs to the simulation were measured kinematics and outputs included muscle, ground reaction, ligament, and joint contact forces. A full body musculoskeletal model with subject specific lower extremity geometries was developed in the multibody framework. A compliant contact was defined between the prosthetic femoral component and tibia insert geometries. Ligament structures were modeled with a nonlinear force-strain relationship. The model included 45 muscles on the right lower leg. During forward dynamics simulations a feedback control scheme calculated muscle forces using the error signal between the current muscle lengths and the lengths recorded during inverse kinematics simulations. Predicted tibio-femoral contact force, ground reaction forces, and muscle forces were compared to experimental measurements for six different gait trials using three different gait types (normal, trunk sway, and medial thrust). The mean average deviation (MAD) and root mean square deviation (RMSD) over one gait cycle are reported. The muscle driven forward dynamics simulations were computationally efficient and consistently reproduced the inverse kinematics motion. The forward simulations also predicted total knee contact forces (166N

Research on the infiltration processes of lawn soils of the Babao River in the Qilian Mountain.

PubMed

Li, GuangWen; Feng, Qi; Zhang, FuPing; Cheng, AiFang

2014-01-01

Using a Guelph Permeameter, the soil water infiltration processes were analyzed in the Babao River of the Qilian Mountain in China. The results showed that the average soil initial infiltration and the steady infiltration rates in the upstream reaches of the Babao River are 1.93 and 0.99 cm/min, whereas those of the middle area are 0.48 cm/min and 0.21 cm/min, respectively. The infiltration processes can be divided into three stages: the rapidly changing stage (0-10 min), the slowly changing stage (10-30 min) and the stabilization stage (after 30 min). We used field data collected from lawn soils and evaluated the performances of the infiltration models of Philip, Kostiakov and Horton with the sum of squared error, the root mean square error, the coefficient of determination, the mean error, the model efficiency and Willmott's index of agreement. The results indicated that the Kostiakov model was most suitable for studying the infiltration process in the alpine lawn soils.

Determining particle size and water content by near-infrared spectroscopy in the granulation of naproxen sodium.

PubMed

Bär, David; Debus, Heiko; Brzenczek, Sina; Fischer, Wolfgang; Imming, Peter

2018-03-20

Near-infrared spectroscopy is frequently used by the pharmaceutical industry to monitor and optimize several production processes. In combination with chemometrics, a mathematical-statistical technique, the following advantages of near-infrared spectroscopy can be applied: It is a fast, non-destructive, non-invasive, and economical analytical method. One of the most advanced and popular chemometric technique is the partial least square algorithm with its best applicability in routine and its results. The required reference analytic enables the analysis of various parameters of interest, for example, moisture content, particle size, and many others. Parameters like the correlation coefficient, root mean square error of prediction, root mean square error of calibration, and root mean square error of validation have been used for evaluating the applicability and robustness of these analytical methods developed. This study deals with investigating a Naproxen Sodium granulation process using near-infrared spectroscopy and the development of water content and particle-size methods. For the water content method, one should consider a maximum water content of about 21% in the granulation process, which must be confirmed by the loss on drying. Further influences to be considered are the constantly changing product temperature, rising to about 54 °C, the creation of hydrated states of Naproxen Sodium when using a maximum of about 21% water content, and the large quantity of about 87% Naproxen Sodium in the formulation. It was considered to use a combination of these influences in developing the near-infrared spectroscopy method for the water content of Naproxen Sodium granules. The "Root Mean Square Error" was 0.25% for calibration dataset and 0.30% for the validation dataset, which was obtained after different stages of optimization by multiplicative scatter correction and the first derivative. Using laser diffraction, the granules have been analyzed for particle sizes and obtaining the summary sieve sizes of >63 μm and >100 μm. The following influences should be considered for application in routine production: constant changes in water content up to 21% and a product temperature up to 54 °C. The different stages of optimization result in a "Root Mean Square Error" of 2.54% for the calibration data set and 3.53% for the validation set by using the Kubelka-Munk conversion and first derivative for the near-infrared spectroscopy method for a particle size >63 μm. For the near-infrared spectroscopy method using a particle size >100 μm, the "Root Mean Square Error" was 3.47% for the calibration data set and 4.51% for the validation set, while using the same pre-treatments. - The robustness and suitability of this methodology has already been demonstrated by its recent successful implementation in a routine granulate production process. Copyright © 2018 Elsevier B.V. All rights reserved.

Statistical models for estimating daily streamflow in Michigan

USGS Publications Warehouse

Holtschlag, D.J.; Salehi, Habib

1992-01-01

Statistical models for estimating daily streamflow were analyzed for 25 pairs of streamflow-gaging stations in Michigan. Stations were paired by randomly choosing a station operated in 1989 at which 10 or more years of continuous flow data had been collected and at which flow is virtually unregulated; a nearby station was chosen where flow characteristics are similar. Streamflow data from the 25 randomly selected stations were used as the response variables; streamflow data at the nearby stations were used to generate a set of explanatory variables. Ordinary-least squares regression (OLSR) equations, autoregressive integrated moving-average (ARIMA) equations, and transfer function-noise (TFN) equations were developed to estimate the log transform of flow for the 25 randomly selected stations. The precision of each type of equation was evaluated on the basis of the standard deviation of the estimation errors. OLSR equations produce one set of estimation errors; ARIMA and TFN models each produce l sets of estimation errors corresponding to the forecast lead. The lead-l forecast is the estimate of flow l days ahead of the most recent streamflow used as a response variable in the estimation. In this analysis, the standard deviation of lead l ARIMA and TFN forecast errors were generally lower than the standard deviation of OLSR errors for l < 2 days and l < 9 days, respectively. Composite estimates were computed as a weighted average of forecasts based on TFN equations and backcasts (forecasts of the reverse-ordered series) based on ARIMA equations. The standard deviation of composite errors varied throughout the length of the estimation interval and generally was at maximum near the center of the interval. For comparison with OLSR errors, the mean standard deviation of composite errors were computed for intervals of length 1 to 40 days. The mean standard deviation of length-l composite errors were generally less than the standard deviation of the OLSR errors for l < 32 days. In addition, the composite estimates ensure a gradual transition between periods of estimated and measured flows. Model performance among stations of differing model error magnitudes were compared by computing ratios of the mean standard deviation of the length l composite errors to the standard deviation of OLSR errors. The mean error ratio for the set of 25 selected stations was less than 1 for intervals l < 32 days. Considering the frequency characteristics of the length of intervals of estimated record in Michigan, the effective mean error ratio for intervals < 30 days was 0.52. Thus, for intervals of estimation of 1 month or less, the error of the composite estimate is substantially lower than error of the OLSR estimate.

Near infrared spectroscopy combined with multivariate analysis for monitoring the ethanol precipitation process of fraction I + II + III supernatant in human albumin separation

NASA Astrophysics Data System (ADS)

Li, Can; Wang, Fei; Zang, Lixuan; Zang, Hengchang; Alcalà, Manel; Nie, Lei; Wang, Mingyu; Li, Lian

2017-03-01

Nowadays, as a powerful process analytical tool, near infrared spectroscopy (NIRS) has been widely applied in process monitoring. In present work, NIRS combined with multivariate analysis was used to monitor the ethanol precipitation process of fraction I + II + III (FI + II + III) supernatant in human albumin (HA) separation to achieve qualitative and quantitative monitoring at the same time and assure the product's quality. First, a qualitative model was established by using principal component analysis (PCA) with 6 of 8 normal batches samples, and evaluated by the remaining 2 normal batches and 3 abnormal batches. The results showed that the first principal component (PC1) score chart could be successfully used for fault detection and diagnosis. Then, two quantitative models were built with 6 of 8 normal batches to determine the content of the total protein (TP) and HA separately by using partial least squares regression (PLS-R) strategy, and the models were validated by 2 remaining normal batches. The determination coefficient of validation (Rp2), root mean square error of cross validation (RMSECV), root mean square error of prediction (RMSEP) and ratio of performance deviation (RPD) were 0.975, 0.501 g/L, 0.465 g/L and 5.57 for TP, and 0.969, 0.530 g/L, 0.341 g/L and 5.47 for HA, respectively. The results showed that the established models could give a rapid and accurate measurement of the content of TP and HA. The results of this study indicated that NIRS is an effective tool and could be successfully used for qualitative and quantitative monitoring the ethanol precipitation process of FI + II + III supernatant simultaneously. This research has significant reference value for assuring the quality and improving the recovery ratio of HA in industrialization scale by using NIRS.

Near infrared spectroscopy combined with multivariate analysis for monitoring the ethanol precipitation process of fraction I+II+III supernatant in human albumin separation.

PubMed

Li, Can; Wang, Fei; Zang, Lixuan; Zang, Hengchang; Alcalà, Manel; Nie, Lei; Wang, Mingyu; Li, Lian

2017-03-15

Nowadays, as a powerful process analytical tool, near infrared spectroscopy (NIRS) has been widely applied in process monitoring. In present work, NIRS combined with multivariate analysis was used to monitor the ethanol precipitation process of fraction I+II+III (FI+II+III) supernatant in human albumin (HA) separation to achieve qualitative and quantitative monitoring at the same time and assure the product's quality. First, a qualitative model was established by using principal component analysis (PCA) with 6 of 8 normal batches samples, and evaluated by the remaining 2 normal batches and 3 abnormal batches. The results showed that the first principal component (PC1) score chart could be successfully used for fault detection and diagnosis. Then, two quantitative models were built with 6 of 8 normal batches to determine the content of the total protein (TP) and HA separately by using partial least squares regression (PLS-R) strategy, and the models were validated by 2 remaining normal batches. The determination coefficient of validation (R p 2 ), root mean square error of cross validation (RMSECV), root mean square error of prediction (RMSEP) and ratio of performance deviation (RPD) were 0.975, 0.501g/L, 0.465g/L and 5.57 for TP, and 0.969, 0.530g/L, 0.341g/L and 5.47 for HA, respectively. The results showed that the established models could give a rapid and accurate measurement of the content of TP and HA. The results of this study indicated that NIRS is an effective tool and could be successfully used for qualitative and quantitative monitoring the ethanol precipitation process of FI+II+III supernatant simultaneously. This research has significant reference value for assuring the quality and improving the recovery ratio of HA in industrialization scale by using NIRS. Copyright © 2016 Elsevier B.V. All rights reserved.

Visible and Near-Infrared Spectroscopy Analysis of a Polycyclic Aromatic Hydrocarbon in Soils

PubMed Central

Okparanma, Reuben N.; Mouazen, Abdul M.

2013-01-01

Visible and near-infrared (VisNIR) spectroscopy is becoming recognised by soil scientists as a rapid and cost-effective measurement method for hydrocarbons in petroleum-contaminated soils. This study investigated the potential application of VisNIR spectroscopy (350–2500 nm) for the prediction of phenanthrene, a polycyclic aromatic hydrocarbon (PAH), in soils. A total of 150 diesel-contaminated soil samples were used in the investigation. Partial least-squares (PLS) regression analysis with full cross-validation was used to develop models to predict the PAH compound. Results showed that the PAH compound was predicted well with residual prediction deviation of 2.0–2.32, root-mean-square error of prediction of 0.21–0.25 mg kg−1, and coefficient of determination (r 2) of 0.75–0.83. The mechanism of prediction was attributed to covariation of the PAH with clay and soil organic carbon. Overall, the results demonstrated that the methodology may be used for predicting phenanthrene in soils utilizing the interrelationship between clay and soil organic carbon. PMID:24453798

Evaluation of chemical parameters in soft mold-ripened cheese during ripening by mid-infrared spectroscopy.

PubMed

Martín-del-Campo, S T; Picque, D; Cosío-Ramírez, R; Corrieu, G

2007-06-01

The suitability of mid-infrared spectroscopy (MIR) to follow the evolution throughout ripening of specific physicochemical parameters in Camembert-type cheeses was evaluated. The infrared spectra were obtained directly from raw cheese samples deposited on an attenuated total reflectance crystal. Significant correlations were observed between physicochemical data, pH, acid-soluble nitrogen, nonprotein nitrogen, ammonia (NH4+), lactose, and lactic acid. Dry matter showed significant correlation only with lactose and nonprotein nitrogen. Principal components analysis factorial maps of physicochemical data showed a ripening evolution in 2 steps, from d 1 to d 7 and from d 8 to d 27, similar to that observed previously from infrared spectral data. Partial least squares regressions made it possible to obtain good prediction models for dry matter, acid-soluble nitrogen, nonprotein nitrogen, lactose, lactic acid, and NH4+ values from spectral data of raw cheese. The values of 3 statistical parameters (coefficient of determination, root mean square error of cross validation, and ratio prediction deviation) are satisfactory. Less precise models were obtained for pH.

Combination of multiple model population analysis and mid-infrared technology for the estimation of copper content in Tegillarca granosa

NASA Astrophysics Data System (ADS)

Hu, Meng-Han; Chen, Xiao-Jing; Ye, Peng-Chao; Chen, Xi; Shi, Yi-Jian; Zhai, Guang-Tao; Yang, Xiao-Kang

2016-11-01

The aim of this study was to use mid-infrared spectroscopy coupled with multiple model population analysis based on Monte Carlo-uninformative variable elimination for rapidly estimating the copper content of Tegillarca granosa. Copper-specific wavelengths were first extracted from the whole spectra, and subsequently, a least square-support vector machine was used to develop the prediction models. Compared with the prediction model based on full wavelengths, models that used 100 multiple MC-UVE selected wavelengths without and with bin operation showed comparable performances with Rp (root mean square error of Prediction) of 0.97 (14.60 mg/kg) and 0.94 (20.85 mg/kg) versus 0.96 (17.27 mg/kg), as well as ratio of percent deviation (number of wavelength) of 2.77 (407) and 1.84 (45) versus 2.32 (1762). The obtained results demonstrated that the mid-infrared technique could be used for estimating copper content in T. granosa. In addition, the proposed multiple model population analysis can eliminate uninformative, weakly informative and interfering wavelengths effectively, that substantially reduced the model complexity and computation time.

A QSAR study of integrase strand transfer inhibitors based on a large set of pyrimidine, pyrimidone, and pyridopyrazine carboxamide derivatives

NASA Astrophysics Data System (ADS)

de Campos, Luana Janaína; de Melo, Eduardo Borges

2017-08-01

In the present study, 199 compounds derived from pyrimidine, pyrimidone and pyridopyrazine carboxamides with inhibitory activity against HIV-1 integrase were modeled. Subsequently, a multivariate QSAR study was conducted with 54 molecules employed by Ordered Predictors Selection (OPS) and Partial Least Squares (PLS) for the selection of variables and model construction, respectively. Topological, electrotopological, geometric, and molecular descriptors were used. The selected real model was robust and free from chance correlation; in addition, it demonstrated favorable internal and external statistical quality. Once statistically validated, the training model was used to predict the activity of a second data set (n = 145). The root mean square deviation (RMSD) between observed and predicted values was 0.698. Although it is a value outside of the standards, only 15 (10.34%) of the samples exhibited higher residual values than 1 log unit, a result considered acceptable. Results of Williams and Euclidean applicability domains relative to the prediction showed that the predictions did not occur by extrapolation and that the model is representative of the chemical space of test compounds.

Oceanwide gravity anomalies from Geos-3, Seasat and Geosat altimeter data

NASA Technical Reports Server (NTRS)

Rapp, Richard H.; Basic, Tomislav

1992-01-01

Three kinds of satellite altimeter data have been combined, along with 5 x 5 arcmin bathymetric data, to calculate a 0.125 deg ocean wide gridded set of 2.3 x 10 exp 6 free-air gravity anomalies. The procedure used was least squares collocation that yields the predicted anomaly and standard deviation. The value of including the bathymetric data was shown in a test around the Dowd Seamount where the root mean square (rms) difference between ship gravity measurements decreased from +/- 40 mgal to +/- 20 mgal when the bathymetry was included. Comparisons between the predicted anomalies and ship gravity data is described in three cases. In the Banda Sea the rms differences were +/- 20 mgal for two lines. In the South Atlantic rms differences over lines of 2000 km in length were +/- 7 mgal. For cruise data in the Antarctica region the discrepancies were +/- 12 mgal. Comparisons of anomalies derived from the Geosat geodetic mission data by Marks and McAdoo (1992) with ship dta gave differences of +/- 6 mgal showing the value of the much denser Geosat geodetic mission altimeter data.

A feasibility study on the measurement of tree trunks in forests using multi-scale vertical images

NASA Astrophysics Data System (ADS)

Berveglieri, A.; Oliveira, R. O.; Tommaselli, A. M. G.

2014-06-01

The determination of the Diameter at Breast Height (DBH) is an important variable that contributes to several studies on forest, e.g., environmental monitoring, tree growth, volume of wood, and biomass estimation. This paper presents a preliminary technique for the measurement of tree trunks using terrestrial images collected with a panoramic camera in nadir view. A multi-scale model is generated with these images. Homologue points on the trunk surface are measured over the images and their ground coordinates are determined by intersection of rays. The resulting XY coordinates of each trunk, defining an arc shape, can be used as observations in a circle fitting by least squares. Then, the DBH of each trunk is calculated using an estimated radius. Experiments were performed in two urban forest areas to assess the approach. In comparison with direct measurements on the trunks taken with a measuring tape, the discrepancies presented a Root Mean Square Error (RMSE) of 1.8 cm with a standard deviation of 0.7 cm. These results demonstrate compatibility with manual measurements and confirm the feasibility of the proposed technique.

Analysis of Femtosecond Laser Assisted Capsulotomy Cutting Edges and Manual Capsulorhexis Using Environmental Scanning Electron Microscopy

PubMed Central

Serrao, Sebastiano; Lombardo, Giuseppe; Desiderio, Giovanni; Buratto, Lucio; Schiano-Lomoriello, Domenico; Pileri, Marco; Lombardo, Marco

2014-01-01

Purpose. To investigate the structure and irregularity of the capsulotomy cutting edges created by two femtosecond (FS) laser platforms in comparison with manual continuous circular capsulorhexis (CCC) using environmental scanning electron microscopy (eSEM). Methods. Ten anterior capsulotomies were obtained using two different FS laser cataract platforms (LenSx, n = 5, and Victus, n = 5). In addition, five manual CCC (n = 5) were obtained using a rhexis forceps. The specimens were imaged by eSEM (FEI Quanta 400, OR, USA). Objective metrics, which included the arithmetic mean deviation of the surface (Sa) and the root-mean-square deviation of the surface (Sq), were used to evaluate the irregularity of both the FS laser capsulotomies and the manual CCC cutting edges. Results. Several microirregularities were shown across the FS laser capsulotomy cutting edges. The edges of manually torn capsules were shown, by comparison of Sa and Sq values, to be smoother (P < 0.05) than the FS laser capsulotomy edges. Conclusions. Work is needed to understand whether the FS laser capsulotomy edge microirregularities, not seen in manual CCC, may act as focal points for the concentration of stress that would increase the risk of capsular tear during phacoemulsification as recently reported in the literature. PMID:25505977

Analysis of femtosecond laser assisted capsulotomy cutting edges and manual capsulorhexis using environmental scanning electron microscopy.

PubMed

Serrao, Sebastiano; Lombardo, Giuseppe; Desiderio, Giovanni; Buratto, Lucio; Schiano-Lomoriello, Domenico; Pileri, Marco; Lombardo, Marco

2014-01-01

Purpose. To investigate the structure and irregularity of the capsulotomy cutting edges created by two femtosecond (FS) laser platforms in comparison with manual continuous circular capsulorhexis (CCC) using environmental scanning electron microscopy (eSEM). Methods. Ten anterior capsulotomies were obtained using two different FS laser cataract platforms (LenSx, n = 5, and Victus, n = 5). In addition, five manual CCC (n = 5) were obtained using a rhexis forceps. The specimens were imaged by eSEM (FEI Quanta 400, OR, USA). Objective metrics, which included the arithmetic mean deviation of the surface (Sa) and the root-mean-square deviation of the surface (Sq), were used to evaluate the irregularity of both the FS laser capsulotomies and the manual CCC cutting edges. Results. Several microirregularities were shown across the FS laser capsulotomy cutting edges. The edges of manually torn capsules were shown, by comparison of Sa and Sq values, to be smoother (P < 0.05) than the FS laser capsulotomy edges. Conclusions. Work is needed to understand whether the FS laser capsulotomy edge microirregularities, not seen in manual CCC, may act as focal points for the concentration of stress that would increase the risk of capsular tear during phacoemulsification as recently reported in the literature.

Quality of corneal lamellar cuts quantified using atomic force microscopy

PubMed Central

Ziebarth, Noël M.; Dias, Janice; Hürmeriç, Volkan; Shousha, Mohamed Abou; Yau, Chiyat Ben; Moy, Vincent T.; Culbertson, William; Yoo, Sonia H.

2012-01-01

PURPOSE To quantify the cut quality of lamellar dissections made with the femtosecond laser using atomic force microscopy (AFM). SETTING Bascom Palmer Eye Institute, University of Miami Miller School of Medicine, Miami, Florida, USA. DESIGN Experimental study. METHODS Experiments were performed on 3 pairs of human cadaver eyes. The cornea was thinned to physiologic levels by placing the globe, cornea side down, in 25% dextran for 24 hours. The eyes were reinflated to normal pressures by injecting a balanced salt solution into the vitreous cavity. The eyes were placed in a holder, the epithelium was removed, and the eyes were cut with a Visumax femtosecond laser. The energy level was 180 nJ for the right eye and 340 nJ for the left eye of each pair. The cut depths were 200 μm, 300 μm, and 400 μm, with the cut depth maintained for both eyes of each pair. A 12.0 mm trephination was then performed. The anterior portion of the lamellar surface was placed in a balanced salt solution and imaged with AFM. As a control, the posterior surface was placed in 2% formalin and imaged with environmental scanning electron microscopy (SEM). Four quantitative parameters (root-mean-square deviation, average deviation, skewness, kurtosis) were calculated from the AFM images. RESULTS From AFM, the 300 μm low-energy cuts were the smoothest. Similar results were seen qualitatively in the environmental SEM images. CONCLUSION Atomic force microscopy provided quantitative information on the quality of lamellar dissections made using a femtosecond laser, which is useful in optimizing patient outcomes in refractive and lamellar keratoplasty surgeries. PMID:23141078

Listening to Mozart K.448 decreases electroencephalography oscillatory power associated with an increase in sympathetic tone in adults: a post-intervention study

PubMed Central

Lin, Lung-Chang; Ouyang, Chen-Sen; Chiang, Ching-Tai; Wu, Rong-Ching; Wu, Hui-Chuan

2014-01-01

Summary Objective Listening to Mozart K.448 has been demonstrated to improve spatial task scores, leading to what is known as the Mozart Effect. However, most of these reports only describe the phenomena but lack the scientific evidence needed to properly investigate the mechanism of Mozart Effect. In this study, we used electroencephalography (EEG) and heart rate variability (HRV) to evaluate the effects of Mozart K.448 on healthy volunteers to explore Mozart Effect. Design An EEG-based post-intervention analysis. Setting Kaohsiung Medical University Hospital, Kaohsiung, Taiwan. Participants Twenty-nine college students were enrolled. They received EEG and electrocardiogram examinations simultaneously before, during and after listening to the first movement of Mozart K.448. Main outcome measure EEG alpha, theta and beta power and HRV were compared in each stage. Results The results showed a significant decrease in alpha, theta and beta power when they listened to Mozart K.448. In addition, the average root mean square successive difference, the proportion derived by dividing NN50 by the total number of NN intervals, standard deviations of NN intervals and standard deviations of differences between adjacent NN intervals showed a significant decrease, while the high frequency revealed a significant decrease with a significantly elevated low-frequency/high-frequency ratio. Conclusion Listening to Mozart K.448 significantly decreased EEG alpha, theta and beta power and HRV. This study indicates that there is brain cortical function and sympathetic tone activation in healthy adults when listening to Mozart K.448, which may play an important role in the mechanism of Mozart Effect. PMID:25383198

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.

[NIR Assignment of Magnolol by 2D-COS Technology and Model Application Huoxiangzhengqi Oral Liduid].

PubMed

Pei, Yan-ling; Wu, Zhi-sheng; Shi, Xin-yuan; Pan, Xiao-ning; Peng, Yan-fang; Qiao, Yan-jiang

2015-08-01

Near infrared (NIR) spectroscopy assignment of Magnolol was performed using deuterated chloroform solvent and two-dimensional correlation spectroscopy (2D-COS) technology. According to the synchronous spectra of deuterated chloroform solvent and Magnolol, 1365~1455, 1600~1720, 2000~2181 and 2275~2465 nm were the characteristic absorption of Magnolol. Connected with the structure of Magnolol, 1440 nm was the stretching vibration of phenolic group O-H, 1679 nm was the stretching vibration of aryl and methyl which connected with aryl, 2117, 2304, 2339 and 2370 nm were the combination of the stretching vibration, bending vibration and deformation vibration for aryl C-H, 2445 nm were the bending vibration of methyl which linked with aryl group, these bands attribut to the characteristics of Magnolol. Huoxiangzhengqi Oral Liduid was adopted to study the Magnolol, the characteristic band by spectral assignment and the band by interval Partial Least Squares (iPLS) and Synergy interval Partial Least Squares (SiPLS) were used to establish Partial Least Squares (PLS) quantitative model, the coefficient of determination Rcal(2) and Rpre(2) were greater than 0.99, the Root Mean of Square Error of Calibration (RM-SEC), Root Mean of Square Error of Cross Validation (RMSECV) and Root Mean of Square Error of Prediction (RMSEP) were very small. It indicated that the characteristic band by spectral assignment has the same results with the Chemometrics in PLS model. It provided a reference for NIR spectral assignment of chemical compositions in Chinese Materia Medica, and the band filters of NIR were interpreted.

Gloss measurements and rugometric inspection in dental biomaterials

NASA Astrophysics Data System (ADS)

Fernández-Oliveras, Alicia; Costa, Manuel F. M.; Yebra, Ana; Rubiño, Manuel; Pérez, María. M.

2013-11-01

In dental applications, optimizing appearance is desirable and increasingly demanded by patients. The specular gloss is among the major appearance properties of dental biomaterials, and its relationship with surface roughness has been reported. Roughness and gloss are key surface aspects that complement each other. We have experimentally analyzed the specular gloss and surface roughness of two different types of dental-resin composites and pre-sintered and sintered zirconia ceramics. We have studied two shades of both composite types and two sintered zirconia ceramics: colored and uncolored. Moreover, a surface treatment was applied to one specimen of each dental resin. Gloss measurements were performed with a standardized reflectometer and the corresponding gloss percentages were calculated. All the samples were submitted to rugometric non-invasive inspection with the MICROTOP.06.MFC laser microtopographer in order to determine meaningful statistical parameters such as the average roughness (Ra) and the root-mean-square deviation (Rq). For a comparison of the different biomaterials, the uncertainties associated to the measure of the surface gloss and roughness were also determined. The differences between the two shades of both kinds of composites proved significant in the case of the roughness parameters but not for the specular gloss. The surface treatment applied to the dental-resin composites increased the average roughness but the changes in the specular gloss were significant only for the A2 enamel nano-composite. For the zirconia ceramic the sintered process resulted in an increase in the surface roughness with a decrease of the specular gloss, corroborating that the relationship between the gloss and the roughness shows the expected behavior.

Using soft computing techniques to predict corrected air permeability using Thomeer parameters, air porosity and grain density

NASA Astrophysics Data System (ADS)

Nooruddin, Hasan A.; Anifowose, Fatai; Abdulraheem, Abdulazeez

2014-03-01

Soft computing techniques are recently becoming very popular in the oil industry. A number of computational intelligence-based predictive methods have been widely applied in the industry with high prediction capabilities. Some of the popular methods include feed-forward neural networks, radial basis function network, generalized regression neural network, functional networks, support vector regression and adaptive network fuzzy inference system. A comparative study among most popular soft computing techniques is presented using a large dataset published in literature describing multimodal pore systems in the Arab D formation. The inputs to the models are air porosity, grain density, and Thomeer parameters obtained using mercury injection capillary pressure profiles. Corrected air permeability is the target variable. Applying developed permeability models in recent reservoir characterization workflow ensures consistency between micro and macro scale information represented mainly by Thomeer parameters and absolute permeability. The dataset was divided into two parts with 80% of data used for training and 20% for testing. The target permeability variable was transformed to the logarithmic scale as a pre-processing step and to show better correlations with the input variables. Statistical and graphical analysis of the results including permeability cross-plots and detailed error measures were created. In general, the comparative study showed very close results among the developed models. The feed-forward neural network permeability model showed the lowest average relative error, average absolute relative error, standard deviations of error and root means squares making it the best model for such problems. Adaptive network fuzzy inference system also showed very good results.

Application of a spectrum standardization method for carbon analysis in coal using laser-induced breakdown spectroscopy (LIBS).

PubMed

Li, Xiongwei; Wang, Zhe; Fu, Yangting; Li, Zheng; Liu, Jianmin; Ni, Weidou

2014-01-01

Measurement of coal carbon content using laser-induced breakdown spectroscopy (LIBS) is limited by its low precision and accuracy. A modified spectrum standardization method was proposed to achieve both reproducible and accurate results for the quantitative analysis of carbon content in coal using LIBS. The proposed method used the molecular emissions of diatomic carbon (C2) and cyanide (CN) to compensate for the diminution of atomic carbon emissions in high volatile content coal samples caused by matrix effect. The compensated carbon line intensities were further converted into an assumed standard state with standard plasma temperature, electron number density, and total number density of carbon, under which the carbon line intensity is proportional to its concentration in the coal samples. To obtain better compensation for fluctuations of total carbon number density, the segmental spectral area was used and an iterative algorithm was applied that is different from our previous spectrum standardization calculations. The modified spectrum standardization model was applied to the measurement of carbon content in 24 bituminous coal samples. The results demonstrate that the proposed method has superior performance over the generally applied normalization methods. The average relative standard deviation was 3.21%, the coefficient of determination was 0.90, the root mean square error of prediction was 2.24%, and the average maximum relative error for the modified model was 12.18%, showing an overall improvement over the corresponding values for the normalization with segmental spectrum area, 6.00%, 0.75, 3.77%, and 15.40%, respectively.

Nonrigid motion compensation in B-mode and contrast enhanced ultrasound image sequences of the carotid artery

NASA Astrophysics Data System (ADS)

Carvalho, Diego D. B.; Akkus, Zeynettin; Bosch, Johan G.; van den Oord, Stijn C. H.; Niessen, Wiro J.; Klein, Stefan

2014-03-01

In this work, we investigate nonrigid motion compensation in simultaneously acquired (side-by-side) B-mode ultrasound (BMUS) and contrast enhanced ultrasound (CEUS) image sequences of the carotid artery. These images are acquired to study the presence of intraplaque neovascularization (IPN), which is a marker of plaque vulnerability. IPN quantification is visualized by performing the maximum intensity projection (MIP) on the CEUS image sequence over time. As carotid images contain considerable motion, accurate global nonrigid motion compensation (GNMC) is required prior to the MIP. Moreover, we demonstrate that an improved lumen and plaque differentiation can be obtained by averaging the motion compensated BMUS images over time. We propose to use a previously published 2D+t nonrigid registration method, which is based on minimization of pixel intensity variance over time, using a spatially and temporally smooth B-spline deformation model. The validation compares displacements of plaque points with manual trackings by 3 experts in 11 carotids. The average (+/- standard deviation) root mean square error (RMSE) was 99+/-74μm for longitudinal and 47+/-18μm for radial displacements. These results were comparable with the interobserver variability, and with results of a local rigid registration technique based on speckle tracking, which estimates motion in a single point, whereas our approach applies motion compensation to the entire image. In conclusion, we evaluated that the GNMC technique produces reliable results. Since this technique tracks global deformations, it can aid in the quantification of IPN and the delineation of lumen and plaque contours.

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.

How do physicians become medical experts? A test of three competing theories: distinct domains, independent influence and encapsulation models.

PubMed

Violato, Claudio; Gao, Hong; O'Brien, Mary Claire; Grier, David; Shen, E

2018-05-01

The distinction between basic sciences and clinical knowledge which has led to a theoretical debate on how medical expertise is developed has implications for medical school and lifelong medical education. This longitudinal, population based observational study was conducted to test the fit of three theories-knowledge encapsulation, independent influence, distinct domains-of the development of medical expertise employing structural equation modelling. Data were collected from 548 physicians (292 men-53.3%; 256 women-46.7%; mean age = 24.2 years on admission) who had graduated from medical school 2009-2014. They included (1) Admissions data of undergraduate grade point average and Medical College Admission Test sub-test scores, (2) Course performance data from years 1, 2, and 3 of medical school, and (3) Performance on the NBME exams (i.e., Step 1, Step 2 CK, and Step 3). Statistical fit indices (Goodness of Fit Index-GFI; standardized root mean squared residual-SRMR; root mean squared error of approximation-RSMEA) and comparative fit [Formula: see text] of three theories of cognitive development of medical expertise were used to assess model fit. There is support for the knowledge encapsulation three factor model of clinical competency (GFI = 0.973, SRMR = 0.043, RSMEA = 0.063) which had superior fit indices to both the independent influence and distinct domains theories ([Formula: see text] vs [Formula: see text] [[Formula: see text

Statistical properties of solar granulation from the SOUP instrument on Spacelab 2

NASA Astrophysics Data System (ADS)

Topka, K.; Title, A.; Tarbell, T.; Ferguson, S.; Shine, R.

1988-11-01

The Solar Optical Universal Polarimeter (SOUP) on Spacelab 2 collected movies of solar granulation completely free from atmospheric blurring, and are not degraded by pointint jitter (the pointing stability was 0.003 sec root mean square). The movies illustrate that the solar five minute oscillation has a major role in the appearance of solar granulation and that exploding granules are a common feature of the granule evolution. Using 3-D Fourier filtering techniques the oscillations were removed and it was demonstrated that the autocorrelation lifetime of granulation is a factor of two greater in magnetic field regions than in field-free quiet sun. Horizontal velocities were measured and flow patterns were observed on the scale of meso- and super granulation. In quiet regions the mean flow velocity is 370 m/s while in the magnetic regions it is about 125 m/s. It was also found that the root mean square (RMS) fluctuating horizonal velocity field is substantially greater in quiet sun than in strong magnetic field regions. By superimposing the location of exploding granules on the average flow maps it was found that they appear almost exclusively in the center of mesogranulation size flow cells. Because of the nonuniformity of the distribution of exploding granules, the evolution of the granulation pattern in mesogranule cell centers and boundaries differs fundamentally. It is clear from this study there is neither a typical granule nor a typical granule evolution.

Statistical properties of solar granulation from the SOUP instrument on Spacelab 2

NASA Technical Reports Server (NTRS)

Topka, K.; Title, A.; Tarbell, T.; Ferguson, S.; Shine, R.

1988-01-01

The Solar Optical Universal Polarimeter (SOUP) on Spacelab 2 collected movies of solar granulation completely free from atmospheric blurring, and are not degraded by pointint jitter (the pointing stability was 0.003 sec root mean square). The movies illustrate that the solar five minute oscillation has a major role in the appearance of solar granulation and that exploding granules are a common feature of the granule evolution. Using 3-D Fourier filtering techniques the oscillations were removed and it was demonstrated that the autocorrelation lifetime of granulation is a factor of two greater in magnetic field regions than in field-free quiet sun. Horizontal velocities were measured and flow patterns were observed on the scale of meso- and super granulation. In quiet regions the mean flow velocity is 370 m/s while in the magnetic regions it is about 125 m/s. It was also found that the root mean square (RMS) fluctuating horizonal velocity field is substantially greater in quiet sun than in strong magnetic field regions. By superimposing the location of exploding granules on the average flow maps it was found that they appear almost exclusively in the center of mesogranulation size flow cells. Because of the nonuniformity of the distribution of exploding granules, the evolution of the granulation pattern in mesogranule cell centers and boundaries differs fundamentally. It is clear from this study there is neither a typical granule nor a typical granule evolution.

Parameterizing the binding properties of dissolved organic matter with default values skews the prediction of copper solution speciation and ecotoxicity in soil.

PubMed

Djae, Tanalou; Bravin, Matthieu N; Garnier, Cédric; Doelsch, Emmanuel

2017-04-01

Parameterizing speciation models by setting the percentage of dissolved organic matter (DOM) that is reactive (% r-DOM) toward metal cations at a single 65% default value is very common in predictive ecotoxicology. The authors tested this practice by comparing the free copper activity (pCu 2+  = -log 10 [Cu 2+ ]) measured in 55 soil sample solutions with pCu 2+ predicted with the Windermere humic aqueous model (WHAM) parameterized by default. Predictions of Cu toxicity to soil organisms based on measured or predicted pCu 2+ were also compared. Default WHAM parameterization substantially skewed the prediction of measured pCu 2+ by up to 2.7 pCu 2+ units (root mean square residual = 0.75-1.3) and subsequently the prediction of Cu toxicity for microbial functions, invertebrates, and plants by up to 36%, 45%, and 59% (root mean square residuals ≤9 %, 11%, and 17%), respectively. Reparametrizing WHAM by optimizing the 2 DOM binding properties (i.e., % r-DOM and the Cu complexation constant) within a physically realistic value range much improved the prediction of measured pCu 2+ (root mean square residual = 0.14-0.25). Accordingly, this WHAM parameterization successfully predicted Cu toxicity for microbial functions, invertebrates, and plants (root mean square residual ≤3.4%, 4.4%, and 5.8%, respectively). Thus, it is essential to account for the real heterogeneity in DOM binding properties for relatively accurate prediction of Cu speciation in soil solution and Cu toxic effects on soil organisms. Environ Toxicol Chem 2017;36:898-905. © 2016 SETAC. © 2016 SETAC.

Analysis of S-box in Image Encryption Using Root Mean Square Error Method

NASA Astrophysics Data System (ADS)

Hussain, Iqtadar; Shah, Tariq; Gondal, Muhammad Asif; Mahmood, Hasan

2012-07-01

The use of substitution boxes (S-boxes) in encryption applications has proven to be an effective nonlinear component in creating confusion and randomness. The S-box is evolving and many variants appear in literature, which include advanced encryption standard (AES) S-box, affine power affine (APA) S-box, Skipjack S-box, Gray S-box, Lui J S-box, residue prime number S-box, Xyi S-box, and S8 S-box. These S-boxes have algebraic and statistical properties which distinguish them from each other in terms of encryption strength. In some circumstances, the parameters from algebraic and statistical analysis yield results which do not provide clear evidence in distinguishing an S-box for an application to a particular set of data. In image encryption applications, the use of S-boxes needs special care because the visual analysis and perception of a viewer can sometimes identify artifacts embedded in the image. In addition to existing algebraic and statistical analysis already used for image encryption applications, we propose an application of root mean square error technique, which further elaborates the results and enables the analyst to vividly distinguish between the performances of various S-boxes. While the use of the root mean square error analysis in statistics has proven to be effective in determining the difference in original data and the processed data, its use in image encryption has shown promising results in estimating the strength of the encryption method. In this paper, we show the application of the root mean square error analysis to S-box image encryption. The parameters from this analysis are used in determining the strength of S-boxes

Empirical mass formula with proton-neutron interaction

NASA Astrophysics Data System (ADS)

Tachibana, Takahiro; Uno, Masahiro; Yamada, So; Yamada, Masami

1987-12-01

An atomic mass formula consisting of a gross part, and averge even-odd part and an empirical shell part is studied. The gross part is, apart from a small atomic term, taken to be the sum of nucleon rest masses. Coulomb energies and a polynomial in A1/3 and ‖N-Z‖/A. The shell part includes, in addition to proton and neutron support of nuclear magicities and the cooperative deformation effect. After the first construction of such a formula, refinements have been made in two respects. One is a separate treatment of Z=N odd-odd nuclei suggested by a quartet model, and the other is an improvement of the proton neutron interaction term. By these refinements the root-mean-square deviation of calculated masses from the 1986 Audi-Wapstra masses has been reduced from 538 keV to 460 keV.

Non-common path aberration correction in an adaptive optics scanning ophthalmoscope.

PubMed

Sulai, Yusufu N; Dubra, Alfredo

2014-09-01

The correction of non-common path aberrations (NCPAs) between the imaging and wavefront sensing channel in a confocal scanning adaptive optics ophthalmoscope is demonstrated. NCPA correction is achieved by maximizing an image sharpness metric while the confocal detection aperture is temporarily removed, effectively minimizing the monochromatic aberrations in the illumination path of the imaging channel. Comparison of NCPA estimated using zonal and modal orthogonal wavefront corrector bases provided wavefronts that differ by ~λ/20 in root-mean-squared (~λ/30 standard deviation). Sequential insertion of a cylindrical lens in the illumination and light collection paths of the imaging channel was used to compare image resolution after changing the wavefront correction to maximize image sharpness and intensity metrics. Finally, the NCPA correction was incorporated into the closed-loop adaptive optics control by biasing the wavefront sensor signals without reducing its bandwidth.

Femtosecond-level timing fluctuation suppression in atmospheric frequency transfer with passive phase conjunction correction.

PubMed

Sun, Fuyu; Hou, Dong; Zhang, Danian; Tian, Jie; Hu, Jianguo; Huang, Xianhe; Chen, Shijun

2017-09-04

We demonstrate femtosecond-level timing fluctuation suppression in indoor atmospheric comb-based frequency transfer with a passive phase conjunction correction technique. Timing fluctuations and Allan deviations are both measured to characterize the excess frequency instability incurred during the frequency transfer process. By transferring a 2 GHz microwave over a 52-m long free-space link in 5000 s, the total root-mean-square (RMS) timing fluctuation was measured to be about 280 fs with a fractional frequency instability on the order of 3 × 10 -13 at 1 s and 6 × 10 -17 at 1000 s. This atmospheric comb-based frequency transfer with passive phase conjunction correction can be used to build an atomic clock-based free-space frequency transmission link because its instability is less than that of a commercial Cs or H-master clock.

Detection of genetically modified soybean in crude soybean oil.

PubMed

Nikolić, Zorica; Vasiljević, Ivana; Zdjelar, Gordana; Ðorđević, Vuk; Ignjatov, Maja; Jovičić, Dušica; Milošević, Dragana

2014-02-15

In order to detect presence and quantity of Roundup Ready (RR) soybean in crude oil extracted from soybean seed with a different percentage of GMO seed two extraction methods were used, CTAB and DNeasy Plant Mini Kit. The amplifications of lectin gene, used to check the presence of soybean DNA, were not achieved in all CTAB extracts of DNA, while commercial kit gave satisfactory results. Comparing actual and estimated GMO content between two extraction methods, root mean square deviation for kit is 0.208 and for CTAB is 2.127, clearly demonstrated superiority of kit over CTAB extraction. The results of quantification evidently showed that if the oil samples originate from soybean seed with varying percentage of RR, it is possible to monitor the GMO content at the first stage of processing crude oil. Copyright © 2013 Elsevier Ltd. All rights reserved.

MoFvAb: Modeling the Fv region of antibodies

PubMed Central

Bujotzek, Alexander; Fuchs, Angelika; Qu, Changtao; Benz, Jörg; Klostermann, Stefan; Antes, Iris; Georges, Guy

2015-01-01

Knowledge of the 3-dimensional structure of the antigen-binding region of antibodies enables numerous useful applications regarding the design and development of antibody-based drugs. We present a knowledge-based antibody structure prediction methodology that incorporates concepts that have arisen from an applied antibody engineering environment. The protocol exploits the rich and continuously growing supply of experimentally derived antibody structures available to predict CDR loop conformations and the packing of heavy and light chain quickly and without user intervention. The homology models are refined by a novel antibody-specific approach to adapt and rearrange sidechains based on their chemical environment. The method achieves very competitive all-atom root mean square deviation values in the order of 1.5 Å on different evaluation datasets consisting of both known and previously unpublished antibody crystal structures. PMID:26176812

Markov state models of protein misfolding

NASA Astrophysics Data System (ADS)

Sirur, Anshul; De Sancho, David; Best, Robert B.

2016-02-01

Markov state models (MSMs) are an extremely useful tool for understanding the conformational dynamics of macromolecules and for analyzing MD simulations in a quantitative fashion. They have been extensively used for peptide and protein folding, for small molecule binding, and for the study of native ensemble dynamics. Here, we adapt the MSM methodology to gain insight into the dynamics of misfolded states. To overcome possible flaws in root-mean-square deviation (RMSD)-based metrics, we introduce a novel discretization approach, based on coarse-grained contact maps. In addition, we extend the MSM methodology to include "sink" states in order to account for the irreversibility (on simulation time scales) of processes like protein misfolding. We apply this method to analyze the mechanism of misfolding of tandem repeats of titin domains, and how it is influenced by confinement in a chaperonin-like cavity.

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.

Predicting Stability Constants for Uranyl Complexes Using Density Functional Theory

DOE PAGES

Vukovic, Sinisa; Hay, Benjamin P.; Bryantsev, Vyacheslav S.

2015-04-02

The ability to predict the equilibrium constants for the formation of 1:1 uranyl:ligand complexes (log K 1 values) provides the essential foundation for the rational design of ligands with enhanced uranyl affinity and selectivity. We also use density functional theory (B3LYP) and the IEFPCM continuum solvation model to compute aqueous stability constants for UO 2 2+ complexes with 18 donor ligands. Theoretical calculations permit reasonably good estimates of relative binding strengths, while the absolute log K 1 values are significantly overestimated. Accurate predictions of the absolute log K 1 values (root mean square deviation from experiment < 1.0 for logmore » K 1 values ranging from 0 to 16.8) can be obtained by fitting the experimental data for two groups of mono and divalent negative oxygen donor ligands. The utility of correlations is demonstrated for amidoxime and imide dioxime ligands, providing a useful means of screening for new ligands with strong chelate capability to uranyl.« less

Large-aperture space optical system testing based on the scanning Hartmann.

PubMed

Wei, Haisong; Yan, Feng; Chen, Xindong; Zhang, Hao; Cheng, Qiang; Xue, Donglin; Zeng, Xuefeng; Zhang, Xuejun

2017-03-10

Based on the Hartmann testing principle, this paper proposes a novel image quality testing technology which applies to a large-aperture space optical system. Compared with the traditional testing method through a large-aperture collimator, the scanning Hartmann testing technology has great advantages due to its simple structure, low cost, and ability to perform wavefront measurement of an optical system. The basic testing principle of the scanning Hartmann testing technology, data processing method, and simulation process are presented in this paper. Certain simulation results are also given to verify the feasibility of this technology. Furthermore, a measuring system is developed to conduct a wavefront measurement experiment for a 200 mm aperture optical system. The small deviation (6.3%) of root mean square (RMS) between experimental results and interferometric results indicates that the testing system can measure low-order aberration correctly, which means that the scanning Hartmann testing technology has the ability to test the imaging quality of a large-aperture space optical system.

Development of the Chinese version of the Hospital Autonomy Questionnaire: a cross-sectional study in Guangdong Province

PubMed Central

Liu, Zifeng; Yuan, Lianxiong; Huang, Yixiang; Zhang, Lingling; Luo, Futian

2016-01-01

Objective We aimed to develop a questionnaire for quantitative evaluation of the autonomy of public hospitals in China. Method An extensive literature review was conducted to select possible items for inclusion in the questionnaire, which was then reviewed by 5 experts. After a two-round Delphi method, we distributed the questionnaire to 404 secondary and tertiary hospitals in Guangdong Province, China, and 379 completed questionnaires were collected. The final questionnaire was then developed on the basis of the results of exploratory and confirmatory factor analysis. Results Analysis suggested that all internal consistency reliabilities exceeded the minimum reliability standard of 0.70 for the α coefficient. The overall scale coefficient was 0.87, and 6 subscale coefficients were 0.92 (strategic management), 0.81 (budget and expenditure), 0.85 (financing), 0.75 (financing, medical management), 0.86 (human resources) and 0.86 (accountability). Correlation coefficients between and among items and their hypothesised subscales were higher than those with other subscales. The value of average variance extracted (AVE) was higher than 0.5, the value of construct reliability (CR) was higher than 0.7, and the square roots of the AVE of each subscale were larger than the correlation of the specific subscale with the other subscales, supporting the convergent and discriminant validity of the Chinese version of the Hospital Autonomy Questionnaire (CVHAQ). The model fit indices were all acceptable: χ2/df=1.73, Goodness of Fit Index (GFI) = 0.93, Adjusted Goodness of Fit Index (AGFI) = 0.91, Non-Normed Fit Index (NNFI) = 0.96, Comparative Fit Index (CFI) = 0.97, Root Mean Square Error of Approximation (RMSEA) = 0.04, Standardised Root Mean Square Residual (SRMR) = 0.07. Conclusions This study demonstrated the reliability and validity of a CVHAQ and provides a quantitative method for the assessment of hospital autonomy. PMID:26911587

Characterizing the relative contributions of large vessels to total ocean noise fields: a case study using the Gerry E. Studds Stellwagen Bank National Marine Sanctuary.

PubMed

Hatch, Leila; Clark, Christopher; Merrick, Richard; Van Parijs, Sofie; Ponirakis, Dimitri; Schwehr, Kurt; Thompson, Michael; Wiley, David

2008-11-01

In 2006, we used the U.S. Coast Guard's Automatic Identification System (AIS) to describe patterns of large commercial ship traffic within a U.S. National Marine Sanctuary located off the coast of Massachusetts. We found that 541 large commercial vessels transited the greater sanctuary 3413 times during the year. Cargo ships, tankers, and tug/tows constituted 78% of the vessels and 82% of the total transits. Cargo ships, tankers, and cruise ships predominantly used the designated Boston Traffic Separation Scheme, while tug/tow traffic was concentrated in the western and northern portions of the sanctuary. We combined AIS data with low-frequency acoustic data from an array of nine autonomous recording units analyzed for 2 months in 2006. Analysis of received sound levels (10-1000 Hz, root-mean-square pressure re 1 microPa +/- SE) averaged 119.5 +/- 0.3 dB at high-traffic locations. High-traffic locations experienced double the acoustic power of less trafficked locations for the majority of the time period analyzed. Average source level estimates (71-141 Hz, root-mean-square pressure re 1 microPa +/- SE) for individual vessels ranged from 158 +/- 2 dB (research vessel) to 186 +/- 2 dB (oil tanker). Tankers were estimated to contribute 2 times more acoustic power to the region than cargo ships, and more than 100 times more than research vessels. Our results indicate that noise produced by large commercial vessels was at levels and within frequencies that warrant concern among managers regarding the ability of endangered whales to maintain acoustic contact within greater sanctuary waters.

Effects of Prolonged Spaceflight on Atrial Size, Atrial Electrophysiology, and Risk of Atrial Fibrillation.

PubMed

Khine, Htet W; Steding-Ehrenborg, Katarina; Hastings, Jeffrey L; Kowal, Jamie; Daniels, James D; Page, Richard L; Goldberger, Jeffery J; Ng, Jason; Adams-Huet, Beverley; Bungo, Michael W; Levine, Benjamin D

2018-05-01

The prevalence of atrial fibrillation (AF) in active astronauts is ≈5%, similar to the general population but at a younger age. Risk factors for AF include left atrial enlargement, increased number of premature atrial complexes, and certain parameters on signal-averaged electrocardiography, such as P-wave duration, root mean square voltage for the terminal 20 ms of the signal-averaged P wave, and P-wave amplitude. We aimed to evaluate changes in atrial structure, supraventricular beats, and atrial electrophysiology to determine whether spaceflight could increase the risk of AF. Thirteen astronauts underwent cardiac magnetic resonance imaging to assess atrial structure and function before and after 6 months in space and high-resolution Holter monitoring for multiple 48-hour time periods before flight, during flight, and on landing day. Left atrial volume transiently increased after 6 months in space (12±18 mL; P =0.03) without changing atrial function. Right atrial size remained unchanged. No changes in supraventricular beats were noted. One astronaut had a large increase in supraventricular ectopic beats but none developed AF. Filtered P-wave duration did not change over time, but root mean square voltage for the terminal 20 ms decreased on all fight days except landing day. No changes in P-wave amplitude were seen in leads II or V 1 except landing day for lead V 1 . Six months of spaceflight may be sufficient to cause transient changes in left atrial structure and atrial electrophysiology that increase the risk of AF. However, there was no definite evidence of increased supraventricular arrhythmias and no identified episodes of AF. © 2018 American Heart Association, Inc.

Atomic charge transfer-counter polarization effects determine infrared CH intensities of hydrocarbons: a quantum theory of atoms in molecules model.

PubMed

Silva, Arnaldo F; Richter, Wagner E; Meneses, Helen G C; Bruns, Roy E

2014-11-14

Atomic charge transfer-counter polarization effects determine most of the infrared fundamental CH intensities of simple hydrocarbons, methane, ethylene, ethane, propyne, cyclopropane and allene. The quantum theory of atoms in molecules/charge-charge flux-dipole flux model predicted the values of 30 CH intensities ranging from 0 to 123 km mol(-1) with a root mean square (rms) error of only 4.2 km mol(-1) without including a specific equilibrium atomic charge term. Sums of the contributions from terms involving charge flux and/or dipole flux averaged 20.3 km mol(-1), about ten times larger than the average charge contribution of 2.0 km mol(-1). The only notable exceptions are the CH stretching and bending intensities of acetylene and two of the propyne vibrations for hydrogens bound to sp hybridized carbon atoms. Calculations were carried out at four quantum levels, MP2/6-311++G(3d,3p), MP2/cc-pVTZ, QCISD/6-311++G(3d,3p) and QCISD/cc-pVTZ. The results calculated at the QCISD level are the most accurate among the four with root mean square errors of 4.7 and 5.0 km mol(-1) for the 6-311++G(3d,3p) and cc-pVTZ basis sets. These values are close to the estimated aggregate experimental error of the hydrocarbon intensities, 4.0 km mol(-1). The atomic charge transfer-counter polarization effect is much larger than the charge effect for the results of all four quantum levels. Charge transfer-counter polarization effects are expected to also be important in vibrations of more polar molecules for which equilibrium charge contributions can be large.

Effects of an Off-Axis Pivoting Elliptical Training Program on Gait Function in Persons With Spastic Cerebral Palsy: A Preliminary Study.

PubMed

Tsai, Liang-Ching; Ren, Yupeng; Gaebler-Spira, Deborah J; Revivo, Gadi A; Zhang, Li-Qun

2017-07-01

This preliminary study examined the effects of off-axis elliptical training on reducing transverse-plane gait deviations and improving gait function in 8 individuals with cerebral palsy (CP) (15.5 ± 4.1 years) who completed an training program using a custom-made elliptical trainer that allows transverse-plane pivoting of the footplates during exercise. Lower-extremity off-axis control during elliptical exercise was evaluated by quantifying the root-mean-square and maximal angular displacement of the footplate pivoting angle. Lower-extremity pivoting strength was assessed. Gait function and balance were evaluated using 10-m walk test, 6-minute-walk test, and Pediatric Balance Scale. Toe-in angles during gait were quantified. Participants with CP demonstrated a significant decrease in the pivoting angle (root mean square and maximal angular displacement; effect size, 1.00-2.00) and increase in the lower-extremity pivoting strength (effect size = 0.91-1.09) after training. Reduced 10-m walk test time (11.9 ± 3.7 seconds vs. 10.8 ± 3.0 seconds; P = 0.004; effect size = 1.46), increased Pediatric Balance Scale score (43.6 ± 12.9 vs. 45.6 ± 10.8; P = 0.042; effect size = 0.79), and decreased toe-in angle (3.7 ± 10.5 degrees vs. 0.7 ± 11.7 degrees; P = 0.011; effect size = 1.22) were observed after training. We present an intervention to challenge lower-extremity off-axis control during a weight-bearing and functional activity for individuals with CP. Our preliminary findings suggest that this intervention was effective in enhancing off-axis control, gait function, and balance and reducing in-toeing gait in persons with CP.

Deciphering the Dynamics of Non-Covalent Interactions Affecting Thermal Stability of a Protein: Molecular Dynamics Study on Point Mutant of Thermus thermophilus Isopropylmalate Dehydrogenase.

PubMed

Sharma, Reetu; Sastry, G Narahari

2015-01-01

Thermus thermophilius isopropylmalate dehydrogenase catalyzes oxidative decarboxylation and dehydrogenation of isopropylmalate. Substitution of leucine to alanine at position 172 enhances the thermal stability among the known point mutants. Exploring the dynamic properties of non-covalent interactions such as saltbridges, hydrogen bonds and hydrophobic interactions to explain thermal stability of a protein is interesting in its own right. In this study dynamic changes in the non-covalent interactions are studied to decipher the deterministic features of thermal stability of a protein considering a case study of a point mutant in Thermus thermophilus isopropylmalate dehydrogenase. A total of four molecular dynamic simulations of 0.2 μs were carried out on wild type and mutant's functional dimers at 300 K and 337 K. Higher thermal stability of the mutant as compared to wild type is revealed by root mean square deviation, root mean square fluctuations and Cα-Cα distance with an increase in temperature from 300 K to 337 K. Most of the regions of wild type fluctuate higher than the corresponding regions of mutant with an increase in temperature. Cα-Cα distance analysis suggests that long distance networks are significantly affected in wild type as compared to the mutant. Short lived contacts are higher in wild type, while long lived contacts are lost at 337 K. The mutant forms less hydrogen bonds with water as compared to wild type at 337 K. In contrast to wild type, the mutant shows significant increase in unique saltbridges, hydrogen bonds and hydrophobic contacts at 337 K. The current study indicates that there is a strong inter-dependence of thermal stability on the way in which non-covalent interactions reorganize, and it is rewarding to explore this connection in single mutant studies.

Disruption of redox catalytic functions of peroxiredoxin-thioredoxin complex in Mycobacterium tuberculosis H37Rv using small interface binding molecules.

PubMed

Gurung, Arun Bahadur; Das, Amit Kumar; Bhattacharjee, Atanu

2017-04-01

Mycobacterium tuberculosis has distinctive ability to detoxify various microbicidal superoxides and hydroperoxides via a redox catalytic cycle involving thiol reductants of peroxiredoxin (Prx) and thioredoxin (Trx) systems which has conferred on it resistance against oxidative killing and survivability within host. We have used computational approach to disrupt catalytic functions of Prx-Trx complex which can possibly render the pathogen vulnerable to oxidative killing in the host. Using protein-protein docking method, we have successfully constructed the Prx-Trx complex. Statistics of interface region revealed contact area of each monomer less than 1500Å 2 and enriched in polar amino acids indicating transient interaction between Prx and Trx. We have identified ZINC40139449 as a potent interface binding molecule through virtual screening of drug-like compounds from ZINC database. Molecular dynamics (MD) simulation studies showed differences in structural properties of Prx-Trx complex both in apo and ligand bound states with regard to root mean square deviation (RMSD), radius of gyration (Rg), root mean square fluctuations (RMSF), solvent accessible surface area (SASA) and number of hydrogen bonds (NHBs). Interestingly, we found stability of two conserved catalytic residues Cys61 and Cys174 of Prx and conserved catalytic motif, WCXXC of Trx upon binding of ZINC40139449. The time dependent displacement study reveals that the compound is quite stable in the interface binding region till 30ns of MD simulation. The structural properties were further validated by principal component analysis (PCA). We report ZINC40139449 as promising lead which can be further evaluated by in vitro or in vivo enzyme inhibition assays. Copyright © 2016 Elsevier Ltd. All rights reserved.

Improving thermostability of phosphatidylinositol-synthesizing Streptomyces phospholipase D.

PubMed

Damnjanović, Jasmina; Takahashi, Rie; Suzuki, Atsuo; Nakano, Hideo; Iwasaki, Yugo

2012-08-01

Aimed to produce thermostable phosphatidylinositol (PI)-synthesizing phospholipase D (PLD), we initiated site-directed combinatorial mutagenesis followed by high-throughput screening. Previous site-directed combinatorial mutagenesis of wild-type Streptomyces PLD produced a mutant, DYR (W187D/Y191Y/Y385R) with PI-synthesizing ability. Deriving PI as a product of transphosphatidylation between phosphatidylcholine and myo-inositol, with myo-inositol in excess at high-temperature reaction conditions can increase yield due to enhanced solubility of this substrate. Thus, we improved DYR's thermostability by introduction of random mutations into selected amino acid positions having high B-factor. Screening of the libraries under restricted conditions yielded single-point mutants, specifically D40H, T291Y and R329G. Combinations of these point mutations yielded double (D40H/T291Y, D40H/R329G and T291Y/R329G) and triple (D40H/T291Y/R329G) mutants. PI synthesis at elevated temperatures pointed at D40H/T291Y as the most efficient enzyme. Circular dichroism analysis revealed D40H/T291Y to have increased melting temperature and postponed onset of thermal unfolding compared with DYR. Thermal tolerance study at 65°C confirmed D40H/T291Y's thermostability as its half-inactivation time was 8.7 min longer compared with DYR. This mutant had significantly less root-mean-square deviation change compared with DYR and showed no change in root-mean-square fluctuation when temperature shifts from 40 to 60°C, as determined by molecular dynamics analysis. Acquired different degrees of thermostability were also observed for several other DYR mutants.

VP40 of the Ebola Virus as a Target for EboV Therapy: Comprehensive Conformational and Inhibitor Binding Landscape from Accelerated Molecular Dynamics.

PubMed

Balmith, Marissa; Soliman, Mahmoud E S

2017-03-01

The first account of the dynamic features of the loop region of VP40 of the Ebola virus was studied using accelerated molecular dynamics simulations and reported herein. Among the proteins of the Ebola virus, the matrix protein (VP40) plays a significant role in the virus lifecycle thereby making it a promising therapeutic target. Of interest is the newly elucidated N-terminal domain loop region of VP40 comprising residues K127, T129, and N130 which when mutated to alanine have demonstrated an unrecognized role for N-terminal domain-plasma membrane interaction for efficient VP40-plasma membrane localization, oligomerization, matrix assembly, and egress. The molecular understanding of the conformational features of VP40 in complex with a known inhibitor still remains elusive. Using accelerated molecular dynamics approaches, we conducted a comparative study on VP40 apo and bound systems to understand the conformational features of VP40 at the molecular level and to determine the effect of inhibitor binding with the aid of a number of post-dynamic analytical tools. Significant features were seen in the presence of an inhibitor as per molecular mechanics/generalized born surface area binding free energy calculations. Results revealed that inhibitor binding to VP40 reduces the flexibility and mobility of the protein as supported by root mean square fluctuation and root mean square deviation calculations. The study revealed a characteristic "twisting" motion and coiling of the loop region of VP40 accompanied by conformational changes in the dimer interface upon inhibitor binding. We believe that results presented in this study will ultimately provide useful insight into the binding landscape of VP40 which could assist researchers in the discovery of potent Ebola virus inhibitors for anti-Ebola therapies.

Identification of new benzamide inhibitor against α-subunit of tryptophan synthase from Mycobacterium tuberculosis through structure-based virtual screening, anti-tuberculosis activity and molecular dynamics simulations.

PubMed

Naz, Sadia; Farooq, Umar; Ali, Sajid; Sarwar, Rizwana; Khan, Sara; Abagyan, Ruben

2018-03-13

Multi-drug-resistant tuberculosis and extensively drug-resistant tuberculosis has emerged as global health threat, causing millions of deaths worldwide. Identification of new drug candidates for tuberculosis (TB) by targeting novel and less explored protein targets will be invaluable for antituberculosis drug discovery. We performed structure-based virtual screening of eMolecules database against a homology model of relatively unexplored protein target: the α-subunit of tryptophan synthase (α-TRPS) from Mycobacterium tuberculosis essential for bacterial survival. Based on physiochemical properties analysis and molecular docking, the seven candidate compounds were selected and evaluated through whole cell-based activity against the H37Rv strain of M. tuberculosis. A new Benzamide inhibitor against α-subunit of tryptophan synthase (α-TRPS) from M. tuberculosis has been identified causing 100% growth inhibition at 25 μg/ml and visible bactericidal activity at 6 μg/ml. This benzamide inhibitor displayed a good predicted binding score (-48.24 kcal/mol) with the α-TRPS binding pocket and has logP value (2.95) comparable to Rifampicin. Further refinement of docking results and evaluation of inhibitor-protein complex stability were investigated through Molecular dynamic (MD) simulations studies. Following MD simulations, Root mean square deviation, Root mean square fluctuation and secondary structure analysis confirmed that protein did not unfold and ligand stayed inside the active pocket of protein during the explored time scale. This identified benzamide inhibitor against the α-subunit of TRPS from M. tuberculosis could be considered as candidate for drug discovery against TB and will be further evaluated for enzyme-based inhibition in future studies.

Prediction of functionally significant single nucleotide polymorphisms in PTEN tumor suppressor gene: An in silico approach.

PubMed

Khan, Imran; Ansari, Irfan A; Singh, Pratichi; Dass J, Febin Prabhu

2017-09-01

The phosphatase and tensin homolog (PTEN) gene plays a crucial role in signal transduction by negatively regulating the PI3K signaling pathway. It is the most frequent mutated gene in many human-related cancers. Considering its critical role, a functional analysis of missense mutations of PTEN gene was undertaken in this study. Thirty five nonsynonymous single nucleotide polymorphisms (nsSNPs) within the coding region of the PTEN gene were selected for our in silico investigation, and five nsSNPs (G129E, C124R, D252G, H61D, and R130G) were found to be deleterious based on combinatorial predictions of different computational tools. Moreover, molecular dynamics (MD) simulation was performed to investigate the conformational variation between native and all the five mutant PTEN proteins having predicted deleterious nsSNPs. The results of MD simulation of all mutant models illustrated variation in structural attributes such as root-mean-square deviation, root-mean-square fluctuation, radius of gyration, and total energy; which depicts the structural stability of PTEN protein. Furthermore, mutant PTEN protein structures also showed a significant variation in the solvent accessible surface area and hydrogen bond frequencies from the native PTEN structure. In conclusion, results of this study have established the deleterious effect of the all the five predicted nsSNPs on the PTEN protein structure. Thus, results of the current study can pave a new platform to sort out nsSNPs that can be undertaken for the confirmation of their phenotype and their correlation with diseased status in case of control studies. © 2016 International Union of Biochemistry and Molecular Biology, Inc.

Identification of potential isoform-selective histone deacetylase inhibitors for cancer therapy: a combined approach of structure-based virtual screening, ADMET prediction and molecular dynamics simulation assay.

PubMed

Uba, Abdullahi Ibrahim; Yelekçi, Kemal

2017-10-23

Histone deacetylases (HDACs) have gained increased attention as targets for anticancer drug design and development. HDAC inhibitors have proven to be effective for reversing the malignant phenotype in HDAC-dependent cancer cases. However, lack of selectivity of the many HDAC inhibitors in clinical use and trials contributes to toxicities to healthy cells. It is believed that, the continued identification of isoform-selective inhibitors will eliminate these undesirable adverse effects - a task that remains a major challenge to HDAC inhibitor designs. Here, in an attempt to identify isoform-selective inhibitors, a large compound library containing 2,703,000 compounds retrieved from Otava database was screened against class I HDACs by exhaustive approach of structure-based virtual screening using rDOCK and Autodock Vina. A total of 41 compounds were found to show high-isoform selectivity and were further redocked into their respective targets using Autodock4. Thirty-six compounds showed remarkable isoform selectivity and passed drug-likeness and absorption, distribution, metabolism, elimination and toxicity prediction tests using ADMET Predictor™ and admetSAR. Furthermore, to study the stability of ligand binding modes, 10 ns-molecular dynamics (MD) simulations of the free HDAC isoforms and their complexes with respective best-ranked ligands were performed using nanoscale MD software. The inhibitors remained bound to their respective targets over time of the simulation and the overall potential energy, root-mean-square deviation, root-mean-square fluctuation profiles suggested that the detected compounds may be potential isoform-selective HDAC inhibitors or serve as promising scaffolds for further optimization towards the design of selective inhibitors for cancer therapy.

Mutational analysis of microbial hydroxycinnamoyl-CoA hydratase-lyase (HCHL) towards enhancement of binding affinity: A computational approach.

PubMed

Kumar, Pravin; Ghosh Sachan, Shashwati; Poddar, Raju

2017-10-01

Improving the industrial enzyme for better yield of the product is important and a challenging task. One of such important industrial enzymes is microbial Hydroxycinnamoyl-CoA hydratase-lyase (HCHL). It converts feruloyl-CoA to vanillin. We place our efforts towards the improvement of its catalytic activity with comprehensive computational investigation. Catalytic core of the HCHL was explored with molecular modeling and docking approaches. Site-directed mutations were introduced in the catalytic site of HCHL in a sequential manner to generate different mutants of HCHL. Basis of mutation is to increase the interaction between HCHL and substrate feruloyl-CoA through interatomic forces and hydrogen bond formation. A rigorous molecular dynamics (MD) simulation was performed to check the stability of mutant's structure. Root mean square deviation (RMSD), root mean square fluctuation (RMSF), dynamic cross correlation (DCCM) and principal component analysis (PCA) were also performed to analyze flexibility and stability of structures. Docking studies were carried out between different mutants of HCHL and feruloyl-CoA. Investigation of the different binding sites and the interactions with mutant HCHLs and substrate allowed us to highlight the improved performance of mutants than wild type HCHL. This was further validated with MD simulation of complex consisting of different mutants and substrate. It further confirms all the structures are stable. However, mutant-2 showed better affinity towards substrate by forming hydrogen bond between active site and feruloyl-CoA. We propose that increase in hydrogen bond formation might facilitate in dissociation of vanillin from feruloyl-CoA. The current work may be useful for the future development of 'tailor-made' enzymes for better yield of vanillin. Copyright © 2017 Elsevier Inc. All rights reserved.

Molecular dynamics simulations and principal component analysis on human laforin mutation W32G and W32G/K87A.

PubMed

Srikumar, P S; Rohini, K; Rajesh, Perumbilavil Kaithamanakallam

2014-06-01

Mutations in human laforin lead to an autosomal neurodegenerative disorder Lafora disease. In N-terminal carbohydrate binding domain of laforin, two mutations W32G and K87A are reported as highly disease causing laforin mutants. Experimental studies reported that mutations are responsible for the abolishment of glycogen binding which is a critical function of laforin. Our current computational study focused on the role of conformational changes in human laforin structure due to existing single mutation W32G and prepared double mutation W32G/K87A related to loss of glycogen binding. We performed 10 ns molecular dynamics (MD) simulation studies in the Gromacs package for both mutations and analyzed the trajectories. From the results, the global properties like root mean square deviation, root mean square fluctuation, radius of gyration, solvent accessible surface area and hydrogen bonds showed structural changes in atomic level observed in W32G and W32G/K87A laforin mutants. The conformational change induced by mutants influenced the loss of the overall stability of the native laforin. Moreover, the change in overall motion of protein was analyzed by principal component analysis and results showed protein clusters expanded more than native and also change in direction in case of double mutant in conformational space. Overall, our report provides theoretical information on loss of structure-function relationship due to flexible nature of laforin mutants. In conclusion, comparative MD simulation studies support the experimental data on W32G and W32G/K87A related to the lafora disease mechanism on glycogen binding.

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.

Computational screening and molecular dynamics simulation of disease associated nsSNPs in CENP-E.

PubMed

Kumar, Ambuj; Purohit, Rituraj

2012-01-01

Aneuploidy and chromosomal instability (CIN) are hallmarks of most solid tumors. Mutations in centroemere proteins have been observed in promoting aneuploidy and tumorigenesis. Recent studies reported that Centromere-associated protein-E (CENP-E) is involved in inducing cancers. In this study we investigated the pathogenic effect of 132 nsSNPs reported in CENP-E using computational platform. Y63H point mutation found to be associated with cancer using SIFT, Polyphen, PhD-SNP, MutPred, CanPredict and Dr. Cancer tools. Further we investigated the binding affinity of ATP molecule to the CENP-E motor domain. Complementarity scores obtained from docking studies showed significant loss in ATP binding affinity of mutant structure. Molecular dynamics simulation was carried to examine the structural consequences of Y63H mutation. Root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (R(g)), solvent accessibility surface area (SASA), energy value, hydrogen bond (NH Bond), eigenvector projection, trace of covariance matrix and atom density analysis results showed notable loss in stability for mutant structure. Y63H mutation was also shown to disrupt the native conformation of ATP binding region in CENP-E motor domain. Docking studies for remaining 18 mutations at 63rd residue position as well as other two computationally predicted disease associated mutations S22L and P69S were also carried to investigate their affect on ATP binding affinity of CENP-E motor domain. Our study provided a promising computational methodology to study the tumorigenic consequences of nsSNPs that have not been characterized and clear clue to the wet lab scientist. Copyright © 2012 Elsevier B.V. All rights reserved.

Molecular dynamics simulation studies of novel β-lactamase inhibitor.

PubMed

Ul Haq, Farhan; Abro, Asma; Raza, Saad; Liedl, Klaus R; Azam, Syed Sikander

2017-06-01

New Delhi Metallo-β-Lactamase-1 (NDM-1) has drawn great attention due to its diverse antibiotic resistant activity. It can hydrolyze almost all clinically available β-lactam antibiotics. To inhibit the activity of NDM-1 a new strategy is proposed using computational methods. Molecular dynamics (MD) simulations are used to analyze the molecular interactions between selected inhibitor candidates and NDM-1 structure. The enzyme-ligand complex is subject to binding free energy calculations using MM(PB/GB)SA methods. The role of each residue of the active site contributing in ligand binding affinity is explored using energy decomposition analysis. Furthermore, a hydrogen bonding network between ligand and enzyme active site is observed and key residues are identified ensuring that the ligand stays inside the active site and maintains its movement towards the active site pocket. A production run of 150ns is carried out and results are analyzed using root mean square deviation (RMSD), root mean square fluctuation (RMSF), and radius of gyration (Rg) to explain the stability of enzyme ligand complex. Important active site residue e.g. PHE70, VAL73, TRP93, HIS122, GLN123, ASP124, HIS189, LYS216, CYS208, LYS211, ALA215, HIS250, and SER251 were observed to be involved in ligand attachemet inside the active site pocket, hence depicting its inhibitor potential. Hydrogen bonds involved in structural stability are analyzed through radial distribution function (RDF) and contribution of important residues involved in ligand movement is explained using a novel analytical tool, axial frequency distribution (AFD) to observe the role of important hydrogen bonding partners between ligand atoms and active site residues. Copyright © 2017 Elsevier Inc. All rights reserved.

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.

Insights into RpoB clinical mutants in mediating rifampicin resistance in Mycobacterium tuberculosis.

PubMed

Nusrath Unissa, Ameeruddin; Hassan, Sameer; Indira Kumari, Venkatesan; Revathy, Ravi; Hanna, Luke Elizabeth

2016-06-01

Rifampicin (RIF) an essential first-line anti-tuberculosis (TB) drug, resistance to RIF is a potential threat to TB control program and widely considered as surrogate marker for detection of multi-drug resistant-TB (MDR-TB), molecular understanding of which is the utmost need of the hour. Mutations at RIF resistance-determining region (RRDR) of 81-bp in the rpoB gene coding for β subunit or RpoB protein is the major cause of RIF resistance in Mycobacterium tuberculosis (MTB). Mutation at positions 526 and 531 are generally associated with high-level RIF resistance and at codons 516, 521 and 533 with low-level resistance. Thus, in order to understand the interactions between the clinical mutants (MTs) of RpoB and RIF which are responsible for mediating both levels of RIF resistance from MTB. In the present study, models of wild type (WT) and seven MTs (D516V, L521M, H526D, H526R, H526Y, S531L and L533P) of RpoB from MTB were generated using crystal structure of 2A68 and 4KBM as templates, for deducing 3 domains structure. Molecular docking between RpoB proteins and RIF was carried out, which showed higher values for WT compared to MTs. The high score in WT may be due to the presence of favorable interactions with RIF and MT-L521M which lacks in other MTs. Molecular dynamics (MD) simulation was performed for over 10 nanoseconds, which suggest the root mean square deviation (RMSD) was more and root mean square fluctuation (RMSF) was less in WT compared to MTs. The ligand RMSD exhibited very unique deviation with the MT-D516V compared to other MTs and WT. The RMSF for MTs such as H526R-H526D, L521M and D516V were higher for residues such as 152, 265, 352, 402, 513, 552, and 577 compared to WT. Hydrogen bond interactions at RIF binding site after MD simulations were found comparatively lower in WT than MTs. Similarly, the binding energy of WT was observed to be lesser in comparison to MTs. All MTs demonstrated certain (2Å) degree of structural deviation from the WT. Overall, these results suggest that RIF binding ability shows differences between WT and MTs, which could be because of different substitutions affecting the conformation of the MT proteins, leading to changes in binding interactions with RIF, eventually to the cause of RIF resistance. Copyright © 2016 Elsevier Inc. All rights reserved.

[Gaussian process regression and its application in near-infrared spectroscopy analysis].

PubMed

Feng, Ai-Ming; Fang, Li-Min; Lin, Min

2011-06-01

Gaussian process (GP) is applied in the present paper as a chemometric method to explore the complicated relationship between the near infrared (NIR) spectra and ingredients. After the outliers were detected by Monte Carlo cross validation (MCCV) method and removed from dataset, different preprocessing methods, such as multiplicative scatter correction (MSC), smoothing and derivate, were tried for the best performance of the models. Furthermore, uninformative variable elimination (UVE) was introduced as a variable selection technique and the characteristic wavelengths obtained were further employed as input for modeling. A public dataset with 80 NIR spectra of corn was introduced as an example for evaluating the new algorithm. The optimal models for oil, starch and protein were obtained by the GP regression method. The performance of the final models were evaluated according to the root mean square error of calibration (RMSEC), root mean square error of cross-validation (RMSECV), root mean square error of prediction (RMSEP) and correlation coefficient (r). The models give good calibration ability with r values above 0.99 and the prediction ability is also satisfactory with r values higher than 0.96. The overall results demonstrate that GP algorithm is an effective chemometric method and is promising for the NIR analysis.

Classic electrocardiogram-based and mobile technology derived approaches to heart rate variability are not equivalent.

PubMed

Guzik, Przemyslaw; Piekos, Caroline; Pierog, Olivia; Fenech, Naiman; Krauze, Tomasz; Piskorski, Jaroslaw; Wykretowicz, Andrzej

2018-05-01

We compared classic ECG-derived versus a mobile approach to heart rate variability (HRV) measurement. 29 young adult healthy volunteers underwent a simultaneous recording of heart rate using an ECG and a chest heart rate monitor at supine rest, during mental stress and active standing. Mean RR interval, Standard Deviation of Normal-to-Normal (SDNN) of RR intervals, and Root Mean Square of the Successive Differences (RMSSD) between RR intervals were computed in 168 pairs of 5-minute epochs by in-house software on a PC (only sinus beats) and by mobile application "ELITEHRV" on a smartphone (no beat type identification). ECG analysis showed that 33.9% of the recordings contained at least one non-sinus beat or artefact, the mobile app did not report this. The mean RR intervals were significantly longer (p = 0.0378), while SDNN (p = 0.0001) and RMSSD (p = 0.0199) were smaller for the mobile approach. Measures of identical HRV parameters by ECG-based and mobile approaches are not equivalent. Copyright © 2018 Elsevier B.V. All rights reserved.

Steady-state distributions of probability fluxes on complex networks

NASA Astrophysics Data System (ADS)

Chełminiak, Przemysław; Kurzyński, Michał

2017-02-01

We consider a simple model of the Markovian stochastic dynamics on complex networks to examine the statistical properties of the probability fluxes. The additional transition, called hereafter a gate, powered by the external constant force breaks a detailed balance in the network. We argue, using a theoretical approach and numerical simulations, that the stationary distributions of the probability fluxes emergent under such conditions converge to the Gaussian distribution. By virtue of the stationary fluctuation theorem, its standard deviation depends directly on the square root of the mean flux. In turn, the nonlinear relation between the mean flux and the external force, which provides the key result of the present study, allows us to calculate the two parameters that entirely characterize the Gaussian distribution of the probability fluxes both close to as well as far from the equilibrium state. Also, the other effects that modify these parameters, such as the addition of shortcuts to the tree-like network, the extension and configuration of the gate and a change in the network size studied by means of computer simulations are widely discussed in terms of the rigorous theoretical predictions.

Road traffic accidents prediction modelling: An analysis of Anambra State, Nigeria.

PubMed

Ihueze, Chukwutoo C; Onwurah, Uchendu O

2018-03-01

One of the major problems in the world today is the rate of road traffic crashes and deaths on our roads. Majority of these deaths occur in low-and-middle income countries including Nigeria. This study analyzed road traffic crashes in Anambra State, Nigeria with the intention of developing accurate predictive models for forecasting crash frequency in the State using autoregressive integrated moving average (ARIMA) and autoregressive integrated moving average with explanatory variables (ARIMAX) modelling techniques. The result showed that ARIMAX model outperformed the ARIMA (1,1,1) model generated when their performances were compared using the lower Bayesian information criterion, mean absolute percentage error, root mean square error; and higher coefficient of determination (R-Squared) as accuracy measures. The findings of this study reveal that incorporating human, vehicle and environmental related factors in time series analysis of crash dataset produces a more robust predictive model than solely using aggregated crash count. This study contributes to the body of knowledge on road traffic safety and provides an approach to forecasting using many human, vehicle and environmental factors. The recommendations made in this study if applied will help in reducing the number of road traffic crashes in Nigeria. Copyright © 2017 Elsevier Ltd. All rights reserved.

Absolute binding free energy calculations of CBClip host–guest systems in the SAMPL5 blind challenge

PubMed Central

Tofoleanu, Florentina; Pickard, Frank C.; König, Gerhard; Huang, Jing; Damjanović, Ana; Baek, Minkyung; Seok, Chaok; Brooks, Bernard R.

2016-01-01

Herein, we report the absolute binding free energy calculations of CBClip complexes in the SAMPL5 blind challenge. Initial conformations of CBClip complexes were obtained using docking and molecular dynamics simulations. Free energy calculations were performed using thermodynamic integration (TI) with soft-core potentials and Bennett’s acceptance ratio (BAR) method based on a serial insertion scheme. We compared the results obtained with TI simulations with soft-core potentials and Hamiltonian replica exchange simulations with the serial insertion method combined with the BAR method. The results show that the difference between the two methods can be mainly attributed to the van der Waals free energies, suggesting that either the simulations used for TI or the simulations used for BAR, or both are not fully converged and the two sets of simulations may have sampled difference phase space regions. The penalty scores of force field parameters of the 10 guest molecules provided by CHARMM Generalized Force Field can be an indicator of the accuracy of binding free energy calculations. Among our submissions, the combination of docking and TI performed best, which yielded the root mean square deviation of 2.94 kcal/mol and an average unsigned error of 3.41 kcal/mol for the ten guest molecules. These values were best overall among all participants. However, our submissions had little correlation with experiments. PMID:27677749

A python-based docking program utilizing a receptor bound ligand shape: PythDock.

PubMed

Chung, Jae Yoon; Cho, Seung Joo; Hah, Jung-Mi

2011-09-01

PythDock is a heuristic docking program that uses Python programming language with a simple scoring function and a population based search engine. The scoring function considers electrostatic and dispersion/repulsion terms. The search engine utilizes a particle swarm optimization algorithm. A grid potential map is generated using the shape information of a bound ligand within the active site. Therefore, the searching area is more relevant to the ligand binding. To evaluate the docking performance of PythDock, two well-known docking programs (AutoDock and DOCK) were also used with the same data. The accuracy of docked results were measured by the difference of the ligand structure between x-ray structure, and docked pose, i.e., average root mean squared deviation values of the bound ligand were compared for fourteen protein-ligand complexes. Since the number of ligands' rotational flexibility is an important factor affecting the accuracy of a docking, the data set was chosen to have various degrees of flexibility. Although PythDock has a scoring function simpler than those of other programs (AutoDock and DOCK), our results showed that PythDock predicted more accurate poses than both AutoDock4.2 and DOCK6.2. This indicates that PythDock could be a useful tool to study ligand-receptor interactions and could also be beneficial in structure based drug design.

[A preliminary study on the forming quality of titanium alloy removable partial denture frameworks fabricated by selective laser melting].

PubMed

Liu, Y F; Yu, H; Wang, W N; Gao, B

2017-06-09

Objective: To evaluate the processing accuracy, internal quality and suitability of the titanium alloy frameworks of removable partial denture (RPD) fabricated by selective laser melting (SLM) technique, and to provide reference for clinical application. Methods: The plaster model of one clinical patient was used as the working model, and was scanned and reconstructed into a digital working model. A RPD framework was designed on it. Then, eight corresponding RPD frameworks were fabricated using SLM technique. Three-dimensional (3D) optical scanner was used to scan and obtain the 3D data of the frameworks and the data was compared with the original computer aided design (CAD) model to evaluate their processing precision. The traditional casting pure titanium frameworks was used as the control group, and the internal quality was analyzed by X-ray examination. Finally, the fitness of the frameworks was examined on the plaster model. Results: The overall average deviation of the titanium alloy RPD framework fabricated by SLM technology was (0.089±0.076) mm, the root mean square error was 0.103 mm. No visible pores, cracks and other internal defects was detected in the frameworks. The framework fits on the plaster model completely, and its tissue surface fitted on the plaster model well. There was no obvious movement. Conclusions: The titanium alloy RPD framework fabricated by SLM technology is of good quality.

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.

Application of Artificial Neural Network to Predict Colour Change, Shrinkage and Texture of Osmotically Dehydrated Pumpkin

NASA Astrophysics Data System (ADS)

Tang, S. Y.; Lee, J. S.; Loh, S. P.; Tham, H. J.

2017-06-01

The objectives of this study were to use Artificial Neural Network (ANN) to predict colour change, shrinkage and texture of osmotically dehydrated pumpkin slices. The effects of process variables such as concentration of osmotic solution, immersion temperature and immersion time on the above mentioned physical properties were studied. The colour of the samples was measured using a colorimeter and the net colour difference changes, ΔE were determined. The texture was measured in terms of hardness by using a Texture Analyzer. As for the shrinkage, displacement of volume method was applied and percentage of shrinkage was obtained in terms of volume changes. A feed-forward backpropagation network with sigmoidal function was developed and best network configuration was chosen based on the highest correlation coefficients between the experimental values versus predicted values. As a comparison, Response Surface Methodology (RSM) statistical analysis was also employed. The performances of both RSM and ANN modelling were evaluated based on absolute average deviation (AAD), correlation of determination (R2) and root mean square error (RMSE). The results showed that ANN has higher prediction capability as compared to RSM. The relative importance of the variables on the physical properties were also determined by using connection weight approach in ANN. It was found that solution concentration showed the highest influence on all three physical properties.

A molecular dynamics study of the pores formed by Escherichia coli OmpF porin in a fully hydrated palmitoyloleoylphosphatidylcholine bilayer.

PubMed

Tieleman, D P; Berendsen, H J

1998-06-01

In this paper we study the properties of pores formed by OmpF porin from Escherichia coli, based on a molecular dynamics simulation of the OmpF trimer, 318 palmitoyl-oleoyl-phosphatidylethanolamine lipids, 27 Na+ ions, and 12,992 water molecules. After equilibration and a nanosecond production run, the OmpF trimer exhibits a C-alpha root mean square deviation from the crystal structure of 0.23 nm and a stable secondary structure. No evidence is found for large-scale motions of the L3 loop. We investigate the pore dimensions, conductance, and the properties of water inside the pore. This water forms a complicated pattern, even when averaged over 1 ns of simulation time. Around the pore constriction zone the water dipoles are highly structured in the plane of the membrane, oriented by the strong transversal electric field. In addition, there is a net orientation along the pore axis pointing from the extracellular to the intracellular side of the bilayer. The diffusion coefficients of water inside the pore are greatly reduced compared to bulk. We compare our results to results from model pores (Breed et al., 1996. Biophys. J. 70:1 643-1 661; Sansom et al. 1997. Biophys. J. 73:2404-241 5) and discuss implications for further theoretical work.

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.

A hybrid experimental-numerical technique for determining 3D velocity fields from planar 2D PIV data

NASA Astrophysics Data System (ADS)

Eden, A.; Sigurdson, M.; Mezić, I.; Meinhart, C. D.

2016-09-01

Knowledge of 3D, three component velocity fields is central to the understanding and development of effective microfluidic devices for lab-on-chip mixing applications. In this paper we present a hybrid experimental-numerical method for the generation of 3D flow information from 2D particle image velocimetry (PIV) experimental data and finite element simulations of an alternating current electrothermal (ACET) micromixer. A numerical least-squares optimization algorithm is applied to a theory-based 3D multiphysics simulation in conjunction with 2D PIV data to generate an improved estimation of the steady state velocity field. This 3D velocity field can be used to assess mixing phenomena more accurately than would be possible through simulation alone. Our technique can also be used to estimate uncertain quantities in experimental situations by fitting the gathered field data to a simulated physical model. The optimization algorithm reduced the root-mean-squared difference between the experimental and simulated velocity fields in the target region by more than a factor of 4, resulting in an average error less than 12% of the average velocity magnitude.

Red Wine Age Estimation by the Alteration of Its Color Parameters: Fourier Transform Infrared Spectroscopy as a Tool to Monitor Wine Maturation Time

PubMed Central

Basalekou, M.; Pappas, C.; Kotseridis, Y.; Tarantilis, P. A.; Kontaxakis, E.

2017-01-01

Color, phenolic content, and chemical age values of red wines made from Cretan grape varieties (Kotsifali, Mandilari) were evaluated over nine months of maturation in different containers for two vintages. The wines differed greatly on their anthocyanin profiles. Mid-IR spectra were also recorded with the use of a Fourier Transform Infrared Spectrophotometer in ZnSe disk mode. Analysis of Variance was used to explore the parameter's dependency on time. Determination models were developed for the chemical age indexes using Partial Least Squares (PLS) (TQ Analyst software) considering the spectral region 1830–1500 cm−1. The correlation coefficients (r) for chemical age index i were 0.86 for Kotsifali (Root Mean Square Error of Calibration (RMSEC) = 0.067, Root Mean Square Error of Prediction (RMSEP) = 0,115, and Root Mean Square Error of Validation (RMSECV) = 0.164) and 0.90 for Mandilari (RMSEC = 0.050, RMSEP = 0.040, and RMSECV = 0.089). For chemical age index ii the correlation coefficients (r) were 0.86 and 0.97 for Kotsifali (RMSEC 0.044, RMSEP = 0.087, and RMSECV = 0.214) and Mandilari (RMSEC = 0.024, RMSEP = 0.033, and RMSECV = 0.078), respectively. The proposed method is simpler, less time consuming, and more economical and does not require chemical reagents. PMID:29225994

Application of near-infrared spectroscopy for the rapid quality assessment of Radix Paeoniae Rubra

NASA Astrophysics Data System (ADS)

Zhan, Hao; Fang, Jing; Tang, Liying; Yang, Hongjun; Li, Hua; Wang, Zhuju; Yang, Bin; Wu, Hongwei; Fu, Meihong

2017-08-01

Near-infrared (NIR) spectroscopy with multivariate analysis was used to quantify gallic acid, catechin, albiflorin, and paeoniflorin in Radix Paeoniae Rubra, and the feasibility to classify the samples originating from different areas was investigated. A new high-performance liquid chromatography method was developed and validated to analyze gallic acid, catechin, albiflorin, and paeoniflorin in Radix Paeoniae Rubra as the reference. Partial least squares (PLS), principal component regression (PCR), and stepwise multivariate linear regression (SMLR) were performed to calibrate the regression model. Different data pretreatments such as derivatives (1st and 2nd), multiplicative scatter correction, standard normal variate, Savitzky-Golay filter, and Norris derivative filter were applied to remove the systematic errors. The performance of the model was evaluated according to the root mean square of calibration (RMSEC), root mean square error of prediction (RMSEP), root mean square error of cross-validation (RMSECV), and correlation coefficient (r). The results show that compared to PCR and SMLR, PLS had a lower RMSEC, RMSECV, and RMSEP and higher r for all the four analytes. PLS coupled with proper pretreatments showed good performance in both the fitting and predicting results. Furthermore, the original areas of Radix Paeoniae Rubra samples were partly distinguished by principal component analysis. This study shows that NIR with PLS is a reliable, inexpensive, and rapid tool for the quality assessment of Radix Paeoniae Rubra.

Statistical modeling of temperature, humidity and wind fields in the atmospheric boundary layer over the Siberian region

NASA Astrophysics Data System (ADS)

Lomakina, N. Ya.

2017-11-01

The work presents the results of the applied climatic division of the Siberian region into districts based on the methodology of objective classification of the atmospheric boundary layer climates by the "temperature-moisture-wind" complex realized with using the method of principal components and the special similarity criteria of average profiles and the eigen values of correlation matrices. On the territory of Siberia, it was identified 14 homogeneous regions for winter season and 10 regions were revealed for summer. The local statistical models were constructed for each region. These include vertical profiles of mean values, mean square deviations, and matrices of interlevel correlation of temperature, specific humidity, zonal and meridional wind velocity. The advantage of the obtained local statistical models over the regional models is shown.

A hybrid SVM-FFA method for prediction of monthly mean global solar radiation

NASA Astrophysics Data System (ADS)

Shamshirband, Shahaboddin; Mohammadi, Kasra; Tong, Chong Wen; Zamani, Mazdak; Motamedi, Shervin; Ch, Sudheer

2016-07-01

In this study, a hybrid support vector machine-firefly optimization algorithm (SVM-FFA) model is proposed to estimate monthly mean horizontal global solar radiation (HGSR). The merit of SVM-FFA is assessed statistically by comparing its performance with three previously used approaches. Using each approach and long-term measured HGSR, three models are calibrated by considering different sets of meteorological parameters measured for Bandar Abbass situated in Iran. It is found that the model (3) utilizing the combination of relative sunshine duration, difference between maximum and minimum temperatures, relative humidity, water vapor pressure, average temperature, and extraterrestrial solar radiation shows superior performance based upon all approaches. Moreover, the extraterrestrial radiation is introduced as a significant parameter to accurately estimate the global solar radiation. The survey results reveal that the developed SVM-FFA approach is greatly capable to provide favorable predictions with significantly higher precision than other examined techniques. For the SVM-FFA (3), the statistical indicators of mean absolute percentage error (MAPE), root mean square error (RMSE), relative root mean square error (RRMSE), and coefficient of determination ( R 2) are 3.3252 %, 0.1859 kWh/m2, 3.7350 %, and 0.9737, respectively which according to the RRMSE has an excellent performance. As a more evaluation of SVM-FFA (3), the ratio of estimated to measured values is computed and found that 47 out of 48 months considered as testing data fall between 0.90 and 1.10. Also, by performing a further verification, it is concluded that SVM-FFA (3) offers absolute superiority over the empirical models using relatively similar input parameters. In a nutshell, the hybrid SVM-FFA approach would be considered highly efficient to estimate the HGSR.

Validation of the angular measurements of a new inertial-measurement-unit based rehabilitation system: comparison with state-of-the-art gait analysis.

PubMed

Leardini, Alberto; Lullini, Giada; Giannini, Sandro; Berti, Lisa; Ortolani, Maurizio; Caravaggi, Paolo

2014-09-11

Several rehabilitation systems based on inertial measurement units (IMU) are entering the market for the control of exercises and to measure performance progression, particularly for recovery after lower limb orthopaedic treatments. IMU are easy to wear also by the patient alone, but the extent to which IMU's malpositioning in routine use can affect the accuracy of the measurements is not known. A new such system (Riablo™, CoRehab, Trento, Italy), using audio-visual biofeedback based on videogames, was assessed against state-of-the-art gait analysis as the gold standard. The sensitivity of the system to errors in the IMU's position and orientation was measured in 5 healthy subjects performing two hip joint motion exercises. Root mean square deviation was used to assess differences in the system's kinematic output between the erroneous and correct IMU position and orientation.In order to estimate the system's accuracy, thorax and knee joint motion of 17 healthy subjects were tracked during the execution of standard rehabilitation tasks and compared with the corresponding measurements obtained with an established gait protocol using stereophotogrammetry. A maximum mean error of 3.1 ± 1.8 deg and 1.9 ± 0.8 deg from the angle trajectory with correct IMU position was recorded respectively in the medio-lateral malposition and frontal-plane misalignment tests. Across the standard rehabilitation tasks, the mean distance between the IMU and gait analysis systems was on average smaller than 5°. These findings showed that the tested IMU based system has the necessary accuracy to be safely utilized in rehabilitation programs after orthopaedic treatments of the lower limb.

In vivo precision of the GE Lunar iDXA densitometer for the measurement of total-body, lumbar spine, and femoral bone mineral density in adults.

PubMed

Hind, Karen; Oldroyd, Brian; Truscott, John G

2010-01-01

Knowledge of precision is integral to the monitoring of bone mineral density (BMD) changes using dual-energy X-ray absorptiometry (DXA). We evaluated the precision for bone measurements acquired using a GE Lunar iDXA (GE Healthcare, Waukesha, WI) in self-selected men and women, with mean age of 34.8 yr (standard deviation [SD]: 8.4; range: 20.1-50.5), heterogeneous in terms of body mass index (mean: 25.8 kg/m(2); SD: 5.1; range: 16.7-42.7 kg/m(2)). Two consecutive iDXA scans (with repositioning) of the total body, lumbar spine, and femur were conducted within 1h, for each subject. The coefficient of variation (CV), the root-mean-square (RMS) averages of SDs of repeated measurements, and the corresponding 95% least significant change were calculated. Linear regression analyses were also undertaken. We found a high level of precision for BMD measurements, particularly for scans of the total body, lumbar spine, and total hip (RMS: 0.007, 0.004, and 0.007 g/cm(2); CV: 0.63%, 0.41%, and 0.53%, respectively). Precision error for the femoral neck was higher but still represented good reproducibility (RMS: 0.014 g/cm(2); CV: 1.36%). There were associations between body size and total-body BMD and total-hip BMD SD precisions (r=0.534-0.806, p<0.05) in male subjects. Regression parameters showed good association between consecutive measurements for all body sites (r(2)=0.98-0.99). The Lunar iDXA provided excellent precision for BMD measurements of the total body, lumbar spine, femoral neck, and total hip. Copyright © 2010 The International Society for Clinical Densitometry. Published by Elsevier Inc. All rights reserved.

Reliability of assessing postural control during seated balancing using a physical human-robot interaction.

PubMed

Ramadan, Ahmed; Cholewicki, Jacek; Radcliffe, Clark J; Popovich, John M; Reeves, N Peter; Choi, Jongeun

2017-11-07

This study evaluated the within- and between-visit reliability of a seated balance test for quantifying trunk motor control using input-output data. Thirty healthy subjects performed a seated balance test under three conditions: eyes open (EO), eyes closed (EC), and eyes closed with vibration to the lumbar muscles (VIB). Each subject performed three trials of each condition on three different visits. The seated balance test utilized a torque-controlled robotic seat, which together with a sitting subject resulted in a physical human-robot interaction (pHRI) (two degrees-of-freedom with upper and lower body rotations). Subjects balanced the pHRI by controlling trunk rotation in response to pseudorandom torque perturbations applied to the seat in the coronal plane. Performance error was expressed as the root mean square (RMSE) of deviations from the upright position in the time domain and as the mean bandpass signal energy (E mb ) in the frequency domain. Intra-class correlation coefficients (ICC) quantified the between-visit reliability of both RMSE and E mb . The empirical transfer function estimates (ETFE) from the perturbation input to each of the two rotational outputs were calculated. Coefficients of multiple correlation (CMC) quantified the within- and between-visit reliability of the averaged ETFE. ICCs of RMSE and E mb for all conditions were ≥0.84. The mean within- and between-visit CMCs were all ≥0.96 for the lower body rotation and ≥0.89 for the upper body rotation. Therefore, our seated balance test consisting of pHRI to assess coronal plane trunk motor control is reliable. Copyright © 2017 Elsevier Ltd. All rights reserved.

Measurement of stream channel habitat using sonar

USGS Publications Warehouse

Flug, Marshall; Seitz, Heather; Scott, John

1998-01-01

An efficient and low cost technique using a sonar system was evaluated for describing channel geometry and quantifying inundated area in a large river. The boat-mounted portable sonar equipment was used to record water depths and river width measurements for direct storage on a laptop computer. The field data collected from repeated traverses at a cross-section were evaluated to determine the precision of the system and field technique. Results from validation at two different sites showed average sample standard deviations (S.D.s) of 0.12 m for these complete cross-sections, with coefficient of variations of 10%. Validation using only the mid-channel river cross-section data yields an average sample S.D. of 0.05 m, with a coefficient of variation below 5%, at a stable and gauged river site using only measurements of water depths greater than 0.6 m. Accuracy of the sonar system was evaluated by comparison to traditionally surveyed transect data from a regularly gauged site. We observed an average mean squared deviation of 46.0 cm2, considering only that portion of the cross-section inundated by more than 0.6 m of water. Our procedure proved to be a reliable, accurate, safe, quick, and economic method to record river depths, discharges, bed conditions, and substratum composition necessary for stream habitat studies.

Nondestructive quantification of the soluble-solids content and the available acidity of apples by Fourier-transform near-infrared spectroscopy

NASA Astrophysics Data System (ADS)

Ying, Yibin; Liu, Yande; Tao, Yang

2005-09-01

This research evaluated the feasibility of using Fourier-transform near-infrared (FT-NIR) spectroscopy to quantify the soluble-solids content (SSC) and the available acidity (VA) in intact apples. Partial least-squares calibration models, obtained from several preprocessing techniques (smoothing, derivative, etc.) in several wave-number ranges were compared. The best models were obtained with the high coefficient determination (r) 0.940 for the SSC and a moderate r of 0.801 for the VA, root-mean-square errors of prediction of 0.272% and 0.053%, and root-mean-square errors of calibration of 0.261% and 0.046%, respectively. The results indicate that the FT-NIR spectroscopy yields good predictions of the SSC and also showed the feasibility of using it to predict the VA of apples.

Monthly streamflow forecasting with auto-regressive integrated moving average

NASA Astrophysics Data System (ADS)

Nasir, Najah; Samsudin, Ruhaidah; Shabri, Ani

2017-09-01

Forecasting of streamflow is one of the many ways that can contribute to better decision making for water resource management. The auto-regressive integrated moving average (ARIMA) model was selected in this research for monthly streamflow forecasting with enhancement made by pre-processing the data using singular spectrum analysis (SSA). This study also proposed an extension of the SSA technique to include a step where clustering was performed on the eigenvector pairs before reconstruction of the time series. The monthly streamflow data of Sungai Muda at Jeniang, Sungai Muda at Jambatan Syed Omar and Sungai Ketil at Kuala Pegang was gathered from the Department of Irrigation and Drainage Malaysia. A ratio of 9:1 was used to divide the data into training and testing sets. The ARIMA, SSA-ARIMA and Clustered SSA-ARIMA models were all developed in R software. Results from the proposed model are then compared to a conventional auto-regressive integrated moving average model using the root-mean-square error and mean absolute error values. It was found that the proposed model can outperform the conventional model.

ECG artifact cancellation in surface EMG signals by fractional order calculus application.

PubMed

Miljković, Nadica; Popović, Nenad; Djordjević, Olivera; Konstantinović, Ljubica; Šekara, Tomislav B

2017-03-01

New aspects for automatic electrocardiography artifact removal from surface electromyography signals by application of fractional order calculus in combination with linear and nonlinear moving window filters are explored. Surface electromyography recordings of skeletal trunk muscles are commonly contaminated with spike shaped artifacts. This artifact originates from electrical heart activity, recorded by electrocardiography, commonly present in the surface electromyography signals recorded in heart proximity. For appropriate assessment of neuromuscular changes by means of surface electromyography, application of a proper filtering technique of electrocardiography artifact is crucial. A novel method for automatic artifact cancellation in surface electromyography signals by applying fractional order calculus and nonlinear median filter is introduced. The proposed method is compared with the linear moving average filter, with and without prior application of fractional order calculus. 3D graphs for assessment of window lengths of the filters, crest factors, root mean square differences, and fractional calculus orders (called WFC and WRC graphs) have been introduced. For an appropriate quantitative filtering evaluation, the synthetic electrocardiography signal and analogous semi-synthetic dataset have been generated. The examples of noise removal in 10 able-bodied subjects and in one patient with muscle dystrophy are presented for qualitative analysis. The crest factors, correlation coefficients, and root mean square differences of the recorded and semi-synthetic electromyography datasets showed that the most successful method was the median filter in combination with fractional order calculus of the order 0.9. Statistically more significant (p < 0.001) ECG peak reduction was obtained by the median filter application compared to the moving average filter in the cases of low level amplitude of muscle contraction compared to ECG spikes. The presented results suggest that the novel method combining a median filter and fractional order calculus can be used for automatic filtering of electrocardiography artifacts in the surface electromyography signal envelopes recorded in trunk muscles. Copyright © 2017 Elsevier Ireland Ltd. All rights reserved.

Analysis of concentric and eccentric contractions in biceps brachii muscles using surface electromyography signals and multifractal analysis.

PubMed

Marri, Kiran; Swaminathan, Ramakrishnan

2016-06-23

Muscle contractions can be categorized into isometric, isotonic (concentric and eccentric) and isokinetic contractions. The eccentric contractions are very effective for promoting muscle hypertrophy and produce larger forces when compared to the concentric or isometric contractions. Surface electromyography signals are widely used for analyzing muscle activities. These signals are nonstationary, nonlinear and exhibit self-similar multifractal behavior. The research on surface electromyography signals using multifractal analysis is not well established for concentric and eccentric contractions. In this study, an attempt has been made to analyze the concentric and eccentric contractions associated with biceps brachii muscles using surface electromyography signals and multifractal detrended moving average algorithm. Surface electromyography signals were recorded from 20 healthy individuals while performing a single curl exercise. The preprocessed signals were divided into concentric and eccentric cycles and in turn divided into phases based on range of motion: lower (0°-90°) and upper (>90°). The segments of surface electromyography signal were subjected to multifractal detrended moving average algorithm, and multifractal features such as strength of multifractality, peak exponent value, maximum exponent and exponent index were extracted in addition to conventional linear features such as root mean square and median frequency. The results show that surface electromyography signals exhibit multifractal behavior in both concentric and eccentric cycles. The mean strength of multifractality increased by 15% in eccentric contraction compared to concentric contraction. The lowest and highest exponent index values are observed in the upper concentric and lower eccentric contractions, respectively. The multifractal features are observed to be helpful in differentiating surface electromyography signals along the range of motion as compared to root mean square and median frequency. It appears that these multifractal features extracted from the concentric and eccentric contractions can be useful in the assessment of surface electromyography signals in sports medicine and training and also in rehabilitation programs. © IMechE 2016.

Automated time series forecasting for biosurveillance.

PubMed

Burkom, Howard S; Murphy, Sean Patrick; Shmueli, Galit

2007-09-30

For robust detection performance, traditional control chart monitoring for biosurveillance is based on input data free of trends, day-of-week effects, and other systematic behaviour. Time series forecasting methods may be used to remove this behaviour by subtracting forecasts from observations to form residuals for algorithmic input. We describe three forecast methods and compare their predictive accuracy on each of 16 authentic syndromic data streams. The methods are (1) a non-adaptive regression model using a long historical baseline, (2) an adaptive regression model with a shorter, sliding baseline, and (3) the Holt-Winters method for generalized exponential smoothing. Criteria for comparing the forecasts were the root-mean-square error, the median absolute per cent error (MedAPE), and the median absolute deviation. The median-based criteria showed best overall performance for the Holt-Winters method. The MedAPE measures over the 16 test series averaged 16.5, 11.6, and 9.7 for the non-adaptive regression, adaptive regression, and Holt-Winters methods, respectively. The non-adaptive regression forecasts were degraded by changes in the data behaviour in the fixed baseline period used to compute model coefficients. The mean-based criterion was less conclusive because of the effects of poor forecasts on a small number of calendar holidays. The Holt-Winters method was also most effective at removing serial autocorrelation, with most 1-day-lag autocorrelation coefficients below 0.15. The forecast methods were compared without tuning them to the behaviour of individual series. We achieved improved predictions with such tuning of the Holt-Winters method, but practical use of such improvements for routine surveillance will require reliable data classification methods.

Tailor-made force fields for crystal-structure prediction.

PubMed

Neumann, Marcus A

2008-08-14

A general procedure is presented to derive a complete set of force-field parameters for flexible molecules in the crystalline state on a case-by-case basis. The force-field parameters are fitted to the electrostatic potential as well as to accurate energies and forces generated by means of a hybrid method that combines solid-state density functional theory (DFT) calculations with an empirical van der Waals correction. All DFT calculations are carried out with the VASP program. The mathematical structure of the force field, the generation of reference data, the choice of the figure of merit, the optimization algorithm, and the parameter-refinement strategy are discussed in detail. The approach is applied to cyclohexane-1,4-dione, a small flexible ring. The tailor-made force field obtained for cyclohexane-1,4-dione is used to search for low-energy crystal packings in all 230 space groups with one molecule per asymmetric unit, and the most stable crystal structures are reoptimized in a second step with the hybrid method. The experimental crystal structure is found as the most stable predicted crystal structure both with the tailor-made force field and the hybrid method. The same methodology has also been applied successfully to the four compounds of the fourth CCDC blind test on crystal-structure prediction. For the five aforementioned compounds, the root-mean-square deviations between lattice energies calculated with the tailor-made force fields and the hybrid method range from 0.024 to 0.053 kcal/mol per atom around an average value of 0.034 kcal/mol per atom.

Improved liver R2* mapping by pixel-wise curve fitting with adaptive neighborhood regularization.

PubMed

Wang, Changqing; Zhang, Xinyuan; Liu, Xiaoyun; He, Taigang; Chen, Wufan; Feng, Qianjin; Feng, Yanqiu

2018-08-01

To improve liver R2* mapping by incorporating adaptive neighborhood regularization into pixel-wise curve fitting. Magnetic resonance imaging R2* mapping remains challenging because of the serial images with low signal-to-noise ratio. In this study, we proposed to exploit the neighboring pixels as regularization terms and adaptively determine the regularization parameters according to the interpixel signal similarity. The proposed algorithm, called the pixel-wise curve fitting with adaptive neighborhood regularization (PCANR), was compared with the conventional nonlinear least squares (NLS) and nonlocal means filter-based NLS algorithms on simulated, phantom, and in vivo data. Visually, the PCANR algorithm generates R2* maps with significantly reduced noise and well-preserved tiny structures. Quantitatively, the PCANR algorithm produces R2* maps with lower root mean square errors at varying R2* values and signal-to-noise-ratio levels compared with the NLS and nonlocal means filter-based NLS algorithms. For the high R2* values under low signal-to-noise-ratio levels, the PCANR algorithm outperforms the NLS and nonlocal means filter-based NLS algorithms in the accuracy and precision, in terms of mean and standard deviation of R2* measurements in selected region of interests, respectively. The PCANR algorithm can reduce the effect of noise on liver R2* mapping, and the improved measurement precision will benefit the assessment of hepatic iron in clinical practice. Magn Reson Med 80:792-801, 2018. © 2018 International Society for Magnetic Resonance in Medicine. © 2018 International Society for Magnetic Resonance in Medicine.

An investigation of the unsteady flow associated with plume induced flow separation

NASA Technical Reports Server (NTRS)

Boggess, A. L., Jr.

1972-01-01

A wind tunnel study of the basic nature of plume induced flow separation is reported with emphasis on the unsteady aspects of the flow. Testing was conducted in a 6 inch by 6 inch blow-down supersonic wind tunnel. A cone-cylinder model with a pluming jet was used as the test model. Tests were conducted with a systematic variation in Mach number and plume pressure. Results of the tests are presented in the form of root-mean-squared surface pressure levels, power spectral densities, photographs of the flow field from which shock angles and separation lengths were taken, and time-averaged surface pressure profiles.

Systems for measuring response statistics of gigahertz bandwidth photomultipliers

NASA Technical Reports Server (NTRS)

Abshire, J. B.; Rowe, H. E.

1977-01-01

New systems have been developed for measuring the average impulse response, the pulse-height spectrum, the transit-time statistics as a function of signal level, and the dark-count spectrum of gigahertz bandwidth photomultipliers. Measurements showed that the 0.53 microns pulse used as an optical test source had a 30 picoseconds and less than 70 ps pulse width. Calibration data showed the system resolution to be less than 20 ps for root mean square transit-time measurements. Test data for a static crossed-field photomultiplier showed 2-photoelectron resolution and less than 30-ps time jitter over the 1- to 100-photoelectron range.

[Simulation of cropland soil moisture based on an ensemble Kalman filter].

PubMed

Liu, Zhao; Zhou, Yan-Lian; Ju, Wei-Min; Gao, Ping

2011-11-01

By using an ensemble Kalman filter (EnKF) to assimilate the observed soil moisture data, the modified boreal ecosystem productivity simulator (BEPS) model was adopted to simulate the dynamics of soil moisture in winter wheat root zones at Xuzhou Agro-meteorological Station, Jiangsu Province of China during the growth seasons in 2000-2004. After the assimilation of observed data, the determination coefficient, root mean square error, and average absolute error of simulated soil moisture were in the ranges of 0.626-0.943, 0.018-0.042, and 0.021-0.041, respectively, with the simulation precision improved significantly, as compared with that before assimilation, indicating the applicability of data assimilation in improving the simulation of soil moisture. The experimental results at single point showed that the errors in the forcing data and observations and the frequency and soil depth of the assimilation of observed data all had obvious effects on the simulated soil moisture.

On some labelings of triangular snake and central graph of triangular snake graph

NASA Astrophysics Data System (ADS)

Agasthi, P.; Parvathi, N.

2018-04-01

A Triangular snake Tn is obtained from a path u 1 u 2 … u n by joining ui and u i+1 to a new vertex wi for 1≤i≤n‑1. A Central graph of Triangular snake C(T n ) is obtained by subdividing each edge of Tn exactly once and joining all the non adjacent vertices of Tn . In this paper the ways to construct square sum, square difference, Root Mean square, strongly Multiplicative, Even Mean and Odd Mean labeling for Triangular Snake and Central graph of Triangular Snake graphs are reported.

Investigation of the relation between the return periods of major drought characteristics using copula functions

NASA Astrophysics Data System (ADS)

Hüsami Afşar, Mehdi; Unal Şorman, Ali; Tugrul Yilmaz, Mustafa

2016-04-01

Different drought characteristics (e.g. duration, average severity, and average areal extent) often have monotonic relation that increased magnitude of one often follows a similar increase in the magnitude of the other drought characteristic. Hence it is viable to establish a relationship between different drought characteristics with the goal of predicting one using other ones. Copula functions that relate different variables using their joint and conditional cumulative probability distributions are often used to statistically model the drought characteristics. In this study bivariate and trivariate joint probabilities of these characteristics are obtained over Ankara (Turkey) between 1960 and 2013. Copula-based return period estimation of drought characteristics of duration, average severity, and average areal extent show joint probabilities of these characteristics can be satisfactorily achieved. Among different copula families investigated in this study, elliptical family (i.e. including normal and t-student copula functions) resulted in the lowest root mean square error. "This study was supported by TUBITAK fund #114Y676)."

MO-FG-CAMPUS-TeP3-01: A Model of Baseline Shift to Improve Robustness of Proton Therapy Treatments of Moving Tumors

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

Souris, K; Barragan Montero, A; Di Perri, D

Purpose: The shift in mean position of a moving tumor also known as “baseline shift”, has been modeled, in order to automatically generate uncertainty scenarios for the assessment and robust optimization of proton therapy treatments in lung cancer. Methods: An average CT scan and a Mid-Position CT scan (MidPCT) of the patient at the planning time are first generated from a 4D-CT data. The mean position of the tumor along the breathing cycle is represented by the GTV contour in the MidPCT. Several studies reported both systematic and random variations of the mean tumor position from fraction to fraction. Ourmore » model can simulate this baseline shift by generating a local deformation field that moves the tumor on all phases of the 4D-CT, without creating any non-physical artifact. The deformation field is comprised of normal and tangential components with respect to the lung wall in order to allow the tumor to slip within the lung instead of deforming the lung surface. The deformation field is eventually smoothed in order to enforce its continuity. Two 4D-CT series acquired at 1 week of interval were used to validate the model. Results: Based on the first 4D-CT set, the model was able to generate a third 4D-CT that reproduced the 5.8 mm baseline-shift measured in the second 4D-CT. Water equivalent thickness (WET) of the voxels have been computed for the 3 average CTs. The root mean square deviation of the WET in the GTV is 0.34 mm between week 1 and week 2, and 0.08 mm between the simulated data and week 2. Conclusion: Our model can be used to automatically generate uncertainty scenarios for robustness analysis of a proton therapy plan. The generated scenarios can also feed a TPS equipped with a robust optimizer. Kevin Souris, Ana Barragan, and Dario Di Perri are financially supported by Televie Grants from F.R.S.-FNRS.« less

Validation of Core Temperature Estimation Algorithm

DTIC Science & Technology

2016-01-29

plot of observed versus estimated core temperature with the line of identity (dashed) and the least squares regression line (solid) and line equation...estimated PSI with the line of identity (dashed) and the least squares regression line (solid) and line equation in the top left corner. (b) Bland...for comparison. The root mean squared error (RMSE) was also computed, as given by Equation 2.

A model-constrained Monte Carlo method for blind arterial input function estimation in dynamic contrast-enhanced MRI: II. In vivo results

NASA Astrophysics Data System (ADS)

Schabel, Matthias C.; DiBella, Edward V. R.; Jensen, Randy L.; Salzman, Karen L.

2010-08-01

Accurate quantification of pharmacokinetic model parameters in tracer kinetic imaging experiments requires correspondingly accurate determination of the arterial input function (AIF). Despite significant effort expended on methods of directly measuring patient-specific AIFs in modalities as diverse as dynamic contrast-enhanced magnetic resonance imaging (DCE-MRI), dynamic positron emission tomography (PET), and perfusion computed tomography (CT), fundamental and technical difficulties have made consistent and reliable achievement of that goal elusive. Here, we validate a new algorithm for AIF determination, the Monte Carlo blind estimation (MCBE) method (which is described in detail and characterized by extensive simulations in a companion paper), by comparing AIFs measured in DCE-MRI studies of eight brain tumor patients with results of blind estimation. Blind AIFs calculated with the MCBE method using a pool of concentration-time curves from a region of normal brain tissue were found to be quite similar to the measured AIFs, with statistically significant decreases in fit residuals observed in six of eight patients. Biases between the blind and measured pharmacokinetic parameters were the dominant source of error. Averaged over all eight patients, the mean biases were +7% in K trans, 0% in kep, -11% in vp and +10% in ve. Corresponding uncertainties (median absolute deviation from the best fit line) were 0.0043 min-1 in K trans, 0.0491 min-1 in kep, 0.29% in vp and 0.45% in ve. The use of a published population-averaged AIF resulted in larger mean biases in three of the four parameters (-23% in K trans, -22% in kep, -63% in vp), with the bias in ve unchanged, and led to larger uncertainties in all four parameters (0.0083 min-1 in K trans, 0.1038 min-1 in kep, 0.31% in vp and 0.95% in ve). When blind AIFs were calculated from a region of tumor tissue, statistically significant decreases in fit residuals were observed in all eight patients despite larger deviations of these blind AIFs from the measured AIFs. The observed decrease in root-mean-square fit residuals between the normal brain and tumor tissue blind AIFs suggests that the local blood supply in tumors is measurably different from that in normal brain tissue and that the proposed method is able to discriminate between the two. We have shown the feasibility of applying the MCBE algorithm to DCE-MRI data acquired in brain, finding generally good agreement with measured AIFs and decreased biases and uncertainties relative to the use of a population-averaged AIF. These results demonstrate that the MCBE algorithm is a useful alternative to direct AIF measurement in cases where acquisition of high-quality arterial input function data is difficult or impossible.

Design and resolution analysis of parabolic mirror spectrometer

NASA Astrophysics Data System (ADS)

Wu, Su; Wang, Guodong; Xia, Guo; Sun, Yanchao; Hu, Mingyong

2017-10-01

In order to further eliminate aberration and improve resolution, the paper employs parabolic mirror as the collimating mirror and the focusing mirror to design "Z" configuration and "U" configuration optical structure of parabolic spectrometer with the F number 2.5 and the spectral range varying from 250 nm to 850 nm. We conduct experiments on ZEMAX to simulate and optimize the initial parameters of two structures with the root-mean-square (RMS) radius of spots along Y axis as the optimization goal. Through analyzing the spot diagram and the root-mean-square (RMS) of Y axis, we can see that the "U" configuration spectrometers can achieve much better spectral resolution than the "Z" configuration.