Sample records for accurate analytic expressions

  1. Highly Accurate Analytical Approximate Solution to a Nonlinear Pseudo-Oscillator

    NASA Astrophysics Data System (ADS)

    Wu, Baisheng; Liu, Weijia; Lim, C. W.

    2017-07-01

    A second-order Newton method is presented to construct analytical approximate solutions to a nonlinear pseudo-oscillator in which the restoring force is inversely proportional to the dependent variable. The nonlinear equation is first expressed in a specific form, and it is then solved in two steps, a predictor and a corrector step. In each step, the harmonic balance method is used in an appropriate manner to obtain a set of linear algebraic equations. With only one simple second-order Newton iteration step, a short, explicit, and highly accurate analytical approximate solution can be derived. The approximate solutions are valid for all amplitudes of the pseudo-oscillator. Furthermore, the method incorporates second-order Taylor expansion in a natural way, and it is of significant faster convergence rate.

  2. Accurate expressions for solar cell fill factors including series and shunt resistances

    NASA Astrophysics Data System (ADS)

    Green, Martin A.

    2016-02-01

    Together with open-circuit voltage and short-circuit current, fill factor is a key solar cell parameter. In their classic paper on limiting efficiency, Shockley and Queisser first investigated this factor's analytical properties showing, for ideal cells, it could be expressed implicitly in terms of the maximum power point voltage. Subsequently, fill factors usually have been calculated iteratively from such implicit expressions or from analytical approximations. In the absence of detrimental series and shunt resistances, analytical fill factor expressions have recently been published in terms of the Lambert W function available in most mathematical computing software. Using a recently identified perturbative relationship, exact expressions in terms of this function are derived in technically interesting cases when both series and shunt resistances are present but have limited impact, allowing a better understanding of their effect individually and in combination. Approximate expressions for arbitrary shunt and series resistances are then deduced, which are significantly more accurate than any previously published. A method based on the insights developed is also reported for deducing one-diode fits to experimental data.

  3. Highly accurate analytic formulae for projectile motion subjected to quadratic drag

    NASA Astrophysics Data System (ADS)

    Turkyilmazoglu, Mustafa

    2016-05-01

    The classical phenomenon of motion of a projectile fired (thrown) into the horizon through resistive air charging a quadratic drag onto the object is revisited in this paper. No exact solution is known that describes the full physical event under such an exerted resistance force. Finding elegant analytical approximations for the most interesting engineering features of dynamical behavior of the projectile is the principal target. Within this purpose, some analytical explicit expressions are derived that accurately predict the maximum height, its arrival time as well as the flight range of the projectile at the highest ascent. The most significant property of the proposed formulas is that they are not restricted to the initial speed and firing angle of the object, nor to the drag coefficient of the medium. In combination with the available approximations in the literature, it is possible to gain information about the flight and complete the picture of a trajectory with high precision, without having to numerically simulate the full governing equations of motion.

  4. Accurate mass measurements and their appropriate use for reliable analyte identification.

    PubMed

    Godfrey, A Ruth; Brenton, A Gareth

    2012-09-01

    Accurate mass instrumentation is becoming increasingly available to non-expert users. This data can be mis-used, particularly for analyte identification. Current best practice in assigning potential elemental formula for reliable analyte identification has been described with modern informatic approaches to analyte elucidation, including chemometric characterisation, data processing and searching using facilities such as the Chemical Abstracts Service (CAS) Registry and Chemspider.

  5. Accurate analytical modeling of junctionless DG-MOSFET by green's function approach

    NASA Astrophysics Data System (ADS)

    Nandi, Ashutosh; Pandey, Nilesh

    2017-11-01

    An accurate analytical model of Junctionless double gate MOSFET (JL-DG-MOSFET) in the subthreshold regime of operation is developed in this work using green's function approach. The approach considers 2-D mixed boundary conditions and multi-zone techniques to provide an exact analytical solution to 2-D Poisson's equation. The Fourier coefficients are calculated correctly to derive the potential equations that are further used to model the channel current and subthreshold slope of the device. The threshold voltage roll-off is computed from parallel shifts of Ids-Vgs curves between the long channel and short-channel devices. It is observed that the green's function approach of solving 2-D Poisson's equation in both oxide and silicon region can accurately predict channel potential, subthreshold current (Isub), threshold voltage (Vt) roll-off and subthreshold slope (SS) of both long & short channel devices designed with different doping concentrations and higher as well as lower tsi/tox ratio. All the analytical model results are verified through comparisons with TCAD Sentaurus simulation results. It is observed that the model matches quite well with TCAD device simulations.

  6. Analytical expressions for the nonlinear interference in dispersion managed transmission coherent optical systems

    NASA Astrophysics Data System (ADS)

    Qiao, Yaojun; Li, Ming; Yang, Qiuhong; Xu, Yanfei; Ji, Yuefeng

    2015-01-01

    Closed-form expressions of nonlinear interference of dense wavelength-division-multiplexed (WDM) systems with dispersion managed transmission (DMT) are derived. We carry out a simulative validation by addressing an ample and significant set of the Nyquist-WDM systems based on polarization multiplexed quadrature phase-shift keying (PM-QPSK) subcarriers at a baud rate of 32 Gbaud per channel. Simulation results show the simple closed-form analytical expressions can provide an effective tool for the quick and accurate prediction of system performance in DMT coherent optical systems.

  7. An analytic model for accurate spring constant calibration of rectangular atomic force microscope cantilevers.

    PubMed

    Li, Rui; Ye, Hongfei; Zhang, Weisheng; Ma, Guojun; Su, Yewang

    2015-10-29

    Spring constant calibration of the atomic force microscope (AFM) cantilever is of fundamental importance for quantifying the force between the AFM cantilever tip and the sample. The calibration within the framework of thin plate theory undoubtedly has a higher accuracy and broader scope than that within the well-established beam theory. However, thin plate theory-based accurate analytic determination of the constant has been perceived as an extremely difficult issue. In this paper, we implement the thin plate theory-based analytic modeling for the static behavior of rectangular AFM cantilevers, which reveals that the three-dimensional effect and Poisson effect play important roles in accurate determination of the spring constants. A quantitative scaling law is found that the normalized spring constant depends only on the Poisson's ratio, normalized dimension and normalized load coordinate. Both the literature and our refined finite element model validate the present results. The developed model is expected to serve as the benchmark for accurate calibration of rectangular AFM cantilevers.

  8. Development and application of accurate analytical models for single active electron potentials

    NASA Astrophysics Data System (ADS)

    Miller, Michelle; Jaron-Becker, Agnieszka; Becker, Andreas

    2015-05-01

    The single active electron (SAE) approximation is a theoretical model frequently employed to study scenarios in which inner-shell electrons may productively be treated as frozen spectators to a physical process of interest, and accurate analytical approximations for these potentials are sought as a useful simulation tool. Density function theory is often used to construct a SAE potential, requiring that a further approximation for the exchange correlation functional be enacted. In this study, we employ the Krieger, Li, and Iafrate (KLI) modification to the optimized-effective-potential (OEP) method to reduce the complexity of the problem to the straightforward solution of a system of linear equations through simple arguments regarding the behavior of the exchange-correlation potential in regions where a single orbital dominates. We employ this method for the solution of atomic and molecular potentials, and use the resultant curve to devise a systematic construction for highly accurate and useful analytical approximations for several systems. Supported by the U.S. Department of Energy (Grant No. DE-FG02-09ER16103), and the U.S. National Science Foundation (Graduate Research Fellowship, Grants No. PHY-1125844 and No. PHY-1068706).

  9. Realistic Analytical Polyhedral MRI Phantoms

    PubMed Central

    Ngo, Tri M.; Fung, George S. K.; Han, Shuo; Chen, Min; Prince, Jerry L.; Tsui, Benjamin M. W.; McVeigh, Elliot R.; Herzka, Daniel A.

    2015-01-01

    Purpose Analytical phantoms have closed form Fourier transform expressions and are used to simulate MRI acquisitions. Existing 3D analytical phantoms are unable to accurately model shapes of biomedical interest. It is demonstrated that polyhedral analytical phantoms have closed form Fourier transform expressions and can accurately represent 3D biomedical shapes. Theory The derivations of the Fourier transform of a polygon and polyhedron are presented. Methods The Fourier transform of a polyhedron was implemented and its accuracy in representing faceted and smooth surfaces was characterized. Realistic anthropomorphic polyhedral brain and torso phantoms were constructed and their use in simulated 3D/2D MRI acquisitions was described. Results Using polyhedra, the Fourier transform of faceted shapes can be computed to within machine precision. Smooth surfaces can be approximated with increasing accuracy by increasing the number of facets in the polyhedron; the additional accumulated numerical imprecision of the Fourier transform of polyhedra with many faces remained small. Simulations of 3D/2D brain and 2D torso cine acquisitions produced realistic reconstructions free of high frequency edge aliasing as compared to equivalent voxelized/rasterized phantoms. Conclusion Analytical polyhedral phantoms are easy to construct and can accurately simulate shapes of biomedical interest. PMID:26479724

  10. Accurate Identification of Fear Facial Expressions Predicts Prosocial Behavior

    PubMed Central

    Marsh, Abigail A.; Kozak, Megan N.; Ambady, Nalini

    2009-01-01

    The fear facial expression is a distress cue that is associated with the provision of help and prosocial behavior. Prior psychiatric studies have found deficits in the recognition of this expression by individuals with antisocial tendencies. However, no prior study has shown accuracy for recognition of fear to predict actual prosocial or antisocial behavior in an experimental setting. In 3 studies, the authors tested the prediction that individuals who recognize fear more accurately will behave more prosocially. In Study 1, participants who identified fear more accurately also donated more money and time to a victim in a classic altruism paradigm. In Studies 2 and 3, participants’ ability to identify the fear expression predicted prosocial behavior in a novel task designed to control for confounding variables. In Study 3, accuracy for recognizing fear proved a better predictor of prosocial behavior than gender, mood, or scores on an empathy scale. PMID:17516803

  11. Accurate identification of fear facial expressions predicts prosocial behavior.

    PubMed

    Marsh, Abigail A; Kozak, Megan N; Ambady, Nalini

    2007-05-01

    The fear facial expression is a distress cue that is associated with the provision of help and prosocial behavior. Prior psychiatric studies have found deficits in the recognition of this expression by individuals with antisocial tendencies. However, no prior study has shown accuracy for recognition of fear to predict actual prosocial or antisocial behavior in an experimental setting. In 3 studies, the authors tested the prediction that individuals who recognize fear more accurately will behave more prosocially. In Study 1, participants who identified fear more accurately also donated more money and time to a victim in a classic altruism paradigm. In Studies 2 and 3, participants' ability to identify the fear expression predicted prosocial behavior in a novel task designed to control for confounding variables. In Study 3, accuracy for recognizing fear proved a better predictor of prosocial behavior than gender, mood, or scores on an empathy scale.

  12. Analytic expressions for ULF wave radiation belt radial diffusion coefficients

    PubMed Central

    Ozeke, Louis G; Mann, Ian R; Murphy, Kyle R; Jonathan Rae, I; Milling, David K

    2014-01-01

    We present analytic expressions for ULF wave-derived radiation belt radial diffusion coefficients, as a function of L and Kp, which can easily be incorporated into global radiation belt transport models. The diffusion coefficients are derived from statistical representations of ULF wave power, electric field power mapped from ground magnetometer data, and compressional magnetic field power from in situ measurements. We show that the overall electric and magnetic diffusion coefficients are to a good approximation both independent of energy. We present example 1-D radial diffusion results from simulations driven by CRRES-observed time-dependent energy spectra at the outer boundary, under the action of radial diffusion driven by the new ULF wave radial diffusion coefficients and with empirical chorus wave loss terms (as a function of energy, Kp and L). There is excellent agreement between the differential flux produced by the 1-D, Kp-driven, radial diffusion model and CRRES observations of differential electron flux at 0.976 MeV—even though the model does not include the effects of local internal acceleration sources. Our results highlight not only the importance of correct specification of radial diffusion coefficients for developing accurate models but also show significant promise for belt specification based on relatively simple models driven by solar wind parameters such as solar wind speed or geomagnetic indices such as Kp. Key Points Analytic expressions for the radial diffusion coefficients are presented The coefficients do not dependent on energy or wave m value The electric field diffusion coefficient dominates over the magnetic PMID:26167440

  13. A Machine Learned Classifier That Uses Gene Expression Data to Accurately Predict Estrogen Receptor Status

    PubMed Central

    Bastani, Meysam; Vos, Larissa; Asgarian, Nasimeh; Deschenes, Jean; Graham, Kathryn; Mackey, John; Greiner, Russell

    2013-01-01

    Background Selecting the appropriate treatment for breast cancer requires accurately determining the estrogen receptor (ER) status of the tumor. However, the standard for determining this status, immunohistochemical analysis of formalin-fixed paraffin embedded samples, suffers from numerous technical and reproducibility issues. Assessment of ER-status based on RNA expression can provide more objective, quantitative and reproducible test results. Methods To learn a parsimonious RNA-based classifier of hormone receptor status, we applied a machine learning tool to a training dataset of gene expression microarray data obtained from 176 frozen breast tumors, whose ER-status was determined by applying ASCO-CAP guidelines to standardized immunohistochemical testing of formalin fixed tumor. Results This produced a three-gene classifier that can predict the ER-status of a novel tumor, with a cross-validation accuracy of 93.17±2.44%. When applied to an independent validation set and to four other public databases, some on different platforms, this classifier obtained over 90% accuracy in each. In addition, we found that this prediction rule separated the patients' recurrence-free survival curves with a hazard ratio lower than the one based on the IHC analysis of ER-status. Conclusions Our efficient and parsimonious classifier lends itself to high throughput, highly accurate and low-cost RNA-based assessments of ER-status, suitable for routine high-throughput clinical use. This analytic method provides a proof-of-principle that may be applicable to developing effective RNA-based tests for other biomarkers and conditions. PMID:24312637

  14. Branch and bound algorithm for accurate estimation of analytical isotropic bidirectional reflectance distribution function models.

    PubMed

    Yu, Chanki; Lee, Sang Wook

    2016-05-20

    We present a reliable and accurate global optimization framework for estimating parameters of isotropic analytical bidirectional reflectance distribution function (BRDF) models. This approach is based on a branch and bound strategy with linear programming and interval analysis. Conventional local optimization is often very inefficient for BRDF estimation since its fitting quality is highly dependent on initial guesses due to the nonlinearity of analytical BRDF models. The algorithm presented in this paper employs L1-norm error minimization to estimate BRDF parameters in a globally optimal way and interval arithmetic to derive our feasibility problem and lower bounding function. Our method is developed for the Cook-Torrance model but with several normal distribution functions such as the Beckmann, Berry, and GGX functions. Experiments have been carried out to validate the presented method using 100 isotropic materials from the MERL BRDF database, and our experimental results demonstrate that the L1-norm minimization provides a more accurate and reliable solution than the L2-norm minimization.

  15. Arbitrarily accurate twin composite π -pulse sequences

    NASA Astrophysics Data System (ADS)

    Torosov, Boyan T.; Vitanov, Nikolay V.

    2018-04-01

    We present three classes of symmetric broadband composite pulse sequences. The composite phases are given by analytic formulas (rational fractions of π ) valid for any number of constituent pulses. The transition probability is expressed by simple analytic formulas and the order of pulse area error compensation grows linearly with the number of pulses. Therefore, any desired compensation order can be produced by an appropriate composite sequence; in this sense, they are arbitrarily accurate. These composite pulses perform equally well as or better than previously published ones. Moreover, the current sequences are more flexible as they allow total pulse areas of arbitrary integer multiples of π .

  16. Analytical Expressions for Thermo-Osmotic Permeability of Clays

    NASA Astrophysics Data System (ADS)

    Gonçalvès, J.; Ji Yu, C.; Matray, J.-M.; Tremosa, J.

    2018-01-01

    In this study, a new formulation for the thermo-osmotic permeability of natural pore solutions containing monovalent and divalent cations is proposed. The mathematical formulation proposed here is based on the theoretical framework supporting thermo-osmosis which relies on water structure alteration in the pore space of surface-charged materials caused by solid-fluid electrochemical interactions. The ionic content balancing the surface charge of clay minerals causes a disruption in the hydrogen bond network when more structured water is present at the clay surface. Analytical expressions based on our heuristic model are proposed and compared to the available data for NaCl solutions. It is shown that the introduction of divalent cations reduces the thermo-osmotic permeability by one third compared to the monovalent case. The analytical expressions provided here can be used to advantage for safety calculations in deep underground nuclear waste repositories.

  17. An accurate analytic description of neutrino oscillations in matter

    NASA Astrophysics Data System (ADS)

    Akhmedov, E. Kh.; Niro, Viviana

    2008-12-01

    A simple closed-form analytic expression for the probability of two-flavour neutrino oscillations in a matter with an arbitrary density profile is derived. Our formula is based on a perturbative expansion and allows an easy calculation of higher order corrections. The expansion parameter is small when the density changes relatively slowly along the neutrino path and/or neutrino energy is not very close to the Mikheyev-Smirnov-Wolfenstein (MSW) resonance energy. Our approximation is not equivalent to the adiabatic approximation and actually goes beyond it. We demonstrate the validity of our results using a few model density profiles, including the PREM density profile of the Earth. It is shown that by combining the results obtained from the expansions valid below and above the MSW resonance one can obtain a very good description of neutrino oscillations in matter in the entire energy range, including the resonance region.

  18. Generating Facial Expressions Using an Anatomically Accurate Biomechanical Model.

    PubMed

    Wu, Tim; Hung, Alice; Mithraratne, Kumar

    2014-11-01

    This paper presents a computational framework for modelling the biomechanics of human facial expressions. A detailed high-order (Cubic-Hermite) finite element model of the human head was constructed using anatomical data segmented from magnetic resonance images. The model includes a superficial soft-tissue continuum consisting of skin, the subcutaneous layer and the superficial Musculo-Aponeurotic system. Embedded within this continuum mesh, are 20 pairs of facial muscles which drive facial expressions. These muscles were treated as transversely-isotropic and their anatomical geometries and fibre orientations were accurately depicted. In order to capture the relative composition of muscles and fat, material heterogeneity was also introduced into the model. Complex contact interactions between the lips, eyelids, and between superficial soft tissue continuum and deep rigid skeletal bones were also computed. In addition, this paper investigates the impact of incorporating material heterogeneity and contact interactions, which are often neglected in similar studies. Four facial expressions were simulated using the developed model and the results were compared with surface data obtained from a 3D structured-light scanner. Predicted expressions showed good agreement with the experimental data.

  19. Analytical Expressions for Deformation from an Arbitrarily Oriented Spheroid in a Half-Space

    NASA Astrophysics Data System (ADS)

    Cervelli, P. F.

    2013-12-01

    Deformation from magma chambers can be modeled by an elastic half-space with an embedded cavity subject to uniform pressure change along its interior surface. For a small number of cavity shapes, such as a sphere or a prolate spheroid, closed-form, analytical expressions for deformation have been derived, although these only approximate the uniform-pressure-change boundary condition, with the approximation becoming more accurate as the ratio of source depth to source dimension increases. Using the method of Elshelby [1957] and Yang [1988], which consists of a distribution of double forces and centers of dilatation along the vertical axis, I have derived expressions for displacement from a finite spheroid of arbitrary orientation and aspect ratio that are exact in an infinite elastic medium and approximate in a half-space. The approximation, like those for other cavity shapes, becomes increasingly accurate as the depth to source ratio grows larger, and is accurate to within a few percent in most real-world cases. I have also derived expressions for the deformation-gradient tensor, i.e., the derivatives of each component of displacement with respect to each coordinate direction. These can be transformed easily into the strain and stress tensors. The expressions give deformation both at the surface and at any point within the half-space, and include conditional statements that account for limiting cases that would otherwise prove singular. I have developed MATLAB code for these expressions (and their derivatives), which I use to demonstrate the accuracy of the approximation by showing how well the uniform-pressure-change boundary condition is satisfied in a variety of cases. I also show that a vertical, oblate spheroid with a zero-length vertical axis is equivalent to the penny-shaped crack of Fialko [2001] in an infinite medium and an excellent approximation in a half-space. Finally, because, in many cases, volume change is more tangible than pressure change, I have

  20. Self-Expression on Social Media: Do Tweets Present Accurate and Positive Portraits of Impulsivity, Self-Esteem, and Attachment Style?

    PubMed

    Orehek, Edward; Human, Lauren J

    2017-01-01

    Self-expression values are at an all-time high, and people are increasingly relying upon social media platforms to express themselves positively and accurately. We examined whether self-expression on the social media platform Twitter elicits positive and accurate social perceptions. Eleven perceivers rated 128 individuals (targets; total dyadic impressions = 1,408) on their impulsivity, self-esteem, and attachment style, based solely on the information provided in targets' 10 most recent tweets. Targets were on average perceived normatively and with distinctive self-other agreement, indicating both positive and accurate social perceptions. There were also individual differences in how positively and accurately targets were perceived, which exploratory analyses indicated may be partially driven by differential word usage, such as the use of positive emotion words and self- versus other-focus. This study demonstrates that self-expression on social media can elicit both positive and accurate perceptions and begins to shed light on how to curate such perceptions.

  1. Approximate analytical relationships for linear optimal aeroelastic flight control laws

    NASA Astrophysics Data System (ADS)

    Kassem, Ayman Hamdy

    1998-09-01

    This dissertation introduces new methods to uncover functional relationships between design parameters of a contemporary control design technique and the resulting closed-loop properties. Three new methods are developed for generating such relationships through analytical expressions: the Direct Eigen-Based Technique, the Order of Magnitude Technique, and the Cost Function Imbedding Technique. Efforts concentrated on the linear-quadratic state-feedback control-design technique applied to an aeroelastic flight control task. For this specific application, simple and accurate analytical expressions for the closed-loop eigenvalues and zeros in terms of basic parameters such as stability and control derivatives, structural vibration damping and natural frequency, and cost function weights are generated. These expressions explicitly indicate how the weights augment the short period and aeroelastic modes, as well as the closed-loop zeros, and by what physical mechanism. The analytical expressions are used to address topics such as damping, nonminimum phase behavior, stability, and performance with robustness considerations, and design modifications. This type of knowledge is invaluable to the flight control designer and would be more difficult to formulate when obtained from numerical-based sensitivity analysis.

  2. Fast and accurate computation of projected two-point functions

    NASA Astrophysics Data System (ADS)

    Grasshorn Gebhardt, Henry S.; Jeong, Donghui

    2018-01-01

    We present the two-point function from the fast and accurate spherical Bessel transformation (2-FAST) algorithmOur code is available at https://github.com/hsgg/twoFAST. for a fast and accurate computation of integrals involving one or two spherical Bessel functions. These types of integrals occur when projecting the galaxy power spectrum P (k ) onto the configuration space, ξℓν(r ), or spherical harmonic space, Cℓ(χ ,χ'). First, we employ the FFTLog transformation of the power spectrum to divide the calculation into P (k )-dependent coefficients and P (k )-independent integrations of basis functions multiplied by spherical Bessel functions. We find analytical expressions for the latter integrals in terms of special functions, for which recursion provides a fast and accurate evaluation. The algorithm, therefore, circumvents direct integration of highly oscillating spherical Bessel functions.

  3. Accurate monoenergetic electron parameters of laser wakefield in a bubble model

    NASA Astrophysics Data System (ADS)

    Raheli, A.; Rahmatallahpur, S. H.

    2012-11-01

    A reliable analytical expression for the potential of plasma waves with phase velocities near the speed of light is derived. The presented spheroid cavity model is more consistent than the previous spherical and ellipsoidal model and it explains the mono-energetic electron trajectory more accurately, especially at the relativistic region. As a result, the quasi-mono-energetic electrons output beam interacting with the laser plasma can be more appropriately described with this model.

  4. Analytical formulation of impulsive collision avoidance dynamics

    NASA Astrophysics Data System (ADS)

    Bombardelli, Claudio

    2014-02-01

    The paper deals with the problem of impulsive collision avoidance between two colliding objects in three dimensions and assuming elliptical Keplerian orbits. Closed-form analytical expressions are provided that accurately predict the relative dynamics of the two bodies in the encounter b-plane following an impulsive delta-V manoeuvre performed by one object at a given orbit location prior to the impact and with a generic three-dimensional orientation. After verifying the accuracy of the analytical expressions for different orbital eccentricities and encounter geometries the manoeuvre direction that maximises the miss distance is obtained numerically as a function of the arc length separation between the manoeuvre point and the predicted collision point. The provided formulas can be used for high-accuracy instantaneous estimation of the outcome of a generic impulsive collision avoidance manoeuvre and its optimisation.

  5. A highly accurate analytical solution for the surface fields of a short vertical wire antenna lying on a multilayer ground

    NASA Astrophysics Data System (ADS)

    Parise, M.

    2018-01-01

    A highly accurate analytical solution is derived to the electromagnetic problem of a short vertical wire antenna located on a stratified ground. The derivation consists of three steps. First, the integration path of the integrals describing the fields of the dipole is deformed and wrapped around the pole singularities and the two vertical branch cuts of the integrands located in the upper half of the complex plane. This allows to decompose the radiated field into its three contributions, namely the above-surface ground wave, the lateral wave, and the trapped surface waves. Next, the square root terms responsible for the branch cuts are extracted from the integrands of the branch-cut integrals. Finally, the extracted square roots are replaced with their rational representations according to Newton's square root algorithm, and residue theorem is applied to give explicit expressions, in series form, for the fields. The rigorous integration procedure and the convergence of square root algorithm ensure that the obtained formulas converge to the exact solution. Numerical simulations are performed to show the validity and robustness of the developed formulation, as well as its advantages in terms of time cost over standard numerical integration procedures.

  6. Accurate Estimate of Some Propagation Characteristics for the First Higher Order Mode in Graded Index Fiber with Simple Analytic Chebyshev Method

    NASA Astrophysics Data System (ADS)

    Dutta, Ivy; Chowdhury, Anirban Roy; Kumbhakar, Dharmadas

    2013-03-01

    Using Chebyshev power series approach, accurate description for the first higher order (LP11) mode of graded index fibers having three different profile shape functions are presented in this paper and applied to predict their propagation characteristics. These characteristics include fractional power guided through the core, excitation efficiency and Petermann I and II spot sizes with their approximate analytic formulations. We have shown that where two and three Chebyshev points in LP11 mode approximation present fairly accurate results, the values based on our calculations involving four Chebyshev points match excellently with available exact numerical results.

  7. Analytical Validation of a Highly Quantitative, Sensitive, Accurate, and Reproducible Assay (HERmark) for the Measurement of HER2 Total Protein and HER2 Homodimers in FFPE Breast Cancer Tumor Specimens.

    PubMed

    Larson, Jeffrey S; Goodman, Laurie J; Tan, Yuping; Defazio-Eli, Lisa; Paquet, Agnes C; Cook, Jennifer W; Rivera, Amber; Frankson, Kristi; Bose, Jolly; Chen, Lili; Cheung, Judy; Shi, Yining; Irwin, Sarah; Kiss, Linda D B; Huang, Weidong; Utter, Shannon; Sherwood, Thomas; Bates, Michael; Weidler, Jodi; Parry, Gordon; Winslow, John; Petropoulos, Christos J; Whitcomb, Jeannette M

    2010-06-28

    We report here the results of the analytical validation of assays that measure HER2 total protein (H2T) and HER2 homodimer (H2D) expression in Formalin Fixed Paraffin Embedded (FFPE) breast cancer tumors as well as cell line controls. The assays are based on the VeraTag technology platform and are commercially available through a central CAP-accredited clinical reference laboratory. The accuracy of H2T measurements spans a broad dynamic range (2-3 logs) as evaluated by comparison with cross-validating technologies. The measurement of H2T expression demonstrates a sensitivity that is approximately 7-10 times greater than conventional immunohistochemistry (IHC) (HercepTest). The HERmark assay is a quantitative assay that sensitively and reproducibly measures continuous H2T and H2D protein expression levels and therefore may have the potential to stratify patients more accurately with respect to response to HER2-targeted therapies than current methods which rely on semiquantitative protein measurements (IHC) or on indirect assessments of gene amplification (FISH).

  8. Simple Analytic Expressions for the Magnetic Field of a Circular Current Loop

    NASA Technical Reports Server (NTRS)

    Simpson, James C.; Lane, John E.; Immer, Christopher D.; Youngquist, Robert C.

    2001-01-01

    Analytic expressions for the magnetic induction (magnetic flux density, B) of a simple planar circular current loop have been published in Cartesian and cylindrical coordinates [1,2], and are also known implicitly in spherical coordinates [3]. In this paper, we present explicit analytic expressions for B and its spatial derivatives in Cartesian, cylindrical, and spherical coordinates for a filamentary current loop. These results were obtained with extensive use of Mathematica "TM" and are exact throughout all space outside of the conductor. The field expressions reduce to the well-known limiting cases and satisfy V · B = 0 and V x B = 0 outside the conductor. These results are general and applicable to any model using filamentary circular current loops. Solenoids of arbitrary size may be easily modeled by approximating the total magnetic induction as the sum of those for the individual loops. The inclusion of the spatial derivatives expands their utility to magnetohydrodynamics where the derivatives are required. The equations can be coded into any high-level programming language. It is necessary to numerically evaluate complete elliptic integrals of the first and second kind, but this capability is now available with most programming packages.

  9. Analytical expressions for stability regions in the Ince-Strutt diagram of Mathieu equation

    NASA Astrophysics Data System (ADS)

    Butikov, Eugene I.

    2018-04-01

    Simple analytical expressions are suggested for transition curves that separate, in the Ince-Strutt diagram, different types of solutions to the famous Mathieu equation. The derivations of these expressions in this paper rely on physically meaningful periodic solutions describing various regular motions of a familiar nonlinear mechanical system—a rigid planar pendulum with a vertically oscillating pivot. The paper is accompanied by a relevant simulation program.

  10. Analytical expressions for the evolution of many-body quantum systems quenched far from equilibrium

    NASA Astrophysics Data System (ADS)

    Santos, Lea F.; Torres-Herrera, E. Jonathan

    2017-12-01

    Possible strategies to describe analytically the dynamics of many-body quantum systems out of equilibrium include the use of solvable models and of full random matrices. None of the two approaches represent actual realistic systems, but they serve as references for the studies of these ones. We take the second path and obtain analytical expressions for the survival probability, density imbalance, and out-of-time-ordered correlator. Using these findings, we then propose an approximate expression that matches very well numerical results for the evolution of realistic finite quantum systems that are strongly chaotic and quenched far from equilibrium. In the case of the survival probability, the expression proposed covers all different time scales, from the moment the system is taken out of equilibrium to the moment it reaches a new equilibrium. The realistic systems considered are described by one-dimensional spin-1/2 models.

  11. Analytical expressions for the log-amplitude correlation function of a plane wave through anisotropic atmospheric refractive turbulence.

    PubMed

    Gudimetla, V S Rao; Holmes, Richard B; Smith, Carey; Needham, Gregory

    2012-05-01

    The effect of anisotropic Kolmogorov turbulence on the log-amplitude correlation function for plane-wave fields is investigated using analysis, numerical integration, and simulation. A new analytical expression for the log-amplitude correlation function is derived for anisotropic Kolmogorov turbulence. The analytic results, based on the Rytov approximation, agree well with a more general wave-optics simulation based on the Fresnel approximation as well as with numerical evaluations, for low and moderate strengths of turbulence. The new expression reduces correctly to previously published analytic expressions for isotropic turbulence. The final results indicate that, as asymmetry becomes greater, the Rytov variance deviates from that given by the standard formula. This deviation becomes greater with stronger turbulence, up to moderate turbulence strengths. The anisotropic effects on the log-amplitude correlation function are dominant when the separation of the points is within the Fresnel length. In the direction of stronger turbulence, there is an enhanced dip in the correlation function at a separation close to the Fresnel length. The dip is diminished in the weak-turbulence axis, suggesting that energy redistribution via focusing and defocusing is dominated by the strong-turbulence axis. The new analytical expression is useful when anisotropy is observed in relevant experiments. © 2012 Optical Society of America

  12. Accurate quantification of PGE2 in the polyposis in rat colon (Pirc) model by surrogate analyte-based UPLC-MS/MS.

    PubMed

    Yun, Changhong; Dashwood, Wan-Mohaiza; Kwong, Lawrence N; Gao, Song; Yin, Taijun; Ling, Qinglan; Singh, Rashim; Dashwood, Roderick H; Hu, Ming

    2018-01-30

    An accurate and reliable UPLC-MS/MS method is reported for the quantification of endogenous Prostaglandin E2 (PGE 2 ) in rat colonic mucosa and polyps. This method adopted the "surrogate analyte plus authentic bio-matrix" approach, using two different stable isotopic labeled analogs - PGE 2 -d9 as the surrogate analyte and PGE 2 -d4 as the internal standard. A quantitative standard curve was constructed with the surrogate analyte in colonic mucosa homogenate, and the method was successfully validated with the authentic bio-matrix. Concentrations of endogenous PGE 2 in both normal and inflammatory tissue homogenates were back-calculated based on the regression equation. Because of no endogenous interference on the surrogate analyte determination, the specificity was particularly good. By using authentic bio-matrix for validation, the matrix effect and exaction recovery are identically same for the quantitative standard curve and actual samples - this notably increased the assay accuracy. The method is easy, fast, robust and reliable for colon PGE 2 determination. This "surrogate analyte" approach was applied to measure the Pirc (an Apc-mutant rat kindred that models human FAP) mucosa and polyps PGE 2 , one of the strong biomarkers of colorectal cancer. A similar concept could be applied to endogenous biomarkers in other tissues. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Analytical Validation of a Highly Quantitative, Sensitive, Accurate, and Reproducible Assay (HERmark®) for the Measurement of HER2 Total Protein and HER2 Homodimers in FFPE Breast Cancer Tumor Specimens

    PubMed Central

    Larson, Jeffrey S.; Goodman, Laurie J.; Tan, Yuping; Defazio-Eli, Lisa; Paquet, Agnes C.; Cook, Jennifer W.; Rivera, Amber; Frankson, Kristi; Bose, Jolly; Chen, Lili; Cheung, Judy; Shi, Yining; Irwin, Sarah; Kiss, Linda D. B.; Huang, Weidong; Utter, Shannon; Sherwood, Thomas; Bates, Michael; Weidler, Jodi; Parry, Gordon; Winslow, John; Petropoulos, Christos J.; Whitcomb, Jeannette M.

    2010-01-01

    We report here the results of the analytical validation of assays that measure HER2 total protein (H2T) and HER2 homodimer (H2D) expression in Formalin Fixed Paraffin Embedded (FFPE) breast cancer tumors as well as cell line controls. The assays are based on the VeraTag technology platform and are commercially available through a central CAP-accredited clinical reference laboratory. The accuracy of H2T measurements spans a broad dynamic range (2-3 logs) as evaluated by comparison with cross-validating technologies. The measurement of H2T expression demonstrates a sensitivity that is approximately 7–10 times greater than conventional immunohistochemistry (IHC) (HercepTest). The HERmark assay is a quantitative assay that sensitively and reproducibly measures continuous H2T and H2D protein expression levels and therefore may have the potential to stratify patients more accurately with respect to response to HER2-targeted therapies than current methods which rely on semiquantitative protein measurements (IHC) or on indirect assessments of gene amplification (FISH). PMID:21151530

  14. Analytic expression for poloidal flow velocity in the banana regime

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

    Taguchi, M.

    The poloidal flow velocity in the banana regime is calculated by improving the l = 1 approximation for the Fokker-Planck collision operator [M. Taguchi, Plasma Phys. Controlled Fusion 30, 1897 (1988)]. The obtained analytic expression for this flow, which can be used for general axisymmetric toroidal plasmas, agrees quite well with the recently calculated numerical results by Parker and Catto [Plasma Phys. Controlled Fusion 54, 085011 (2012)] in the full range of aspect ratio.

  15. Wideband analytical equivalent circuit for one-dimensional periodic stacked arrays.

    PubMed

    Molero, Carlos; Rodríguez-Berral, Raúl; Mesa, Francisco; Medina, Francisco; Yakovlev, Alexander B

    2016-01-01

    A wideband equivalent circuit is proposed for the accurate analysis of scattering from a set of stacked slit gratings illuminated by a plane wave with transverse magnetic or electric polarization that impinges normally or obliquely along one of the principal planes of the structure. The slit gratings are printed on dielectric slabs of arbitrary thickness, including the case of closely spaced gratings that interact by higher-order modes. A Π-circuit topology is obtained for a pair of coupled arrays, with fully analytical expressions for all the circuit elements. This equivalent Π circuit is employed as the basis to derive the equivalent circuit of finite stacks with any given number of gratings. Analytical expressions for the Brillouin diagram and the Bloch impedance are also obtained for infinite periodic stacks.

  16. Analytical expression for Risken-Nummedal-Graham-Haken instability threshold in quantum cascade lasers.

    PubMed

    Vukovic, N; Radovanovic, J; Milanovic, V; Boiko, D L

    2016-11-14

    We have obtained a closed-form expression for the threshold of Risken-Nummedal-Graham-Haken (RNGH) multimode instability in a Fabry-Pérot (FP) cavity quantum cascade laser (QCL). This simple analytical expression is a versatile tool that can easily be applied in practical situations which require analysis of QCL dynamic behavior and estimation of its RNGH multimode instability threshold. Our model for a FP cavity laser accounts for the carrier coherence grating and carrier population grating as well as their relaxation due to carrier diffusion. In the model, the RNGH instability threshold is analyzed using a second-order bi-orthogonal perturbation theory and we confirm our analytical solution by a comparison with the numerical simulations. In particular, the model predicts a low RNGH instability threshold in QCLs. This agrees very well with experimental data available in the literature.

  17. Explicit analytical expression for the condition number of polynomials in power form

    NASA Astrophysics Data System (ADS)

    Rack, Heinz-Joachim

    2017-07-01

    In his influential papers [1-3] W. Gautschi has defined and reshaped the condition number κ∞ of polynomials Pn of degree ≤ n which are represented in power form on a zero-symmetric interval [-ω, ω]. Basically, κ∞ is expressed as the product of two operator norms: an explicit factor times an implicit one (the l∞-norm of the coefficient vector of the n-th Chebyshev polynomial of the first kind relative to [-ω, ω]). We provide a new proof, economize the second factor and express it by an explicit analytical formula.

  18. Analytical model of diffuse reflectance spectrum of skin tissue

    NASA Astrophysics Data System (ADS)

    Lisenko, S. A.; Kugeiko, M. M.; Firago, V. A.; Sobchuk, A. N.

    2014-01-01

    We have derived simple analytical expressions that enable highly accurate calculation of diffusely reflected light signals of skin in the spectral range from 450 to 800 nm at a distance from the region of delivery of exciting radiation. The expressions, taking into account the dependence of the detected signals on the refractive index, transport scattering coefficient, absorption coefficient and anisotropy factor of the medium, have been obtained in the approximation of a two-layer medium model (epidermis and dermis) for the same parameters of light scattering but different absorption coefficients of layers. Numerical experiments on the retrieval of the skin biophysical parameters from the diffuse reflectance spectra simulated by the Monte Carlo method show that commercially available fibre-optic spectrophotometers with a fixed distance between the radiation source and detector can reliably determine the concentration of bilirubin, oxy- and deoxyhaemoglobin in the dermis tissues and the tissue structure parameter characterising the size of its effective scatterers. We present the examples of quantitative analysis of the experimental data, confirming the correctness of estimates of biophysical parameters of skin using the obtained analytical expressions.

  19. Analytical expression for position sensitivity of linear response beam position monitor having inter-electrode cross talk

    NASA Astrophysics Data System (ADS)

    Kumar, Mukesh; Ojha, A.; Garg, A. D.; Puntambekar, T. A.; Senecha, V. K.

    2017-02-01

    According to the quasi electrostatic model of linear response capacitive beam position monitor (BPM), the position sensitivity of the device depends only on the aperture of the device and it is independent of processing frequency and load impedance. In practice, however, due to the inter-electrode capacitive coupling (cross talk), the actual position sensitivity of the device decreases with increasing frequency and load impedance. We have taken into account the inter-electrode capacitance to derive and propose a new analytical expression for the position sensitivity as a function of frequency and load impedance. The sensitivity of a linear response shoe-box type BPM has been obtained through simulation using CST Studio Suite to verify and confirm the validity of the new analytical equation. Good agreement between the simulation results and the new analytical expression suggest that this method can be exploited for proper designing of BPM.

  20. Quo vadis, analytical chemistry?

    PubMed

    Valcárcel, Miguel

    2016-01-01

    This paper presents an open, personal, fresh approach to the future of Analytical Chemistry in the context of the deep changes Science and Technology are anticipated to experience. Its main aim is to challenge young analytical chemists because the future of our scientific discipline is in their hands. A description of not completely accurate overall conceptions of our discipline, both past and present, to be avoided is followed by a flexible, integral definition of Analytical Chemistry and its cornerstones (viz., aims and objectives, quality trade-offs, the third basic analytical reference, the information hierarchy, social responsibility, independent research, transfer of knowledge and technology, interfaces to other scientific-technical disciplines, and well-oriented education). Obsolete paradigms, and more accurate general and specific that can be expected to provide the framework for our discipline in the coming years are described. Finally, the three possible responses of analytical chemists to the proposed changes in our discipline are discussed.

  1. Analytical method for the accurate determination of tricothecenes in grains using LC-MS/MS: a comparison between MRM transition and MS3 quantitation.

    PubMed

    Lim, Chee Wei; Tai, Siew Hoon; Lee, Lin Min; Chan, Sheot Harn

    2012-07-01

    The current food crisis demands unambiguous determination of mycotoxin contamination in staple foods to achieve safer food for consumption. This paper describes the first accurate LC-MS/MS method developed to analyze tricothecenes in grains by applying multiple reaction monitoring (MRM) transition and MS(3) quantitation strategies in tandem. The tricothecenes are nivalenol, deoxynivalenol, deoxynivalenol-3-glucoside, fusarenon X, 3-acetyl-deoxynivalenol, 15-acetyldeoxynivalenol, diacetoxyscirpenol, and HT-2 and T-2 toxins. Acetic acid and ammonium acetate were used to convert the analytes into their respective acetate adducts and ammonium adducts under negative and positive MS polarity conditions, respectively. The mycotoxins were separated by reversed-phase LC in a 13.5-min run, ionized using electrospray ionization, and detected by tandem mass spectrometry. Analyte-specific mass-to-charge (m/z) ratios were used to perform quantitation under MRM transition and MS(3) (linear ion trap) modes. Three experiments were made for each quantitation mode and matrix in batches over 6 days for recovery studies. The matrix effect was investigated at concentration levels of 20, 40, 80, 120, 160, and 200 μg kg(-1) (n = 3) in 5 g corn flour and rice flour. Extraction with acetonitrile provided a good overall recovery range of 90-108% (n = 3) at three levels of spiking concentration of 40, 80, and 120 μg kg(-1). A quantitation limit of 2-6 μg kg(-1) was achieved by applying an MRM transition quantitation strategy. Under MS(3) mode, a quantitation limit of 4-10 μg kg(-1) was achieved. Relative standard deviations of 2-10% and 2-11% were reported for MRM transition and MS(3) quantitation, respectively. The successful utilization of MS(3) enabled accurate analyte fragmentation pattern matching and its quantitation, leading to the development of analytical methods in fields that demand both analyte specificity and fragmentation fingerprint-matching capabilities that are

  2. Petermann I and II spot size: Accurate semi analytical description involving Nelder-Mead method of nonlinear unconstrained optimization and three parameter fundamental modal field

    NASA Astrophysics Data System (ADS)

    Roy Choudhury, Raja; Roy Choudhury, Arundhati; Kanti Ghose, Mrinal

    2013-01-01

    A semi-analytical model with three optimizing parameters and a novel non-Gaussian function as the fundamental modal field solution has been proposed to arrive at an accurate solution to predict various propagation parameters of graded-index fibers with less computational burden than numerical methods. In our semi analytical formulation the optimization of core parameter U which is usually uncertain, noisy or even discontinuous, is being calculated by Nelder-Mead method of nonlinear unconstrained minimizations as it is an efficient and compact direct search method and does not need any derivative information. Three optimizing parameters are included in the formulation of fundamental modal field of an optical fiber to make it more flexible and accurate than other available approximations. Employing variational technique, Petermann I and II spot sizes have been evaluated for triangular and trapezoidal-index fibers with the proposed fundamental modal field. It has been demonstrated that, the results of the proposed solution identically match with the numerical results over a wide range of normalized frequencies. This approximation can also be used in the study of doped and nonlinear fiber amplifier.

  3. An Analytical State Transition Matrix for Orbits Perturbed by an Oblate Spheroid

    NASA Technical Reports Server (NTRS)

    Mueller, A. C.

    1977-01-01

    An analytical state transition matrix and its inverse, which include the short period and secular effects of the second zonal harmonic, were developed from the nonsingular PS satellite theory. The fact that the independent variable in the PS theory is not time is in no respect disadvantageous, since any explicit analytical solution must be expressed in the true or eccentric anomaly. This is shown to be the case for the simple conic matrix. The PS theory allows for a concise, accurate, and algorithmically simple state transition matrix. The improvement over the conic matrix ranges from 2 to 4 digits accuracy.

  4. Analytical expressions for the correlation function of a hard sphere dimer fluid

    NASA Astrophysics Data System (ADS)

    Kim, Soonho; Chang, Jaeeon; Kim, Hwayong

    A closed form expression is given for the correlation function of a hard sphere dimer fluid. A set of integral equations is obtained from Wertheim's multidensity Ornstein-Zernike integral equation theory with Percus-Yevick approximation. Applying the Laplace transformation method to the integral equations and then solving the resulting equations algebraically, the Laplace transforms of the individual correlation functions are obtained. By the inverse Laplace transformation, the radial distribution function (RDF) is obtained in closed form out to 3D (D is the segment diameter). The analytical expression for the RDF of the hard dimer should be useful in developing the perturbation theory of dimer fluids.

  5. Analytical expression for the correlation function of a hard sphere chain fluid

    NASA Astrophysics Data System (ADS)

    Chang, Jaeeon; Kim, Hwayong

    A closed form expression is given for the correlation function of flexible hard sphere chain fluid. A set of integral equations obtained from Wertheim's multidensity Ornstein-Zernike integral equation theory with the polymer Percus-Yevick ideal chain approximation is considered. Applying the Laplace transformation method to the integral equations and then solving the resulting equations algebraically, the Laplace transforms of individual correlation functions are obtained. By inverse Laplace transformation the inter- and intramolecular radial distribution functions (RDFs) are obtained in closed forms up to 3D(D is segment diameter). These analytical expressions for the RDFs would be useful in developing the perturbation theory of chain fluids.

  6. An Accurate Analytic Approximation for Light Scattering by Non-absorbing Spherical Aerosol Particles

    NASA Astrophysics Data System (ADS)

    Lewis, E. R.

    2017-12-01

    The scattering of light by particles in the atmosphere is a ubiquitous and important phenomenon, with applications to numerous fields of science and technology. The problem of scattering of electromagnetic radiation by a uniform spherical particle can be solved by the method of Mie and Debye as a series of terms depending on the size parameter, x=2πr/λ, and the complex index of refraction, m. However, this solution does not provide insight into the dependence of the scattering on the radius of the particle, the wavelength, or the index of refraction, or how the scattering varies with relative humidity. Van de Hulst demonstrated that the scattering efficiency (the scattering cross section divided by the geometric cross section) of a non-absorbing sphere, over a wide range of particle sizes of atmospheric importance, depends not on x and m separately, but on the quantity 2x(m-1); this is the basis for the anomalous diffraction approximation. Here an analytic approximation for the scattering efficiency of a non-absorbing spherical particle is presented in terms of this new quantity that is accurate over a wide range of particle sizes of atmospheric importance and which readily displays the dependences of the scattering efficiency on particle radius, index of refraction, and wavelength. For an aerosol for which the particle size distribution is parameterized as a gamma function, this approximation also yields analytical results for the scattering coefficient and for the Ångström exponent, with the dependences of scattering properties on wavelength and index of refraction clearly displayed. This approximation provides insight into the dependence of light scattering properties on factors such as relative humidity, readily enables conversion of scattering from one index of refraction to another, and demonstrates the conditions under which the aerosol index (the product of the aerosol optical depth and the Ångström exponent) is a useful proxy for the number of cloud

  7. Recursively constructing analytic expressions for equilibrium distributions of stochastic biochemical reaction networks

    PubMed Central

    Baetica, Ania-Ariadna; Singhal, Vipul; Murray, Richard M.

    2017-01-01

    Noise is often indispensable to key cellular activities, such as gene expression, necessitating the use of stochastic models to capture its dynamics. The chemical master equation (CME) is a commonly used stochastic model of Kolmogorov forward equations that describe how the probability distribution of a chemically reacting system varies with time. Finding analytic solutions to the CME can have benefits, such as expediting simulations of multiscale biochemical reaction networks and aiding the design of distributional responses. However, analytic solutions are rarely known. A recent method of computing analytic stationary solutions relies on gluing simple state spaces together recursively at one or two states. We explore the capabilities of this method and introduce algorithms to derive analytic stationary solutions to the CME. We first formally characterize state spaces that can be constructed by performing single-state gluing of paths, cycles or both sequentially. We then study stochastic biochemical reaction networks that consist of reversible, elementary reactions with two-dimensional state spaces. We also discuss extending the method to infinite state spaces and designing the stationary behaviour of stochastic biochemical reaction networks. Finally, we illustrate the aforementioned ideas using examples that include two interconnected transcriptional components and biochemical reactions with two-dimensional state spaces. PMID:28566513

  8. Recursively constructing analytic expressions for equilibrium distributions of stochastic biochemical reaction networks.

    PubMed

    Meng, X Flora; Baetica, Ania-Ariadna; Singhal, Vipul; Murray, Richard M

    2017-05-01

    Noise is often indispensable to key cellular activities, such as gene expression, necessitating the use of stochastic models to capture its dynamics. The chemical master equation (CME) is a commonly used stochastic model of Kolmogorov forward equations that describe how the probability distribution of a chemically reacting system varies with time. Finding analytic solutions to the CME can have benefits, such as expediting simulations of multiscale biochemical reaction networks and aiding the design of distributional responses. However, analytic solutions are rarely known. A recent method of computing analytic stationary solutions relies on gluing simple state spaces together recursively at one or two states. We explore the capabilities of this method and introduce algorithms to derive analytic stationary solutions to the CME. We first formally characterize state spaces that can be constructed by performing single-state gluing of paths, cycles or both sequentially. We then study stochastic biochemical reaction networks that consist of reversible, elementary reactions with two-dimensional state spaces. We also discuss extending the method to infinite state spaces and designing the stationary behaviour of stochastic biochemical reaction networks. Finally, we illustrate the aforementioned ideas using examples that include two interconnected transcriptional components and biochemical reactions with two-dimensional state spaces. © 2017 The Author(s).

  9. Derivation of an analytic expression for the error associated with the noise reduction rating

    NASA Astrophysics Data System (ADS)

    Murphy, William J.

    2005-04-01

    Hearing protection devices are assessed using the Real Ear Attenuation at Threshold (REAT) measurement procedure for the purpose of estimating the amount of noise reduction provided when worn by a subject. The rating number provided on the protector label is a function of the mean and standard deviation of the REAT results achieved by the test subjects. If a group of subjects have a large variance, then it follows that the certainty of the rating should be correspondingly lower. No estimate of the error of a protector's rating is given by existing standards or regulations. Propagation of errors was applied to the Noise Reduction Rating to develop an analytic expression for the hearing protector rating error term. Comparison of the analytic expression for the error to the standard deviation estimated from Monte Carlo simulation of subject attenuations yielded a linear relationship across several protector types and assumptions for the variance of the attenuations.

  10. Recommendations for Accurate Resolution of Gene and Isoform Allele-Specific Expression in RNA-Seq Data

    PubMed Central

    Wood, David L. A.; Nones, Katia; Steptoe, Anita; Christ, Angelika; Harliwong, Ivon; Newell, Felicity; Bruxner, Timothy J. C.; Miller, David; Cloonan, Nicole; Grimmond, Sean M.

    2015-01-01

    Genetic variation modulates gene expression transcriptionally or post-transcriptionally, and can profoundly alter an individual’s phenotype. Measuring allelic differential expression at heterozygous loci within an individual, a phenomenon called allele-specific expression (ASE), can assist in identifying such factors. Massively parallel DNA and RNA sequencing and advances in bioinformatic methodologies provide an outstanding opportunity to measure ASE genome-wide. In this study, matched DNA and RNA sequencing, genotyping arrays and computationally phased haplotypes were integrated to comprehensively and conservatively quantify ASE in a single human brain and liver tissue sample. We describe a methodological evaluation and assessment of common bioinformatic steps for ASE quantification, and recommend a robust approach to accurately measure SNP, gene and isoform ASE through the use of personalized haplotype genome alignment, strict alignment quality control and intragenic SNP aggregation. Our results indicate that accurate ASE quantification requires careful bioinformatic analyses and is adversely affected by sample specific alignment confounders and random sampling even at moderate sequence depths. We identified multiple known and several novel ASE genes in liver, including WDR72, DSP and UBD, as well as genes that contained ASE SNPs with imbalance direction discordant with haplotype phase, explainable by annotated transcript structure, suggesting isoform derived ASE. The methods evaluated in this study will be of use to researchers performing highly conservative quantification of ASE, and the genes and isoforms identified as ASE of interest to researchers studying those loci. PMID:25965996

  11. On the analytical form of the Earth's magnetic attraction expressed as a function of time

    NASA Technical Reports Server (NTRS)

    Carlheim-Gyllenskold, V.

    1983-01-01

    An attempt is made to express the Earth's magnetic attraction in simple analytical form using observations during the 16th to 19th centuries. Observations of the magnetic inclination in the 16th and 17th centuries are discussed.

  12. Expressions of homosexuality and the perspective of analytical psychology.

    PubMed

    Miller, Barry

    2010-02-01

    Homosexuality, as a description and category of human experience, has a long, complicated and problematic history. It has been utilized as a carrier of theological, political, and psychological ideologies of all sorts, with varying and contradictory influences into the lives of us all. Analytical psychology, emphasizing the purposiveness found in manifestations of the psyche, offers a unique approach to this subject. The focus moves from causation to the meanings embedded in erotic expressions, fantasies, and dreams. Consequently, homosexuality loses its predetermined meaning and finds its definition in the psychology of the individual. Categories of 'sexual orientation' may defend against personal analysis, deflecting the essential fluidity and mystery of Eros. This is illustrated with samples of the variety found in 'homosexual' material.

  13. A practical model of thin disk regenerative amplifier based on analytical expression of ASE lifetime

    NASA Astrophysics Data System (ADS)

    Zhou, Huang; Chyla, Michal; Nagisetty, Siva Sankar; Chen, Liyuan; Endo, Akira; Smrz, Martin; Mocek, Tomas

    2017-12-01

    In this paper, a practical model of a thin disk regenerative amplifier has been developed based on an analytical approach, in which Drew A. Copeland [1] had evaluated the loss rate of the upper state laser level due to ASE and derived the analytical expression of the effective life-time of the upper-state laser level by taking the Lorentzian stimulated emission line-shape and total internal reflection into account. By adopting the analytical expression of effective life-time in the rate equations, we have developed a less numerically intensive model for predicting and analyzing the performance of a thin disk regenerative amplifier. Thanks to the model, optimized combination of various parameters can be obtained to avoid saturation, period-doubling bifurcation or first pulse suppression prior to experiments. The effective life-time due to ASE is also analyzed against various parameters. The simulated results fit well with experimental data. By fitting more experimental results with numerical model, we can improve the parameters of the model, such as reflective factor which is used to determine the weight of boundary reflection within the influence of ASE. This practical model will be used to explore the scaling limits imposed by ASE of the thin disk regenerative amplifier being developed in HiLASE Centre.

  14. The need for accurate total cholesterol measurement. Recommended analytical goals, current state of reliability, and guidelines for better determinations.

    PubMed

    Naito, H K

    1989-03-01

    We have approached a dawn of a new era in detection, evaluation, treatment, and monitoring of individuals with elevated blood cholesterol levels who are at increased risk for CHD. The NHLBI's National Cholesterol Education Program will be the major force underlying this national awareness program, which is dependent on the clinical laboratories providing reliable data. Precision or reproducibility of results is not a problem for most of the laboratories, but accuracy is a major concern. Both the manufacturers and laboratorians need to standardize the measurement for cholesterol so that the accuracy base is traceable to the NCCLS NRS/CHOL. The manufacturers need to adopt a uniform policy that will ensure that the values assigned to calibration, quality control, and quality assurance or survey materials are accurate and traceable to the NCCLS/CHOL. Since, at present, there are some limitations of these materials caused by matrix effects, laboratories are encouraged to use the CDC-NHLBI National Reference Laboratory Network to evaluate and monitor their ability to measure patient blood cholesterol levels accurately. Major areas of analytical problems are identified and general, as well as specific, recommendations are provided to help ensure reliable measurement of cholesterol in patient specimens.

  15. Facing mixed emotions: Analytic and holistic perception of facial emotion expressions engages separate brain networks.

    PubMed

    Meaux, Emilie; Vuilleumier, Patrik

    2016-11-01

    The ability to decode facial emotions is of primary importance for human social interactions; yet, it is still debated how we analyze faces to determine their expression. Here we compared the processing of emotional face expressions through holistic integration and/or local analysis of visual features, and determined which brain systems mediate these distinct processes. Behavioral, physiological, and brain responses to happy and angry faces were assessed by presenting congruent global configurations of expressions (e.g., happy top+happy bottom), incongruent composite configurations (e.g., angry top+happy bottom), and isolated features (e.g. happy top only). Top and bottom parts were always from the same individual. Twenty-six healthy volunteers were scanned using fMRI while they classified the expression in either the top or the bottom face part but ignored information in the other non-target part. Results indicate that the recognition of happy and anger expressions is neither strictly holistic nor analytic Both routes were involved, but with a different role for analytic and holistic information depending on the emotion type, and different weights of local features between happy and anger expressions. Dissociable neural pathways were engaged depending on emotional face configurations. In particular, regions within the face processing network differed in their sensitivity to holistic expression information, which predominantly activated fusiform, inferior occipital areas and amygdala when internal features were congruent (i.e. template matching), whereas more local analysis of independent features preferentially engaged STS and prefrontal areas (IFG/OFC) in the context of full face configurations, but early visual areas and pulvinar when seen in isolated parts. Collectively, these findings suggest that facial emotion recognition recruits separate, but interactive dorsal and ventral routes within the face processing networks, whose engagement may be shaped by

  16. Robust Accurate Non-Invasive Analyte Monitor

    DOEpatents

    Robinson, Mark R.

    1998-11-03

    An improved method and apparatus for determining noninvasively and in vivo one or more unknown values of a known characteristic, particularly the concentration of an analyte in human tissue. The method includes: (1) irradiating the tissue with infrared energy (400 nm-2400 nm) having at least several wavelengths in a given range of wavelengths so that there is differential absorption of at least some of the wavelengths by the tissue as a function of the wavelengths and the known characteristic, the differential absorption causeing intensity variations of the wavelengths incident from the tissue; (2) providing a first path through the tissue; (3) optimizing the first path for a first sub-region of the range of wavelengths to maximize the differential absorption by at least some of the wavelengths in the first sub-region; (4) providing a second path through the tissue; and (5) optimizing the second path for a second sub-region of the range, to maximize the differential absorption by at least some of the wavelengths in the second sub-region. In the preferred embodiment a third path through the tissue is provided for, which path is optimized for a third sub-region of the range. With this arrangement, spectral variations which are the result of tissue differences (e.g., melanin and temperature) can be reduced. At least one of the paths represents a partial transmission path through the tissue. This partial transmission path may pass through the nail of a finger once and, preferably, twice. Also included are apparatus for: (1) reducing the arterial pulsations within the tissue; and (2) maximizing the blood content i the tissue.

  17. Sad people are more accurate at expression identification with a smaller own-ethnicity bias than happy people.

    PubMed

    Hills, Peter J; Hill, Dominic M

    2017-07-12

    Sad individuals perform more accurately at face identity recognition (Hills, Werno, & Lewis, 2011), possibly because they scan more of the face during encoding. During expression identification tasks, sad individuals do not fixate on the eyes as much as happier individuals (Wu, Pu, Allen, & Pauli, 2012). Fixating on features other than the eyes leads to a reduced own-ethnicity bias (Hills & Lewis, 2006). This background indicates that sad individuals would not view the eyes as much as happy individuals and this would result in improved expression recognition and a reduced own-ethnicity bias. This prediction was tested using an expression identification task, with eye tracking. We demonstrate that sad-induced participants show enhanced expression recognition and a reduced own-ethnicity bias than happy-induced participants due to scanning more facial features. We conclude that mood affects eye movements and face encoding by causing a wider sampling strategy and deeper encoding of facial features diagnostic for expression identification.

  18. Analytic expressions for Atomic Layer Deposition: coverage, throughput, and materials utilization in cross-flow, particle coating, and spatial ALD

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

    Yanguas-Gil, Angel; Elam, Jeffrey W.

    2014-05-01

    In this work, the authors present analytic models for atomic layer deposition (ALD) in three common experimental configurations: cross-flow, particle coating, and spatial ALD. These models, based on the plug-flow and well-mixed approximations, allow us to determine the minimum dose times and materials utilization for all three configurations. A comparison between the three models shows that throughput and precursor utilization can each be expressed by universal equations, in which the particularity of the experimental system is contained in a single parameter related to the residence time of the precursor in the reactor. For the case of cross-flow reactors, the authorsmore » show how simple analytic expressions for the reactor saturation profiles agree well with experimental results. Consequently, the analytic model can be used to extract information about the ALD surface chemistry (e. g., the reaction probability) by comparing the analytic and experimental saturation profiles, providing a useful tool for characterizing new and existing ALD processes. (C) 2014 American Vacuum Society« less

  19. Partially Coherent Scattering in Stellar Chromospheres. Part 4; Analytic Wing Approximations

    NASA Technical Reports Server (NTRS)

    Gayley, K. G.

    1993-01-01

    Simple analytic expressions are derived to understand resonance-line wings in stellar chromospheres and similar astrophysical plasmas. The results are approximate, but compare well with accurate numerical simulations. The redistribution is modeled using an extension of the partially coherent scattering approximation (PCS) which we term the comoving-frame partially coherent scattering approximation (CPCS). The distinction is made here because Doppler diffusion is included in the coherent/noncoherent decomposition, in a form slightly improved from the earlier papers in this series.

  20. Analytical solution for wave propagation through a graded index interface between a right-handed and a left-handed material.

    PubMed

    Dalarsson, Mariana; Tassin, Philippe

    2009-04-13

    We have investigated the transmission and reflection properties of structures incorporating left-handed materials with graded index of refraction. We present an exact analytical solution to Helmholtz' equation for a graded index profile changing according to a hyperbolic tangent function along the propagation direction. We derive expressions for the field intensity along the graded index structure, and we show excellent agreement between the analytical solution and the corresponding results obtained by accurate numerical simulations. Our model straightforwardly allows for arbitrary spectral dispersion.

  1. Analytical Expressions for the Mixed-Order Kinetics Parameters of TL Glow Peaks Based on the two Heating Rates Method.

    PubMed

    Maghrabi, Mufeed; Al-Abdullah, Tariq; Khattari, Ziad

    2018-03-24

    The two heating rates method (originally developed for first-order glow peaks) was used for the first time to evaluate the activation energy (E) from glow peaks obeying mixed-order (MO) kinetics. The derived expression for E has an insignificant additional term (on the scale of a few meV) when compared with the first-order case. Hence, the original expression for E using the two heating rates method can be used with excellent accuracy in the case of MO glow peaks. In addition, we derived a simple analytical expression for the MO parameter. The present procedure has the advantage that the MO parameter can now be evaluated using analytical expression instead of using the graphical representation between the geometrical factor and the MO parameter as given by the existing peak shape methods. The applicability of the derived expressions for real samples was demonstrated for the glow curve of Li 2 B 4 O 7 :Mn single crystal. The obtained parameters compare very well with those obtained by glow curve fitting and with the available published data.

  2. Analytic model for the long-term evolution of circular Earth satellite orbits including lunar node regression

    NASA Astrophysics Data System (ADS)

    Zhu, Ting-Lei; Zhao, Chang-Yin; Zhang, Ming-Jiang

    2017-04-01

    This paper aims to obtain an analytic approximation to the evolution of circular orbits governed by the Earth's J2 and the luni-solar gravitational perturbations. Assuming that the lunar orbital plane coincides with the ecliptic plane, Allan and Cook (Proc. R. Soc. A, Math. Phys. Eng. Sci. 280(1380):97, 1964) derived an analytic solution to the orbital plane evolution of circular orbits. Using their result as an intermediate solution, we establish an approximate analytic model with lunar orbital inclination and its node regression be taken into account. Finally, an approximate analytic expression is derived, which is accurate compared to the numerical results except for the resonant cases when the period of the reference orbit approximately equals the integer multiples (especially 1 or 2 times) of lunar node regression period.

  3. Introducing GAMER: A Fast and Accurate Method for Ray-tracing Galaxies Using Procedural Noise

    NASA Astrophysics Data System (ADS)

    Groeneboom, N. E.; Dahle, H.

    2014-03-01

    We developed a novel approach for fast and accurate ray-tracing of galaxies using procedural noise fields. Our method allows for efficient and realistic rendering of synthetic galaxy morphologies, where individual components such as the bulge, disk, stars, and dust can be synthesized in different wavelengths. These components follow empirically motivated overall intensity profiles but contain an additional procedural noise component that gives rise to complex natural patterns that mimic interstellar dust and star-forming regions. These patterns produce more realistic-looking galaxy images than using analytical expressions alone. The method is fully parallelized and creates accurate high- and low- resolution images that can be used, for example, in codes simulating strong and weak gravitational lensing. In addition to having a user-friendly graphical user interface, the C++ software package GAMER is easy to implement into an existing code.

  4. Finding accurate frontiers: A knowledge-intensive approach to relational learning

    NASA Technical Reports Server (NTRS)

    Pazzani, Michael; Brunk, Clifford

    1994-01-01

    An approach to analytic learning is described that searches for accurate entailments of a Horn Clause domain theory. A hill-climbing search, guided by an information based evaluation function, is performed by applying a set of operators that derive frontiers from domain theories. The analytic learning system is one component of a multi-strategy relational learning system. We compare the accuracy of concepts learned with this analytic strategy to concepts learned with an analytic strategy that operationalizes the domain theory.

  5. The analytical validation of the Oncotype DX Recurrence Score assay

    PubMed Central

    Baehner, Frederick L

    2016-01-01

    In vitro diagnostic multivariate index assays are highly complex molecular assays that can provide clinically actionable information regarding the underlying tumour biology and facilitate personalised treatment. These assays are only useful in clinical practice if all of the following are established: analytical validation (i.e., how accurately/reliably the assay measures the molecular characteristics), clinical validation (i.e., how consistently/accurately the test detects/predicts the outcomes of interest), and clinical utility (i.e., how likely the test is to significantly improve patient outcomes). In considering the use of these assays, clinicians often focus primarily on the clinical validity/utility; however, the analytical validity of an assay (e.g., its accuracy, reproducibility, and standardisation) should also be evaluated and carefully considered. This review focuses on the rigorous analytical validation and performance of the Oncotype DX® Breast Cancer Assay, which is performed at the Central Clinical Reference Laboratory of Genomic Health, Inc. The assay process includes tumour tissue enrichment (if needed), RNA extraction, gene expression quantitation (using a gene panel consisting of 16 cancer genes plus 5 reference genes and quantitative real-time RT-PCR), and an automated computer algorithm to produce a Recurrence Score® result (scale: 0–100). This review presents evidence showing that the Recurrence Score result reported for each patient falls within a tight clinically relevant confidence interval. Specifically, the review discusses how the development of the assay was designed to optimise assay performance, presents data supporting its analytical validity, and describes the quality control and assurance programmes that ensure optimal test performance over time. PMID:27729940

  6. The analytical validation of the Oncotype DX Recurrence Score assay.

    PubMed

    Baehner, Frederick L

    2016-01-01

    In vitro diagnostic multivariate index assays are highly complex molecular assays that can provide clinically actionable information regarding the underlying tumour biology and facilitate personalised treatment. These assays are only useful in clinical practice if all of the following are established: analytical validation (i.e., how accurately/reliably the assay measures the molecular characteristics), clinical validation (i.e., how consistently/accurately the test detects/predicts the outcomes of interest), and clinical utility (i.e., how likely the test is to significantly improve patient outcomes). In considering the use of these assays, clinicians often focus primarily on the clinical validity/utility; however, the analytical validity of an assay (e.g., its accuracy, reproducibility, and standardisation) should also be evaluated and carefully considered. This review focuses on the rigorous analytical validation and performance of the Oncotype DX ® Breast Cancer Assay, which is performed at the Central Clinical Reference Laboratory of Genomic Health, Inc. The assay process includes tumour tissue enrichment (if needed), RNA extraction, gene expression quantitation (using a gene panel consisting of 16 cancer genes plus 5 reference genes and quantitative real-time RT-PCR), and an automated computer algorithm to produce a Recurrence Score ® result (scale: 0-100). This review presents evidence showing that the Recurrence Score result reported for each patient falls within a tight clinically relevant confidence interval. Specifically, the review discusses how the development of the assay was designed to optimise assay performance, presents data supporting its analytical validity, and describes the quality control and assurance programmes that ensure optimal test performance over time.

  7. A highly sensitive and accurate gene expression analysis by sequencing ("bead-seq") for a single cell.

    PubMed

    Matsunaga, Hiroko; Goto, Mari; Arikawa, Koji; Shirai, Masataka; Tsunoda, Hiroyuki; Huang, Huan; Kambara, Hideki

    2015-02-15

    Analyses of gene expressions in single cells are important for understanding detailed biological phenomena. Here, a highly sensitive and accurate method by sequencing (called "bead-seq") to obtain a whole gene expression profile for a single cell is proposed. A key feature of the method is to use a complementary DNA (cDNA) library on magnetic beads, which enables adding washing steps to remove residual reagents in a sample preparation process. By adding the washing steps, the next steps can be carried out under the optimal conditions without losing cDNAs. Error sources were carefully evaluated to conclude that the first several steps were the key steps. It is demonstrated that bead-seq is superior to the conventional methods for single-cell gene expression analyses in terms of reproducibility, quantitative accuracy, and biases caused during sample preparation and sequencing processes. Copyright © 2014 Elsevier Inc. All rights reserved.

  8. Analytic expression for the giant fieldlike spin torque in spin-filter magnetic tunnel junctions

    NASA Astrophysics Data System (ADS)

    Tang, Y.-H.; Huang, Z.-W.; Huang, B.-H.

    2017-08-01

    We propose analytic expressions for fieldlike, T⊥, and spin-transfer, T∥, spin torque components in the spin-filter-based magnetic tunnel junction (SFMTJ), by using the single-band tight-binding model with the nonequilibrium Keldysh formalism. In consideration of multireflection processes between noncollinear magnetization of the spin-filter (SF) barrier and the ferromagnetic (FM) electrode, the central spin-selective SF barrier plays an active role in the striking discovery T⊥≫T∥ , which can be further identified by the unusual barrier thickness dependence of giant T⊥. Our general expressions reveal the sinusoidal angular dependence of both spin torque components, even in the presence of the SF barrier.

  9. Palm: Easing the Burden of Analytical Performance Modeling

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

    Tallent, Nathan R.; Hoisie, Adolfy

    2014-06-01

    Analytical (predictive) application performance models are critical for diagnosing performance-limiting resources, optimizing systems, and designing machines. Creating models, however, is difficult because they must be both accurate and concise. To ease the burden of performance modeling, we developed Palm, a modeling tool that combines top-down (human-provided) semantic insight with bottom-up static and dynamic analysis. To express insight, Palm defines a source code modeling annotation language. By coordinating models and source code, Palm's models are `first-class' and reproducible. Unlike prior work, Palm formally links models, functions, and measurements. As a result, Palm (a) uses functions to either abstract or express complexitymore » (b) generates hierarchical models (representing an application's static and dynamic structure); and (c) automatically incorporates measurements to focus attention, represent constant behavior, and validate models. We discuss generating models for three different applications.« less

  10. Fluorescence polarization immunoassays for rapid, accurate, and sensitive determination of mycotoxins

    USDA-ARS?s Scientific Manuscript database

    Analytical methods for the determination of mycotoxins in foods are commonly based on chromatographic techniques (GC, HPLC or LC-MS). Although these methods permit a sensitive and accurate determination of the analyte, they require skilled personnel and are time-consuming, expensive, and unsuitable ...

  11. Visual analytics of brain networks.

    PubMed

    Li, Kaiming; Guo, Lei; Faraco, Carlos; Zhu, Dajiang; Chen, Hanbo; Yuan, Yixuan; Lv, Jinglei; Deng, Fan; Jiang, Xi; Zhang, Tuo; Hu, Xintao; Zhang, Degang; Miller, L Stephen; Liu, Tianming

    2012-05-15

    Identification of regions of interest (ROIs) is a fundamental issue in brain network construction and analysis. Recent studies demonstrate that multimodal neuroimaging approaches and joint analysis strategies are crucial for accurate, reliable and individualized identification of brain ROIs. In this paper, we present a novel approach of visual analytics and its open-source software for ROI definition and brain network construction. By combining neuroscience knowledge and computational intelligence capabilities, visual analytics can generate accurate, reliable and individualized ROIs for brain networks via joint modeling of multimodal neuroimaging data and an intuitive and real-time visual analytics interface. Furthermore, it can be used as a functional ROI optimization and prediction solution when fMRI data is unavailable or inadequate. We have applied this approach to an operation span working memory fMRI/DTI dataset, a schizophrenia DTI/resting state fMRI (R-fMRI) dataset, and a mild cognitive impairment DTI/R-fMRI dataset, in order to demonstrate the effectiveness of visual analytics. Our experimental results are encouraging. Copyright © 2012 Elsevier Inc. All rights reserved.

  12. Introducing GAMER: A fast and accurate method for ray-tracing galaxies using procedural noise

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

    Groeneboom, N. E.; Dahle, H., E-mail: nicolaag@astro.uio.no

    2014-03-10

    We developed a novel approach for fast and accurate ray-tracing of galaxies using procedural noise fields. Our method allows for efficient and realistic rendering of synthetic galaxy morphologies, where individual components such as the bulge, disk, stars, and dust can be synthesized in different wavelengths. These components follow empirically motivated overall intensity profiles but contain an additional procedural noise component that gives rise to complex natural patterns that mimic interstellar dust and star-forming regions. These patterns produce more realistic-looking galaxy images than using analytical expressions alone. The method is fully parallelized and creates accurate high- and low- resolution images thatmore » can be used, for example, in codes simulating strong and weak gravitational lensing. In addition to having a user-friendly graphical user interface, the C++ software package GAMER is easy to implement into an existing code.« less

  13. Gender differences in emotion expression in children: a meta-analytic review.

    PubMed

    Chaplin, Tara M; Aldao, Amelia

    2013-07-01

    Emotion expression is an important feature of healthy child development that has been found to show gender differences. However, there has been no empirical review of the literature on gender and facial, vocal, and behavioral expressions of different types of emotions in children. The present study constitutes a comprehensive meta-analytic review of gender differences and moderators of differences in emotion expression from infancy through adolescence. We analyzed 555 effect sizes from 166 studies with a total of 21,709 participants. Significant but very small gender differences were found overall, with girls showing more positive emotions (g = -.08) and internalizing emotions (e.g., sadness, anxiety, sympathy; g = -.10) than boys, and boys showing more externalizing emotions (e.g., anger; g = .09) than girls. Notably, gender differences were moderated by age, interpersonal context, and task valence, underscoring the importance of contextual factors in gender differences. Gender differences in positive emotions were more pronounced with increasing age, with girls showing more positive emotions than boys in middle childhood (g = -.20) and adolescence (g = -.28). Boys showed more externalizing emotions than girls at toddler/preschool age (g = .17) and middle childhood (g = .13) and fewer externalizing emotions than girls in adolescence (g = -.27). Gender differences were less pronounced with parents and were more pronounced with unfamiliar adults (for positive emotions) and with peers/when alone (for externalizing emotions). Our findings of gender differences in emotion expression in specific contexts have important implications for gender differences in children's healthy and maladaptive development. 2013 APA, all rights reserved

  14. Gender Differences in Emotion Expression in Children: A Meta-Analytic Review

    PubMed Central

    Chaplin, Tara M.; Aldao, Amelia

    2012-01-01

    Emotion expression is an important feature of healthy child development that has been found to show gender differences. However, there has been no empirical review of the literature on gender and facial, vocal, and behavioral expressions of different types of emotions in children. The present study constitutes a comprehensive meta-analytic review of gender differences, and moderators of differences, in emotion expression from infancy through adolescence. We analyzed 555 effect sizes from 166 studies with a total of 21,709 participants. Significant, but very small, gender differences were found overall, with girls showing more positive emotions (g = −.08) and internalizing emotions (e.g., sadness, anxiety, sympathy; g = −.10) than boys, and boys showing more externalizing emotions (e.g., anger; g = .09) than girls. Notably, gender differences were moderated by age, interpersonal context, and task valence, underscoring the importance of contextual factors in gender differences. Gender differences in positive emotions were more pronounced with increasing age, with girls showing more positive emotions than boys in middle childhood (g = −.20) and adolescence (g = −.28). Boys showed more externalizing emotions than girls at toddler/preschool age (g = .17) and middle childhood (g = .13) and fewer externalizing emotions than girls in adolescence (g = −.27). Gender differences were less pronounced with parents and were more pronounced with unfamiliar adults (for positive emotions) and with peers/when alone (for externalizing emotions). Our findings of gender differences in emotion expression in specific contexts have important implications for gender differences in children’s healthy and maladaptive development. PMID:23231534

  15. Moving Toward Integrating Gene Expression Profiling Into High-Throughput Testing: A Gene Expression Biomarker Accurately Predicts Estrogen Receptor α Modulation in a Microarray Compendium

    PubMed Central

    Ryan, Natalia; Chorley, Brian; Tice, Raymond R.; Judson, Richard; Corton, J. Christopher

    2016-01-01

    Microarray profiling of chemical-induced effects is being increasingly used in medium- and high-throughput formats. Computational methods are described here to identify molecular targets from whole-genome microarray data using as an example the estrogen receptor α (ERα), often modulated by potential endocrine disrupting chemicals. ERα biomarker genes were identified by their consistent expression after exposure to 7 structurally diverse ERα agonists and 3 ERα antagonists in ERα-positive MCF-7 cells. Most of the biomarker genes were shown to be directly regulated by ERα as determined by ESR1 gene knockdown using siRNA as well as through chromatin immunoprecipitation coupled with DNA sequencing analysis of ERα-DNA interactions. The biomarker was evaluated as a predictive tool using the fold-change rank-based Running Fisher algorithm by comparison to annotated gene expression datasets from experiments using MCF-7 cells, including those evaluating the transcriptional effects of hormones and chemicals. Using 141 comparisons from chemical- and hormone-treated cells, the biomarker gave a balanced accuracy for prediction of ERα activation or suppression of 94% and 93%, respectively. The biomarker was able to correctly classify 18 out of 21 (86%) ER reference chemicals including “very weak” agonists. Importantly, the biomarker predictions accurately replicated predictions based on 18 in vitro high-throughput screening assays that queried different steps in ERα signaling. For 114 chemicals, the balanced accuracies were 95% and 98% for activation or suppression, respectively. These results demonstrate that the ERα gene expression biomarker can accurately identify ERα modulators in large collections of microarray data derived from MCF-7 cells. PMID:26865669

  16. Analytic expressions for the black-sky and white-sky albedos of the cosine lobe model.

    PubMed

    Goodin, Christopher

    2013-05-01

    The cosine lobe model is a bidirectional reflectance distribution function (BRDF) that is commonly used in computer graphics to model specular reflections. The model is both simple and physically plausible, but physical quantities such as albedo have not been related to the parameterization of the model. In this paper, analytic expressions for calculating the black-sky and white-sky albedos from the cosine lobe BRDF model with integer exponents will be derived, to the author's knowledge for the first time. These expressions for albedo can be used to place constraints on physics-based simulations of radiative transfer such as high-fidelity ray-tracing simulations.

  17. Analytic materials

    PubMed Central

    2016-01-01

    The theory of inhomogeneous analytic materials is developed. These are materials where the coefficients entering the equations involve analytic functions. Three types of analytic materials are identified. The first two types involve an integer p. If p takes its maximum value, then we have a complete analytic material. Otherwise, it is incomplete analytic material of rank p. For two-dimensional materials, further progress can be made in the identification of analytic materials by using the well-known fact that a 90° rotation applied to a divergence-free field in a simply connected domain yields a curl-free field, and this can then be expressed as the gradient of a potential. Other exact results for the fields in inhomogeneous media are reviewed. Also reviewed is the subject of metamaterials, as these materials provide a way of realizing desirable coefficients in the equations. PMID:27956882

  18. Fast and accurate Voronoi density gridding from Lagrangian hydrodynamics data

    NASA Astrophysics Data System (ADS)

    Petkova, Maya A.; Laibe, Guillaume; Bonnell, Ian A.

    2018-01-01

    Voronoi grids have been successfully used to represent density structures of gas in astronomical hydrodynamics simulations. While some codes are explicitly built around using a Voronoi grid, others, such as Smoothed Particle Hydrodynamics (SPH), use particle-based representations and can benefit from constructing a Voronoi grid for post-processing their output. So far, calculating the density of each Voronoi cell from SPH data has been done numerically, which is both slow and potentially inaccurate. This paper proposes an alternative analytic method, which is fast and accurate. We derive an expression for the integral of a cubic spline kernel over the volume of a Voronoi cell and link it to the density of the cell. Mass conservation is ensured rigorously by the procedure. The method can be applied more broadly to integrate a spherically symmetric polynomial function over the volume of a random polyhedron.

  19. Insight solutions are correct more often than analytic solutions

    PubMed Central

    Salvi, Carola; Bricolo, Emanuela; Kounios, John; Bowden, Edward; Beeman, Mark

    2016-01-01

    How accurate are insights compared to analytical solutions? In four experiments, we investigated how participants’ solving strategies influenced their solution accuracies across different types of problems, including one that was linguistic, one that was visual and two that were mixed visual-linguistic. In each experiment, participants’ self-judged insight solutions were, on average, more accurate than their analytic ones. We hypothesised that insight solutions have superior accuracy because they emerge into consciousness in an all-or-nothing fashion when the unconscious solving process is complete, whereas analytic solutions can be guesses based on conscious, prematurely terminated, processing. This hypothesis is supported by the finding that participants’ analytic solutions included relatively more incorrect responses (i.e., errors of commission) than timeouts (i.e., errors of omission) compared to their insight responses. PMID:27667960

  20. Moving Toward Integrating Gene Expression Profiling Into High-Throughput Testing: A Gene Expression Biomarker Accurately Predicts Estrogen Receptor α Modulation in a Microarray Compendium.

    PubMed

    Ryan, Natalia; Chorley, Brian; Tice, Raymond R; Judson, Richard; Corton, J Christopher

    2016-05-01

    Microarray profiling of chemical-induced effects is being increasingly used in medium- and high-throughput formats. Computational methods are described here to identify molecular targets from whole-genome microarray data using as an example the estrogen receptor α (ERα), often modulated by potential endocrine disrupting chemicals. ERα biomarker genes were identified by their consistent expression after exposure to 7 structurally diverse ERα agonists and 3 ERα antagonists in ERα-positive MCF-7 cells. Most of the biomarker genes were shown to be directly regulated by ERα as determined by ESR1 gene knockdown using siRNA as well as through chromatin immunoprecipitation coupled with DNA sequencing analysis of ERα-DNA interactions. The biomarker was evaluated as a predictive tool using the fold-change rank-based Running Fisher algorithm by comparison to annotated gene expression datasets from experiments using MCF-7 cells, including those evaluating the transcriptional effects of hormones and chemicals. Using 141 comparisons from chemical- and hormone-treated cells, the biomarker gave a balanced accuracy for prediction of ERα activation or suppression of 94% and 93%, respectively. The biomarker was able to correctly classify 18 out of 21 (86%) ER reference chemicals including "very weak" agonists. Importantly, the biomarker predictions accurately replicated predictions based on 18 in vitro high-throughput screening assays that queried different steps in ERα signaling. For 114 chemicals, the balanced accuracies were 95% and 98% for activation or suppression, respectively. These results demonstrate that the ERα gene expression biomarker can accurately identify ERα modulators in large collections of microarray data derived from MCF-7 cells. Published by Oxford University Press on behalf of the Society of Toxicology 2016. This work is written by US Government employees and is in the public domain in the US.

  1. An analytical model for scanning electron microscope Type I magnetic contrast with energy filtering

    NASA Astrophysics Data System (ADS)

    Chim, W. K.

    1994-02-01

    In this article, a theoretical model for type I magnetic contrast calculations in the scanning electron microscope with energy filtering is presented. This model uses an approximate form of the secondary electron (SE) energy distribution by Chung and Everhart [M. S. Chung and T. E. Everhart, J. Appl. Phys. 45, 707 (1974). Closed form analytical expressions for the contrast and quality factors, which take into consideration the work function and field-distance integral of the material being studied, are obtained. This analytical model is compared with that of a more accurate numerical model. Results showed that the contrast and quality factors for the analytical model differed by not more than 20% from the numerical model, with the actual difference depending on the range of filtered SE energies considered. This model has also been extended to the situation of a two-detector (i.e., detector A and B) configuration, in which enhanced magnetic contrast and quality factor can be obtained by operating in the ``A-B'' mode.

  2. Online Analytical Processing (OLAP): A Fast and Effective Data Mining Tool for Gene Expression Databases

    PubMed Central

    2005-01-01

    Gene expression databases contain a wealth of information, but current data mining tools are limited in their speed and effectiveness in extracting meaningful biological knowledge from them. Online analytical processing (OLAP) can be used as a supplement to cluster analysis for fast and effective data mining of gene expression databases. We used Analysis Services 2000, a product that ships with SQLServer2000, to construct an OLAP cube that was used to mine a time series experiment designed to identify genes associated with resistance of soybean to the soybean cyst nematode, a devastating pest of soybean. The data for these experiments is stored in the soybean genomics and microarray database (SGMD). A number of candidate resistance genes and pathways were found. Compared to traditional cluster analysis of gene expression data, OLAP was more effective and faster in finding biologically meaningful information. OLAP is available from a number of vendors and can work with any relational database management system through OLE DB. PMID:16046824

  3. The Analytical Solution of the Transient Radial Diffusion Equation with a Nonuniform Loss Term.

    NASA Astrophysics Data System (ADS)

    Loridan, V.; Ripoll, J. F.; De Vuyst, F.

    2017-12-01

    Many works have been done during the past 40 years to perform the analytical solution of the radial diffusion equation that models the transport and loss of electrons in the magnetosphere, considering a diffusion coefficient proportional to a power law in shell and a constant loss term. Here, we propose an original analytical method to address this challenge with a nonuniform loss term. The strategy is to match any L-dependent electron losses with a piecewise constant function on M subintervals, i.e., dealing with a constant lifetime on each subinterval. Applying an eigenfunction expansion method, the eigenvalue problem becomes presently a Sturm-Liouville problem with M interfaces. Assuming the continuity of both the distribution function and its first spatial derivatives, we are able to deal with a well-posed problem and to find the full analytical solution. We further show an excellent agreement between both the analytical solutions and the solutions obtained directly from numerical simulations for different loss terms of various shapes and with a diffusion coefficient DLL L6. We also give two expressions for the required number of eigenmodes N to get an accurate snapshot of the analytical solution, highlighting that N is proportional to 1/√t0, where t0 is a time of interest, and that N increases with the diffusion power. Finally, the equilibrium time, defined as the time to nearly reach the steady solution, is estimated by a closed-form expression and discussed. Applications to Earth and also Jupiter and Saturn are discussed.

  4. Analytical Model and Optimized Design of Power Transmitting Coil for Inductively Coupled Endoscope Robot.

    PubMed

    Ke, Quan; Luo, Weijie; Yan, Guozheng; Yang, Kai

    2016-04-01

    A wireless power transfer system based on the weakly inductive coupling makes it possible to provide the endoscope microrobot (EMR) with infinite power. To facilitate the patients' inspection with the EMR system, the diameter of the transmitting coil is enlarged to 69 cm. Due to the large transmitting range, a high quality factor of the Litz-wire transmitting coil is a necessity to ensure the intensity of magnetic field generated efficiently. Thus, this paper builds an analytical model of the transmitting coil, and then, optimizes the parameters of the coil by enlarging the quality factor. The lumped model of the transmitting coil includes three parameters: ac resistance, self-inductance, and stray capacitance. Based on the exact two-dimension solution, the accurate analytical expression of ac resistance is derived. Several transmitting coils of different specifications are utilized to verify this analytical expression, being in good agreements with the measured results except the coils with a large number of strands. Then, the quality factor of transmitting coils can be well predicted with the available analytical expressions of self- inductance and stray capacitance. Owing to the exact estimation of quality factor, the appropriate coil turns of the transmitting coil is set to 18-40 within the restrictions of transmitting circuit and human tissue issues. To supply enough energy for the next generation of the EMR equipped with a Ø9.5×10.1 mm receiving coil, the coil turns of the transmitting coil is optimally set to 28, which can transfer a maximum power of 750 mW with the remarkable delivering efficiency of 3.55%.

  5. Analytic integrable systems: Analytic normalization and embedding flows

    NASA Astrophysics Data System (ADS)

    Zhang, Xiang

    In this paper we mainly study the existence of analytic normalization and the normal form of finite dimensional complete analytic integrable dynamical systems. More details, we will prove that any complete analytic integrable diffeomorphism F(x)=Bx+f(x) in (Cn,0) with B having eigenvalues not modulus 1 and f(x)=O(|) is locally analytically conjugate to its normal form. Meanwhile, we also prove that any complete analytic integrable differential system x˙=Ax+f(x) in (Cn,0) with A having nonzero eigenvalues and f(x)=O(|) is locally analytically conjugate to its normal form. Furthermore we will prove that any complete analytic integrable diffeomorphism defined on an analytic manifold can be embedded in a complete analytic integrable flow. We note that parts of our results are the improvement of Moser's one in J. Moser, The analytic invariants of an area-preserving mapping near a hyperbolic fixed point, Comm. Pure Appl. Math. 9 (1956) 673-692 and of Poincaré's one in H. Poincaré, Sur l'intégration des équations différentielles du premier order et du premier degré, II, Rend. Circ. Mat. Palermo 11 (1897) 193-239. These results also improve the ones in Xiang Zhang, Analytic normalization of analytic integrable systems and the embedding flows, J. Differential Equations 244 (2008) 1080-1092 in the sense that the linear part of the systems can be nonhyperbolic, and the one in N.T. Zung, Convergence versus integrability in Poincaré-Dulac normal form, Math. Res. Lett. 9 (2002) 217-228 in the way that our paper presents the concrete expression of the normal form in a restricted case.

  6. Analytical modeling and analysis of magnetic field and torque for novel axial flux eddy current couplers with PM excitation

    NASA Astrophysics Data System (ADS)

    Li, Zhao; Wang, Dazhi; Zheng, Di; Yu, Linxin

    2017-10-01

    Rotational permanent magnet eddy current couplers are promising devices for torque and speed transmission without any mechanical contact. In this study, flux-concentration disk-type permanent magnet eddy current couplers with double conductor rotor are investigated. Given the drawback of the accurate three-dimensional finite element method, this paper proposes a mixed two-dimensional analytical modeling approach. Based on this approach, the closed-form expressions of magnetic field, eddy current, electromagnetic force and torque for such devices are obtained. Finally, a three-dimensional finite element method is employed to validate the analytical results. Besides, a prototype is manufactured and tested for the torque-speed characteristic.

  7. The Analytical Limits of Modeling Short Diffusion Timescales

    NASA Astrophysics Data System (ADS)

    Bradshaw, R. W.; Kent, A. J.

    2016-12-01

    Chemical and isotopic zoning in minerals is widely used to constrain the timescales of magmatic processes such as magma mixing and crystal residence, etc. via diffusion modeling. Forward modeling of diffusion relies on fitting diffusion profiles to measured compositional gradients. However, an individual measurement is essentially an average composition for a segment of the gradient defined by the spatial resolution of the analysis. Thus there is the potential for the analytical spatial resolution to limit the timescales that can be determined for an element of given diffusivity, particularly where the scale of the gradient approaches that of the measurement. Here we use a probabilistic modeling approach to investigate the effect of analytical spatial resolution on estimated timescales from diffusion modeling. Our method investigates how accurately the age of a synthetic diffusion profile can be obtained by modeling an "unknown" profile derived from discrete sampling of the synthetic compositional gradient at a given spatial resolution. We also include the effects of analytical uncertainty and the position of measurements relative to the diffusion gradient. We apply this method to the spatial resolutions of common microanalytical techniques (LA-ICP-MS, SIMS, EMP, NanoSIMS). Our results confirm that for a given diffusivity, higher spatial resolution gives access to shorter timescales, and that each analytical spacing has a minimum timescale, below which it overestimates the timescale. For example, for Ba diffusion in plagioclase at 750 °C timescales are accurate (within 20%) above 10, 100, 2,600, and 71,000 years at 0.3, 1, 5, and 25 mm spatial resolution, respectively. For Sr diffusion in plagioclase at 750 °C, timescales are accurate above 0.02, 0.2, 4, and 120 years at the same spatial resolutions. Our results highlight the importance of selecting appropriate analytical techniques to estimate accurate diffusion-based timescales.

  8. Accurate Mars Express orbits to improve the determination of the mass and ephemeris of the Martian moons

    NASA Astrophysics Data System (ADS)

    Rosenblatt, P.; Lainey, V.; Le Maistre, S.; Marty, J. C.; Dehant, V.; Pätzold, M.; Van Hoolst, T.; Häusler, B.

    2008-05-01

    The determination of the ephemeris of the Martian moons has benefited from observations of their plane-of-sky positions derived from images taken by cameras onboard spacecraft orbiting Mars. Images obtained by the Super Resolution Camera (SRC) onboard Mars Express (MEX) have been used to derive moon positions relative to Mars on the basis of a fit of a complete dynamical model of their motion around Mars. Since, these positions are computed from the relative position of the spacecraft when the images are taken, those positions need to be known as accurately as possible. An accurate MEX orbit is obtained by fitting two years of tracking data of the Mars Express Radio Science (MaRS) experiment onboard MEX. The average accuracy of the orbits has been estimated to be around 20-25 m. From these orbits, we have re-derived the positions of Phobos and Deimos at the epoch of the SRC observations and compared them with the positions derived by using the MEX orbits provided by the ESOC navigation team. After fit of the orbital model of Phobos and Deimos, the gain in precision in the Phobos position is roughly 30 m, corresponding to the estimated gain of accuracy of the MEX orbits. A new solution of the GM of the Martian moons has also been obtained from the accurate MEX orbits, which is consistent with previous solutions and, for Phobos, is more precise than the solution from the Mars Global Surveyor (MGS) and Mars Odyssey (ODY) tracking data. It will be further improved with data from MEX-Phobos closer encounters (at a distance less than 300 km). This study also demonstrates the advantage of combining observations of the moon positions from a spacecraft and from the Earth to assess the real accuracy of the spacecraft orbit. In turn, the natural satellite ephemerides can be improved and participate to a better knowledge of the origin and evolution of the Martian moons.

  9. A gene expression biomarker accurately predicts estrogen ...

    EPA Pesticide Factsheets

    The EPA’s vision for the Endocrine Disruptor Screening Program (EDSP) in the 21st Century (EDSP21) includes utilization of high-throughput screening (HTS) assays coupled with computational modeling to prioritize chemicals with the goal of eventually replacing current Tier 1 screening tests. The ToxCast program currently includes 18 HTS in vitro assays that evaluate the ability of chemicals to modulate estrogen receptor α (ERα), an important endocrine target. We propose microarray-based gene expression profiling as a complementary approach to predict ERα modulation and have developed computational methods to identify ERα modulators in an existing database of whole-genome microarray data. The ERα biomarker consisted of 46 ERα-regulated genes with consistent expression patterns across 7 known ER agonists and 3 known ER antagonists. The biomarker was evaluated as a predictive tool using the fold-change rank-based Running Fisher algorithm by comparison to annotated gene expression data sets from experiments in MCF-7 cells. Using 141 comparisons from chemical- and hormone-treated cells, the biomarker gave a balanced accuracy for prediction of ERα activation or suppression of 94% or 93%, respectively. The biomarker was able to correctly classify 18 out of 21 (86%) OECD ER reference chemicals including “very weak” agonists and replicated predictions based on 18 in vitro ER-associated HTS assays. For 114 chemicals present in both the HTS data and the MCF-7 c

  10. An Analytical Time–Domain Expression for the Net Ripple Produced by Parallel Interleaved Converters

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

    Johnson, Brian B.; Krein, Philip T.

    We apply modular arithmetic and Fourier series to analyze the superposition of N interleaved triangular waveforms with identical amplitudes and duty-ratios. Here, interleaving refers to the condition when a collection of periodic waveforms with identical periods are each uniformly phase-shifted across one period. The main result is a time-domain expression which provides an exact representation of the summed and interleaved triangular waveforms, where the peak amplitude and parameters of the time-periodic component are all specified in closed-form. Analysis is general and can be used to study various applications in multi-converter systems. This model is unique not only in that itmore » reveals a simple and intuitive expression for the net ripple, but its derivation via modular arithmetic and Fourier series is distinct from prior approaches. The analytical framework is experimentally validated with a system of three parallel converters under time-varying operating conditions.« less

  11. Analytical pair correlations in ideal quantum gases: temperature-dependent bunching and antibunching.

    PubMed

    Bosse, J; Pathak, K N; Singh, G S

    2011-10-01

    The fluctuation-dissipation theorem together with the exact density response spectrum for ideal quantum gases has been utilized to yield a new expression for the static structure factor, which we use to derive exact analytical expressions for the temperature-dependent pair distribution function g(r) of the ideal gases. The plots of bosonic and fermionic g(r) display "Bose pile" and "Fermi hole" typically akin to bunching and antibunching as observed experimentally for ultracold atomic gases. The behavior of spin-scaled pair correlation for fermions is almost featureless, but bosons show a rich structure including long-range correlations near T(c). The coherent state at T=0 shows no correlation at all, just like single-mode lasers. The depicted decreasing trend in correlation with decrease in temperature for Taccurate experiments.

  12. Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction

    PubMed Central

    Schmidt, Florian; Gasparoni, Nina; Gasparoni, Gilles; Gianmoena, Kathrin; Cadenas, Cristina; Polansky, Julia K.; Ebert, Peter; Nordström, Karl; Barann, Matthias; Sinha, Anupam; Fröhler, Sebastian; Xiong, Jieyi; Dehghani Amirabad, Azim; Behjati Ardakani, Fatemeh; Hutter, Barbara; Zipprich, Gideon; Felder, Bärbel; Eils, Jürgen; Brors, Benedikt; Chen, Wei; Hengstler, Jan G.; Hamann, Alf; Lengauer, Thomas; Rosenstiel, Philip; Walter, Jörn; Schulz, Marcel H.

    2017-01-01

    The binding and contribution of transcription factors (TF) to cell specific gene expression is often deduced from open-chromatin measurements to avoid costly TF ChIP-seq assays. Thus, it is important to develop computational methods for accurate TF binding prediction in open-chromatin regions (OCRs). Here, we report a novel segmentation-based method, TEPIC, to predict TF binding by combining sets of OCRs with position weight matrices. TEPIC can be applied to various open-chromatin data, e.g. DNaseI-seq and NOMe-seq. Additionally, Histone-Marks (HMs) can be used to identify candidate TF binding sites. TEPIC computes TF affinities and uses open-chromatin/HM signal intensity as quantitative measures of TF binding strength. Using machine learning, we find low affinity binding sites to improve our ability to explain gene expression variability compared to the standard presence/absence classification of binding sites. Further, we show that both footprints and peaks capture essential TF binding events and lead to a good prediction performance. In our application, gene-based scores computed by TEPIC with one open-chromatin assay nearly reach the quality of several TF ChIP-seq data sets. Finally, these scores correctly predict known transcriptional regulators as illustrated by the application to novel DNaseI-seq and NOMe-seq data for primary human hepatocytes and CD4+ T-cells, respectively. PMID:27899623

  13. The MGGB equation-of-state for multifield applications: a numerical recipe for analytic expression of sesame EOS data

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

    Kashiwa, B. A.

    2010-12-01

    Abstract A thermodynamically consistent and fully general equation–of– state (EOS) for multifield applications is described. EOS functions are derived from a Helmholtz free energy expressed as the sum of thermal (fluctuational) and collisional (condensed–phase) contributions; thus the free energy is of the Mie–Gr¨uneisen1 form. The phase–coexistence region is defined using a parameterized saturation curve by extending the form introduced by Guggenheim,2 which scales the curve relative to conditions at the critical point. We use the zero–temperature condensed–phase contribution developed by Barnes,3 which extends the Thomas–Fermi–Dirac equation to zero pressure. Thus, the functional form of the EOS could be called MGGBmore » (for Mie– Gr¨uneisen–Guggenheim–Barnes). Substance–specific parameters are obtained by fitting the low–density energy to data from the Sesame4 library; fitting the zero–temperature pressure to the Sesame cold curve; and fitting the saturation curve and latent heat to laboratory data,5 if available. When suitable coexistence data, or Sesame data, are not available, then we apply the Principle of Corresponding States.2 Thus MGGB can be thought of as a numerical recipe for rendering the tabular Sesame EOS data in an analytic form that includes a proper coexistence region, and which permits the accurate calculation of derivatives associated with compressibility, expansivity, Joule coefficient, and specific heat, all of which are required for multifield applications. 1« less

  14. Modern analytical chemistry in the contemporary world

    NASA Astrophysics Data System (ADS)

    Šíma, Jan

    2016-12-01

    Students not familiar with chemistry tend to misinterpret analytical chemistry as some kind of the sorcery where analytical chemists working as modern wizards handle magical black boxes able to provide fascinating results. However, this approach is evidently improper and misleading. Therefore, the position of modern analytical chemistry among sciences and in the contemporary world is discussed. Its interdisciplinary character and the necessity of the collaboration between analytical chemists and other experts in order to effectively solve the actual problems of the human society and the environment are emphasized. The importance of the analytical method validation in order to obtain the accurate and precise results is highlighted. The invalid results are not only useless; they can often be even fatal (e.g., in clinical laboratories). The curriculum of analytical chemistry at schools and universities is discussed. It is referred to be much broader than traditional equilibrium chemistry coupled with a simple description of individual analytical methods. Actually, the schooling of analytical chemistry should closely connect theory and practice.

  15. Analytical results for a stochastic model of gene expression with arbitrary partitioning of proteins

    NASA Astrophysics Data System (ADS)

    Tschirhart, Hugo; Platini, Thierry

    2018-05-01

    In biophysics, the search for analytical solutions of stochastic models of cellular processes is often a challenging task. In recent work on models of gene expression, it was shown that a mapping based on partitioning of Poisson arrivals (PPA-mapping) can lead to exact solutions for previously unsolved problems. While the approach can be used in general when the model involves Poisson processes corresponding to creation or degradation, current applications of the method and new results derived using it have been limited to date. In this paper, we present the exact solution of a variation of the two-stage model of gene expression (with time dependent transition rates) describing the arbitrary partitioning of proteins. The methodology proposed makes full use of the PPA-mapping by transforming the original problem into a new process describing the evolution of three biological switches. Based on a succession of transformations, the method leads to a hierarchy of reduced models. We give an integral expression of the time dependent generating function as well as explicit results for the mean, variance, and correlation function. Finally, we discuss how results for time dependent parameters can be extended to the three-stage model and used to make inferences about models with parameter fluctuations induced by hidden stochastic variables.

  16. Simple, accurate formula for the average bit error probability of multiple-input multiple-output free-space optical links over negative exponential turbulence channels.

    PubMed

    Peppas, Kostas P; Lazarakis, Fotis; Alexandridis, Antonis; Dangakis, Kostas

    2012-08-01

    In this Letter we investigate the error performance of multiple-input multiple-output free-space optical communication systems employing intensity modulation/direct detection and operating over strong atmospheric turbulence channels. Atmospheric-induced strong turbulence fading is modeled using the negative exponential distribution. For the considered system, an approximate yet accurate analytical expression for the average bit error probability is derived and an efficient method for its numerical evaluation is proposed. Numerically evaluated and computer simulation results are further provided to demonstrate the validity of the proposed mathematical analysis.

  17. PyVCI: A flexible open-source code for calculating accurate molecular infrared spectra

    NASA Astrophysics Data System (ADS)

    Sibaev, Marat; Crittenden, Deborah L.

    2016-06-01

    The PyVCI program package is a general purpose open-source code for simulating accurate molecular spectra, based upon force field expansions of the potential energy surface in normal mode coordinates. It includes harmonic normal coordinate analysis and vibrational configuration interaction (VCI) algorithms, implemented primarily in Python for accessibility but with time-consuming routines written in C. Coriolis coupling terms may be optionally included in the vibrational Hamiltonian. Non-negligible VCI matrix elements are stored in sparse matrix format to alleviate the diagonalization problem. CPU and memory requirements may be further controlled by algorithmic choices and/or numerical screening procedures, and recommended values are established by benchmarking using a test set of 44 molecules for which accurate analytical potential energy surfaces are available. Force fields in normal mode coordinates are obtained from the PyPES library of high quality analytical potential energy surfaces (to 6th order) or by numerical differentiation of analytic second derivatives generated using the GAMESS quantum chemical program package (to 4th order).

  18. Collaborative Visual Analytics: A Health Analytics Approach to Injury Prevention

    PubMed Central

    Fisher, Brian; Smith, Jennifer; Pike, Ian

    2017-01-01

    Background: Accurate understanding of complex health data is critical in order to deal with wicked health problems and make timely decisions. Wicked problems refer to ill-structured and dynamic problems that combine multidimensional elements, which often preclude the conventional problem solving approach. This pilot study introduces visual analytics (VA) methods to multi-stakeholder decision-making sessions about child injury prevention; Methods: Inspired by the Delphi method, we introduced a novel methodology—group analytics (GA). GA was pilot-tested to evaluate the impact of collaborative visual analytics on facilitating problem solving and supporting decision-making. We conducted two GA sessions. Collected data included stakeholders’ observations, audio and video recordings, questionnaires, and follow up interviews. The GA sessions were analyzed using the Joint Activity Theory protocol analysis methods; Results: The GA methodology triggered the emergence of ‘common ground’ among stakeholders. This common ground evolved throughout the sessions to enhance stakeholders’ verbal and non-verbal communication, as well as coordination of joint activities and ultimately collaboration on problem solving and decision-making; Conclusions: Understanding complex health data is necessary for informed decisions. Equally important, in this case, is the use of the group analytics methodology to achieve ‘common ground’ among diverse stakeholders about health data and their implications. PMID:28895928

  19. Collaborative Visual Analytics: A Health Analytics Approach to Injury Prevention.

    PubMed

    Al-Hajj, Samar; Fisher, Brian; Smith, Jennifer; Pike, Ian

    2017-09-12

    Background : Accurate understanding of complex health data is critical in order to deal with wicked health problems and make timely decisions. Wicked problems refer to ill-structured and dynamic problems that combine multidimensional elements, which often preclude the conventional problem solving approach. This pilot study introduces visual analytics (VA) methods to multi-stakeholder decision-making sessions about child injury prevention; Methods : Inspired by the Delphi method, we introduced a novel methodology-group analytics (GA). GA was pilot-tested to evaluate the impact of collaborative visual analytics on facilitating problem solving and supporting decision-making. We conducted two GA sessions. Collected data included stakeholders' observations, audio and video recordings, questionnaires, and follow up interviews. The GA sessions were analyzed using the Joint Activity Theory protocol analysis methods; Results : The GA methodology triggered the emergence of ' common g round ' among stakeholders. This common ground evolved throughout the sessions to enhance stakeholders' verbal and non-verbal communication, as well as coordination of joint activities and ultimately collaboration on problem solving and decision-making; Conclusion s : Understanding complex health data is necessary for informed decisions. Equally important, in this case, is the use of the group analytics methodology to achieve ' common ground' among diverse stakeholders about health data and their implications.

  20. Combining transcription factor binding affinities with open-chromatin data for accurate gene expression prediction.

    PubMed

    Schmidt, Florian; Gasparoni, Nina; Gasparoni, Gilles; Gianmoena, Kathrin; Cadenas, Cristina; Polansky, Julia K; Ebert, Peter; Nordström, Karl; Barann, Matthias; Sinha, Anupam; Fröhler, Sebastian; Xiong, Jieyi; Dehghani Amirabad, Azim; Behjati Ardakani, Fatemeh; Hutter, Barbara; Zipprich, Gideon; Felder, Bärbel; Eils, Jürgen; Brors, Benedikt; Chen, Wei; Hengstler, Jan G; Hamann, Alf; Lengauer, Thomas; Rosenstiel, Philip; Walter, Jörn; Schulz, Marcel H

    2017-01-09

    The binding and contribution of transcription factors (TF) to cell specific gene expression is often deduced from open-chromatin measurements to avoid costly TF ChIP-seq assays. Thus, it is important to develop computational methods for accurate TF binding prediction in open-chromatin regions (OCRs). Here, we report a novel segmentation-based method, TEPIC, to predict TF binding by combining sets of OCRs with position weight matrices. TEPIC can be applied to various open-chromatin data, e.g. DNaseI-seq and NOMe-seq. Additionally, Histone-Marks (HMs) can be used to identify candidate TF binding sites. TEPIC computes TF affinities and uses open-chromatin/HM signal intensity as quantitative measures of TF binding strength. Using machine learning, we find low affinity binding sites to improve our ability to explain gene expression variability compared to the standard presence/absence classification of binding sites. Further, we show that both footprints and peaks capture essential TF binding events and lead to a good prediction performance. In our application, gene-based scores computed by TEPIC with one open-chromatin assay nearly reach the quality of several TF ChIP-seq data sets. Finally, these scores correctly predict known transcriptional regulators as illustrated by the application to novel DNaseI-seq and NOMe-seq data for primary human hepatocytes and CD4+ T-cells, respectively. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  1. QUESP and QUEST revisited - fast and accurate quantitative CEST experiments.

    PubMed

    Zaiss, Moritz; Angelovski, Goran; Demetriou, Eleni; McMahon, Michael T; Golay, Xavier; Scheffler, Klaus

    2018-03-01

    Chemical exchange saturation transfer (CEST) NMR or MRI experiments allow detection of low concentrated molecules with enhanced sensitivity via their proton exchange with the abundant water pool. Be it endogenous metabolites or exogenous contrast agents, an exact quantification of the actual exchange rate is required to design optimal pulse sequences and/or specific sensitive agents. Refined analytical expressions allow deeper insight and improvement of accuracy for common quantification techniques. The accuracy of standard quantification methodologies, such as quantification of exchange rate using varying saturation power or varying saturation time, is improved especially for the case of nonequilibrium initial conditions and weak labeling conditions, meaning the saturation amplitude is smaller than the exchange rate (γB 1  < k). The improved analytical 'quantification of exchange rate using varying saturation power/time' (QUESP/QUEST) equations allow for more accurate exchange rate determination, and provide clear insights on the general principles to execute the experiments and to perform numerical evaluation. The proposed methodology was evaluated on the large-shift regime of paramagnetic chemical-exchange-saturation-transfer agents using simulated data and data of the paramagnetic Eu(III) complex of DOTA-tetraglycineamide. The refined formulas yield improved exchange rate estimation. General convergence intervals of the methods that would apply for smaller shift agents are also discussed. Magn Reson Med 79:1708-1721, 2018. © 2017 International Society for Magnetic Resonance in Medicine. © 2017 International Society for Magnetic Resonance in Medicine.

  2. Analytic expressions for perturbations and partial derivatives of range and range rate of a spacecraft with respect to the coefficient of the second harmonic

    NASA Technical Reports Server (NTRS)

    Georgevic, R. M.

    1973-01-01

    Closed-form analytic expressions for the time variations of instantaneous orbital parameters and of the topocentric range and range rate of a spacecraft moving in the gravitational field of an oblate large body are derived using a first-order variation of parameters technique. In addition, the closed-form analytic expressions for the partial derivatives of the topocentric range and range rate are obtained, with respect to the coefficient of the second harmonic of the potential of the central body (J sub 2). The results are applied to the motion of a point-mass spacecraft moving in the orbit around the equatorially elliptic, oblate sun, with J sub 2 approximately equal to .000027.

  3. Analytic Validation of RNA In Situ Hybridization (RISH) for AR and AR-V7 Expression in Human Prostate Cancer

    PubMed Central

    Guedes, Liana B.; Morais, Carlos L.; Almutairi, Fawaz; Haffner, Michael C.; Zheng, Qizhi; Isaacs, John T.; Antonarakis, Emmanuel S.; Lu, Changxue; Tsai, Harrison; Luo, Jun; De Marzo, Angelo M.; Lotan, Tamara L.

    2016-01-01

    Purpose RNA expression of androgen receptor splice variants may be a biomarker of resistance to novel androgen deprivation therapies in castrate resistant prostate cancer (CRPC). We analytically validated an RNA in situ hybridization (RISH) assay for total AR and AR-V7 for use in formalin fixed paraffin embedded (FFPE) prostate tumors. Experimental Design We used prostate cell lines and xenografts to validate chromogenic RISH to detect RNA containing AR exon 1 (AR-E1, surrogate for total AR RNA species) and cryptic exon 3 (AR-CE3, surrogate for AR-V7 expression). RISH signals were quantified in FFPE primary tumors and CRPC specimens, comparing to known AR and AR-V7 status by immunohistochemistry and RT-PCR. Results The quantified RISH results correlated significantly with total AR and AR-V7 levels by RT-PCR in cell lines, xenografts and autopsy metastases. Both AR-E1 and AR-CE3 RISH signals were localized in nuclear punctae in addition to the expected cytoplasmic speckles. Compared to admixed benign glands, AR-E1 expression was significantly higher in primary tumor cells with a median fold increase of 3.0 and 1.4 in two independent cohorts (p<0.0001 and p=0.04, respectively). While AR-CE3 expression was detectable in primary prostatic tumors, levels were substantially higher in a subset of CRPC metastases and cell lines, and were correlated with AR-E1 expression. Conclusions RISH for AR-E1 and AR-CE3 is an analytically valid method to examine total AR and AR-V7 RNA levels in FFPE tissues. Future clinical validation studies are required to determine whether AR RISH is a prognostic or predictive biomarker in specific clinical contexts. PMID:27166397

  4. Piecewise linear emulator of the nonlinear Schrödinger equation and the resulting analytic solutions for Bose-Einstein condensates.

    PubMed

    Theodorakis, Stavros

    2003-06-01

    We emulate the cubic term Psi(3) in the nonlinear Schrödinger equation by a piecewise linear term, thus reducing the problem to a set of uncoupled linear inhomogeneous differential equations. The resulting analytic expressions constitute an excellent approximation to the exact solutions, as is explicitly shown in the case of the kink, the vortex, and a delta function trap. Such a piecewise linear emulation can be used for any differential equation where the only nonlinearity is a Psi(3) one. In particular, it can be used for the nonlinear Schrödinger equation in the presence of harmonic traps, giving analytic Bose-Einstein condensate solutions that reproduce very accurately the numerically calculated ones in one, two, and three dimensions.

  5. Machine-learning approach identifies a pattern of gene expression in peripheral blood that can accurately detect ischaemic stroke

    PubMed Central

    O’Connell, Grant C; Petrone, Ashley B; Treadway, Madison B; Tennant, Connie S; Lucke-Wold, Noelle; Chantler, Paul D; Barr, Taura L

    2016-01-01

    Early and accurate diagnosis of stroke improves the probability of positive outcome. The objective of this study was to identify a pattern of gene expression in peripheral blood that could potentially be optimised to expedite the diagnosis of acute ischaemic stroke (AIS). A discovery cohort was recruited consisting of 39 AIS patients and 24 neurologically asymptomatic controls. Peripheral blood was sampled at emergency department admission, and genome-wide expression profiling was performed via microarray. A machine-learning technique known as genetic algorithm k-nearest neighbours (GA/kNN) was then used to identify a pattern of gene expression that could optimally discriminate between groups. This pattern of expression was then assessed via qRT-PCR in an independent validation cohort, where it was evaluated for its ability to discriminate between an additional 39 AIS patients and 30 neurologically asymptomatic controls, as well as 20 acute stroke mimics. GA/kNN identified 10 genes (ANTXR2, STK3, PDK4, CD163, MAL, GRAP, ID3, CTSZ, KIF1B and PLXDC2) whose coordinate pattern of expression was able to identify 98.4% of discovery cohort subjects correctly (97.4% sensitive, 100% specific). In the validation cohort, the expression levels of the same 10 genes were able to identify 95.6% of subjects correctly when comparing AIS patients to asymptomatic controls (92.3% sensitive, 100% specific), and 94.9% of subjects correctly when comparing AIS patients with stroke mimics (97.4% sensitive, 90.0% specific). The transcriptional pattern identified in this study shows strong diagnostic potential, and warrants further evaluation to determine its true clinical efficacy. PMID:29263821

  6. A study of density effects in plasmas using analytical approximations for the self-consistent potential

    NASA Astrophysics Data System (ADS)

    Poirier, M.

    2015-06-01

    Density effects in ionized matter require particular attention since they modify energies, wavefunctions and transition rates with respect to the isolated-ion situation. The approach chosen in this paper is based on the ion-sphere model involving a Thomas-Fermi-like description for free electrons, the bound electrons being described by a full quantum mechanical formalism. This permits to deal with plasmas out of thermal local equilibrium, assuming only a Maxwell distribution for free electrons. For H-like ions, such a theory provides simple and rather accurate analytical approximations for the potential created by free electrons. Emphasis is put on the plasma potential rather than on the electron density, since the energies and wavefunctions depend directly on this potential. Beyond the uniform electron gas model, temperature effects may be analyzed. In the case of H-like ions, this formalism provides analytical perturbative expressions for the energies, wavefunctions and transition rates. Explicit expressions are given in the case of maximum orbital quantum number, and compare satisfactorily with results from a direct integration of the radial Schrödinger equation. Some formulas for lower orbital quantum numbers are also proposed.

  7. New analytical model for the ozone electronic ground state potential surface and accurate ab initio vibrational predictions at high energy range.

    PubMed

    Tyuterev, Vladimir G; Kochanov, Roman V; Tashkun, Sergey A; Holka, Filip; Szalay, Péter G

    2013-10-07

    An accurate description of the complicated shape of the potential energy surface (PES) and that of the highly excited vibration states is of crucial importance for various unsolved issues in the spectroscopy and dynamics of ozone and remains a challenge for the theory. In this work a new analytical representation is proposed for the PES of the ground electronic state of the ozone molecule in the range covering the main potential well and the transition state towards the dissociation. This model accounts for particular features specific to the ozone PES for large variations of nuclear displacements along the minimum energy path. The impact of the shape of the PES near the transition state (existence of the "reef structure") on vibration energy levels was studied for the first time. The major purpose of this work was to provide accurate theoretical predictions for ozone vibrational band centres at the energy range near the dissociation threshold, which would be helpful for understanding the very complicated high-resolution spectra and its analyses currently in progress. Extended ab initio electronic structure calculations were carried out enabling the determination of the parameters of a minimum energy path PES model resulting in a new set of theoretical vibrational levels of ozone. A comparison with recent high-resolution spectroscopic data on the vibrational levels gives the root-mean-square deviations below 1 cm(-1) for ozone band centres up to 90% of the dissociation energy. New ab initio vibrational predictions represent a significant improvement with respect to all previously available calculations.

  8. Temporal Learning Analytics for Adaptive Assessment

    ERIC Educational Resources Information Center

    Papamitsiou, Zacharoula; Economides, Anastasios A.

    2014-01-01

    Accurate and early predictions of student performance could significantly affect interventions during teaching and assessment, which gradually could lead to improved learning outcomes. In our research, we seek to identify and formalize temporal parameters as predictors of performance ("temporal learning analytics" or TLA) and examine…

  9. Simple Expressions for the Design of Linear Tapers in Overmoded Corrugated Waveguides

    DOE PAGES

    Schaub, S. C.; Shapiro, M. A.; Temkin, R. J.

    2015-08-16

    In this paper, simple analytical formulae are presented for the design of linear tapers with very low mode conversion loss in overmoded corrugated waveguides. For tapers from waveguide radius a2 to a1, with a11a 2/λ. Here, λ is the wavelength of radiation. The fractional loss of the HE 11 mode in an optimized taper is 0.0293(a 2-a 1) 4/amore » $$2\\atop{1}$$1a$$2\\atop{2}$$. These formulae are accurate when a2≲2a 1. Slightly more complex formulae, accurate for a 2≤4a 1, are also presented in this paper. The loss in an overmoded corrugated linear taper is less than 1 % when a 2≤2.12a 1 and less than 0.1 % when a 2≤1.53a 1. The present analytic results have been benchmarked against a rigorous mode matching code and have been found to be very accurate. The results for linear tapers are compared with the analogous expressions for parabolic tapers. Finally, parabolic tapers may provide lower loss, but linear tapers with moderate values of a 2/a 1 may be attractive because of their simplicity of fabrication.« less

  10. Analytic Expressions for the Gravity Gradient Tensor of 3D Prisms with Depth-Dependent Density

    NASA Astrophysics Data System (ADS)

    Jiang, Li; Liu, Jie; Zhang, Jianzhong; Feng, Zhibing

    2017-12-01

    Variable-density sources have been paid more attention in gravity modeling. We conduct the computation of gravity gradient tensor of given mass sources with variable density in this paper. 3D rectangular prisms, as simple building blocks, can be used to approximate well 3D irregular-shaped sources. A polynomial function of depth can represent flexibly the complicated density variations in each prism. Hence, we derive the analytic expressions in closed form for computing all components of the gravity gradient tensor due to a 3D right rectangular prism with an arbitrary-order polynomial density function of depth. The singularity of the expressions is analyzed. The singular points distribute at the corners of the prism or on some of the lines through the edges of the prism in the lower semi-space containing the prism. The expressions are validated, and their numerical stability is also evaluated through numerical tests. The numerical examples with variable-density prism and basin models show that the expressions within their range of numerical stability are superior in computational accuracy and efficiency to the common solution that sums up the effects of a collection of uniform subprisms, and provide an effective method for computing gravity gradient tensor of 3D irregular-shaped sources with complicated density variation. In addition, the tensor computed with variable density is different in magnitude from that with constant density. It demonstrates the importance of the gravity gradient tensor modeling with variable density.

  11. Current projects in Pre-analytics: where to go?

    PubMed

    Sapino, Anna; Annaratone, Laura; Marchiò, Caterina

    2015-01-01

    The current clinical practice of tissue handling and sample preparation is multifaceted and lacks strict standardisation: this scenario leads to significant variability in the quality of clinical samples. Poor tissue preservation has a detrimental effect thus leading to morphological artefacts, hampering the reproducibility of immunocytochemical and molecular diagnostic results (protein expression, DNA gene mutations, RNA gene expression) and affecting the research outcomes with irreproducible gene expression and post-transcriptional data. Altogether, this limits the opportunity to share and pool national databases into European common databases. At the European level, standardization of pre-analytical steps is just at the beginning and issues regarding bio-specimen collection and management are still debated. A joint (public-private) project entitled on standardization of tissue handling in pre-analytical procedures has been recently funded in Italy with the aim of proposing novel approaches to the neglected issue of pre-analytical procedures. In this chapter, we will show how investing in pre-analytics may impact both public health problems and practical innovation in solid tumour processing.

  12. Approximate analytic expression for the Skyrmions crystal

    NASA Astrophysics Data System (ADS)

    Grandi, Nicolás; Sturla, Mauricio

    2018-01-01

    We find approximate solutions for the two-dimensional nonlinear Σ-model with Dzyalioshinkii-Moriya term, representing magnetic Skyrmions. They are built in an analytic form, by pasting different approximate solutions found in different regions of space. We verify that our construction reproduces the phenomenology known from numerical solutions and Monte Carlo simulations, giving rise to a Skyrmion lattice at an intermediate range of magnetic field, flanked by spiral and spin-polarized phases for low and high magnetic fields, respectively.

  13. Creating analytically divergence-free velocity fields from grid-based data

    NASA Astrophysics Data System (ADS)

    Ravu, Bharath; Rudman, Murray; Metcalfe, Guy; Lester, Daniel R.; Khakhar, Devang V.

    2016-10-01

    We present a method, based on B-splines, to calculate a C2 continuous analytic vector potential from discrete 3D velocity data on a regular grid. A continuous analytically divergence-free velocity field can then be obtained from the curl of the potential. This field can be used to robustly and accurately integrate particle trajectories in incompressible flow fields. Based on the method of Finn and Chacon (2005) [10] this new method ensures that the analytic velocity field matches the grid values almost everywhere, with errors that are two to four orders of magnitude lower than those of existing methods. We demonstrate its application to three different problems (each in a different coordinate system) and provide details of the specifics required in each case. We show how the additional accuracy of the method results in qualitatively and quantitatively superior trajectories that results in more accurate identification of Lagrangian coherent structures.

  14. Toward more accurate loss tangent measurements in reentrant cavities

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

    Moyer, R. D.

    1980-05-01

    Karpova has described an absolute method for measurement of dielectric properties of a solid in a coaxial reentrant cavity. His cavity resonance equation yields very accurate results for dielectric constants. However, he presented only approximate expressions for the loss tangent. This report presents more exact expressions for that quantity and summarizes some experimental results.

  15. Analytic family of post-merger template waveforms

    NASA Astrophysics Data System (ADS)

    Del Pozzo, Walter; Nagar, Alessandro

    2017-06-01

    Building on the analytical description of the post-merger (ringdown) waveform of coalescing, nonprecessing, spinning binary black holes introduced by Damour and Nagar [Phys. Rev. D 90, 024054 (2014), 10.1103/PhysRevD.90.024054], we propose an analytic, closed form, time-domain, representation of the ℓ=m =2 gravitational radiation mode emitted after merger. This expression is given as a function of the component masses and dimensionless spins (m1 ,2,χ1 ,2) of the two inspiraling objects, as well as of the mass MBH and (complex) frequency σ1 of the fundamental quasinormal mode of the remnant black hole. Our proposed template is obtained by fitting the post-merger waveform part of several publicly available numerical relativity simulations from the Simulating eXtreme Spacetimes (SXS) catalog and then suitably interpolating over (symmetric) mass ratio and spins. We show that this analytic expression accurately reproduces (˜0.01 rad ) the phasing of the post-merger data of other data sets not used in its construction. This is notably the case of the spin-aligned run SXS:BBH:0305, whose intrinsic parameters are consistent with the 90% credible intervals reported in the parameter-estimation followup of GW150914 by B.P. Abbott et al. [Phys. Rev. Lett. 116, 241102 (2016), 10.1103/PhysRevLett.116.241102]. Using SXS waveforms as "experimental" data, we further show that our template could be used on the actual GW150914 data to perform a new measure of the complex frequency of the fundamental quasinormal mode so as to exploit the complete (high signal-to-noise-ratio) post-merger waveform. We assess the usefulness of our proposed template by analyzing, in a realistic setting, SXS full inspiral-merger-ringdown waveforms and constructing posterior probability distribution functions for the central frequency damping time of the first overtone of the fundamental quasinormal mode as well as for the physical parameters of the systems. We also briefly explore the possibility

  16. Building pit dewatering: application of transient analytic elements.

    PubMed

    Zaadnoordijk, Willem J

    2006-01-01

    Analytic elements are well suited for the design of building pit dewatering. Wells and drains can be modeled accurately by analytic elements, both nearby to determine the pumping level and at some distance to verify the targeted drawdown at the building site and to estimate the consequences in the vicinity. The ability to shift locations of wells or drains easily makes the design process very flexible. The temporary pumping has transient effects, for which transient analytic elements may be used. This is illustrated using the free, open-source, object-oriented analytic element simulator Tim(SL) for the design of a building pit dewatering near a canal. Steady calculations are complemented with transient calculations. Finally, the bandwidths of the results are estimated using linear variance analysis.

  17. Microemulsification: an approach for analytical determinations.

    PubMed

    Lima, Renato S; Shiroma, Leandro Y; Teixeira, Alvaro V N C; de Toledo, José R; do Couto, Bruno C; de Carvalho, Rogério M; Carrilho, Emanuel; Kubota, Lauro T; Gobbi, Angelo L

    2014-09-16

    We address a novel method for analytical determinations that combines simplicity, rapidity, low consumption of chemicals, and portability with high analytical performance taking into account parameters such as precision, linearity, robustness, and accuracy. This approach relies on the effect of the analyte content over the Gibbs free energy of dispersions, affecting the thermodynamic stabilization of emulsions or Winsor systems to form microemulsions (MEs). Such phenomenon was expressed by the minimum volume fraction of amphiphile required to form microemulsion (Φ(ME)), which was the analytical signal of the method. Thus, the measurements can be taken by visually monitoring the transition of the dispersions from cloudy to transparent during the microemulsification, like a titration. It bypasses the employment of electric energy. The performed studies were: phase behavior, droplet dimension by dynamic light scattering, analytical curve, and robustness tests. The reliability of the method was evaluated by determining water in ethanol fuels and monoethylene glycol in complex samples of liquefied natural gas. The dispersions were composed of water-chlorobenzene (water analysis) and water-oleic acid (monoethylene glycol analysis) with ethanol as the hydrotrope phase. The mean hydrodynamic diameter values for the nanostructures in the droplet-based water-chlorobenzene MEs were in the range of 1 to 11 nm. The procedures of microemulsification were conducted by adding ethanol to water-oleic acid (W-O) mixtures with the aid of micropipette and shaking. The Φ(ME) measurements were performed in a thermostatic water bath at 23 °C by direct observation that is based on the visual analyses of the media. The experiments to determine water demonstrated that the analytical performance depends on the composition of ME. It shows flexibility in the developed method. The linear range was fairly broad with limits of linearity up to 70.00% water in ethanol. For monoethylene glycol in

  18. 1NON-INVASIVE RADIOIODINE IMAGING FOR ACCURATE QUANTITATION OF NIS REPORTER GENE EXPRESSION IN TRANSPLANTED HEARTS

    PubMed Central

    Ricci, Davide; Mennander, Ari A; Pham, Linh D; Rao, Vinay P; Miyagi, Naoto; Byrne, Guerard W; Russell, Stephen J; McGregor, Christopher GA

    2008-01-01

    Objectives We studied the concordance of transgene expression in the transplanted heart using bicistronic adenoviral vector coding for a transgene of interest (human carcinoembryonic antigen: hCEA - beta human chorionic gonadotropin: βhCG) and for a marker imaging transgene (human sodium iodide symporter: hNIS). Methods Inbred Lewis rats were used for syngeneic heterotopic cardiac transplantation. Donor rat hearts were perfused ex vivo for 30 minutes prior to transplantation with University of Wisconsin (UW) solution (n=3), with 109 pfu/ml of adenovirus expressing hNIS (Ad-NIS; n=6), hNIS-hCEA (Ad-NIS-CEA; n=6) and hNIS-βhCG (Ad-NIS-CG; n=6). On post-operative day (POD) 5, 10, 15 all animals underwent micro-SPECT/CT imaging of the donor hearts after tail vein injection of 1000 μCi 123I and blood sample collection for hCEA and βhCG quantification. Results Significantly higher image intensity was noted in the hearts perfused with Ad-NIS (1.1±0.2; 0.9±0.07), Ad-NIS-CEA (1.2±0.3; 0.9±0.1) and Ad-NIS-CG (1.1±0.1; 0.9±0.1) compared to UW group (0.44±0.03; 0.47±0.06) on POD 5 and 10 (p<0.05). Serum levels of hCEA and βhCG increased in animals showing high cardiac 123I uptake, but not in those with lower uptake. Above this threshold, image intensities correlated well with serum levels of hCEA and βhCG (R2=0.99 and R2=0.96 respectively). Conclusions These data demonstrate that hNIS is an excellent reporter gene for the transplanted heart. The expression level of hNIS can be accurately and non-invasively monitored by serial radioisotopic single photon emission computed tomography (SPECT) imaging. High concordance has been demonstrated between imaging and soluble marker peptides at the maximum transgene expression on POD 5. PMID:17980613

  19. Piezoresistive Cantilever Performance—Part I: Analytical Model for Sensitivity

    PubMed Central

    Park, Sung-Jin; Doll, Joseph C.; Pruitt, Beth L.

    2010-01-01

    An accurate analytical model for the change in resistance of a piezoresistor is necessary for the design of silicon piezoresistive transducers. Ion implantation requires a high-temperature oxidation or annealing process to activate the dopant atoms, and this treatment results in a distorted dopant profile due to diffusion. Existing analytical models do not account for the concentration dependence of piezoresistance and are not accurate for nonuniform dopant profiles. We extend previous analytical work by introducing two nondimensional factors, namely, the efficiency and geometry factors. A practical benefit of this efficiency factor is that it separates the process parameters from the design parameters; thus, designers may address requirements for cantilever geometry and fabrication process independently. To facilitate the design process, we provide a lookup table for the efficiency factor over an extensive range of process conditions. The model was validated by comparing simulation results with the experimentally determined sensitivities of piezoresistive cantilevers. We performed 9200 TSUPREM4 simulations and fabricated 50 devices from six unique process flows; we systematically explored the design space relating process parameters and cantilever sensitivity. Our treatment focuses on piezoresistive cantilevers, but the analytical sensitivity model is extensible to other piezoresistive transducers such as membrane pressure sensors. PMID:20336183

  20. Piezoresistive Cantilever Performance-Part I: Analytical Model for Sensitivity.

    PubMed

    Park, Sung-Jin; Doll, Joseph C; Pruitt, Beth L

    2010-02-01

    An accurate analytical model for the change in resistance of a piezoresistor is necessary for the design of silicon piezoresistive transducers. Ion implantation requires a high-temperature oxidation or annealing process to activate the dopant atoms, and this treatment results in a distorted dopant profile due to diffusion. Existing analytical models do not account for the concentration dependence of piezoresistance and are not accurate for nonuniform dopant profiles. We extend previous analytical work by introducing two nondimensional factors, namely, the efficiency and geometry factors. A practical benefit of this efficiency factor is that it separates the process parameters from the design parameters; thus, designers may address requirements for cantilever geometry and fabrication process independently. To facilitate the design process, we provide a lookup table for the efficiency factor over an extensive range of process conditions. The model was validated by comparing simulation results with the experimentally determined sensitivities of piezoresistive cantilevers. We performed 9200 TSUPREM4 simulations and fabricated 50 devices from six unique process flows; we systematically explored the design space relating process parameters and cantilever sensitivity. Our treatment focuses on piezoresistive cantilevers, but the analytical sensitivity model is extensible to other piezoresistive transducers such as membrane pressure sensors.

  1. Accurate Sloshing Modes Modeling: A New Analytical Solution and its Consequences on Control

    NASA Astrophysics Data System (ADS)

    Gonidou, Luc-Olivier; Desmariaux, Jean

    2014-06-01

    This study addresses the issue of sloshing modes modeling for GNC analyses purposes. On European launchers, equivalent mechanical systems are commonly used for modeling sloshing effects on launcher dynamics. The representativeness of such a methodology is discussed here. First an exact analytical formulation of the launcher dynamics fitted with sloshing modes is proposed and discrepancies with equivalent mechanical system approach are emphasized. Then preliminary comparative GNC analyses are performed using the different models of dynamics in order to evaluate the impact of the aforementioned discrepancies from GNC standpoint. Special attention is paid to system stability.

  2. Importance of accurate measurements in nutrition research: dietary flavonoids as a case study

    USDA-ARS?s Scientific Manuscript database

    Accurate measurements of the secondary metabolites in natural products and plant foods are critical to establishing diet/health relationships. There are as many as 50,000 secondary metabolites which may influence human health. Their structural and chemical diversity present a challenge to analytic...

  3. The Analytic Hierarchy Process and Participatory Decisionmaking

    Treesearch

    Daniel L. Schmoldt; Daniel L. Peterson; Robert L. Smith

    1995-01-01

    Managing natural resource lands requires social, as well as biophysical, considerations. Unfortunately, it is extremely difficult to accurately assess and quantify changing social preferences, and to aggregate conflicting opinions held by diverse social groups. The Analytic Hierarchy Process (AHP) provides a systematic, explicit, rigorous, and robust mechanism for...

  4. Meta-analytic framework for liquid association.

    PubMed

    Wang, Lin; Liu, Silvia; Ding, Ying; Yuan, Shin-Sheng; Ho, Yen-Yi; Tseng, George C

    2017-07-15

    Although coexpression analysis via pair-wise expression correlation is popularly used to elucidate gene-gene interactions at the whole-genome scale, many complicated multi-gene regulations require more advanced detection methods. Liquid association (LA) is a powerful tool to detect the dynamic correlation of two gene variables depending on the expression level of a third variable (LA scouting gene). LA detection from single transcriptomic study, however, is often unstable and not generalizable due to cohort bias, biological variation and limited sample size. With the rapid development of microarray and NGS technology, LA analysis combining multiple gene expression studies can provide more accurate and stable results. In this article, we proposed two meta-analytic approaches for LA analysis (MetaLA and MetaMLA) to combine multiple transcriptomic studies. To compensate demanding computing, we also proposed a two-step fast screening algorithm for more efficient genome-wide screening: bootstrap filtering and sign filtering. We applied the methods to five Saccharomyces cerevisiae datasets related to environmental changes. The fast screening algorithm reduced 98% of running time. When compared with single study analysis, MetaLA and MetaMLA provided stronger detection signal and more consistent and stable results. The top triplets are highly enriched in fundamental biological processes related to environmental changes. Our method can help biologists understand underlying regulatory mechanisms under different environmental exposure or disease states. A MetaLA R package, data and code for this article are available at http://tsenglab.biostat.pitt.edu/software.htm. ctseng@pitt.edu. Supplementary data are available at Bioinformatics online. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

  5. Validation of biomarkers to predict response to immunotherapy in cancer: Volume I - pre-analytical and analytical validation.

    PubMed

    Masucci, Giuseppe V; Cesano, Alessandra; Hawtin, Rachael; Janetzki, Sylvia; Zhang, Jenny; Kirsch, Ilan; Dobbin, Kevin K; Alvarez, John; Robbins, Paul B; Selvan, Senthamil R; Streicher, Howard Z; Butterfield, Lisa H; Thurin, Magdalena

    2016-01-01

    Immunotherapies have emerged as one of the most promising approaches to treat patients with cancer. Recently, there have been many clinical successes using checkpoint receptor blockade, including T cell inhibitory receptors such as cytotoxic T-lymphocyte-associated antigen 4 (CTLA-4) and programmed cell death-1 (PD-1). Despite demonstrated successes in a variety of malignancies, responses only typically occur in a minority of patients in any given histology. Additionally, treatment is associated with inflammatory toxicity and high cost. Therefore, determining which patients would derive clinical benefit from immunotherapy is a compelling clinical question. Although numerous candidate biomarkers have been described, there are currently three FDA-approved assays based on PD-1 ligand expression (PD-L1) that have been clinically validated to identify patients who are more likely to benefit from a single-agent anti-PD-1/PD-L1 therapy. Because of the complexity of the immune response and tumor biology, it is unlikely that a single biomarker will be sufficient to predict clinical outcomes in response to immune-targeted therapy. Rather, the integration of multiple tumor and immune response parameters, such as protein expression, genomics, and transcriptomics, may be necessary for accurate prediction of clinical benefit. Before a candidate biomarker and/or new technology can be used in a clinical setting, several steps are necessary to demonstrate its clinical validity. Although regulatory guidelines provide general roadmaps for the validation process, their applicability to biomarkers in the cancer immunotherapy field is somewhat limited. Thus, Working Group 1 (WG1) of the Society for Immunotherapy of Cancer (SITC) Immune Biomarkers Task Force convened to address this need. In this two volume series, we discuss pre-analytical and analytical (Volume I) as well as clinical and regulatory (Volume II) aspects of the validation process as applied to predictive biomarkers

  6. An accurate behavioral model for single-photon avalanche diode statistical performance simulation

    NASA Astrophysics Data System (ADS)

    Xu, Yue; Zhao, Tingchen; Li, Ding

    2018-01-01

    An accurate behavioral model is presented to simulate important statistical performance of single-photon avalanche diodes (SPADs), such as dark count and after-pulsing noise. The derived simulation model takes into account all important generation mechanisms of the two kinds of noise. For the first time, thermal agitation, trap-assisted tunneling and band-to-band tunneling mechanisms are simultaneously incorporated in the simulation model to evaluate dark count behavior of SPADs fabricated in deep sub-micron CMOS technology. Meanwhile, a complete carrier trapping and de-trapping process is considered in afterpulsing model and a simple analytical expression is derived to estimate after-pulsing probability. In particular, the key model parameters of avalanche triggering probability and electric field dependence of excess bias voltage are extracted from Geiger-mode TCAD simulation and this behavioral simulation model doesn't include any empirical parameters. The developed SPAD model is implemented in Verilog-A behavioral hardware description language and successfully operated on commercial Cadence Spectre simulator, showing good universality and compatibility. The model simulation results are in a good accordance with the test data, validating high simulation accuracy.

  7. Analytical workflow profiling gene expression in murine macrophages

    PubMed Central

    Nixon, Scott E.; González-Peña, Dianelys; Lawson, Marcus A.; McCusker, Robert H.; Hernandez, Alvaro G.; O’Connor, Jason C.; Dantzer, Robert; Kelley, Keith W.

    2015-01-01

    Comprehensive and simultaneous analysis of all genes in a biological sample is a capability of RNA-Seq technology. Analysis of the entire transcriptome benefits from summarization of genes at the functional level. As a cellular response of interest not previously explored with RNA-Seq, peritoneal macrophages from mice under two conditions (control and immunologically challenged) were analyzed for gene expression differences. Quantification of individual transcripts modeled RNA-Seq read distribution and uncertainty (using a Beta Negative Binomial distribution), then tested for differential transcript expression (False Discovery Rate-adjusted p-value < 0.05). Enrichment of functional categories utilized the list of differentially expressed genes. A total of 2079 differentially expressed transcripts representing 1884 genes were detected. Enrichment of 92 categories from Gene Ontology Biological Processes and Molecular Functions, and KEGG pathways were grouped into 6 clusters. Clusters included defense and inflammatory response (Enrichment Score = 11.24) and ribosomal activity (Enrichment Score = 17.89). Our work provides a context to the fine detail of individual gene expression differences in murine peritoneal macrophages during immunological challenge with high throughput RNA-Seq. PMID:25708305

  8. Correction for isotopic interferences between analyte and internal standard in quantitative mass spectrometry by a nonlinear calibration function.

    PubMed

    Rule, Geoffrey S; Clark, Zlatuse D; Yue, Bingfang; Rockwood, Alan L

    2013-04-16

    Stable isotope-labeled internal standards are of great utility in providing accurate quantitation in mass spectrometry (MS). An implicit assumption has been that there is no "cross talk" between signals of the internal standard and the target analyte. In some cases, however, naturally occurring isotopes of the analyte do contribute to the signal of the internal standard. This phenomenon becomes more pronounced for isotopically rich compounds, such as those containing sulfur, chlorine, or bromine, higher molecular weight compounds, and those at high analyte/internal standard concentration ratio. This can create nonlinear calibration behavior that may bias quantitative results. Here, we propose the use of a nonlinear but more accurate fitting of data for these situations that incorporates one or two constants determined experimentally for each analyte/internal standard combination and an adjustable calibration parameter. This fitting provides more accurate quantitation in MS-based assays where contributions from analyte to stable labeled internal standard signal exist. It can also correct for the reverse situation where an analyte is present in the internal standard as an impurity. The practical utility of this approach is described, and by using experimental data, the approach is compared to alternative fits.

  9. Identification of Emotional Facial Expressions: Effects of Expression, Intensity, and Sex on Eye Gaze.

    PubMed

    Wells, Laura Jean; Gillespie, Steven Mark; Rotshtein, Pia

    2016-01-01

    The identification of emotional expressions is vital for social interaction, and can be affected by various factors, including the expressed emotion, the intensity of the expression, the sex of the face, and the gender of the observer. This study investigates how these factors affect the speed and accuracy of expression recognition, as well as dwell time on the two most significant areas of the face: the eyes and the mouth. Participants were asked to identify expressions from female and male faces displaying six expressions (anger, disgust, fear, happiness, sadness, and surprise), each with three levels of intensity (low, moderate, and normal). Overall, responses were fastest and most accurate for happy expressions, but slowest and least accurate for fearful expressions. More intense expressions were also classified most accurately. Reaction time showed a different pattern, with slowest response times recorded for expressions of moderate intensity. Overall, responses were slowest, but also most accurate, for female faces. Relative to male observers, women showed greater accuracy and speed when recognizing female expressions. Dwell time analyses revealed that attention to the eyes was about three times greater than on the mouth, with fearful eyes in particular attracting longer dwell times. The mouth region was attended to the most for fearful, angry, and disgusted expressions and least for surprise. These results extend upon previous findings to show important effects of expression, emotion intensity, and sex on expression recognition and gaze behaviour, and may have implications for understanding the ways in which emotion recognition abilities break down.

  10. Identification of Emotional Facial Expressions: Effects of Expression, Intensity, and Sex on Eye Gaze

    PubMed Central

    Rotshtein, Pia

    2016-01-01

    The identification of emotional expressions is vital for social interaction, and can be affected by various factors, including the expressed emotion, the intensity of the expression, the sex of the face, and the gender of the observer. This study investigates how these factors affect the speed and accuracy of expression recognition, as well as dwell time on the two most significant areas of the face: the eyes and the mouth. Participants were asked to identify expressions from female and male faces displaying six expressions (anger, disgust, fear, happiness, sadness, and surprise), each with three levels of intensity (low, moderate, and normal). Overall, responses were fastest and most accurate for happy expressions, but slowest and least accurate for fearful expressions. More intense expressions were also classified most accurately. Reaction time showed a different pattern, with slowest response times recorded for expressions of moderate intensity. Overall, responses were slowest, but also most accurate, for female faces. Relative to male observers, women showed greater accuracy and speed when recognizing female expressions. Dwell time analyses revealed that attention to the eyes was about three times greater than on the mouth, with fearful eyes in particular attracting longer dwell times. The mouth region was attended to the most for fearful, angry, and disgusted expressions and least for surprise. These results extend upon previous findings to show important effects of expression, emotion intensity, and sex on expression recognition and gaze behaviour, and may have implications for understanding the ways in which emotion recognition abilities break down. PMID:27942030

  11. Note: Model identification and analysis of bivalent analyte surface plasmon resonance data.

    PubMed

    Tiwari, Purushottam Babu; Üren, Aykut; He, Jin; Darici, Yesim; Wang, Xuewen

    2015-10-01

    Surface plasmon resonance (SPR) is a widely used, affinity based, label-free biophysical technique to investigate biomolecular interactions. The extraction of rate constants requires accurate identification of the particular binding model. The bivalent analyte model involves coupled non-linear differential equations. No clear procedure to identify the bivalent analyte mechanism has been established. In this report, we propose a unique signature for the bivalent analyte model. This signature can be used to distinguish the bivalent analyte model from other biphasic models. The proposed method is demonstrated using experimentally measured SPR sensorgrams.

  12. Biological Matrix Effects in Quantitative Tandem Mass Spectrometry-Based Analytical Methods: Advancing Biomonitoring

    PubMed Central

    Panuwet, Parinya; Hunter, Ronald E.; D’Souza, Priya E.; Chen, Xianyu; Radford, Samantha A.; Cohen, Jordan R.; Marder, M. Elizabeth; Kartavenka, Kostya; Ryan, P. Barry; Barr, Dana Boyd

    2015-01-01

    The ability to quantify levels of target analytes in biological samples accurately and precisely, in biomonitoring, involves the use of highly sensitive and selective instrumentation such as tandem mass spectrometers and a thorough understanding of highly variable matrix effects. Typically, matrix effects are caused by co-eluting matrix components that alter the ionization of target analytes as well as the chromatographic response of target analytes, leading to reduced or increased sensitivity of the analysis. Thus, before the desired accuracy and precision standards of laboratory data are achieved, these effects must be characterized and controlled. Here we present our review and observations of matrix effects encountered during the validation and implementation of tandem mass spectrometry-based analytical methods. We also provide systematic, comprehensive laboratory strategies needed to control challenges posed by matrix effects in order to ensure delivery of the most accurate data for biomonitoring studies assessing exposure to environmental toxicants. PMID:25562585

  13. Solvent effects in time-dependent self-consistent field methods. II. Variational formulations and analytical gradients

    DOE PAGES

    Bjorgaard, J. A.; Velizhanin, K. A.; Tretiak, S.

    2015-08-06

    This study describes variational energy expressions and analytical excited state energy gradients for time-dependent self-consistent field methods with polarizable solvent effects. Linear response, vertical excitation, and state-specific solventmodels are examined. Enforcing a variational ground stateenergy expression in the state-specific model is found to reduce it to the vertical excitation model. Variational excited state energy expressions are then provided for the linear response and vertical excitation models and analytical gradients are formulated. Using semiempiricalmodel chemistry, the variational expressions are verified by numerical and analytical differentiation with respect to a static external electric field. Lastly, analytical gradients are further tested by performingmore » microcanonical excited state molecular dynamics with p-nitroaniline.« less

  14. service line analytics in the new era.

    PubMed

    Spence, Jay; Seargeant, Dan

    2015-08-01

    To succeed under the value-based business model, hospitals and health systems require effective service line analytics that combine inpatient and outpatient data and that incorporate quality metrics for evaluating clinical operations. When developing a framework for collection, analysis, and dissemination of service line data, healthcare organizations should focus on five key aspects of effective service line analytics: Updated service line definitions. Ability to analyze and trend service line net patient revenues by payment source. Access to accurate service line cost information across multiple dimensions with drill-through capabilities. Ability to redesign key reports based on changing requirements. Clear assignment of accountability.

  15. Approximated analytical solution to an Ebola optimal control problem

    NASA Astrophysics Data System (ADS)

    Hincapié-Palacio, Doracelly; Ospina, Juan; Torres, Delfim F. M.

    2016-11-01

    An analytical expression for the optimal control of an Ebola problem is obtained. The analytical solution is found as a first-order approximation to the Pontryagin Maximum Principle via the Euler-Lagrange equation. An implementation of the method is given using the computer algebra system Maple. Our analytical solutions confirm the results recently reported in the literature using numerical methods.

  16. Exact analytical modeling of magnetic vector potential in surface inset permanent magnet DC machines considering magnet segmentation

    NASA Astrophysics Data System (ADS)

    Jabbari, Ali

    2018-01-01

    Surface inset permanent magnet DC machine can be used as an alternative in automation systems due to their high efficiency and robustness. Magnet segmentation is a common technique in order to mitigate pulsating torque components in permanent magnet machines. An accurate computation of air-gap magnetic field distribution is necessary in order to calculate machine performance. An exact analytical method for magnetic vector potential calculation in surface inset permanent magnet machines considering magnet segmentation has been proposed in this paper. The analytical method is based on the resolution of Laplace and Poisson equations as well as Maxwell equation in polar coordinate by using sub-domain method. One of the main contributions of the paper is to derive an expression for the magnetic vector potential in the segmented PM region by using hyperbolic functions. The developed method is applied on the performance computation of two prototype surface inset magnet segmented motors with open circuit and on load conditions. The results of these models are validated through FEM method.

  17. Light-emitting diodes for analytical chemistry.

    PubMed

    Macka, Mirek; Piasecki, Tomasz; Dasgupta, Purnendu K

    2014-01-01

    Light-emitting diodes (LEDs) are playing increasingly important roles in analytical chemistry, from the final analysis stage to photoreactors for analyte conversion to actual fabrication of and incorporation in microdevices for analytical use. The extremely fast turn-on/off rates of LEDs have made possible simple approaches to fluorescence lifetime measurement. Although they are increasingly being used as detectors, their wavelength selectivity as detectors has rarely been exploited. From their first proposed use for absorbance measurement in 1970, LEDs have been used in analytical chemistry in too many ways to make a comprehensive review possible. Hence, we critically review here the more recent literature on their use in optical detection and measurement systems. Cloudy as our crystal ball may be, we express our views on the future applications of LEDs in analytical chemistry: The horizon will certainly become wider as LEDs in the deep UV with sufficient intensity become available.

  18. Pre-analytical and analytical variation of drug determination in segmented hair using ultra-performance liquid chromatography-tandem mass spectrometry.

    PubMed

    Nielsen, Marie Katrine Klose; Johansen, Sys Stybe; Linnet, Kristian

    2014-01-01

    Assessment of total uncertainty of analytical methods for the measurements of drugs in human hair has mainly been derived from the analytical variation. However, in hair analysis several other sources of uncertainty will contribute to the total uncertainty. Particularly, in segmental hair analysis pre-analytical variations associated with the sampling and segmentation may be significant factors in the assessment of the total uncertainty budget. The aim of this study was to develop and validate a method for the analysis of 31 common drugs in hair using ultra-performance liquid chromatography-tandem mass spectrometry (UHPLC-MS/MS) with focus on the assessment of both the analytical and pre-analytical sampling variations. The validated method was specific, accurate (80-120%), and precise (CV≤20%) across a wide linear concentration range from 0.025-25 ng/mg for most compounds. The analytical variation was estimated to be less than 15% for almost all compounds. The method was successfully applied to 25 segmented hair specimens from deceased drug addicts showing a broad pattern of poly-drug use. The pre-analytical sampling variation was estimated from the genuine duplicate measurements of two bundles of hair collected from each subject after subtraction of the analytical component. For the most frequently detected analytes, the pre-analytical variation was estimated to be 26-69%. Thus, the pre-analytical variation was 3-7 folds larger than the analytical variation (7-13%) and hence the dominant component in the total variation (29-70%). The present study demonstrated the importance of including the pre-analytical variation in the assessment of the total uncertainty budget and in the setting of the 95%-uncertainty interval (±2CVT). Excluding the pre-analytical sampling variation could significantly affect the interpretation of results from segmental hair analysis. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

  19. Analytical Energy Gradients for Excited-State Coupled-Cluster Methods

    NASA Astrophysics Data System (ADS)

    Wladyslawski, Mark; Nooijen, Marcel

    The equation-of-motion coupled-cluster (EOM-CC) and similarity transformed equation-of-motion coupled-cluster (STEOM-CC) methods have been firmly established as accurate and routinely applicable extensions of single-reference coupled-cluster theory to describe electronically excited states. An overview of these methods is provided, with emphasis on the many-body similarity transform concept that is the key to a rationalization of their accuracy. The main topic of the paper is the derivation of analytical energy gradients for such non-variational electronic structure approaches, with an ultimate focus on obtaining their detailed algebraic working equations. A general theoretical framework using Lagrange's method of undetermined multipliers is presented, and the method is applied to formulate the EOM-CC and STEOM-CC gradients in abstract operator terms, following the previous work in [P.G. Szalay, Int. J. Quantum Chem. 55 (1995) 151] and [S.R. Gwaltney, R.J. Bartlett, M. Nooijen, J. Chem. Phys. 111 (1999) 58]. Moreover, the systematics of the Lagrange multiplier approach is suitable for automation by computer, enabling the derivation of the detailed derivative equations through a standardized and direct procedure. To this end, we have developed the SMART (Symbolic Manipulation and Regrouping of Tensors) package of automated symbolic algebra routines, written in the Mathematica programming language. The SMART toolkit provides the means to expand, differentiate, and simplify equations by manipulation of the detailed algebraic tensor expressions directly. The Lagrangian multiplier formulation establishes a uniform strategy to perform the automated derivation in a standardized manner: A Lagrange multiplier functional is constructed from the explicit algebraic equations that define the energy in the electronic method; the energy functional is then made fully variational with respect to all of its parameters, and the symbolic differentiations directly yield the explicit

  20. Expressing analytical performance from multi-sample evaluation in laboratory EQA.

    PubMed

    Thelen, Marc H M; Jansen, Rob T P; Weykamp, Cas W; Steigstra, Herman; Meijer, Ron; Cobbaert, Christa M

    2017-08-28

    To provide its participants with an external quality assessment system (EQAS) that can be used to check trueness, the Dutch EQAS organizer, Organization for Quality Assessment of Laboratory Diagnostics (SKML), has innovated its general chemistry scheme over the last decade by introducing fresh frozen commutable samples whose values were assigned by Joint Committee for Traceability in Laboratory Medicine (JCTLM)-listed reference laboratories using reference methods where possible. Here we present some important innovations in our feedback reports that allow participants to judge whether their trueness and imprecision meet predefined analytical performance specifications. Sigma metrics are used to calculate performance indicators named 'sigma values'. Tolerance intervals are based on both Total Error allowable (TEa) according to biological variation data and state of the art (SA) in line with the European Federation of Clinical Chemistry and Laboratory Medicine (EFLM) Milan consensus. The existing SKML feedback reports that express trueness as the agreement between the regression line through the results of the last 12 months and the values obtained from reference laboratories and calculate imprecision from the residuals of the regression line are now enriched with sigma values calculated from the degree to which the combination of trueness and imprecision are within tolerance limits. The information and its conclusion to a simple two-point scoring system are also graphically represented in addition to the existing difference plot. By adding sigma metrics-based performance evaluation in relation to both TEa and SA tolerance intervals to its EQAS schemes, SKML provides its participants with a powerful and actionable check on accuracy.

  1. Analytical expression for the exit probability of the q -voter model in one dimension

    NASA Astrophysics Data System (ADS)

    Timpanaro, André M.; Galam, Serge

    2015-07-01

    We present in this paper an approximation that is able to give an analytical expression for the exit probability of the q -voter model in one dimension. This expression gives a better fit for the more recent data about simulations in large networks [A. M. Timpanaro and C. P. C. do Prado, Phys. Rev. E 89, 052808 (2014), 10.1103/PhysRevE.89.052808] and as such departs from the expression ρ/qρq+(1-ρ ) q found in papers that investigated small networks only [R. Lambiotte and S. Redner, Europhys. Lett. 82, 18007 (2008), 10.1209/0295-5075/82/18007; P. Przybyła et al., Phys. Rev. E 84, 031117 (2011), 10.1103/PhysRevE.84.031117; F. Slanina et al., Europhys. Lett. 82, 18006 (2008), 10.1209/0295-5075/82/18006]. The approximation consists in assuming a large separation on the time scales at which active groups of agents convince inactive ones and the time taken in the competition between active groups. Some interesting findings are that for q =2 we still have ρ/2ρ2+(1-ρ ) 2 as the exit probability and for q >2 we can obtain a lower-order approximation of the form ρ/sρs+(1-ρ ) s with s varying from q for low values of q to q -1/2 for large values of q . As such, this work can also be seen as a deduction for why the exit probability ρ/qρq+(1-ρ ) q gives a good fit, without relying on mean-field arguments or on the assumption that only the first step is nondeterministic, as q and q -1/2 will give very similar results when q →∞ .

  2. An analytical expression for ion velocities at the wall including the sheath electric field and surface biasing for erosion modeling at JET ILW

    DOE PAGES

    Borodkina, I.; Borodin, D.; Brezinsek, S.; ...

    2017-04-12

    For simulation of plasma-facing component erosion in fusion experiments, an analytical expression for the ion velocity just before the surface impact including the local electric field and an optional surface biasing effect is suggested. Energy and angular impact distributions and the resulting effective sputtering yields were produced for several experimental scenarios at JET ILW mostly involving PFCs exposed to an oblique magnetic field. The analytic solution has been applied as an improvement to earlier ERO modelling of localized, Be outer limiter, RF-enhanced erosion, modulated by toggling of a remote, however magnetically connected ICRH antenna. The effective W sputtering yields duemore » to D and Be ion impact in Type-I and Type-III ELMs and inter-ELM conditions were also estimated using the analytical approach and benchmarked by spectroscopy. The intra-ELM W sputtering flux increases almost 10 times in comparison to the inter-ELM flux.« less

  3. How to perform RT-qPCR accurately in plant species? A case study on flower colour gene expression in an azalea (Rhododendron simsii hybrids) mapping population.

    PubMed

    De Keyser, Ellen; Desmet, Laurence; Van Bockstaele, Erik; De Riek, Jan

    2013-06-24

    Flower colour variation is one of the most crucial selection criteria in the breeding of a flowering pot plant, as is also the case for azalea (Rhododendron simsii hybrids). Flavonoid biosynthesis was studied intensively in several species. In azalea, flower colour can be described by means of a 3-gene model. However, this model does not clarify pink-coloration. The last decade gene expression studies have been implemented widely for studying flower colour. However, the methods used were often only semi-quantitative or quantification was not done according to the MIQE-guidelines. We aimed to develop an accurate protocol for RT-qPCR and to validate the protocol to study flower colour in an azalea mapping population. An accurate RT-qPCR protocol had to be established. RNA quality was evaluated in a combined approach by means of different techniques e.g. SPUD-assay and Experion-analysis. We demonstrated the importance of testing noRT-samples for all genes under study to detect contaminating DNA. In spite of the limited sequence information available, we prepared a set of 11 reference genes which was validated in flower petals; a combination of three reference genes was most optimal. Finally we also used plasmids for the construction of standard curves. This allowed us to calculate gene-specific PCR efficiencies for every gene to assure an accurate quantification. The validity of the protocol was demonstrated by means of the study of six genes of the flavonoid biosynthesis pathway. No correlations were found between flower colour and the individual expression profiles. However, the combination of early pathway genes (CHS, F3H, F3'H and FLS) is clearly related to co-pigmentation with flavonols. The late pathway genes DFR and ANS are to a minor extent involved in differentiating between coloured and white flowers. Concerning pink coloration, we could demonstrate that the lower intensity in this type of flowers is correlated to the expression of F3'H. Currently in plant

  4. How to perform RT-qPCR accurately in plant species? A case study on flower colour gene expression in an azalea (Rhododendron simsii hybrids) mapping population

    PubMed Central

    2013-01-01

    Background Flower colour variation is one of the most crucial selection criteria in the breeding of a flowering pot plant, as is also the case for azalea (Rhododendron simsii hybrids). Flavonoid biosynthesis was studied intensively in several species. In azalea, flower colour can be described by means of a 3-gene model. However, this model does not clarify pink-coloration. The last decade gene expression studies have been implemented widely for studying flower colour. However, the methods used were often only semi-quantitative or quantification was not done according to the MIQE-guidelines. We aimed to develop an accurate protocol for RT-qPCR and to validate the protocol to study flower colour in an azalea mapping population. Results An accurate RT-qPCR protocol had to be established. RNA quality was evaluated in a combined approach by means of different techniques e.g. SPUD-assay and Experion-analysis. We demonstrated the importance of testing noRT-samples for all genes under study to detect contaminating DNA. In spite of the limited sequence information available, we prepared a set of 11 reference genes which was validated in flower petals; a combination of three reference genes was most optimal. Finally we also used plasmids for the construction of standard curves. This allowed us to calculate gene-specific PCR efficiencies for every gene to assure an accurate quantification. The validity of the protocol was demonstrated by means of the study of six genes of the flavonoid biosynthesis pathway. No correlations were found between flower colour and the individual expression profiles. However, the combination of early pathway genes (CHS, F3H, F3'H and FLS) is clearly related to co-pigmentation with flavonols. The late pathway genes DFR and ANS are to a minor extent involved in differentiating between coloured and white flowers. Concerning pink coloration, we could demonstrate that the lower intensity in this type of flowers is correlated to the expression of F3'H

  5. Analytical Calculation of the Lower Bound on Timing Resolution for PET Scintillation Detectors Comprising High-Aspect-Ratio Crystal Elements

    PubMed Central

    Cates, Joshua W.; Vinke, Ruud; Levin, Craig S.

    2015-01-01

    Excellent timing resolution is required to enhance the signal-to-noise ratio (SNR) gain available from the incorporation of time-of-flight (ToF) information in image reconstruction for positron emission tomography (PET). As the detector’s timing resolution improves, so does SNR, reconstructed image quality, and accuracy. This directly impacts the challenging detection and quantification tasks in the clinic. The recognition of these benefits has spurred efforts within the molecular imaging community to determine to what extent the timing resolution of scintillation detectors can be improved and develop near-term solutions for advancing ToF-PET. Presented in this work, is a method for calculating the Cramér-Rao lower bound (CRLB) on timing resolution for scintillation detectors with long crystal elements, where the influence of the variation in optical path length of scintillation light on achievable timing resolution is non-negligible. The presented formalism incorporates an accurate, analytical probability density function (PDF) of optical transit time within the crystal to obtain a purely mathematical expression of the CRLB with high-aspect-ratio (HAR) scintillation detectors. This approach enables the statistical limit on timing resolution performance to be analytically expressed for clinically-relevant PET scintillation detectors without requiring Monte Carlo simulation-generated photon transport time distributions. The analytically calculated optical transport PDF was compared with detailed light transport simulations, and excellent agreement was found between the two. The coincidence timing resolution (CTR) between two 3×3×20 mm3 LYSO:Ce crystals coupled to analogue SiPMs was experimentally measured to be 162±1 ps FWHM, approaching the analytically calculated lower bound within 6.5%. PMID:26083559

  6. Analytical calculation of the lower bound on timing resolution for PET scintillation detectors comprising high-aspect-ratio crystal elements

    NASA Astrophysics Data System (ADS)

    Cates, Joshua W.; Vinke, Ruud; Levin, Craig S.

    2015-07-01

    Excellent timing resolution is required to enhance the signal-to-noise ratio (SNR) gain available from the incorporation of time-of-flight (ToF) information in image reconstruction for positron emission tomography (PET). As the detector’s timing resolution improves, so does SNR, reconstructed image quality, and accuracy. This directly impacts the challenging detection and quantification tasks in the clinic. The recognition of these benefits has spurred efforts within the molecular imaging community to determine to what extent the timing resolution of scintillation detectors can be improved and develop near-term solutions for advancing ToF-PET. Presented in this work, is a method for calculating the Cramér-Rao lower bound (CRLB) on timing resolution for scintillation detectors with long crystal elements, where the influence of the variation in optical path length of scintillation light on achievable timing resolution is non-negligible. The presented formalism incorporates an accurate, analytical probability density function (PDF) of optical transit time within the crystal to obtain a purely mathematical expression of the CRLB with high-aspect-ratio (HAR) scintillation detectors. This approach enables the statistical limit on timing resolution performance to be analytically expressed for clinically-relevant PET scintillation detectors without requiring Monte Carlo simulation-generated photon transport time distributions. The analytically calculated optical transport PDF was compared with detailed light transport simulations, and excellent agreement was found between the two. The coincidence timing resolution (CTR) between two 3× 3× 20 mm3 LYSO:Ce crystals coupled to analogue SiPMs was experimentally measured to be 162+/- 1 ps FWHM, approaching the analytically calculated lower bound within 6.5%.

  7. Statistically Qualified Neuro-Analytic system and Method for Process Monitoring

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

    Vilim, Richard B.; Garcia, Humberto E.; Chen, Frederick W.

    1998-11-04

    An apparatus and method for monitoring a process involves development and application of a statistically qualified neuro-analytic (SQNA) model to accurately and reliably identify process change. The development of the SQNA model is accomplished in two steps: deterministic model adaption and stochastic model adaptation. Deterministic model adaption involves formulating an analytic model of the process representing known process characteristics,augmenting the analytic model with a neural network that captures unknown process characteristics, and training the resulting neuro-analytic model by adjusting the neural network weights according to a unique scaled equation emor minimization technique. Stochastic model adaptation involves qualifying any remaining uncertaintymore » in the trained neuro-analytic model by formulating a likelihood function, given an error propagation equation, for computing the probability that the neuro-analytic model generates measured process output. Preferably, the developed SQNA model is validated using known sequential probability ratio tests and applied to the process as an on-line monitoring system.« less

  8. Statistically qualified neuro-analytic failure detection method and system

    DOEpatents

    Vilim, Richard B.; Garcia, Humberto E.; Chen, Frederick W.

    2002-03-02

    An apparatus and method for monitoring a process involve development and application of a statistically qualified neuro-analytic (SQNA) model to accurately and reliably identify process change. The development of the SQNA model is accomplished in two stages: deterministic model adaption and stochastic model modification of the deterministic model adaptation. Deterministic model adaption involves formulating an analytic model of the process representing known process characteristics, augmenting the analytic model with a neural network that captures unknown process characteristics, and training the resulting neuro-analytic model by adjusting the neural network weights according to a unique scaled equation error minimization technique. Stochastic model modification involves qualifying any remaining uncertainty in the trained neuro-analytic model by formulating a likelihood function, given an error propagation equation, for computing the probability that the neuro-analytic model generates measured process output. Preferably, the developed SQNA model is validated using known sequential probability ratio tests and applied to the process as an on-line monitoring system. Illustrative of the method and apparatus, the method is applied to a peristaltic pump system.

  9. An improved 3D MoF method based on analytical partial derivatives

    NASA Astrophysics Data System (ADS)

    Chen, Xiang; Zhang, Xiong

    2016-12-01

    MoF (Moment of Fluid) method is one of the most accurate approaches among various surface reconstruction algorithms. As other second order methods, MoF method needs to solve an implicit optimization problem to obtain the optimal approximate surface. Therefore, the partial derivatives of the objective function have to be involved during the iteration for efficiency and accuracy. However, to the best of our knowledge, the derivatives are currently estimated numerically by finite difference approximation because it is very difficult to obtain the analytical derivatives of the object function for an implicit optimization problem. Employing numerical derivatives in an iteration not only increase the computational cost, but also deteriorate the convergence rate and robustness of the iteration due to their numerical error. In this paper, the analytical first order partial derivatives of the objective function are deduced for 3D problems. The analytical derivatives can be calculated accurately, so they are incorporated into the MoF method to improve its accuracy, efficiency and robustness. Numerical studies show that by using the analytical derivatives the iterations are converged in all mixed cells with the efficiency improvement of 3 to 4 times.

  10. Plant Aquaporins: Genome-Wide Identification, Transcriptomics, Proteomics, and Advanced Analytical Tools.

    PubMed

    Deshmukh, Rupesh K; Sonah, Humira; Bélanger, Richard R

    2016-01-01

    Aquaporins (AQPs) are channel-forming integral membrane proteins that facilitate the movement of water and many other small molecules. Compared to animals, plants contain a much higher number of AQPs in their genome. Homology-based identification of AQPs in sequenced species is feasible because of the high level of conservation of protein sequences across plant species. Genome-wide characterization of AQPs has highlighted several important aspects such as distribution, genetic organization, evolution and conserved features governing solute specificity. From a functional point of view, the understanding of AQP transport system has expanded rapidly with the help of transcriptomics and proteomics data. The efficient analysis of enormous amounts of data generated through omic scale studies has been facilitated through computational advancements. Prediction of protein tertiary structures, pore architecture, cavities, phosphorylation sites, heterodimerization, and co-expression networks has become more sophisticated and accurate with increasing computational tools and pipelines. However, the effectiveness of computational approaches is based on the understanding of physiological and biochemical properties, transport kinetics, solute specificity, molecular interactions, sequence variations, phylogeny and evolution of aquaporins. For this purpose, tools like Xenopus oocyte assays, yeast expression systems, artificial proteoliposomes, and lipid membranes have been efficiently exploited to study the many facets that influence solute transport by AQPs. In the present review, we discuss genome-wide identification of AQPs in plants in relation with recent advancements in analytical tools, and their availability and technological challenges as they apply to AQPs. An exhaustive review of omics resources available for AQP research is also provided in order to optimize their efficient utilization. Finally, a detailed catalog of computational tools and analytical pipelines is

  11. Plant Aquaporins: Genome-Wide Identification, Transcriptomics, Proteomics, and Advanced Analytical Tools

    PubMed Central

    Deshmukh, Rupesh K.; Sonah, Humira; Bélanger, Richard R.

    2016-01-01

    Aquaporins (AQPs) are channel-forming integral membrane proteins that facilitate the movement of water and many other small molecules. Compared to animals, plants contain a much higher number of AQPs in their genome. Homology-based identification of AQPs in sequenced species is feasible because of the high level of conservation of protein sequences across plant species. Genome-wide characterization of AQPs has highlighted several important aspects such as distribution, genetic organization, evolution and conserved features governing solute specificity. From a functional point of view, the understanding of AQP transport system has expanded rapidly with the help of transcriptomics and proteomics data. The efficient analysis of enormous amounts of data generated through omic scale studies has been facilitated through computational advancements. Prediction of protein tertiary structures, pore architecture, cavities, phosphorylation sites, heterodimerization, and co-expression networks has become more sophisticated and accurate with increasing computational tools and pipelines. However, the effectiveness of computational approaches is based on the understanding of physiological and biochemical properties, transport kinetics, solute specificity, molecular interactions, sequence variations, phylogeny and evolution of aquaporins. For this purpose, tools like Xenopus oocyte assays, yeast expression systems, artificial proteoliposomes, and lipid membranes have been efficiently exploited to study the many facets that influence solute transport by AQPs. In the present review, we discuss genome-wide identification of AQPs in plants in relation with recent advancements in analytical tools, and their availability and technological challenges as they apply to AQPs. An exhaustive review of omics resources available for AQP research is also provided in order to optimize their efficient utilization. Finally, a detailed catalog of computational tools and analytical pipelines is

  12. Stakeholder perspectives on decision-analytic modeling frameworks to assess genetic services policy.

    PubMed

    Guzauskas, Gregory F; Garrison, Louis P; Stock, Jacquie; Au, Sylvia; Doyle, Debra Lochner; Veenstra, David L

    2013-01-01

    Genetic services policymakers and insurers often make coverage decisions in the absence of complete evidence of clinical utility and under budget constraints. We evaluated genetic services stakeholder opinions on the potential usefulness of decision-analytic modeling to inform coverage decisions, and asked them to identify genetic tests for decision-analytic modeling studies. We presented an overview of decision-analytic modeling to members of the Western States Genetic Services Collaborative Reimbursement Work Group and state Medicaid representatives and conducted directed content analysis and an anonymous survey to gauge their attitudes toward decision-analytic modeling. Participants also identified and prioritized genetic services for prospective decision-analytic evaluation. Participants expressed dissatisfaction with current processes for evaluating insurance coverage of genetic services. Some participants expressed uncertainty about their comprehension of decision-analytic modeling techniques. All stakeholders reported openness to using decision-analytic modeling for genetic services assessments. Participants were most interested in application of decision-analytic concepts to multiple-disorder testing platforms, such as next-generation sequencing and chromosomal microarray. Decision-analytic modeling approaches may provide a useful decision tool to genetic services stakeholders and Medicaid decision-makers.

  13. High precision analytical description of the allowed β spectrum shape

    NASA Astrophysics Data System (ADS)

    Hayen, Leendert; Severijns, Nathal; Bodek, Kazimierz; Rozpedzik, Dagmara; Mougeot, Xavier

    2018-01-01

    A fully analytical description of the allowed β spectrum shape is given in view of ongoing and planned measurements. Its study forms an invaluable tool in the search for physics beyond the standard electroweak model and the weak magnetism recoil term. Contributions stemming from finite size corrections, mass effects, and radiative corrections are reviewed. Particular focus is placed on atomic and chemical effects, where the existing description is extended and analytically provided. The effects of QCD-induced recoil terms are discussed, and cross-checks were performed for different theoretical formalisms. Special attention was given to a comparison of the treatment of nuclear structure effects in different formalisms. Corrections were derived for both Fermi and Gamow-Teller transitions, and methods of analytical evaluation thoroughly discussed. In its integrated form, calculated f values were in agreement with the most precise numerical results within the aimed for precision. The need for an accurate evaluation of weak magnetism contributions was stressed, and the possible significance of the oft-neglected induced pseudoscalar interaction was noted. Together with improved atomic corrections, an analytical description was presented of the allowed β spectrum shape accurate to a few parts in 10-4 down to 1 keV for low to medium Z nuclei, thereby extending the work by previous authors by nearly an order of magnitude.

  14. First-and Second-Order Displacement Transfer Functions for Structural Shape Calculations Using Analytically Predicted Surface Strains

    NASA Technical Reports Server (NTRS)

    Ko, William L.; Fleischer, Van Tran

    2012-01-01

    New first- and second-order displacement transfer functions have been developed for deformed shape calculations of nonuniform cross-sectional beam structures such as aircraft wings. The displacement transfer functions are expressed explicitly in terms of beam geometrical parameters and surface strains (uniaxial bending strains) obtained at equally spaced strain stations along the surface of the beam structure. By inputting the measured or analytically calculated surface strains into the displacement transfer functions, one could calculate local slopes, deflections, and cross-sectional twist angles of the nonuniform beam structure for mapping the overall structural deformed shapes for visual display. The accuracy of deformed shape calculations by the first- and second-order displacement transfer functions are determined by comparing these values to the analytically predicted values obtained from finite element analyses. This comparison shows that the new displacement transfer functions could quite accurately calculate the deformed shapes of tapered cantilever tubular beams with different tapered angles. The accuracy of the present displacement transfer functions also are compared to those of the previously developed displacement transfer functions.

  15. MASTERS OF ANALYTICAL TRADECRAFT: CERTIFYING THE STANDARDS AND ANALYTIC RIGOR OF INTELLIGENCE PRODUCTS

    DTIC Science & Technology

    2016-04-01

    Disclaimer The views expressed in this academic research paper are those of the author and do not reflect the official policy or position of the US...10 Figure 2: Proposed MAT Rating Badges..............................................................................16...establishing unit level certified Masters of Analytic Tradecraft (MAT) analysts to be trained and entrusted to evaluate and rate the standards and

  16. Accurate approximation of in-ecliptic trajectories for E-sail with constant pitch angle

    NASA Astrophysics Data System (ADS)

    Huo, Mingying; Mengali, Giovanni; Quarta, Alessandro A.

    2018-05-01

    Propellantless continuous-thrust propulsion systems, such as electric solar wind sails, may be successfully used for new space missions, especially those requiring high-energy orbit transfers. When the mass-to-thrust ratio is sufficiently large, the spacecraft trajectory is characterized by long flight times with a number of revolutions around the Sun. The corresponding mission analysis, especially when addressed within an optimal context, requires a significant amount of simulation effort. Analytical trajectories are therefore useful aids in a preliminary phase of mission design, even though exact solution are very difficult to obtain. The aim of this paper is to present an accurate, analytical, approximation of the spacecraft trajectory generated by an electric solar wind sail with a constant pitch angle, using the latest mathematical model of the thrust vector. Assuming a heliocentric circular parking orbit and a two-dimensional scenario, the simulation results show that the proposed equations are able to accurately describe the actual spacecraft trajectory for a long time interval when the propulsive acceleration magnitude is sufficiently small.

  17. Analytical model of the optical vortex microscope.

    PubMed

    Płocinniczak, Łukasz; Popiołek-Masajada, Agnieszka; Masajada, Jan; Szatkowski, Mateusz

    2016-04-20

    This paper presents an analytical model of the optical vortex scanning microscope. In this microscope the Gaussian beam with an embedded optical vortex is focused into the sample plane. Additionally, the optical vortex can be moved inside the beam, which allows fine scanning of the sample. We provide an analytical solution of the whole path of the beam in the system (within paraxial approximation)-from the vortex lens to the observation plane situated on the CCD camera. The calculations are performed step by step from one optical element to the next. We show that at each step, the expression for light complex amplitude has the same form with only four coefficients modified. We also derive a simple expression for the vortex trajectory of small vortex displacements.

  18. AN ANALYTIC MODEL OF DUSTY, STRATIFIED, SPHERICAL H ii REGIONS

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

    Rodríguez-Ramírez, J. C.; Raga, A. C.; Lora, V.

    2016-12-20

    We study analytically the effect of radiation pressure (associated with photoionization processes and with dust absorption) on spherical, hydrostatic H ii regions. We consider two basic equations, one for the hydrostatic balance between the radiation-pressure components and the gas pressure, and another for the balance among the recombination rate, the dust absorption, and the ionizing photon rate. Based on appropriate mathematical approximations, we find a simple analytic solution for the density stratification of the nebula, which is defined by specifying the radius of the external boundary, the cross section of dust absorption, and the luminosity of the central star. Wemore » compare the analytic solution with numerical integrations of the model equations of Draine, and find a wide range of the physical parameters for which the analytic solution is accurate.« less

  19. Spiral trajectory design: a flexible numerical algorithm and base analytical equations.

    PubMed

    Pipe, James G; Zwart, Nicholas R

    2014-01-01

    Spiral-based trajectories for magnetic resonance imaging can be advantageous, but are often cumbersome to design or create. This work presents a flexible numerical algorithm for designing trajectories based on explicit definition of radial undersampling, and also gives several analytical expressions for charactering the base (critically sampled) class of these trajectories. Expressions for the gradient waveform, based on slew and amplitude limits, are developed such that a desired pitch in the spiral k-space trajectory is followed. The source code for this algorithm, written in C, is publicly available. Analytical expressions approximating the spiral trajectory (ignoring the radial component) are given to characterize measurement time, gradient heating, maximum gradient amplitude, and off-resonance phase for slew-limited and gradient amplitude-limited cases. Several numerically calculated trajectories are illustrated, and base Archimedean spirals are compared with analytically obtained results. Several different waveforms illustrate that the desired slew and amplitude limits are reached, as are the desired undersampling patterns, using the numerical method. For base Archimedean spirals, the results of the numerical and analytical approaches are in good agreement. A versatile numerical algorithm was developed, and was written in publicly available code. Approximate analytical formulas are given that help characterize spiral trajectories. Copyright © 2013 Wiley Periodicals, Inc.

  20. Big data analytics in immunology: a knowledge-based approach.

    PubMed

    Zhang, Guang Lan; Sun, Jing; Chitkushev, Lou; Brusic, Vladimir

    2014-01-01

    With the vast amount of immunological data available, immunology research is entering the big data era. These data vary in granularity, quality, and complexity and are stored in various formats, including publications, technical reports, and databases. The challenge is to make the transition from data to actionable knowledge and wisdom and bridge the knowledge gap and application gap. We report a knowledge-based approach based on a framework called KB-builder that facilitates data mining by enabling fast development and deployment of web-accessible immunological data knowledge warehouses. Immunological knowledge discovery relies heavily on both the availability of accurate, up-to-date, and well-organized data and the proper analytics tools. We propose the use of knowledge-based approaches by developing knowledgebases combining well-annotated data with specialized analytical tools and integrating them into analytical workflow. A set of well-defined workflow types with rich summarization and visualization capacity facilitates the transformation from data to critical information and knowledge. By using KB-builder, we enabled streamlining of normally time-consuming processes of database development. The knowledgebases built using KB-builder will speed up rational vaccine design by providing accurate and well-annotated data coupled with tailored computational analysis tools and workflow.

  1. An accurate computational method for the diffusion regime verification

    NASA Astrophysics Data System (ADS)

    Zhokh, Alexey A.; Strizhak, Peter E.

    2018-04-01

    The diffusion regime (sub-diffusive, standard, or super-diffusive) is defined by the order of the derivative in the corresponding transport equation. We develop an accurate computational method for the direct estimation of the diffusion regime. The method is based on the derivative order estimation using the asymptotic analytic solutions of the diffusion equation with the integer order and the time-fractional derivatives. The robustness and the computational cheapness of the proposed method are verified using the experimental methane and methyl alcohol transport kinetics through the catalyst pellet.

  2. Universal analytical scattering form factor for shell-, core-shell, or homogeneous particles with continuously variable density profile shape.

    PubMed

    Foster, Tobias

    2011-09-01

    A novel analytical and continuous density distribution function with a widely variable shape is reported and used to derive an analytical scattering form factor that allows us to universally describe the scattering from particles with the radial density profile of homogeneous spheres, shells, or core-shell particles. Composed by the sum of two Fermi-Dirac distribution functions, the shape of the density profile can be altered continuously from step-like via Gaussian-like or parabolic to asymptotically hyperbolic by varying a single "shape parameter", d. Using this density profile, the scattering form factor can be calculated numerically. An analytical form factor can be derived using an approximate expression for the original Fermi-Dirac distribution function. This approximation is accurate for sufficiently small rescaled shape parameters, d/R (R being the particle radius), up to values of d/R ≈ 0.1, and thus captures step-like, Gaussian-like, and parabolic as well as asymptotically hyperbolic profile shapes. It is expected that this form factor is particularly useful in a model-dependent analysis of small-angle scattering data since the applied continuous and analytical function for the particle density profile can be compared directly with the density profile extracted from the data by model-free approaches like the generalized inverse Fourier transform method. © 2011 American Chemical Society

  3. Analytical thermal model for end-pumped solid-state lasers

    NASA Astrophysics Data System (ADS)

    Cini, L.; Mackenzie, J. I.

    2017-12-01

    Fundamentally power-limited by thermal effects, the design challenge for end-pumped "bulk" solid-state lasers depends upon knowledge of the temperature gradients within the gain medium. We have developed analytical expressions that can be used to model the temperature distribution and thermal-lens power in end-pumped solid-state lasers. Enabled by the inclusion of a temperature-dependent thermal conductivity, applicable from cryogenic to elevated temperatures, typical pumping distributions are explored and the results compared with accepted models. Key insights are gained through these analytical expressions, such as the dependence of the peak temperature rise in function of the boundary thermal conductance to the heat sink. Our generalized expressions provide simple and time-efficient tools for parametric optimization of the heat distribution in the gain medium based upon the material and pumping constraints.

  4. Estimation of the uncertainty of analyte concentration from the measurement uncertainty.

    PubMed

    Brown, Simon; Cooke, Delwyn G; Blackwell, Leonard F

    2015-09-01

    Ligand-binding assays, such as immunoassays, are usually analysed using standard curves based on the four-parameter and five-parameter logistic models. An estimate of the uncertainty of an analyte concentration obtained from such curves is needed for confidence intervals or precision profiles. Using a numerical simulation approach, it is shown that the uncertainty of the analyte concentration estimate becomes significant at the extremes of the concentration range and that this is affected significantly by the steepness of the standard curve. We also provide expressions for the coefficient of variation of the analyte concentration estimate from which confidence intervals and the precision profile can be obtained. Using three examples, we show that the expressions perform well.

  5. An analytic performance model of disk arrays and its application

    NASA Technical Reports Server (NTRS)

    Lee, Edward K.; Katz, Randy H.

    1991-01-01

    As disk arrays become widely used, tools for understanding and analyzing their performance become increasingly important. In particular, performance models can be invaluable in both configuring and designing disk arrays. Accurate analytic performance models are desirable over other types of models because they can be quickly evaluated, are applicable under a wide range of system and workload parameters, and can be manipulated by a range of mathematical techniques. Unfortunately, analytical performance models of disk arrays are difficult to formulate due to the presence of queuing and fork-join synchronization; a disk array request is broken up into independent disk requests which must all complete to satisfy the original request. We develop, validate, and apply an analytic performance model for disk arrays. We derive simple equations for approximating their utilization, response time, and throughput. We then validate the analytic model via simulation and investigate the accuracy of each approximation used in deriving the analytical model. Finally, we apply the analytical model to derive an equation for the optimal unit of data striping in disk arrays.

  6. Simplified expressions that incorporate finite pulse effects into coherent two-dimensional optical spectra.

    PubMed

    Do, Thanh Nhut; Gelin, Maxim F; Tan, Howe-Siang

    2017-10-14

    We derive general expressions that incorporate finite pulse envelope effects into a coherent two-dimensional optical spectroscopy (2DOS) technique. These expressions are simpler and less computationally intensive than the conventional triple integral calculations needed to simulate 2DOS spectra. The simplified expressions involving multiplications of arbitrary pulse spectra with 2D spectral response function are shown to be exactly equal to the conventional triple integral calculations of 2DOS spectra if the 2D spectral response functions do not vary with population time. With minor modifications, they are also accurate for 2D spectral response functions with quantum beats and exponential decay during population time. These conditions cover a broad range of experimental 2DOS spectra. For certain analytically defined pulse spectra, we also derived expressions of 2D spectra for arbitrary population time dependent 2DOS spectral response functions. Having simpler and more efficient methods to calculate experimentally relevant 2DOS spectra with finite pulse effect considered will be important in the simulation and understanding of the complex systems routinely being studied by using 2DOS.

  7. Analytical performance of a bronchial genomic classifier.

    PubMed

    Hu, Zhanzhi; Whitney, Duncan; Anderson, Jessica R; Cao, Manqiu; Ho, Christine; Choi, Yoonha; Huang, Jing; Frink, Robert; Smith, Kate Porta; Monroe, Robert; Kennedy, Giulia C; Walsh, P Sean

    2016-02-26

    The current standard practice of lung lesion diagnosis often leads to inconclusive results, requiring additional diagnostic follow up procedures that are invasive and often unnecessary due to the high benign rate in such lesions (Chest 143:e78S-e92, 2013). The Percepta bronchial genomic classifier was developed and clinically validated to provide more accurate classification of lung nodules and lesions that are inconclusive by bronchoscopy, using bronchial brushing specimens (N Engl J Med 373:243-51, 2015, BMC Med Genomics 8:18, 2015). The analytical performance of the Percepta test is reported here. Analytical performance studies were designed to characterize the stability of RNA in bronchial brushing specimens during collection and shipment; analytical sensitivity defined as input RNA mass; analytical specificity (i.e. potentially interfering substances) as tested on blood and genomic DNA; and assay performance studies including intra-run, inter-run, and inter-laboratory reproducibility. RNA content within bronchial brushing specimens preserved in RNAprotect is stable for up to 20 days at 4 °C with no changes in RNA yield or integrity. Analytical sensitivity studies demonstrated tolerance to variation in RNA input (157 ng to 243 ng). Analytical specificity studies utilizing cancer positive and cancer negative samples mixed with either blood (up to 10 % input mass) or genomic DNA (up to 10 % input mass) demonstrated no assay interference. The test is reproducible from RNA extraction through to Percepta test result, including variation across operators, runs, reagent lots, and laboratories (standard deviation of 0.26 for scores on > 6 unit scale). Analytical sensitivity, analytical specificity and robustness of the Percepta test were successfully verified, supporting its suitability for clinical use.

  8. Healthcare predictive analytics: An overview with a focus on Saudi Arabia.

    PubMed

    Alharthi, Hana

    2018-03-08

    Despite a newfound wealth of data and information, the healthcare sector is lacking in actionable knowledge. This is largely because healthcare data, though plentiful, tends to be inherently complex and fragmented. Health data analytics, with an emphasis on predictive analytics, is emerging as a transformative tool that can enable more proactive and preventative treatment options. This review considers the ways in which predictive analytics has been applied in the for-profit business sector to generate well-timed and accurate predictions of key outcomes, with a focus on key features that may be applicable to healthcare-specific applications. Published medical research presenting assessments of predictive analytics technology in medical applications are reviewed, with particular emphasis on how hospitals have integrated predictive analytics into their day-to-day healthcare services to improve quality of care. This review also highlights the numerous challenges of implementing predictive analytics in healthcare settings and concludes with a discussion of current efforts to implement healthcare data analytics in the developing country, Saudi Arabia. Copyright © 2018 The Author. Published by Elsevier Ltd.. All rights reserved.

  9. Thermodynamics of Gas Turbine Cycles with Analytic Derivatives in OpenMDAO

    NASA Technical Reports Server (NTRS)

    Gray, Justin; Chin, Jeffrey; Hearn, Tristan; Hendricks, Eric; Lavelle, Thomas; Martins, Joaquim R. R. A.

    2016-01-01

    A new equilibrium thermodynamics analysis tool was built based on the CEA method using the OpenMDAO framework. The new tool provides forward and adjoint analytic derivatives for use with gradient based optimization algorithms. The new tool was validated against the original CEA code to ensure an accurate analysis and the analytic derivatives were validated against finite-difference approximations. Performance comparisons between analytic and finite difference methods showed a significant speed advantage for the analytic methods. To further test the new analysis tool, a sample optimization was performed to find the optimal air-fuel equivalence ratio, , maximizing combustion temperature for a range of different pressures. Collectively, the results demonstrate the viability of the new tool to serve as the thermodynamic backbone for future work on a full propulsion modeling tool.

  10. High-Resolution Metabolomics Assessment of Military Personnel: Evaluating Analytical Strategies for Chemical Detection.

    PubMed

    Liu, Ken H; Walker, Douglas I; Uppal, Karan; Tran, ViLinh; Rohrbeck, Patricia; Mallon, Timothy M; Jones, Dean P

    2016-08-01

    The aim of this study was to maximize detection of serum metabolites with high-resolution metabolomics (HRM). Department of Defense Serum Repository (DoDSR) samples were analyzed using ultrahigh resolution mass spectrometry with three complementary chromatographic phases and four ionization modes. Chemical coverage was evaluated by number of ions detected and accurate mass matches to a human metabolomics database. Individual HRM platforms provided accurate mass matches for up to 58% of the KEGG metabolite database. Combining two analytical methods increased matches to 72% and included metabolites in most major human metabolic pathways and chemical classes. Detection and feature quality varied by analytical configuration. Dual chromatography HRM with positive and negative electrospray ionization provides an effective generalized method for metabolic assessment of military personnel.

  11. High-resolution metabolomics assessment of military personnel: Evaluating analytical strategies for chemical detection

    PubMed Central

    Liu, Ken H.; Walker, Douglas I.; Uppal, Karan; Tran, ViLinh; Rohrbeck, Patricia; Mallon, Timothy M.; Jones, Dean P.

    2016-01-01

    Objective To maximize detection of serum metabolites with high-resolution metabolomics (HRM). Methods Department of Defense Serum Repository (DoDSR) samples were analyzed using ultra-high resolution mass spectrometry with three complementary chromatographic phases and four ionization modes. Chemical coverage was evaluated by number of ions detected and accurate mass matches to a human metabolomics database. Results Individual HRM platforms provided accurate mass matches for up to 58% of the KEGG metabolite database. Combining two analytical methods increased matches to 72%, and included metabolites in most major human metabolic pathways and chemical classes. Detection and feature quality varied by analytical configuration. Conclusions Dual chromatography HRM with positive and negative electrospray ionization provides an effective generalized method for metabolic assessment of military personnel. PMID:27501105

  12. Analytical transmission cross-coefficients for pink beam X-ray microscopy based on compound refractive lenses.

    PubMed

    Falch, Ken Vidar; Detlefs, Carsten; Snigirev, Anatoly; Mathiesen, Ragnvald H

    2018-01-01

    Analytical expressions for the transmission cross-coefficients for x-ray microscopes based on compound refractive lenses are derived based on Gaussian approximations of the source shape and energy spectrum. The effects of partial coherence, defocus, beam convergence, as well as lateral and longitudinal chromatic aberrations are accounted for and discussed. Taking the incoherent limit of the transmission cross-coefficients, a compact analytical expression for the modulation transfer function of the system is obtained, and the resulting point, line and edge spread functions are presented. Finally, analytical expressions for optimal numerical aperture, coherence ratio, and bandwidth are given. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Rapid perfusion quantification using Welch-Satterthwaite approximation and analytical spectral filtering

    NASA Astrophysics Data System (ADS)

    Krishnan, Karthik; Reddy, Kasireddy V.; Ajani, Bhavya; Yalavarthy, Phaneendra K.

    2017-02-01

    CT and MR perfusion weighted imaging (PWI) enable quantification of perfusion parameters in stroke studies. These parameters are calculated from the residual impulse response function (IRF) based on a physiological model for tissue perfusion. The standard approach for estimating the IRF is deconvolution using oscillatory-limited singular value decomposition (oSVD) or Frequency Domain Deconvolution (FDD). FDD is widely recognized as the fastest approach currently available for deconvolution of CT Perfusion/MR PWI. In this work, three faster methods are proposed. The first is a direct (model based) crude approximation to the final perfusion quantities (Blood flow, Blood volume, Mean Transit Time and Delay) using the Welch-Satterthwaite approximation for gamma fitted concentration time curves (CTC). The second method is a fast accurate deconvolution method, we call Analytical Fourier Filtering (AFF). The third is another fast accurate deconvolution technique using Showalter's method, we call Analytical Showalter's Spectral Filtering (ASSF). Through systematic evaluation on phantom and clinical data, the proposed methods are shown to be computationally more than twice as fast as FDD. The two deconvolution based methods, AFF and ASSF, are also shown to be quantitatively accurate compared to FDD and oSVD.

  14. Analytic barrage attack model. Final report, January 1986-January 1989

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

    St Ledger, J.W.; Naegeli, R.E.; Dowden, N.A.

    An analytic model is developed for a nuclear barrage attack, assuming weapons with no aiming error and a cookie-cutter damage function. The model is then extended with approximations for the effects of aiming error and distance damage sigma. The final result is a fast running model which calculates probability of damage for a barrage attack. The probability of damage is accurate to within seven percent or better, for weapon reliabilities of 50 to 100 percent, distance damage sigmas of 0.5 or less, and zero to very large circular error probabilities. FORTRAN 77 coding is included in the report for themore » analytic model and for a numerical model used to check the analytic results.« less

  15. Fas expression in renal cell carcinoma accurately predicts patient survival after radical nephrectomy.

    PubMed

    Sejima, Takehiro; Morizane, Shuichi; Hinata, Nobuyuki; Yao, Akihisa; Isoyama, Tadahiro; Saito, Motoaki; Takenaka, Atsushi

    2012-01-01

    To investigate Fas, Fas ligand (FasL) and Bcl-2 expression, which are considered to be important apoptotic regulatory factors in renal cell carcinomas (RCCs). mRNA quantification and immunohistochemistry allowed for the determination of the expression of these three factors in surgically resected tumors from 82 patients with RCC. The correlation of protein and gene expression with more than 10 years of survival data following nephrectomy (along with clinical and pathologic parameters) was analyzed using uni- and multivariate statistical models. A significantly poorer outcome was observed in patients with tumors expressing high levels of Fas mRNA in the multivariate analysis (p = 0.0002). In addition, patient survival was significantly worse in FasL mRNA-positive tumor cases when compared with FasL mRNA-negative cases (p = 0.0345). Ten cases relapsed more than 5 years after nephrectomy. Among them, the tumors of 8 cases (80%) did not express FasL mRNA. Analysis of Bcl-2 did not show statistical significance of Bcl-2 expression as a prognostic indicator. The data suggest that pronounced Fas expression is a surrogate biomarker of active cancer cell proliferation. Given the FasL tumor counterattack theory, FasL overexpression in RCC may be one of the host immune deficiencies, consequently leading to poor prognosis. Copyright © 2012 S. Karger AG, Basel.

  16. An improved analytic function for predicting light fluence rate in circular fields on a semi-infinite geometry

    NASA Astrophysics Data System (ADS)

    Zhu, Timothy C.; Lu, Amy; Ong, Yi-Hong

    2016-03-01

    Accurate determination of in-vivo light fluence rate is critical for preclinical and clinical studies involving photodynamic therapy (PDT). This study compares the longitudinal light fluence distribution inside biological tissue in the central axis of a 1 cm diameter circular uniform light field for a range of in-vivo tissue optical properties (absorption coefficients (μa) between 0.01 and 1 cm-1 and reduced scattering coefficients (μs') between 2 and 40 cm-1). This was done using Monte-Carlo simulations for a semi-infinite turbid medium in an air-tissue interface. The end goal is to develop an analytical expression that would fit the results from the Monte Carlo simulation for both the 1 cm diameter circular beam and the broad beam. Each of these parameters is expressed as a function of tissue optical properties. These results can then be compared against the existing expressions in the literature for broad beam for analysis in both accuracy and applicable range. Using the 6-parameter model, the range and accuracy for light transport through biological tissue is improved and may be used in the future as a guide in PDT for light fluence distribution for known tissue optical properties.

  17. Analytic TOF PET reconstruction algorithm within DIRECT data partitioning framework

    PubMed Central

    Matej, Samuel; Daube-Witherspoon, Margaret E.; Karp, Joel S.

    2016-01-01

    Iterative reconstruction algorithms are routinely used for clinical practice; however, analytic algorithms are relevant candidates for quantitative research studies due to their linear behavior. While iterative algorithms also benefit from the inclusion of accurate data and noise models the widespread use of TOF scanners with less sensitivity to noise and data imperfections make analytic algorithms even more promising. In our previous work we have developed a novel iterative reconstruction approach (Direct Image Reconstruction for TOF) providing convenient TOF data partitioning framework and leading to very efficient reconstructions. In this work we have expanded DIRECT to include an analytic TOF algorithm with confidence weighting incorporating models of both TOF and spatial resolution kernels. Feasibility studies using simulated and measured data demonstrate that analytic-DIRECT with appropriate resolution and regularization filters is able to provide matched bias vs. variance performance to iterative TOF reconstruction with a matched resolution model. PMID:27032968

  18. Analytic TOF PET reconstruction algorithm within DIRECT data partitioning framework

    NASA Astrophysics Data System (ADS)

    Matej, Samuel; Daube-Witherspoon, Margaret E.; Karp, Joel S.

    2016-05-01

    Iterative reconstruction algorithms are routinely used for clinical practice; however, analytic algorithms are relevant candidates for quantitative research studies due to their linear behavior. While iterative algorithms also benefit from the inclusion of accurate data and noise models the widespread use of time-of-flight (TOF) scanners with less sensitivity to noise and data imperfections make analytic algorithms even more promising. In our previous work we have developed a novel iterative reconstruction approach (DIRECT: direct image reconstruction for TOF) providing convenient TOF data partitioning framework and leading to very efficient reconstructions. In this work we have expanded DIRECT to include an analytic TOF algorithm with confidence weighting incorporating models of both TOF and spatial resolution kernels. Feasibility studies using simulated and measured data demonstrate that analytic-DIRECT with appropriate resolution and regularization filters is able to provide matched bias versus variance performance to iterative TOF reconstruction with a matched resolution model.

  19. Fast analytical scatter estimation using graphics processing units.

    PubMed

    Ingleby, Harry; Lippuner, Jonas; Rickey, Daniel W; Li, Yue; Elbakri, Idris

    2015-01-01

    To develop a fast patient-specific analytical estimator of first-order Compton and Rayleigh scatter in cone-beam computed tomography, implemented using graphics processing units. The authors developed an analytical estimator for first-order Compton and Rayleigh scatter in a cone-beam computed tomography geometry. The estimator was coded using NVIDIA's CUDA environment for execution on an NVIDIA graphics processing unit. Performance of the analytical estimator was validated by comparison with high-count Monte Carlo simulations for two different numerical phantoms. Monoenergetic analytical simulations were compared with monoenergetic and polyenergetic Monte Carlo simulations. Analytical and Monte Carlo scatter estimates were compared both qualitatively, from visual inspection of images and profiles, and quantitatively, using a scaled root-mean-square difference metric. Reconstruction of simulated cone-beam projection data of an anthropomorphic breast phantom illustrated the potential of this method as a component of a scatter correction algorithm. The monoenergetic analytical and Monte Carlo scatter estimates showed very good agreement. The monoenergetic analytical estimates showed good agreement for Compton single scatter and reasonable agreement for Rayleigh single scatter when compared with polyenergetic Monte Carlo estimates. For a voxelized phantom with dimensions 128 × 128 × 128 voxels and a detector with 256 × 256 pixels, the analytical estimator required 669 seconds for a single projection, using a single NVIDIA 9800 GX2 video card. Accounting for first order scatter in cone-beam image reconstruction improves the contrast to noise ratio of the reconstructed images. The analytical scatter estimator, implemented using graphics processing units, provides rapid and accurate estimates of single scatter and with further acceleration and a method to account for multiple scatter may be useful for practical scatter correction schemes.

  20. A new expression of Ns versus Ef to an accurate control charge model for AlGaAs/GaAs

    NASA Astrophysics Data System (ADS)

    Bouneb, I.; Kerrour, F.

    2016-03-01

    Semi-conductor components become the privileged support of information and communication, particularly appreciation to the development of the internet. Today, MOS transistors on silicon dominate largely the semi-conductors market, however the diminution of transistors grid length is not enough to enhance the performances and respect Moore law. Particularly, for broadband telecommunications systems, where faster components are required. For this reason, alternative structures proposed like hetero structures IV-IV or III-V [1] have been.The most effective components in this area (High Electron Mobility Transistor: HEMT) on IIIV substrate. This work investigates an approach for contributing to the development of a numerical model based on physical and numerical modelling of the potential at heterostructure in AlGaAs/GaAs interface. We have developed calculation using projective methods allowed the Hamiltonian integration using Green functions in Schrodinger equation, for a rigorous resolution “self coherent” with Poisson equation. A simple analytical approach for charge-control in quantum well region of an AlGaAs/GaAs HEMT structure was presented. A charge-control equation, accounting for a variable average distance of the 2-DEG from the interface was introduced. Our approach which have aim to obtain ns-Vg characteristics is mainly based on: A new linear expression of Fermi-level variation with two-dimensional electron gas density in high electron mobility and also is mainly based on the notion of effective doping and a new expression of AEc

  1. Rapid analytical assessment of the mechanical perturbations induced by non-isothermal injection into a subsurface formation.

    NASA Astrophysics Data System (ADS)

    De Simone, Silvia; Carrera, Jesús; María Gómez Castro, Berta

    2016-04-01

    Fluid injection into geological formations is required for several engineering operations, e.g. geothermal energy production, hydrocarbon production and storage, CO2 storage, wastewater disposal, etc. Non-isothermal fluid injection causes alterations of the pressure and temperature fields, which affect the mechanical stability of the reservoir. This coupled thermo-hydro-mechanical behavior has become a matter of special interest because of public concern about induced seismicity. The response is complex and its evaluation often requires numerical modeling. Nevertheless, analytical solutions are useful in improving our understanding of interactions, identifying the controlling parameters, testing codes and in providing a rapid assessment of the system response to an alteration. We present an easy-to-use solution to the transient advection-conduction heat transfer problem for parallel and radial flow. The solution is then applied to derive analytical expressions for hydraulic and thermal driven displacements and stresses. The validity is verified by comparison with numerical simulations and yields fairly accurate results. The solution is then used to illustrate some features of the poroelastic and thermoelastic response and, in particular, the sensitivity to the external mechanical constraints and to the reservoir dimension.

  2. Analytic Scattering and Refraction Models for Exoplanet Transit Spectra

    NASA Astrophysics Data System (ADS)

    Robinson, Tyler D.; Fortney, Jonathan J.; Hubbard, William B.

    2017-12-01

    Observations of exoplanet transit spectra are essential to understanding the physics and chemistry of distant worlds. The effects of opacity sources and many physical processes combine to set the shape of a transit spectrum. Two such key processes—refraction and cloud and/or haze forward-scattering—have seen substantial recent study. However, models of these processes are typically complex, which prevents their incorporation into observational analyses and standard transit spectrum tools. In this work, we develop analytic expressions that allow for the efficient parameterization of forward-scattering and refraction effects in transit spectra. We derive an effective slant optical depth that includes a correction for forward-scattered light, and present an analytic form of this correction. We validate our correction against a full-physics transit spectrum model that includes scattering, and we explore the extent to which the omission of forward-scattering effects may bias models. Also, we verify a common analytic expression for the location of a refractive boundary, which we express in terms of the maximum pressure probed in a transit spectrum. This expression is designed to be easily incorporated into existing tools, and we discuss how the detection of a refractive boundary could help indicate the background atmospheric composition by constraining the bulk refractivity of the atmosphere. Finally, we show that opacity from Rayleigh scattering and collision-induced absorption will outweigh the effects of refraction for Jupiter-like atmospheres whose equilibrium temperatures are above 400-500 K.

  3. Analytical procedures for water-soluble vitamins in foods and dietary supplements: a review.

    PubMed

    Blake, Christopher J

    2007-09-01

    Water-soluble vitamins include the B-group vitamins and vitamin C. In order to correctly monitor water-soluble vitamin content in fortified foods for compliance monitoring as well as to establish accurate data banks, an accurate and precise analytical method is a prerequisite. For many years microbiological assays have been used for analysis of B vitamins. However they are no longer considered to be the gold standard in vitamins analysis as many studies have shown up their deficiencies. This review describes the current status of analytical methods, including microbiological assays and spectrophotometric, biosensor and chromatographic techniques. In particular it describes the current status of the official methods and highlights some new developments in chromatographic procedures and detection methods. An overview is made of multivitamin extractions and analyses for foods and supplements.

  4. Accurate modelling of unsteady flows in collapsible tubes.

    PubMed

    Marchandise, Emilie; Flaud, Patrice

    2010-01-01

    The context of this paper is the development of a general and efficient numerical haemodynamic tool to help clinicians and researchers in understanding of physiological flow phenomena. We propose an accurate one-dimensional Runge-Kutta discontinuous Galerkin (RK-DG) method coupled with lumped parameter models for the boundary conditions. The suggested model has already been successfully applied to haemodynamics in arteries and is now extended for the flow in collapsible tubes such as veins. The main difference with cardiovascular simulations is that the flow may become supercritical and elastic jumps may appear with the numerical consequence that scheme may not remain monotone if no limiting procedure is introduced. We show that our second-order RK-DG method equipped with an approximate Roe's Riemann solver and a slope-limiting procedure allows us to capture elastic jumps accurately. Moreover, this paper demonstrates that the complex physics associated with such flows is more accurately modelled than with traditional methods such as finite difference methods or finite volumes. We present various benchmark problems that show the flexibility and applicability of the numerical method. Our solutions are compared with analytical solutions when they are available and with solutions obtained using other numerical methods. Finally, to illustrate the clinical interest, we study the emptying process in a calf vein squeezed by contracting skeletal muscle in a normal and pathological subject. We compare our results with experimental simulations and discuss the sensitivity to parameters of our model.

  5. Analytical estimation on divergence and flutter vibrations of symmetrical three-phase induction stator via field-synchronous coordinates

    NASA Astrophysics Data System (ADS)

    Xia, Ying; Wang, Shiyu; Sun, Wenjia; Xiu, Jie

    2017-01-01

    The electromagnetically induced parametric vibration of the symmetrical three-phase induction stator is examined. While it can be analyzed by an approximate analytical or numerical method, more accurate and simple analytical method is desirable. This work proposes a new method based on the field-synchronous coordinates. A mechanical-electromagnetic coupling model is developed under this frame such that a time-invariant governing equation with gyroscopic term can be developed. With the general vibration theory, the eigenvalue is formulated; the transition curves between the stable and unstable regions, and response are all determined as closed-form expressions of basic mechanical-electromagnetic parameters. The dependence of these parameters on the instability behaviors is demonstrated. The results imply that the divergence and flutter instabilities can occur even for symmetrical motors with balanced, constant amplitude and sinusoidal voltage. To verify the analytical predictions, this work also builds up a time-variant model of the same system under the conventional inertial frame. The Floquét theory is employed to predict the parametric instability and the numerical integration is used to obtain the parametric response. The parametric instability and response are both well compared against those under the field-synchronous coordinates. The proposed field-synchronous coordinates allows a quick estimation on the electromagnetically induced vibration. The convenience offered by the body-fixed coordinates is discussed across various fields.

  6. Pulsed plane wave analytic solutions for generic shapes and the validation of Maxwell's equations solvers

    NASA Technical Reports Server (NTRS)

    Yarrow, Maurice; Vastano, John A.; Lomax, Harvard

    1992-01-01

    Generic shapes are subjected to pulsed plane waves of arbitrary shape. The resulting scattered electromagnetic fields are determined analytically. These fields are then computed efficiently at field locations for which numerically determined EM fields are required. Of particular interest are the pulsed waveform shapes typically utilized by radar systems. The results can be used to validate the accuracy of finite difference time domain Maxwell's equations solvers. A two-dimensional solver which is second- and fourth-order accurate in space and fourth-order accurate in time is examined. Dielectric media properties are modeled by a ramping technique which simplifies the associated gridding of body shapes. The attributes of the ramping technique are evaluated by comparison with the analytic solutions.

  7. Analytical method for the effects of the asteroid belt on planetary orbits

    NASA Technical Reports Server (NTRS)

    Mayo, A. P.

    1979-01-01

    Analytic expressions are derived for the perturbation of planetary orbits due to a thick constant-density asteroid belt. The derivations include extensions and adaptations of Plakhov's (1968) analytic expressions for the perturbations in five of the orbital elements for closed orbits around Saturn's rings. The equations of Plakhov are modified to include the effect of ring thickness, and additional equations are derived for the perturbations in the sixth orbital element, the mean anomaly. The gravitational potential and orbital perturbations are derived for the asteroid belt with and without thickness, and for a hoop approximation to the belt. The procedures are also applicable to Saturn's rings and the newly discovered rings of Uranus. The effects of the asteroid belt thickness on the gravitational potential coefficients and the orbital motions are demonstrated. Comparisons between the Mars orbital perturbations obtained by using the analytic expressions and those obtained by numerical integration are discussed. The effects of the asteroid belt on earth-based ranging to Mars are also demonstrated.

  8. Analytic Expression of Geometric Discord in Arbitrary Mixture of any Two Bi-qubit Product Pure States

    NASA Astrophysics Data System (ADS)

    Xie, Chuan-Mei; Liu, Yi-Min; Xing, Hang; Zhang, Zhan-Jun

    2015-04-01

    Quantum correlations in a family of states comprising any mixture of a pair of arbitrary bi-qubit product pure states are studied by employing geometric discord [Phys. Rev. Lett. 105 (2010) 190502] as the quantifier. First, the inherent symmetry in the family of states about local unitary transformations is revealed. Then, the analytic expression of geometric discords in the states is worked out. Some concrete discussions and analyses on the captured geometric discords are made so that their distinct features are exposed. It is found that, the more averagely the two bi-qubit product states are mixed, the bigger geometric discord the mixed state owns. Moreover, the monotonic relationships of geometric discord with different parameters are revealed. Supported by the National Natural Science Foundation of China (NNSFC) under Grant Nos. 11375011 and 11372122, the Natural Science Foundation of Anhui Province under Grant No. 1408085MA12, and the 211 Project of Anhui University

  9. A singularity free analytical solution of artificial satellite motion with drag

    NASA Technical Reports Server (NTRS)

    Mueller, A.

    1978-01-01

    An analytical satellite theory based on the regular, canonical Poincare-Similar (PS phi) elements is described along with an accurate density model which can be implemented into the drag theory. A computationally efficient manner in which to expand the equations of motion into a fourier series is discussed.

  10. Supersaturation Control using Analytical Crystal Size Distribution Estimator for Temperature Dependent in Nucleation and Crystal Growth Phenomena

    NASA Astrophysics Data System (ADS)

    Zahari, Zakirah Mohd; Zubaidah Adnan, Siti; Kanthasamy, Ramesh; Saleh, Suriyati; Samad, Noor Asma Fazli Abdul

    2018-03-01

    The specification of the crystal product is usually given in terms of crystal size distribution (CSD). To this end, optimal cooling strategy is necessary to achieve the CSD. The direct design control involving analytical CSD estimator is one of the approaches that can be used to generate the set-point. However, the effects of temperature on the crystal growth rate are neglected in the estimator. Thus, the temperature dependence on the crystal growth rate needs to be considered in order to provide an accurate set-point. The objective of this work is to extend the analytical CSD estimator where Arrhenius expression is employed to cover the effects of temperature on the growth rate. The application of this work is demonstrated through a potassium sulphate crystallisation process. Based on specified target CSD, the extended estimator is capable of generating the required set-point where a proposed controller successfully maintained the operation at the set-point to achieve the target CSD. Comparison with other cooling strategies shows a reduction up to 18.2% of the total number of undesirable crystals generated from secondary nucleation using linear cooling strategy is achieved.

  11. Field-driven chiral bubble dynamics analysed by a semi-analytical approach

    NASA Astrophysics Data System (ADS)

    Vandermeulen, J.; Leliaert, J.; Dupré, L.; Van Waeyenberge, B.

    2017-12-01

    Nowadays, field-driven chiral bubble dynamics in the presence of the Dzyaloshinskii-Moriya interaction are a topic of thorough investigation. In this paper, a semi-analytical approach is used to derive equations of motion that express the bubble wall (BW) velocity and the change in in-plane magnetization angle as function of the micromagnetic parameters of the involved interactions, thereby taking into account the two-dimensional nature of the bubble wall. It is demonstrated that the equations of motion enable an accurate description of the expanding and shrinking convex bubble dynamics and an expression for the transition field between shrinkage and expansion is derived. In addition, these equations of motion show that the BW velocity is not only dependent on the driving force, but also on the BW curvature. The absolute BW velocity increases for both a shrinking and an expanding bubble, but for different reasons: for expanding bubbles, it is due to the increasing importance of the driving force, while for shrinking bubbles, it is due to the increasing importance of contributions related to the BW curvature. Finally, using this approach we show how the recently proposed magnetic bubblecade memory can operate in the flow regime in the presence of a tilted sinusoidal magnetic field and at greatly reduced bubble sizes compared to the original device prototype.

  12. Metabolomics and Diabetes: Analytical and Computational Approaches

    PubMed Central

    Sas, Kelli M.; Karnovsky, Alla; Michailidis, George

    2015-01-01

    Diabetes is characterized by altered metabolism of key molecules and regulatory pathways. The phenotypic expression of diabetes and associated complications encompasses complex interactions between genetic, environmental, and tissue-specific factors that require an integrated understanding of perturbations in the network of genes, proteins, and metabolites. Metabolomics attempts to systematically identify and quantitate small molecule metabolites from biological systems. The recent rapid development of a variety of analytical platforms based on mass spectrometry and nuclear magnetic resonance have enabled identification of complex metabolic phenotypes. Continued development of bioinformatics and analytical strategies has facilitated the discovery of causal links in understanding the pathophysiology of diabetes and its complications. Here, we summarize the metabolomics workflow, including analytical, statistical, and computational tools, highlight recent applications of metabolomics in diabetes research, and discuss the challenges in the field. PMID:25713200

  13. Fall Velocities of Hydrometeors in the Atmosphere: Refinements to a Continuous Analytical Power Law.

    NASA Astrophysics Data System (ADS)

    Khvorostyanov, Vitaly I.; Curry, Judith A.

    2005-12-01

    This paper extends the previous research of the authors on the unified representation of fall velocities for both liquid and crystalline particles as a power law over the entire size range of hydrometeors observed in the atmosphere. The power-law coefficients are determined as continuous analytical functions of the Best or Reynolds number or of the particle size. Here, analytical expressions are formulated for the turbulent corrections to the Reynolds number and to the power-law coefficients that describe the continuous transition from the laminar to the turbulent flow around a falling particle. A simple analytical expression is found for the correction of fall velocities for temperature and pressure. These expressions and the resulting fall velocities are compared with observations and other calculations for a range of ice crystal habits and sizes. This approach provides a continuous analytical power-law description of the terminal velocities of liquid and crystalline hydrometeors with sufficiently high accuracy and can be directly used in bin-resolving models or incorporated into parameterizations for cloud- and large-scale models and remote sensing techniques.

  14. That "poker face" just might lose you the game! The impact of expressive suppression and mimicry on sensitivity to facial expressions of emotion.

    PubMed

    Schneider, Kristin G; Hempel, Roelie J; Lynch, Thomas R

    2013-10-01

    Successful interpersonal functioning often requires both the ability to mask inner feelings and the ability to accurately recognize others' expressions--but what if effortful control of emotional expressions impacts the ability to accurately read others? In this study, we examined the influence of self-controlled expressive suppression and mimicry on facial affect sensitivity--the speed with which one can accurately identify gradually intensifying facial expressions of emotion. Muscle activity of the brow (corrugator, related to anger), upper lip (levator, related to disgust), and cheek (zygomaticus, related to happiness) were recorded using facial electromyography while participants randomized to one of three conditions (Suppress, Mimic, and No-Instruction) viewed a series of six distinct emotional expressions (happiness, sadness, fear, anger, surprise, and disgust) as they morphed from neutral to full expression. As hypothesized, individuals instructed to suppress their own facial expressions showed impairment in facial affect sensitivity. Conversely, mimicry of emotion expressions appeared to facilitate facial affect sensitivity. Results suggest that it is difficult for a person to be able to simultaneously mask inner feelings and accurately "read" the facial expressions of others, at least when these expressions are at low intensity. The combined behavioral and physiological data suggest that the strategies an individual selects to control his or her own expression of emotion have important implications for interpersonal functioning.

  15. Substrate mass transfer: analytical approach for immobilized enzyme reactions

    NASA Astrophysics Data System (ADS)

    Senthamarai, R.; Saibavani, T. N.

    2018-04-01

    In this paper, the boundary value problem in immobilized enzyme reactions is formulated and approximate expression for substrate concentration without external mass transfer resistance is presented. He’s variational iteration method is used to give approximate and analytical solutions of non-linear differential equation containing a non linear term related to enzymatic reaction. The relevant analytical solution for the dimensionless substrate concentration profile is discussed in terms of dimensionless reaction parameters α and β.

  16. Analytic theory for the selection of 2-D needle crystal at arbitrary Peclet number

    NASA Technical Reports Server (NTRS)

    Tanveer, Saleh

    1989-01-01

    An accurate analytic theory is presented for the velocity selection of a two-dimensional needle crystal for arbitrary Peclet number for small values of the surface tension parameter. The velocity selection is caused by the effect of transcendentally small terms which are determined by analytic continuation to the complex plane and analysis of nonlinear equations. The work supports the general conclusion of previous small Peclet number analytical results of other investigators, though there are some discrepancies in details. It also addresses questions raised on the validity of selection theory owing to assumptions made on shape corrections at large distances from the tip.

  17. Exact expressions and accurate approximations for the dependences of radius and index of refraction of solutions of inorganic solutes on relative humidity

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

    Lewis, E.R.; Schwartz, S.

    2010-03-15

    Light scattering by aerosols plays an important role in Earth’s radiative balance, and quantification of this phenomenon is important in understanding and accounting for anthropogenic influences on Earth’s climate. Light scattering by an aerosol particle is determined by its radius and index of refraction, and for aerosol particles that are hygroscopic, both of these quantities vary with relative humidity RH. Here exact expressions are derived for the dependences of the radius ratio (relative to the volume-equivalent dry radius) and index of refraction on RH for aqueous solutions of single solutes. Both of these quantities depend on the apparent molal volumemore » of the solute in solution and on the practical osmotic coefficient of the solution, which in turn depend on concentration and thus implicitly on RH. Simple but accurate approximations are also presented for the RH dependences of both radius ratio and index of refraction for several atmospherically important inorganic solutes over the entire range of RH values for which these substances can exist as solution drops. For all substances considered, the radius ratio is accurate to within a few percent, and the index of refraction to within ~0.02, over this range of RH. Such parameterizations will be useful in radiation transfer models and climate models.« less

  18. Accurate radiative transfer calculations for layered media.

    PubMed

    Selden, Adrian C

    2016-07-01

    Simple yet accurate results for radiative transfer in layered media with discontinuous refractive index are obtained by the method of K-integrals. These are certain weighted integrals applied to the angular intensity distribution at the refracting boundaries. The radiative intensity is expressed as the sum of the asymptotic angular intensity distribution valid in the depth of the scattering medium and a transient term valid near the boundary. Integrated boundary equations are obtained, yielding simple linear equations for the intensity coefficients, enabling the angular emission intensity and the diffuse reflectance (albedo) and transmittance of the scattering layer to be calculated without solving the radiative transfer equation directly. Examples are given of half-space, slab, interface, and double-layer calculations, and extensions to multilayer systems are indicated. The K-integral method is orders of magnitude more accurate than diffusion theory and can be applied to layered scattering media with a wide range of scattering albedos, with potential applications to biomedical and ocean optics.

  19. An Analytic Approach to Projectile Motion in a Linear Resisting Medium

    ERIC Educational Resources Information Center

    Stewart, Sean M.

    2006-01-01

    The time of flight, range and the angle which maximizes the range of a projectile in a linear resisting medium are expressed in analytic form in terms of the recently defined Lambert W function. From the closed-form solutions a number of results characteristic to the motion of the projectile in a linear resisting medium are analytically confirmed,…

  20. Collisional evolution - an analytical study for the non steady-state mass distribution.

    NASA Astrophysics Data System (ADS)

    Vieira Martins, R.

    1999-05-01

    To study the collisional evolution of asteroidal groups one can use an analytical solution for the self-similar collision cascades. This solution is suitable to study the steady-state mass distribution of the collisional fragmentation. However, out of the steady-state conditions, this solution is not satisfactory for some values of the collisional parameters. In fact, for some values for the exponent of the mass distribution power law of an asteroidal group and its relation to the exponent of the function which describes "how rocks break" the author arrives at singular points for the equation which describes the collisional evolution. These singularities appear since some approximations are usually made in the laborious evaluation of many integrals that appear in the analytical calculations. They concern the cutoff for the smallest and the largest bodies. These singularities set some restrictions to the study of the analytical solution for the collisional equation. To overcome these singularities the author performed an algebraic computation considering the smallest and the largest bodies and he obtained the analytical expressions for the integrals that describe the collisional evolution without restriction on the parameters. However, the new distribution is more sensitive to the values of the collisional parameters. In particular the steady-state solution for the differential mass distribution has exponents slightly different from 11/6 for the usual parameters in the asteroid belt. The sensitivity of this distribution with respect to the parameters is analyzed for the usual values in the asteroidal groups. With an expression for the mass distribution without singularities, one can evaluate also its time evolution. The author arrives at an analytical expression given by a power series of terms constituted by a small parameter multiplied by the mass to an exponent, which depends on the initial power law distribution. This expression is a formal solution for the

  1. Fast analytical spectral filtering methods for magnetic resonance perfusion quantification.

    PubMed

    Reddy, Kasireddy V; Mitra, Abhishek; Yalavarthy, Phaneendra K

    2016-08-01

    The deconvolution in the perfusion weighted imaging (PWI) plays an important role in quantifying the MR perfusion parameters. The PWI application to stroke and brain tumor studies has become a standard clinical practice. The standard approach for this deconvolution is oscillatory-limited singular value decomposition (oSVD) and frequency domain deconvolution (FDD). The FDD is widely recognized as the fastest approach currently available for deconvolution of MR perfusion data. In this work, two fast deconvolution methods (namely analytical fourier filtering and analytical showalter spectral filtering) are proposed. Through systematic evaluation, the proposed methods are shown to be computationally efficient and quantitatively accurate compared to FDD and oSVD.

  2. Analytical Model For Fluid Dynamics In A Microgravity Environment

    NASA Technical Reports Server (NTRS)

    Naumann, Robert J.

    1995-01-01

    Report presents analytical approximation methodology for providing coupled fluid-flow, heat, and mass-transfer equations in microgravity environment. Experimental engineering estimates accurate to within factor of 2 made quickly and easily, eliminating need for time-consuming and costly numerical modeling. Any proposed experiment reviewed to see how it would perform in microgravity environment. Model applied in commercial setting for preliminary design of low-Grashoff/Rayleigh-number experiments.

  3. Health Informatics for Neonatal Intensive Care Units: An Analytical Modeling Perspective

    PubMed Central

    Mench-Bressan, Nadja; McGregor, Carolyn; Pugh, James Edward

    2015-01-01

    The effective use of data within intensive care units (ICUs) has great potential to create new cloud-based health analytics solutions for disease prevention or earlier condition onset detection. The Artemis project aims to achieve the above goals in the area of neonatal ICUs (NICU). In this paper, we proposed an analytical model for the Artemis cloud project which will be deployed at McMaster Children’s Hospital in Hamilton. We collect not only physiological data but also the infusion pumps data that are attached to NICU beds. Using the proposed analytical model, we predict the amount of storage, memory, and computation power required for the system. Capacity planning and tradeoff analysis would be more accurate and systematic by applying the proposed analytical model in this paper. Numerical results are obtained using real inputs acquired from McMaster Children’s Hospital and a pilot deployment of the system at The Hospital for Sick Children (SickKids) in Toronto. PMID:27170907

  4. Continuous Metabolic Monitoring Based on Multi-Analyte Biomarkers to Predict Exhaustion

    PubMed Central

    Kastellorizios, Michail; Burgess, Diane J.

    2015-01-01

    This work introduces the concept of multi-analyte biomarkers for continuous metabolic monitoring. The importance of using more than one marker lies in the ability to obtain a holistic understanding of the metabolism. This is showcased for the detection and prediction of exhaustion during intense physical exercise. The findings presented here indicate that when glucose and lactate changes over time are combined into multi-analyte biomarkers, their monitoring trends are more sensitive in the subcutaneous tissue, an implantation-friendly peripheral tissue, compared to the blood. This unexpected observation was confirmed in normal as well as type 1 diabetic rats. This study was designed to be of direct value to continuous monitoring biosensor research, where single analytes are typically monitored. These findings can be implemented in new multi-analyte continuous monitoring technologies for more accurate insulin dosing, as well as for exhaustion prediction studies based on objective data rather than the subject’s perception. PMID:26028477

  5. Continuous metabolic monitoring based on multi-analyte biomarkers to predict exhaustion.

    PubMed

    Kastellorizios, Michail; Burgess, Diane J

    2015-06-01

    This work introduces the concept of multi-analyte biomarkers for continuous metabolic monitoring. The importance of using more than one marker lies in the ability to obtain a holistic understanding of the metabolism. This is showcased for the detection and prediction of exhaustion during intense physical exercise. The findings presented here indicate that when glucose and lactate changes over time are combined into multi-analyte biomarkers, their monitoring trends are more sensitive in the subcutaneous tissue, an implantation-friendly peripheral tissue, compared to the blood. This unexpected observation was confirmed in normal as well as type 1 diabetic rats. This study was designed to be of direct value to continuous monitoring biosensor research, where single analytes are typically monitored. These findings can be implemented in new multi-analyte continuous monitoring technologies for more accurate insulin dosing, as well as for exhaustion prediction studies based on objective data rather than the subject's perception.

  6. Assessment of the analytical capabilities of inductively coupled plasma-mass spectrometry

    USGS Publications Warehouse

    Taylor, Howard E.; Garbarino, John R.

    1988-01-01

    A thorough assessment of the analytical capabilities of inductively coupled plasma-mass spectrometry was conducted for selected analytes of importance in water quality applications and hydrologic research. A multielement calibration curve technique was designed to produce accurate and precise results in analysis times of approximately one minute. The suite of elements included Al, As, B, Ba, Be, Cd, Co, Cr, Cu, Hg, Li, Mn, Mo, Ni, Pb, Se, Sr, V, and Zn. The effects of sample matrix composition on the accuracy of the determinations showed that matrix elements (such as Na, Ca, Mg, and K) that may be present in natural water samples at concentration levels greater than 50 mg/L resulted in as much as a 10% suppression in ion current for analyte elements. Operational detection limits are presented.

  7. Real-Time Analytics for the Healthcare Industry: Arrhythmia Detection.

    PubMed

    Agneeswaran, Vijay Srinivas; Mukherjee, Joydeb; Gupta, Ashutosh; Tonpay, Pranay; Tiwari, Jayati; Agarwal, Nitin

    2013-09-01

    It is time for the healthcare industry to move from the era of "analyzing our health history" to the age of "managing the future of our health." In this article, we illustrate the importance of real-time analytics across the healthcare industry by providing a generic mechanism to reengineer traditional analytics expressed in the R programming language into Storm-based real-time analytics code. This is a powerful abstraction, since most data scientists use R to write the analytics and are not clear on how to make the data work in real-time and on high-velocity data. Our paper focuses on the applications necessary to a healthcare analytics scenario, specifically focusing on the importance of electrocardiogram (ECG) monitoring. A physician can use our framework to compare ECG reports by categorization and consequently detect Arrhythmia. The framework can read the ECG signals and uses a machine learning-based categorizer that runs within a Storm environment to compare different ECG signals. The paper also presents some performance studies of the framework to illustrate the throughput and accuracy trade-off in real-time analytics.

  8. Analytic solution of field distribution and demagnetization function of ideal hollow cylindrical field source

    NASA Astrophysics Data System (ADS)

    Xu, Xiaonong; Lu, Dingwei; Xu, Xibin; Yu, Yang; Gu, Min

    2017-09-01

    The Halbach type hollow cylindrical permanent magnet array (HCPMA) is a volume compact and energy conserved field source, which have attracted intense interests in many practical applications. Here, using the complex variable integration method based on the Biot-Savart Law (including current distributions inside the body and on the surfaces of magnet), we derive analytical field solutions to an ideal multipole HCPMA in entire space including the interior of magnet. The analytic field expression inside the array material is used to construct an analytic demagnetization function, with which we can explain the origin of demagnetization phenomena in HCPMA by taking into account an ideal magnetic hysteresis loop with finite coercivity. These analytical field expressions and demagnetization functions provide deeper insight into the nature of such permanent magnet array systems and offer guidance in designing optimized array system.

  9. Two-dimensional analytic weighting functions for limb scattering

    NASA Astrophysics Data System (ADS)

    Zawada, D. J.; Bourassa, A. E.; Degenstein, D. A.

    2017-10-01

    Through the inversion of limb scatter measurements it is possible to obtain vertical profiles of trace species in the atmosphere. Many of these inversion methods require what is often referred to as weighting functions, or derivatives of the radiance with respect to concentrations of trace species in the atmosphere. Several radiative transfer models have implemented analytic methods to calculate weighting functions, alleviating the computational burden of traditional numerical perturbation methods. Here we describe the implementation of analytic two-dimensional weighting functions, where derivatives are calculated relative to atmospheric constituents in a two-dimensional grid of altitude and angle along the line of sight direction, in the SASKTRAN-HR radiative transfer model. Two-dimensional weighting functions are required for two-dimensional inversions of limb scatter measurements. Examples are presented where the analytic two-dimensional weighting functions are calculated with an underlying one-dimensional atmosphere. It is shown that the analytic weighting functions are more accurate than ones calculated with a single scatter approximation, and are orders of magnitude faster than a typical perturbation method. Evidence is presented that weighting functions for stratospheric aerosols calculated under a single scatter approximation may not be suitable for use in retrieval algorithms under solar backscatter conditions.

  10. Modeling Biodegradation and Reactive Transport: Analytical and Numerical Models

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

    Sun, Y; Glascoe, L

    The computational modeling of the biodegradation of contaminated groundwater systems accounting for biochemical reactions coupled to contaminant transport is a valuable tool for both the field engineer/planner with limited computational resources and the expert computational researcher less constrained by time and computer power. There exists several analytical and numerical computer models that have been and are being developed to cover the practical needs put forth by users to fulfill this spectrum of computational demands. Generally, analytical models provide rapid and convenient screening tools running on very limited computational power, while numerical models can provide more detailed information with consequent requirementsmore » of greater computational time and effort. While these analytical and numerical computer models can provide accurate and adequate information to produce defensible remediation strategies, decisions based on inadequate modeling output or on over-analysis can have costly and risky consequences. In this chapter we consider both analytical and numerical modeling approaches to biodegradation and reactive transport. Both approaches are discussed and analyzed in terms of achieving bioremediation goals, recognizing that there is always a tradeoff between computational cost and the resolution of simulated systems.« less

  11. Building the analytical response in frequency domain of AC biased bolometers. Application to Planck/HFI

    NASA Astrophysics Data System (ADS)

    Sauvé, Alexandre; Montier, Ludovic

    2016-12-01

    Context: Bolometers are high sensitivity detector commonly used in Infrared astronomy. The HFI instrument of the Planck satellite makes extensive use of them, but after the satellite launch two electronic related problems revealed critical. First an unexpected excess response of detectors at low optical excitation frequency for ν < 1 Hz, and secondly the Analog To digital Converter (ADC) component had been insufficiently characterized on-ground. These two problems require an exquisite knowledge of detector response. However bolometers have highly nonlinear characteristics, coming from their electrical and thermal coupling making them very difficult to model. Goal: We present a method to build the analytical transfer function in frequency domain which describe the voltage response of an Alternative Current (AC) biased bolometer to optical excitation, based on the standard bolometer model. This model is built using the setup of the Planck/HFI instrument and offers the major improvement of being based on a physical model rather than the currently in use had-hoc model based on Direct Current (DC) bolometer theory. Method: The analytical transfer function expression will be presented in matrix form. For this purpose, we build linearized versions of the bolometer electro thermal equilibrium. A custom description of signals in frequency is used to solve the problem with linear algebra. The model performances is validated using time domain simulations. Results: The provided expression is suitable for calibration and data processing. It can also be used to provide constraints for fitting optical transfer function using real data from steady state electronic response and optical response. The accurate description of electronic response can also be used to improve the ADC nonlinearity correction for quickly varying optical signals.

  12. Semi-Analytic Reconstruction of Flux in Finite Volume Formulations

    NASA Technical Reports Server (NTRS)

    Gnoffo, Peter A.

    2006-01-01

    Semi-analytic reconstruction uses the analytic solution to a second-order, steady, ordinary differential equation (ODE) to simultaneously evaluate the convective and diffusive flux at all interfaces of a finite volume formulation. The second-order ODE is itself a linearized approximation to the governing first- and second- order partial differential equation conservation laws. Thus, semi-analytic reconstruction defines a family of formulations for finite volume interface fluxes using analytic solutions to approximating equations. Limiters are not applied in a conventional sense; rather, diffusivity is adjusted in the vicinity of changes in sign of eigenvalues in order to achieve a sufficiently small cell Reynolds number in the analytic formulation across critical points. Several approaches for application of semi-analytic reconstruction for the solution of one-dimensional scalar equations are introduced. Results are compared with exact analytic solutions to Burger s Equation as well as a conventional, upwind discretization using Roe s method. One approach, the end-point wave speed (EPWS) approximation, is further developed for more complex applications. One-dimensional vector equations are tested on a quasi one-dimensional nozzle application. The EPWS algorithm has a more compact difference stencil than Roe s algorithm but reconstruction time is approximately a factor of four larger than for Roe. Though both are second-order accurate schemes, Roe s method approaches a grid converged solution with fewer grid points. Reconstruction of flux in the context of multi-dimensional, vector conservation laws including effects of thermochemical nonequilibrium in the Navier-Stokes equations is developed.

  13. A Stationary Wavelet Entropy-Based Clustering Approach Accurately Predicts Gene Expression

    PubMed Central

    Nguyen, Nha; Vo, An; Choi, Inchan

    2015-01-01

    Abstract Studying epigenetic landscapes is important to understand the condition for gene regulation. Clustering is a useful approach to study epigenetic landscapes by grouping genes based on their epigenetic conditions. However, classical clustering approaches that often use a representative value of the signals in a fixed-sized window do not fully use the information written in the epigenetic landscapes. Clustering approaches to maximize the information of the epigenetic signals are necessary for better understanding gene regulatory environments. For effective clustering of multidimensional epigenetic signals, we developed a method called Dewer, which uses the entropy of stationary wavelet of epigenetic signals inside enriched regions for gene clustering. Interestingly, the gene expression levels were highly correlated with the entropy levels of epigenetic signals. Dewer separates genes better than a window-based approach in the assessment using gene expression and achieved a correlation coefficient above 0.9 without using any training procedure. Our results show that the changes of the epigenetic signals are useful to study gene regulation. PMID:25383910

  14. Nonlinear modelling of high-speed catenary based on analytical expressions of cable and truss elements

    NASA Astrophysics Data System (ADS)

    Song, Yang; Liu, Zhigang; Wang, Hongrui; Lu, Xiaobing; Zhang, Jing

    2015-10-01

    Due to the intrinsic nonlinear characteristics and complex structure of the high-speed catenary system, a modelling method is proposed based on the analytical expressions of nonlinear cable and truss elements. The calculation procedure for solving the initial equilibrium state is proposed based on the Newton-Raphson iteration method. The deformed configuration of the catenary system as well as the initial length of each wire can be calculated. Its accuracy and validity of computing the initial equilibrium state are verified by comparison with the separate model method, absolute nodal coordinate formulation and other methods in the previous literatures. Then, the proposed model is combined with a lumped pantograph model and a dynamic simulation procedure is proposed. The accuracy is guaranteed by the multiple iterative calculations in each time step. The dynamic performance of the proposed model is validated by comparison with EN 50318, the results of the finite element method software and SIEMENS simulation report, respectively. At last, the influence of the catenary design parameters (such as the reserved sag and pre-tension) on the dynamic performance is preliminarily analysed by using the proposed model.

  15. Compact perturbative expressions for neutrino oscillations in matter

    DOE PAGES

    Denton, Peter B.; Minakata, Hisakazu; Parke, Stephen J.

    2016-06-08

    We further develop and extend a recent perturbative framework for neutrino oscillations in uniform matter density so that the resulting oscillation probabilities are accurate for the complete matter potential versus baseline divided by neutrino energy plane. This extension also gives the exact oscillation probabilities in vacuum for all values of baseline divided by neutrino energy. The expansion parameter used is related to the ratio of the solar to the atmosphericmore » $$\\Delta m^2$$ scales but with a unique choice of the atmospheric $$\\Delta m^2$$ such that certain first-order effects are taken into account in the zeroth-order Hamiltonian. Using a mixing matrix formulation, this framework has the exceptional feature that the neutrino oscillation probability in matter has the same structure as in vacuum, to all orders in the expansion parameter. It also contains all orders in the matter potential and $$\\sin\\theta_{13}$$. It facilitates immediate physical interpretation of the analytic results, and makes the expressions for the neutrino oscillation probabilities extremely compact and very accurate even at zeroth order in our perturbative expansion. Furthermore, the first and second order results are also given which improve the precision by approximately two or more orders of magnitude per perturbative order.« less

  16. Combining Graphical and Analytical Methods with Molecular Simulations To Analyze Time-Resolved FRET Measurements of Labeled Macromolecules Accurately

    PubMed Central

    2017-01-01

    Förster resonance energy transfer (FRET) measurements from a donor, D, to an acceptor, A, fluorophore are frequently used in vitro and in live cells to reveal information on the structure and dynamics of DA labeled macromolecules. Accurate descriptions of FRET measurements by molecular models are complicated because the fluorophores are usually coupled to the macromolecule via flexible long linkers allowing for diffusional exchange between multiple states with different fluorescence properties caused by distinct environmental quenching, dye mobilities, and variable DA distances. It is often assumed for the analysis of fluorescence intensity decays that DA distances and D quenching are uncorrelated (homogeneous quenching by FRET) and that the exchange between distinct fluorophore states is slow (quasistatic). This allows us to introduce the FRET-induced donor decay, εD(t), a function solely depending on the species fraction distribution of the rate constants of energy transfer by FRET, for a convenient joint analysis of fluorescence decays of FRET and reference samples by integrated graphical and analytical procedures. Additionally, we developed a simulation toolkit to model dye diffusion, fluorescence quenching by the protein surface, and FRET. A benchmark study with simulated fluorescence decays of 500 protein structures demonstrates that the quasistatic homogeneous model works very well and recovers for single conformations the average DA distances with an accuracy of < 2%. For more complex cases, where proteins adopt multiple conformations with significantly different dye environments (heterogeneous case), we introduce a general analysis framework and evaluate its power in resolving heterogeneities in DA distances. The developed fast simulation methods, relying on Brownian dynamics of a coarse-grained dye in its sterically accessible volume, allow us to incorporate structural information in the decay analysis for heterogeneous cases by relating dye states

  17. Accurate interatomic force fields via machine learning with covariant kernels

    NASA Astrophysics Data System (ADS)

    Glielmo, Aldo; Sollich, Peter; De Vita, Alessandro

    2017-06-01

    We present a novel scheme to accurately predict atomic forces as vector quantities, rather than sets of scalar components, by Gaussian process (GP) regression. This is based on matrix-valued kernel functions, on which we impose the requirements that the predicted force rotates with the target configuration and is independent of any rotations applied to the configuration database entries. We show that such covariant GP kernels can be obtained by integration over the elements of the rotation group SO (d ) for the relevant dimensionality d . Remarkably, in specific cases the integration can be carried out analytically and yields a conservative force field that can be recast into a pair interaction form. Finally, we show that restricting the integration to a summation over the elements of a finite point group relevant to the target system is sufficient to recover an accurate GP. The accuracy of our kernels in predicting quantum-mechanical forces in real materials is investigated by tests on pure and defective Ni, Fe, and Si crystalline systems.

  18. Integrated Array/Metadata Analytics

    NASA Astrophysics Data System (ADS)

    Misev, Dimitar; Baumann, Peter

    2015-04-01

    Data comes in various forms and types, and integration usually presents a problem that is often simply ignored and solved with ad-hoc solutions. Multidimensional arrays are an ubiquitous data type, that we find at the core of virtually all science and engineering domains, as sensor, model, image, statistics data. Naturally, arrays are richly described by and intertwined with additional metadata (alphanumeric relational data, XML, JSON, etc). Database systems, however, a fundamental building block of what we call "Big Data", lack adequate support for modelling and expressing these array data/metadata relationships. Array analytics is hence quite primitive or non-existent at all in modern relational DBMS. Recognizing this, we extended SQL with a new SQL/MDA part seamlessly integrating multidimensional array analytics into the standard database query language. We demonstrate the benefits of SQL/MDA with real-world examples executed in ASQLDB, an open-source mediator system based on HSQLDB and rasdaman, that already implements SQL/MDA.

  19. Analytic quantum-interference conditions in Coulomb corrected photoelectron holography

    NASA Astrophysics Data System (ADS)

    Maxwell, A. S.; Al-Jawahiry, A.; Lai, X. Y.; Figueira de Morisson Faria, C.

    2018-02-01

    We provide approximate analytic expressions for above-threshold ionization (ATI) transition probabilities and photoelectron angular distributions. These analytic expressions are more general than those existing in the literature and include the residual binding potential in the electron continuum propagation. They successfully reproduce the ATI side lobes and specific holographic structures such as the near-threshold fan-shaped pattern and the spider-like structure that extends up to relatively high photoelectron energies. We compare such expressions with the Coulomb quantum orbit strong-field approximation (CQSFA) and the full solution of the time-dependent Schrödinger equation for different driving-field frequencies and intensities, and provide an in-depth analysis of the physical mechanisms behind specific holographic structures. Our results shed additional light on what aspects of the CQSFA must be prioritized in order to obtain the key holographic features, and highlight the importance of forward scattered trajectories. Furthermore, we find that the holographic patterns change considerably for different field parameters, even if the Keldysh parameter is kept roughly the same.

  20. Analytic Expressions for the Inner-rim Structure of Passively Heated Protoplanetary Disks

    NASA Astrophysics Data System (ADS)

    Ueda, Takahiro; Okuzumi, Satoshi; Flock, Mario

    2017-07-01

    We analytically derive the expressions for the structure of the inner region of protoplanetary disks based on the results from the recent hydrodynamical simulations. The inner part of a disk can be divided into four regions: a dust-free region with a gas temperature in the optically thin limit, an optically thin dust halo, an optically thick condensation front, and the classical, optically thick region, in order from the innermost to the outermost. We derive the dust-to-gas mass ratio profile in the dust halo using the fact that partial dust condensation regulates the temperature relative to the dust evaporation temperature. Beyond the dust halo, there is an optically thick condensation front where all the available silicate gas condenses out. The curvature of the condensation surface is determined by the condition that the surface temperature must be nearly equal to the characteristic temperature ˜1200 K. We derive the midplane temperature in the outer two regions using the two-layer approximation, with the additional heating by the condensation front for the outermost region. As a result, the overall temperature profile is step-like, with steep gradients at the borders between the outer three regions. The borders might act as planet traps where the inward migration of planets due to gravitational interaction with the gas disk stops. The temperature at the border between the two outermost regions coincides with the temperature needed to activate magnetorotational instability, suggesting that the inner edge of the dead zone must lie at this border. The radius of the dead zone inner edge predicted from our solution is ˜2-3 times larger than that expected from the classical optically thick temperature.

  1. An analytic approach for the study of pulsar spindown

    NASA Astrophysics Data System (ADS)

    Chishtie, F. A.; Zhang, Xiyang; Valluri, S. R.

    2018-07-01

    In this work we develop an analytic approach to study pulsar spindown. We use the monopolar spindown model by Alvarez and Carramiñana (2004 Astron. Astrophys. 414 651–8), which assumes an inverse linear law of magnetic field decay of the pulsar, to extract an all-order formula for the spindown parameters using the Taylor series representation of Jaranowski et al (1998 Phys. Rev. D 58 6300). We further extend the analytic model to incorporate the quadrupole term that accounts for the emission of gravitational radiation, and obtain expressions for the period P and frequency f in terms of transcendental equations. We derive the analytic solution for pulsar frequency spindown in the absence of glitches. We examine the different cases that arise in the analysis of the roots in the solution of the non-linear differential equation for pulsar period evolution. We provide expressions for the spin-down parameters and find that the spindown values are in reasonable agreement with observations. A detection of gravitational waves from pulsars will be the next landmark in the field of multi-messenger gravitational wave astronomy.

  2. Analytic representation of FK/Fπ in two loop chiral perturbation theory

    NASA Astrophysics Data System (ADS)

    Ananthanarayan, B.; Bijnens, Johan; Friot, Samuel; Ghosh, Shayan

    2018-05-01

    We present an analytic representation of FK/Fπ as calculated in three-flavor two-loop chiral perturbation theory, which involves expressing three mass scale sunsets in terms of Kampé de Fériet series. We demonstrate how approximations may be made to obtain relatively compact analytic representations. An illustrative set of fits using lattice data is also presented, which shows good agreement with existing fits.

  3. Analytic representations of mK , FK, mη, and Fη in two loop S U (3 ) chiral perturbation theory

    NASA Astrophysics Data System (ADS)

    Ananthanarayan, B.; Bijnens, Johan; Friot, Samuel; Ghosh, Shayan

    2018-06-01

    In this work, we consider expressions for the masses and decay constants of the pseudoscalar mesons in S U (3 ) chiral perturbation theory. These involve sunset diagrams and their derivatives evaluated at p2=mP2 (P =π , K , η ). Recalling that there are three mass scales in this theory, mπ, mK and mη, there are instances when the finite part of the sunset diagrams do not admit an expression in terms of elementary functions, and have therefore been evaluated numerically in the past. In a recent publication, an expansion in the external momentum was performed to obtain approximate analytic expressions for mπ and Fπ, the pion mass and decay constant. We provide fully analytic exact expressions for mK and mη, the kaon and eta masses, and FK and Fη, the kaon and eta decay constants. These expressions, calculated using Mellin-Barnes methods, are in the form of double series in terms of two mass ratios. A numerical analysis of the results to evaluate the relative size of contributions coming from loops, chiral logarithms as well as phenomenological low-energy constants is presented. We also present a set of approximate analytic expressions for mK, FK, mη and Fη that facilitate comparisons with lattice results. Finally, we show how exact analytic expressions for mπ and Fπ may be obtained, the latter having been used in conjunction with the results for FK to produce a recently published analytic representation of FK/Fπ.

  4. Recent trends in analytical procedures in forensic toxicology.

    PubMed

    Van Bocxlaer, Jan F

    2005-12-01

    Forensic toxicology is a very demanding discipline,heavily dependent on good analytical techniques. That is why new trends appear continuously. In the past years. LC-MS has revolutionized target compound analysis and has become the trend, also in toxicology. In LC-MS screening analysis, things are less straightforward and several approaches exist. One promising approach based on accurate LC-MSTOF mass measurements and elemental formula based library searches is discussed. This way of screening has already proven its applicability but at the same time it became obvious that a single accurate mass measurement lacks some specificity when using large compound libraries. CE too is a reemerging approach. The increasingly polar and ionic molecules encountered make it a worthwhile addition to e.g. LC, as illustrated for the analysis of GHB. A third recent trend is the use of MALDI mass spectrometry for small molecules. It is promising for its ease-of-use and high throughput. Unfortunately, re-ports of disappointment but also accomplishment, e.g. the quantitative analysis of LSD as discussed here, alternate, and it remains to be seen whether MALDI really will establish itself. Indeed, not all new trends will prove themselves but the mere fact that many appear in the world of analytical toxicology nowadays is, in itself, encouraging for the future of (forensic) toxicology.

  5. Analytic Reflected Lightcurves for Exoplanets

    NASA Astrophysics Data System (ADS)

    Haggard, Hal M.; Cowan, Nicolas B.

    2018-04-01

    The disk-integrated reflected brightness of an exoplanet changes as a function of time due to orbital and rotational motion coupled with an inhomogeneous albedo map. We have previously derived analytic reflected lightcurves for spherical harmonic albedo maps in the special case of a synchronously-rotating planet on an edge-on orbit (Cowan, Fuentes & Haggard 2013). In this letter, we present analytic reflected lightcurves for the general case of a planet on an inclined orbit, with arbitrary spin period and non-zero obliquity. We do so for two different albedo basis maps: bright points (δ-maps), and spherical harmonics (Y_l^m-maps). In particular, we use Wigner D-matrices to express an harmonic lightcurve for an arbitrary viewing geometry as a non-linear combination of harmonic lightcurves for the simpler edge-on, synchronously rotating geometry. These solutions will enable future exploration of the degeneracies and information content of reflected lightcurves, as well as fast calculation of lightcurves for mapping exoplanets based on time-resolved photometry. To these ends we make available Exoplanet Analytic Reflected Lightcurves (EARL), a simple open-source code that allows rapid computation of reflected lightcurves.

  6. Reliable and accurate extraction of Hamaker constants from surface force measurements.

    PubMed

    Miklavcic, S J

    2018-08-15

    A simple and accurate closed-form expression for the Hamaker constant that best represents experimental surface force data is presented. Numerical comparisons are made with the current standard least squares approach, which falsely assumes error-free separation measurements, and a nonlinear version assuming independent measurements of force and separation are subject to error. The comparisons demonstrate that not only is the proposed formula easily implemented it is also considerably more accurate. This option is appropriate for any value of Hamaker constant, high or low, and certainly for any interacting system exhibiting an inverse square distance dependent van der Waals force. Copyright © 2018 Elsevier Inc. All rights reserved.

  7. Analytical theory of mesoscopic Bose-Einstein condensation in an ideal gas

    NASA Astrophysics Data System (ADS)

    Kocharovsky, Vitaly V.; Kocharovsky, Vladimir V.

    2010-03-01

    We find the universal structure and scaling of the Bose-Einstein condensation (BEC) statistics and thermodynamics (Gibbs free energy, average energy, heat capacity) for a mesoscopic canonical-ensemble ideal gas in a trap with an arbitrary number of atoms, any volume, and any temperature, including the whole critical region. We identify a universal constraint-cutoff mechanism that makes BEC fluctuations strongly non-Gaussian and is responsible for all unusual critical phenomena of the BEC phase transition in the ideal gas. The main result is an analytical solution to the problem of critical phenomena. It is derived by, first, calculating analytically the universal probability distribution of the noncondensate occupation, or a Landau function, and then using it for the analytical calculation of the universal functions for the particular physical quantities via the exact formulas which express the constraint-cutoff mechanism. We find asymptotics of that analytical solution as well as its simple analytical approximations which describe the universal structure of the critical region in terms of the parabolic cylinder or confluent hypergeometric functions. The obtained results for the order parameter, all higher-order moments of BEC fluctuations, and thermodynamic quantities perfectly match the known asymptotics outside the critical region for both low and high temperature limits. We suggest two- and three-level trap models of BEC and find their exact solutions in terms of the cutoff negative binomial distribution (which tends to the cutoff gamma distribution in the continuous limit) and the confluent hypergeometric distribution, respectively. Also, we present an exactly solvable cutoff Gaussian model of BEC in a degenerate interacting gas. All these exact solutions confirm the universality and constraint-cutoff origin of the strongly non-Gaussian BEC statistics. We introduce a regular refinement scheme for the condensate statistics approximations on the basis of the

  8. Analytical collisionless damping rate of geodesic acoustic mode

    NASA Astrophysics Data System (ADS)

    Ren, H.; Xu, X. Q.

    2016-10-01

    Collisionless damping of geodesic acoustic mode (GAM) is analytically investigated by considering the finite-orbit-width (FOW) resonance effect to the 3rd order in the gyro-kinetic equations. A concise and transparent expression for the damping rate is presented for the first time. Good agreement is found between the analytical damping rate and the previous TEMPEST simulation result (Xu 2008 et al Phys. Rev. Lett. 100 215001) for systematic q scans. Our result also shows that it is of sufficient accuracy and has to take into account the FOW effect to the 3rd order.

  9. An analytical model for regular respiratory signals derived from the probability density function of Rayleigh distribution.

    PubMed

    Li, Xin; Li, Ye

    2015-01-01

    Regular respiratory signals (RRSs) acquired with physiological sensing systems (e.g., the life-detection radar system) can be used to locate survivors trapped in debris in disaster rescue, or predict the breathing motion to allow beam delivery under free breathing conditions in external beam radiotherapy. Among the existing analytical models for RRSs, the harmonic-based random model (HRM) is shown to be the most accurate, which, however, is found to be subject to considerable error if the RRS has a slowly descending end-of-exhale (EOE) phase. The defect of the HRM motivates us to construct a more accurate analytical model for the RRS. In this paper, we derive a new analytical RRS model from the probability density function of Rayleigh distribution. We evaluate the derived RRS model by using it to fit a real-life RRS in the sense of least squares, and the evaluation result shows that, our presented model exhibits lower error and fits the slowly descending EOE phases of the real-life RRS better than the HRM.

  10. Comparison of Cluster, Slab, and Analytic Potential Models for the Dimethyl Methylphosphonate (DMMP)/TiO2 (110) Intermolecular Interaction

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

    Yang, Li; Tunega, Daniel; Xu, Lai

    2013-08-29

    In a previous study (J. Phys. Chem. C 2011, 115, 12403) cluster models for the TiO2 rutile (110) surface and MP2 calculations were used to develop an analytic potential energy function for dimethyl methylphosphonate (DMMP) interacting with this surface. In the work presented here, this analytic potential and MP2 cluster models are compared with DFT "slab" calculations for DMMP interacting with the TiO2 (110) surface and with DFT cluster models for the TiO2 (110) surface. The DFT slab calculations were performed with the PW91 and PBE functionals. The analytic potential gives DMMP/ TiO2 (110) potential energy curves in excellent agreementmore » with those obtained from the slab calculations. The cluster models for the TiO2 (110) surface, used for the MP2 calculations, were extended to DFT calculations with the B3LYP, PW91, and PBE functional. These DFT calculations do not give DMMP/TiO2 (110) interaction energies which agree with those from the DFT slab calculations. Analyses of the wave functions for these cluster models show that they do not accurately represent the HOMO and LUMO for the surface, which should be 2p and 3d orbitals, respectively, and the models also do not give an accurate band gap. The MP2 cluster models do not accurately represent the LUMO and that they give accurate DMMP/TiO2 (110) interaction energies is apparently fortuitous, arising from their highly inaccurate band gaps. Accurate cluster models, consisting of 7, 10, and 15 Ti-atoms and which have the correct HOMO and LUMO properties, are proposed. The work presented here illustrates the care that must be taken in "constructing" cluster models which accurately model surfaces.« less

  11. A non-grey analytical model for irradiated atmospheres. II. Analytical vs. numerical solutions

    NASA Astrophysics Data System (ADS)

    Parmentier, Vivien; Guillot, Tristan; Fortney, Jonathan J.; Marley, Mark S.

    2015-02-01

    Context. The recent discovery and characterization of the diversity of the atmospheres of exoplanets and brown dwarfs calls for the development of fast and accurate analytical models. Aims: We wish to assess the goodness of the different approximations used to solve the radiative transfer problem in irradiated atmospheres analytically, and we aim to provide a useful tool for a fast computation of analytical temperature profiles that remains correct over a wide range of atmospheric characteristics. Methods: We quantify the accuracy of the analytical solution derived in paper I for an irradiated, non-grey atmosphere by comparing it to a state-of-the-art radiative transfer model. Then, using a grid of numerical models, we calibrate the different coefficients of our analytical model for irradiated solar-composition atmospheres of giant exoplanets and brown dwarfs. Results: We show that the so-called Eddington approximation used to solve the angular dependency of the radiation field leads to relative errors of up to ~5% on the temperature profile. For grey or semi-grey atmospheres (i.e., when the visible and thermal opacities, respectively, can be considered independent of wavelength), we show that the presence of a convective zone has a limited effect on the radiative atmosphere above it and leads to modifications of the radiative temperature profile of approximately ~2%. However, for realistic non-grey planetary atmospheres, the presence of a convective zone that extends to optical depths smaller than unity can lead to changes in the radiative temperature profile on the order of 20% or more. When the convective zone is located at deeper levels (such as for strongly irradiated hot Jupiters), its effect on the radiative atmosphere is again on the same order (~2%) as in the semi-grey case. We show that the temperature inversion induced by a strong absorber in the optical, such as TiO or VO is mainly due to non-grey thermal effects reducing the ability of the upper

  12. Analytical and finite element simulation of a three-bar torsion spring

    NASA Astrophysics Data System (ADS)

    Rădoi, M.; Cicone, T.

    2016-08-01

    The present study is dedicated to the innovative 3-bar torsion spring used as suspension solution for the first time at Lunokhod-1, the first autonomous vehicle sent for the exploration of the Moon in the early 70-ies by the former USSR. The paper describes a simple analytical model for calculation of spring static characteristics, taking into account both torsion and bending effects. Closed form solutions of this model allows quick and elegant parametric analysis. A comparison with a single torsion bar with the same stiffness reveal an increase of the maximum stress with more than 50%. A 3D finite element (FE) simulation is proposed to evaluate the accuracy of the analytical model. The model was meshed in an automated pattern (sweep for hubs and tetrahedrons for bars) with mesh morphing. Very close results between analytical and numerical solutions have been found, concluding that the analytical model is accurate. The 3-D finite element simulation was used to evaluate the effects of design details like fillet radius of the bars or contact stresses in the hex hub.

  13. Incorporating photon recycling into the analytical drift-diffusion model of high efficiency solar cells

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

    Lumb, Matthew P.; Naval Research Laboratory, Washington, DC 20375; Steiner, Myles A.

    The analytical drift-diffusion formalism is able to accurately simulate a wide range of solar cell architectures and was recently extended to include those with back surface reflectors. However, as solar cells approach the limits of material quality, photon recycling effects become increasingly important in predicting the behavior of these cells. In particular, the minority carrier diffusion length is significantly affected by the photon recycling, with consequences for the solar cell performance. In this paper, we outline an approach to account for photon recycling in the analytical Hovel model and compare analytical model predictions to GaAs-based experimental devices operating close tomore » the fundamental efficiency limit.« less

  14. Nonlinear analyte concentration gradients for one-step kinetic analysis employing optical microring resonators.

    PubMed

    Marty, Michael T; Sloan, Courtney D Kuhnline; Bailey, Ryan C; Sligar, Stephen G

    2012-07-03

    Conventional methods to probe the binding kinetics of macromolecules at biosensor surfaces employ a stepwise titration of analyte concentrations and measure the association and dissociation to the immobilized ligand at each concentration level. It has previously been shown that kinetic rates can be measured in a single step by monitoring binding as the analyte concentration increases over time in a linear gradient. We report here the application of nonlinear analyte concentration gradients for determining kinetic rates and equilibrium binding affinities in a single experiment. A versatile nonlinear gradient maker is presented, which is easily applied to microfluidic systems. Simulations validate that accurate kinetic rates can be extracted for a wide range of association and dissociation rates, gradient slopes, and curvatures, and with models for mass transport. The nonlinear analyte gradient method is demonstrated with a silicon photonic microring resonator platform to measure prostate specific antigen-antibody binding kinetics.

  15. Nonlinear Analyte Concentration Gradients for One-Step Kinetic Analysis Employing Optical Microring Resonators

    PubMed Central

    Marty, Michael T.; Kuhnline Sloan, Courtney D.; Bailey, Ryan C.; Sligar, Stephen G.

    2012-01-01

    Conventional methods to probe the binding kinetics of macromolecules at biosensor surfaces employ a stepwise titration of analyte concentrations and measure the association and dissociation to the immobilized ligand at each concentration level. It has previously been shown that kinetic rates can be measured in a single step by monitoring binding as the analyte concentration increases over time in a linear gradient. We report here the application of nonlinear analyte concentration gradients for determining kinetic rates and equilibrium binding affinities in a single experiment. A versatile nonlinear gradient maker is presented, which is easily applied to microfluidic systems. Simulations validate that accurate kinetic rates can be extracted for a wide range of association and dissociation rates, gradient slopes and curvatures, and with models for mass transport. The nonlinear analyte gradient method is demonstrated with a silicon photonic microring resonator platform to measure prostate specific antigen-antibody binding kinetics. PMID:22686186

  16. Fast-slow asymptotic for semi-analytical ignition criteria in FitzHugh-Nagumo system.

    PubMed

    Bezekci, B; Biktashev, V N

    2017-09-01

    We study the problem of initiation of excitation waves in the FitzHugh-Nagumo model. Our approach follows earlier works and is based on the idea of approximating the boundary between basins of attraction of propagating waves and of the resting state as the stable manifold of a critical solution. Here, we obtain analytical expressions for the essential ingredients of the theory by singular perturbation using two small parameters, the separation of time scales of the activator and inhibitor and the threshold in the activator's kinetics. This results in a closed analytical expression for the strength-duration curve.

  17. Derivation of general analytic gradient expressions for density-fitted post-Hartree-Fock methods: An efficient implementation for the density-fitted second-order Møller–Plesset perturbation theory

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

    Bozkaya, Uğur, E-mail: ugur.bozkaya@atauni.edu.tr

    General analytic gradient expressions (with the frozen-core approximation) are presented for density-fitted post-HF methods. An efficient implementation of frozen-core analytic gradients for the second-order Møller–Plesset perturbation theory (MP2) with the density-fitting (DF) approximation (applying to both reference and correlation energies), which is denoted as DF-MP2, is reported. The DF-MP2 method is applied to a set of alkanes, conjugated dienes, and noncovalent interaction complexes to compare the computational cost of single point analytic gradients with MP2 with the resolution of the identity approach (RI-MP2) [F. Weigend and M. Häser, Theor. Chem. Acc. 97, 331 (1997); R. A. Distasio, R. P. Steele,more » Y. M. Rhee, Y. Shao, and M. Head-Gordon, J. Comput. Chem. 28, 839 (2007)]. In the RI-MP2 method, the DF approach is used only for the correlation energy. Our results demonstrate that the DF-MP2 method substantially accelerate the RI-MP2 method for analytic gradient computations due to the reduced input/output (I/O) time. Because in the DF-MP2 method the DF approach is used for both reference and correlation energies, the storage of 4-index electron repulsion integrals (ERIs) are avoided, 3-index ERI tensors are employed instead. Further, as in case of integrals, our gradient equation is completely avoid construction or storage of the 4-index two-particle density matrix (TPDM), instead we use 2- and 3-index TPDMs. Hence, the I/O bottleneck of a gradient computation is significantly overcome. Therefore, the cost of the generalized-Fock matrix (GFM), TPDM, solution of Z-vector equations, the back transformation of TPDM, and integral derivatives are substantially reduced when the DF approach is used for the entire energy expression. Further application results show that the DF approach introduce negligible errors for closed-shell reaction energies and equilibrium bond lengths.« less

  18. Methods for the accurate estimation of confidence intervals on protein folding ϕ-values

    PubMed Central

    Ruczinski, Ingo; Sosnick, Tobin R.; Plaxco, Kevin W.

    2006-01-01

    ϕ-Values provide an important benchmark for the comparison of experimental protein folding studies to computer simulations and theories of the folding process. Despite the growing importance of ϕ measurements, however, formulas to quantify the precision with which ϕ is measured have seen little significant discussion. Moreover, a commonly employed method for the determination of standard errors on ϕ estimates assumes that estimates of the changes in free energy of the transition and folded states are independent. Here we demonstrate that this assumption is usually incorrect and that this typically leads to the underestimation of ϕ precision. We derive an analytical expression for the precision of ϕ estimates (assuming linear chevron behavior) that explicitly takes this dependence into account. We also describe an alternative method that implicitly corrects for the effect. By simulating experimental chevron data, we show that both methods accurately estimate ϕ confidence intervals. We also explore the effects of the commonly employed techniques of calculating ϕ from kinetics estimated at non-zero denaturant concentrations and via the assumption of parallel chevron arms. We find that these approaches can produce significantly different estimates for ϕ (again, even for truly linear chevron behavior), indicating that they are not equivalent, interchangeable measures of transition state structure. Lastly, we describe a Web-based implementation of the above algorithms for general use by the protein folding community. PMID:17008714

  19. A fully analytic treatment of resonant inductive coupling in the far field

    NASA Astrophysics Data System (ADS)

    Sedwick, Raymond J.

    2012-02-01

    For the application of resonant inductive coupling for wireless power transfer, fabrication of flat spiral coils using ribbon wire allows for analytic expressions of the capacitance and inductance of the coils and therefore the resonant frequency. The expressions can also be used in an approximate way for the analysis of coils constructed from cylindrical wire. Ribbon wire constructed from both standard metals as well as high temperature superconducting material is commercially available, so using these derived expressions as a basis, a fully analytic treatment is presented that allows for design trades to be made for hybrid designs incorporating either technology. The model is then extended to analyze the performance of the technology as applied to inductively coupled communications, which has been demonstrated as having an advantage in circumstances where radiated signals would suffer unacceptable levels of attenuation.

  20. Two Approaches in the Lunar Libration Theory: Analytical vs. Numerical Methods

    NASA Astrophysics Data System (ADS)

    Petrova, Natalia; Zagidullin, Arthur; Nefediev, Yurii; Kosulin, Valerii

    2016-10-01

    Observation of the physical libration of the Moon and the celestial bodies is one of the astronomical methods to remotely evaluate the internal structure of a celestial body without using expensive space experiments. Review of the results obtained due to the physical libration study, is presented in the report.The main emphasis is placed on the description of successful lunar laser ranging for libration determination and on the methods of simulating the physical libration. As a result, estimation of the viscoelastic and dissipative properties of the lunar body, of the lunar core parameters were done. The core's existence was confirmed by the recent reprocessing of seismic data Apollo missions. Attention is paid to the physical interpretation of the phenomenon of free libration and methods of its determination.A significant part of the report is devoted to describing the practical application of the most accurate to date the analytical tables of lunar libration built by comprehensive analytical processing of residual differences obtained when comparing the long-term series of laser observations with numerical ephemeris DE421 [1].In general, the basic outline of the report reflects the effectiveness of two approaches in the libration theory - numerical and analytical solution. It is shown that the two approaches complement each other for the study of the Moon in different aspects: numerical approach provides high accuracy of the theory necessary for adequate treatment of modern high-accurate observations and the analytic approach allows you to see the essence of the various kind manifestations in the lunar rotation, predict and interpret the new effects in observations of physical libration [2].[1] Rambaux, N., J. G. Williams, 2011, The Moon's physical librations and determination of their free modes, Celest. Mech. Dyn. Astron., 109, 85-100.[2] Petrova N., A. Zagidullin, Yu. Nefediev. Analysis of long-periodic variations of lunar libration parameters on the basis of

  1. Accurate quantitation standards of glutathione via traceable sulfur measurement by inductively coupled plasma optical emission spectrometry and ion chromatography

    PubMed Central

    Rastogi, L.; Dash, K.; Arunachalam, J.

    2013-01-01

    The quantitative analysis of glutathione (GSH) is important in different fields like medicine, biology, and biotechnology. Accurate quantitative measurements of this analyte have been hampered by the lack of well characterized reference standards. The proposed procedure is intended to provide an accurate and definitive method for the quantitation of GSH for reference measurements. Measurement of the stoichiometrically existing sulfur content in purified GSH offers an approach for its quantitation and calibration through an appropriate characterized reference material (CRM) for sulfur would provide a methodology for the certification of GSH quantity, that is traceable to SI (International system of units). The inductively coupled plasma optical emission spectrometry (ICP-OES) approach negates the need for any sample digestion. The sulfur content of the purified GSH is quantitatively converted into sulfate ions by microwave-assisted UV digestion in the presence of hydrogen peroxide prior to ion chromatography (IC) measurements. The measurement of sulfur by ICP-OES and IC (as sulfate) using the “high performance” methodology could be useful for characterizing primary calibration standards and certified reference materials with low uncertainties. The relative expanded uncertainties (% U) expressed at 95% confidence interval for ICP-OES analyses varied from 0.1% to 0.3%, while in the case of IC, they were between 0.2% and 1.2%. The described methods are more suitable for characterizing primary calibration standards and certifying reference materials of GSH, than for routine measurements. PMID:29403814

  2. Analytic theory of orbit contraction

    NASA Technical Reports Server (NTRS)

    Vinh, N. X.; Longuski, J. M.; Busemann, A.; Culp, R. D.

    1977-01-01

    The motion of a satellite in orbit, subject to atmospheric force and the motion of a reentry vehicle are governed by gravitational and aerodynamic forces. This suggests the derivation of a uniform set of equations applicable to both cases. For the case of satellite motion, by a proper transformation and by the method of averaging, a technique appropriate for long duration flight, the classical nonlinear differential equation describing the contraction of the major axis is derived. A rigorous analytic solution is used to integrate this equation with a high degree of accuracy, using Poincare's method of small parameters and Lagrange's expansion to explicitly express the major axis as a function of the eccentricity. The solution is uniformly valid for moderate and small eccentricities. For highly eccentric orbits, the asymptotic equation is derived directly from the general equation. Numerical solutions were generated to display the accuracy of the analytic theory.

  3. An analytical model with flexible accuracy for deep submicron DCVSL cells

    NASA Astrophysics Data System (ADS)

    Valiollahi, Sepideh; Ardeshir, Gholamreza

    2018-07-01

    Differential cascoded voltage switch logic (DCVSL) cells are among the best candidates of circuit designers for a wide range of applications due to advantages such as low input capacitance, high switching speed, small area and noise-immunity; nevertheless, a proper model has not yet been developed to analyse them. This paper analyses deep submicron DCVSL cells based on a flexible accuracy-simplicity trade-off including the following key features: (1) the model is capable of producing closed-form expressions with an acceptable accuracy; (2) model equations can be solved numerically to offer higher accuracy; (3) the short-circuit currents occurring in high-low/low-high transitions are accounted in analysis and (4) the changes in the operating modes of transistors during transitions together with an efficient submicron I-V model, which incorporates the most important non-ideal short-channel effects, are considered. The accuracy of the proposed model is validated in IBM 0.13 µm CMOS technology through comparisons with the accurate physically based BSIM3 model. The maximum error caused by analytical solutions is below 10%, while this amount is below 7% for numerical solutions.

  4. Accurate analytic solution of chemical master equations for gene regulation networks in a single cell

    NASA Astrophysics Data System (ADS)

    Huang, Guan-Rong; Saakian, David B.; Hu, Chin-Kun

    2018-01-01

    Studying gene regulation networks in a single cell is an important, interesting, and hot research topic of molecular biology. Such process can be described by chemical master equations (CMEs). We propose a Hamilton-Jacobi equation method with finite-size corrections to solve such CMEs accurately at the intermediate region of switching, where switching rate is comparable to fast protein production rate. We applied this approach to a model of self-regulating proteins [H. Ge et al., Phys. Rev. Lett. 114, 078101 (2015), 10.1103/PhysRevLett.114.078101] and found that as a parameter related to inducer concentration increases the probability of protein production changes from unimodal to bimodal, then to unimodal, consistent with phenotype switching observed in a single cell.

  5. Analytic Expressions for the Inner-rim Structure of Passively Heated Protoplanetary Disks

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

    Ueda, Takahiro; Okuzumi, Satoshi; Flock, Mario, E-mail: t_ueda@geo.titech.ac.jp

    We analytically derive the expressions for the structure of the inner region of protoplanetary disks based on the results from the recent hydrodynamical simulations. The inner part of a disk can be divided into four regions: a dust-free region with a gas temperature in the optically thin limit, an optically thin dust halo, an optically thick condensation front, and the classical, optically thick region, in order from the innermost to the outermost. We derive the dust-to-gas mass ratio profile in the dust halo using the fact that partial dust condensation regulates the temperature relative to the dust evaporation temperature. Beyondmore » the dust halo, there is an optically thick condensation front where all the available silicate gas condenses out. The curvature of the condensation surface is determined by the condition that the surface temperature must be nearly equal to the characteristic temperature ∼1200 K. We derive the midplane temperature in the outer two regions using the two-layer approximation, with the additional heating by the condensation front for the outermost region. As a result, the overall temperature profile is step-like, with steep gradients at the borders between the outer three regions. The borders might act as planet traps where the inward migration of planets due to gravitational interaction with the gas disk stops. The temperature at the border between the two outermost regions coincides with the temperature needed to activate magnetorotational instability, suggesting that the inner edge of the dead zone must lie at this border. The radius of the dead zone inner edge predicted from our solution is ∼2–3 times larger than that expected from the classical optically thick temperature.« less

  6. Accurate interlaminar stress recovery from finite element analysis

    NASA Technical Reports Server (NTRS)

    Tessler, Alexander; Riggs, H. Ronald

    1994-01-01

    The accuracy and robustness of a two-dimensional smoothing methodology is examined for the problem of recovering accurate interlaminar shear stress distributions in laminated composite and sandwich plates. The smoothing methodology is based on a variational formulation which combines discrete least-squares and penalty-constraint functionals in a single variational form. The smoothing analysis utilizes optimal strains computed at discrete locations in a finite element analysis. These discrete strain data are smoothed with a smoothing element discretization, producing superior accuracy strains and their first gradients. The approach enables the resulting smooth strain field to be practically C1-continuous throughout the domain of smoothing, exhibiting superconvergent properties of the smoothed quantity. The continuous strain gradients are also obtained directly from the solution. The recovered strain gradients are subsequently employed in the integration o equilibrium equations to obtain accurate interlaminar shear stresses. The problem is a simply-supported rectangular plate under a doubly sinusoidal load. The problem has an exact analytic solution which serves as a measure of goodness of the recovered interlaminar shear stresses. The method has the versatility of being applicable to the analysis of rather general and complex structures built of distinct components and materials, such as found in aircraft design. For these types of structures, the smoothing is achieved with 'patches', each patch covering the domain in which the smoothed quantity is physically continuous.

  7. Analytical prediction of digital signal crosstalk of FCC

    NASA Technical Reports Server (NTRS)

    Belleisle, A. P.

    1972-01-01

    The results are presented of study effort whose aim was the development of accurate means of analyzing and predicting signal cross-talk in multi-wire digital data cables. A complete analytical model is developed n + 1 wire systems of uniform transmission lines with arbitrary linear boundary conditions. In addition, a minimum set of parameter measurements required for the application of the model are presented. Comparisons between cross-talk predicted by this model and actual measured cross-talk are shown for a six conductor ribbon cable.

  8. Image analysis driven single-cell analytics for systems microbiology.

    PubMed

    Balomenos, Athanasios D; Tsakanikas, Panagiotis; Aspridou, Zafiro; Tampakaki, Anastasia P; Koutsoumanis, Konstantinos P; Manolakos, Elias S

    2017-04-04

    Time-lapse microscopy is an essential tool for capturing and correlating bacterial morphology and gene expression dynamics at single-cell resolution. However state-of-the-art computational methods are limited in terms of the complexity of cell movies that they can analyze and lack of automation. The proposed Bacterial image analysis driven Single Cell Analytics (BaSCA) computational pipeline addresses these limitations thus enabling high throughput systems microbiology. BaSCA can segment and track multiple bacterial colonies and single-cells, as they grow and divide over time (cell segmentation and lineage tree construction) to give rise to dense communities with thousands of interacting cells in the field of view. It combines advanced image processing and machine learning methods to deliver very accurate bacterial cell segmentation and tracking (F-measure over 95%) even when processing images of imperfect quality with several overcrowded colonies in the field of view. In addition, BaSCA extracts on the fly a plethora of single-cell properties, which get organized into a database summarizing the analysis of the cell movie. We present alternative ways to analyze and visually explore the spatiotemporal evolution of single-cell properties in order to understand trends and epigenetic effects across cell generations. The robustness of BaSCA is demonstrated across different imaging modalities and microscopy types. BaSCA can be used to analyze accurately and efficiently cell movies both at a high resolution (single-cell level) and at a large scale (communities with many dense colonies) as needed to shed light on e.g. how bacterial community effects and epigenetic information transfer play a role on important phenomena for human health, such as biofilm formation, persisters' emergence etc. Moreover, it enables studying the role of single-cell stochasticity without losing sight of community effects that may drive it.

  9. Analytical Solution of the Radiative Transfer Equation in a Thin Dusty Circumstellar Shell

    NASA Astrophysics Data System (ADS)

    Cruzalèbes, P.; Sacuto, S.

    The radiative transfer equation can be solved analytically for optically thin shells. The solution leads to a semi-analytical expression of the visibility function, which can be compared to the numerical solution given by the DUSTY code. Best-fit model parameters are given using real measurements of ISO fluxes, ISI and VLTI-MIDI visibilities for 3 late-type stars.

  10. Accurate inspiral-merger-ringdown gravitational waveforms for nonspinning black-hole binaries including the effect of subdominant modes

    NASA Astrophysics Data System (ADS)

    Mehta, Ajit Kumar; Mishra, Chandra Kant; Varma, Vijay; Ajith, Parameswaran

    2017-12-01

    We present an analytical waveform family describing gravitational waves (GWs) from the inspiral, merger, and ringdown of nonspinning black-hole binaries including the effect of several nonquadrupole modes [(ℓ=2 ,m =±1 ),(ℓ=3 ,m =±3 ),(ℓ=4 ,m =±4 ) apart from (ℓ=2 ,m =±2 )]. We first construct spin-weighted spherical harmonics modes of hybrid waveforms by matching numerical-relativity simulations (with mass ratio 1-10) describing the late inspiral, merger, and ringdown of the binary with post-Newtonian/effective-one-body waveforms describing the early inspiral. An analytical waveform family is constructed in frequency domain by modeling the Fourier transform of the hybrid waveforms making use of analytical functions inspired by perturbative calculations. The resulting highly accurate, ready-to-use waveforms are highly faithful (unfaithfulness ≃10-4- 10-2 ) for observation of GWs from nonspinning black-hole binaries and are extremely inexpensive to generate.

  11. Analytical methods for quantitation of prenylated flavonoids from hops.

    PubMed

    Nikolić, Dejan; van Breemen, Richard B

    2013-01-01

    The female flowers of hops ( Humulus lupulus L.) are used as a flavoring agent in the brewing industry. There is growing interest in possible health benefits of hops, particularly as estrogenic and chemopreventive agents. Among the possible active constituents, most of the attention has focused on prenylated flavonoids, which can chemically be classified as prenylated chalcones and prenylated flavanones. Among chalcones, xanthohumol (XN) and desmethylxanthohumol (DMX) have been the most studied, while among flavanones, 8-prenylnaringenin (8-PN) and 6-prenylnaringenin (6-PN) have received the most attention. Because of the interest in medicinal properties of prenylated flavonoids, there is demand for accurate, reproducible and sensitive analytical methods to quantify these compounds in various matrices. Such methods are needed, for example, for quality control and standardization of hop extracts, measurement of the content of prenylated flavonoids in beer, and to determine pharmacokinetic properties of prenylated flavonoids in animals and humans. This review summarizes currently available analytical methods for quantitative analysis of the major prenylated flavonoids, with an emphasis on the LC-MS and LC-MS-MS methods and their recent applications to biomedical research on hops. This review covers all methods in which prenylated flavonoids have been measured, either as the primary analytes or as a part of a larger group of analytes. The review also discusses methodological issues relating to the quantitative analysis of these compounds regardless of the chosen analytical approach.

  12. Analytical drafting curves provide exact equations for plotted data

    NASA Technical Reports Server (NTRS)

    Stewart, R. B.

    1967-01-01

    Analytical drafting curves provide explicit mathematical expressions for any numerical data that appears in the form of graphical plots. The curves each have a reference coordinate axis system indicated on the curve as well as the mathematical equation from which the curve was generated.

  13. Targeted Analyte Detection by Standard Addition Improves Detection Limits in MALDI Mass Spectrometry

    PubMed Central

    Eshghi, Shadi Toghi; Li, Xingde; Zhang, Hui

    2014-01-01

    Matrix-assisted laser desorption/ionization has proven an effective tool for fast and accurate determination of many molecules. However, the detector sensitivity and chemical noise compromise the detection of many invaluable low-abundance molecules from biological and clinical samples. To challenge this limitation, we developed a targeted analyte detection (TAD) technique. In TAD, the target analyte is selectively elevated by spiking a known amount of that analyte into the sample, thereby raising its concentration above the noise level, where we take advantage of the improved sensitivity to detect the presence of the endogenous analyte in the sample. We assessed TAD on three peptides in simple and complex background solutions with various exogenous analyte concentrations in two MALDI matrices. TAD successfully improved the limit of detection (LOD) of target analytes when the target peptides were added to the sample in a concentration close to optimum concentration. The optimum exogenous concentration was estimated through a quantitative method to be approximately equal to the original LOD for each target. Also, we showed that TAD could achieve LOD improvements on an average of 3-fold in a simple and 2-fold in a complex sample. TAD provides a straightforward assay to improve the LOD of generic target analytes without the need for costly hardware modifications. PMID:22877355

  14. Robust and accurate vectorization of line drawings.

    PubMed

    Hilaire, Xavier; Tombre, Karl

    2006-06-01

    This paper presents a method for vectorizing the graphical parts of paper-based line drawings. The method consists of separating the input binary image into layers of homogeneous thickness, skeletonizing each layer, segmenting the skeleton by a method based on random sampling, and simplifying the result. The segmentation method is robust with a best bound of 50 percent noise reached for indefinitely long primitives. Accurate estimation of the recognized vector's parameters is enabled by explicitly computing their feasibility domains. Theoretical performance analysis and expression of the complexity of the segmentation method are derived. Experimental results and comparisons with other vectorization systems are also provided.

  15. Analytical time-domain Green’s functions for power-law media

    PubMed Central

    Kelly, James F.; McGough, Robert J.; Meerschaert, Mark M.

    2008-01-01

    Frequency-dependent loss and dispersion are typically modeled with a power-law attenuation coefficient, where the power-law exponent ranges from 0 to 2. To facilitate analytical solution, a fractional partial differential equation is derived that exactly describes power-law attenuation and the Szabo wave equation [“Time domain wave-equations for lossy media obeying a frequency power-law,” J. Acoust. Soc. Am. 96, 491–500 (1994)] is an approximation to this equation. This paper derives analytical time-domain Green’s functions in power-law media for exponents in this range. To construct solutions, stable law probability distributions are utilized. For exponents equal to 0, 1∕3, 1∕2, 2∕3, 3∕2, and 2, the Green’s function is expressed in terms of Dirac delta, exponential, Airy, hypergeometric, and Gaussian functions. For exponents strictly less than 1, the Green’s functions are expressed as Fox functions and are causal. For exponents greater than or equal than 1, the Green’s functions are expressed as Fox and Wright functions and are noncausal. However, numerical computations demonstrate that for observation points only one wavelength from the radiating source, the Green’s function is effectively causal for power-law exponents greater than or equal to 1. The analytical time-domain Green’s function is numerically verified against the material impulse response function, and the results demonstrate excellent agreement. PMID:19045774

  16. Surrogate matrix and surrogate analyte approaches for definitive quantitation of endogenous biomolecules.

    PubMed

    Jones, Barry R; Schultz, Gary A; Eckstein, James A; Ackermann, Bradley L

    2012-10-01

    Quantitation of biomarkers by LC-MS/MS is complicated by the presence of endogenous analytes. This challenge is most commonly overcome by calibration using an authentic standard spiked into a surrogate matrix devoid of the target analyte. A second approach involves use of a stable-isotope-labeled standard as a surrogate analyte to allow calibration in the actual biological matrix. For both methods, parallelism between calibration standards and the target analyte in biological matrix must be demonstrated in order to ensure accurate quantitation. In this communication, the surrogate matrix and surrogate analyte approaches are compared for the analysis of five amino acids in human plasma: alanine, valine, methionine, leucine and isoleucine. In addition, methodology based on standard addition is introduced, which enables a robust examination of parallelism in both surrogate analyte and surrogate matrix methods prior to formal validation. Results from additional assays are presented to introduce the standard-addition methodology and to highlight the strengths and weaknesses of each approach. For the analysis of amino acids in human plasma, comparable precision and accuracy were obtained by the surrogate matrix and surrogate analyte methods. Both assays were well within tolerances prescribed by regulatory guidance for validation of xenobiotic assays. When stable-isotope-labeled standards are readily available, the surrogate analyte approach allows for facile method development. By comparison, the surrogate matrix method requires greater up-front method development; however, this deficit is offset by the long-term advantage of simplified sample analysis.

  17. GESearch: An Interactive GUI Tool for Identifying Gene Expression Signature.

    PubMed

    Ye, Ning; Yin, Hengfu; Liu, Jingjing; Dai, Xiaogang; Yin, Tongming

    2015-01-01

    The huge amount of gene expression data generated by microarray and next-generation sequencing technologies present challenges to exploit their biological meanings. When searching for the coexpression genes, the data mining process is largely affected by selection of algorithms. Thus, it is highly desirable to provide multiple options of algorithms in the user-friendly analytical toolkit to explore the gene expression signatures. For this purpose, we developed GESearch, an interactive graphical user interface (GUI) toolkit, which is written in MATLAB and supports a variety of gene expression data files. This analytical toolkit provides four models, including the mean, the regression, the delegate, and the ensemble models, to identify the coexpression genes, and enables the users to filter data and to select gene expression patterns by browsing the display window or by importing knowledge-based genes. Subsequently, the utility of this analytical toolkit is demonstrated by analyzing two sets of real-life microarray datasets from cell-cycle experiments. Overall, we have developed an interactive GUI toolkit that allows for choosing multiple algorithms for analyzing the gene expression signatures.

  18. pyJac: Analytical Jacobian generator for chemical kinetics

    NASA Astrophysics Data System (ADS)

    Niemeyer, Kyle E.; Curtis, Nicholas J.; Sung, Chih-Jen

    2017-06-01

    Accurate simulations of combustion phenomena require the use of detailed chemical kinetics in order to capture limit phenomena such as ignition and extinction as well as predict pollutant formation. However, the chemical kinetic models for hydrocarbon fuels of practical interest typically have large numbers of species and reactions and exhibit high levels of mathematical stiffness in the governing differential equations, particularly for larger fuel molecules. In order to integrate the stiff equations governing chemical kinetics, generally reactive-flow simulations rely on implicit algorithms that require frequent Jacobian matrix evaluations. Some in situ and a posteriori computational diagnostics methods also require accurate Jacobian matrices, including computational singular perturbation and chemical explosive mode analysis. Typically, finite differences numerically approximate these, but for larger chemical kinetic models this poses significant computational demands since the number of chemical source term evaluations scales with the square of species count. Furthermore, existing analytical Jacobian tools do not optimize evaluations or support emerging SIMD processors such as GPUs. Here we introduce pyJac, a Python-based open-source program that generates analytical Jacobian matrices for use in chemical kinetics modeling and analysis. In addition to producing the necessary customized source code for evaluating reaction rates (including all modern reaction rate formulations), the chemical source terms, and the Jacobian matrix, pyJac uses an optimized evaluation order to minimize computational and memory operations. As a demonstration, we first establish the correctness of the Jacobian matrices for kinetic models of hydrogen, methane, ethylene, and isopentanol oxidation (number of species ranging 13-360) by showing agreement within 0.001% of matrices obtained via automatic differentiation. We then demonstrate the performance achievable on CPUs and GPUs using py

  19. Mars Analytical Microimager

    NASA Astrophysics Data System (ADS)

    Batory, Krzysztof J.; Govindjee; Andersen, Dale; Presley, John; Lucas, John M.; Sears, S. Kelly; Vali, Hojatollah

    Unambiguous detection of extraterrestrial nitrogenous hydrocarbon microbiology requires an instrument both to recognize potential biogenic specimens and to successfully discriminate them from geochemical settings. Such detection should ideally be in-situ and not jeopardize other experiments by altering samples. Taken individually most biomarkers are inconclusive. For example, since amino acids can be synthesized abiotically they are not always considered reliable biomarkers. An enantiomeric imbalance, which is characteristic of all terrestrial life, may be questioned because chirality can also be altered abiotically. However, current scientific understanding holds that aggregates of identical proteins or proteinaceous complexes, with their well-defined amino acid residue sequences, are indisputable biomarkers. Our paper describes the Mars Analytical Microimager, an instrument for the simultaneous imaging of generic autofluorescent biomarkers and overall morphology. Autofluorescence from ultraviolet to near-infrared is emitted by all known terrestrial biology, and often as consistent complex bands uncharacteristic of abiotic mineral luminescence. The MAM acquires morphology, and even sub-micron morphogenesis, at a 3-centimeter working distance with resolution approaching a laser scanning microscope. Luminescence is simultaneously collected via a 2.5-micron aperture, thereby permitting accurate correlation of multi-dimensional optical behavior with specimen morphology. A variable wavelength excitation source and photospectrometer serve to obtain steady-state and excitation spectra of biotic and luminescent abiotic sources. We believe this is the first time instrumentation for detecting hydrated or desiccated microbiology non-destructively in-situ has been demonstrated. We have obtained excellent preliminary detection of biota and inorganic matrix discrimination from terrestrial polar analogues, and perimetric morphology of individual magnetotactic bacteria. Proposed

  20. Simple and accurate sum rules for highly relativistic systems

    NASA Astrophysics Data System (ADS)

    Cohen, Scott M.

    2005-03-01

    In this paper, I consider the Bethe and Thomas-Reiche-Kuhn sum rules, which together form the foundation of Bethe's theory of energy loss from fast charged particles to matter. For nonrelativistic target systems, the use of closure leads directly to simple expressions for these quantities. In the case of relativistic systems, on the other hand, the calculation of sum rules is fraught with difficulties. Various perturbative approaches have been used over the years to obtain relativistic corrections, but these methods fail badly when the system in question is very strongly bound. Here, I present an approach that leads to relatively simple expressions yielding accurate sums, even for highly relativistic many-electron systems. I also offer an explanation for the difference between relativistic and nonrelativistic sum rules in terms of the Zitterbewegung of the electrons.

  1. Molecular Structures and Momentum Transfer Cross Sections: The Influence of the Analyte Charge Distribution.

    PubMed

    Young, Meggie N; Bleiholder, Christian

    2017-04-01

    Structure elucidation by ion mobility spectrometry-mass spectrometry methods is based on the comparison of an experimentally measured momentum transfer cross-section to cross-sections calculated for model structures. Thus, it is imperative that the calculated cross-section must be accurate. However, it is not fully understood how important it is to accurately model the charge distribution of an analyte ion when calculating momentum transfer cross-sections. Here, we calculate and compare momentum transfer cross-sections for carbon clusters that differ in mass, charge state, and mode of charge distribution, and vary temperature and polarizability of the buffer gas. Our data indicate that the detailed distribution of the ion charge density is intimately linked to the contribution of glancing collisions to the momentum transfer cross-section. The data suggest that analyte ions with molecular mass ~3 kDa or momentum transfer cross-section 400-500 Å 2 would be significantly influenced by the charge distribution in nitrogen buffer gas. Our data further suggest that accurate structure elucidation on the basis of IMS-MS data measured in nitrogen buffer gas must account for the molecular charge distribution even for systems as large as C 960 (~12 kDa) when localized charges are present and/or measurements are conducted under cryogenic temperatures. Finally, our data underscore that accurate structure elucidation is unlikely if ion mobility data recorded in one buffer gas is converted into other buffer gases when electronic properties of the buffer gases differ. Graphical Abstract ᅟ.

  2. Spectral multivariate calibration without laboratory prepared or determined reference analyte values.

    PubMed

    Ottaway, Josh; Farrell, Jeremy A; Kalivas, John H

    2013-02-05

    An essential part to calibration is establishing the analyte calibration reference samples. These samples must characterize the sample matrix and measurement conditions (chemical, physical, instrumental, and environmental) of any sample to be predicted. Calibration usually requires measuring spectra for numerous reference samples in addition to determining the corresponding analyte reference values. Both tasks are typically time-consuming and costly. This paper reports on a method named pure component Tikhonov regularization (PCTR) that does not require laboratory prepared or determined reference values. Instead, an analyte pure component spectrum is used in conjunction with nonanalyte spectra for calibration. Nonanalyte spectra can be from different sources including pure component interference samples, blanks, and constant analyte samples. The approach is also applicable to calibration maintenance when the analyte pure component spectrum is measured in one set of conditions and nonanalyte spectra are measured in new conditions. The PCTR method balances the trade-offs between calibration model shrinkage and the degree of orthogonality to the nonanalyte content (model direction) in order to obtain accurate predictions. Using visible and near-infrared (NIR) spectral data sets, the PCTR results are comparable to those obtained using ridge regression (RR) with reference calibration sets. The flexibility of PCTR also allows including reference samples if such samples are available.

  3. Analytical fitting model for rough-surface BRDF.

    PubMed

    Renhorn, Ingmar G E; Boreman, Glenn D

    2008-08-18

    A physics-based model is developed for rough surface BRDF, taking into account angles of incidence and scattering, effective index, surface autocovariance, and correlation length. Shadowing is introduced on surface correlation length and reflectance. Separate terms are included for surface scatter, bulk scatter and retroreflection. Using the FindFit function in Mathematica, the functional form is fitted to BRDF measurements over a wide range of incident angles. The model has fourteen fitting parameters; once these are fixed, the model accurately describes scattering data over two orders of magnitude in BRDF without further adjustment. The resulting analytical model is convenient for numerical computations.

  4. bigSCale: an analytical framework for big-scale single-cell data.

    PubMed

    Iacono, Giovanni; Mereu, Elisabetta; Guillaumet-Adkins, Amy; Corominas, Roser; Cuscó, Ivon; Rodríguez-Esteban, Gustavo; Gut, Marta; Pérez-Jurado, Luis Alberto; Gut, Ivo; Heyn, Holger

    2018-06-01

    Single-cell RNA sequencing (scRNA-seq) has significantly deepened our insights into complex tissues, with the latest techniques capable of processing tens of thousands of cells simultaneously. Analyzing increasing numbers of cells, however, generates extremely large data sets, extending processing time and challenging computing resources. Current scRNA-seq analysis tools are not designed to interrogate large data sets and often lack sensitivity to identify marker genes. With bigSCale, we provide a scalable analytical framework to analyze millions of cells, which addresses the challenges associated with large data sets. To handle the noise and sparsity of scRNA-seq data, bigSCale uses large sample sizes to estimate an accurate numerical model of noise. The framework further includes modules for differential expression analysis, cell clustering, and marker identification. A directed convolution strategy allows processing of extremely large data sets, while preserving transcript information from individual cells. We evaluated the performance of bigSCale using both a biological model of aberrant gene expression in patient-derived neuronal progenitor cells and simulated data sets, which underlines the speed and accuracy in differential expression analysis. To test its applicability for large data sets, we applied bigSCale to assess 1.3 million cells from the mouse developing forebrain. Its directed down-sampling strategy accumulates information from single cells into index cell transcriptomes, thereby defining cellular clusters with improved resolution. Accordingly, index cell clusters identified rare populations, such as reelin ( Reln )-positive Cajal-Retzius neurons, for which we report previously unrecognized heterogeneity associated with distinct differentiation stages, spatial organization, and cellular function. Together, bigSCale presents a solution to address future challenges of large single-cell data sets. © 2018 Iacono et al.; Published by Cold Spring Harbor

  5. Assessment of analytical quality in Nordic clinical chemistry laboratories using data from contemporary national programs.

    PubMed

    Aronsson, T; Bjørnstad, P; Leskinen, E; Uldall, A; de Verdier, C H

    1984-01-01

    The aim of this investigation was primarily to assess analytical quality expressed as between-laboratory, within-laboratory, and total imprecision, not in order to detect laboratories with poor performance, but in the positive sense to provide data for improving critical steps in analytical methodology. The aim was also to establish the present state of the art in comparison with earlier investigations to see if improvement in analytical quality could be observed.

  6. Online self-expression and experimentation as 'reflectivism': Using text analytics to examine the participatory forum Hello Sunday Morning.

    PubMed

    Carah, Nicholas; Meurk, Carla; Angus, Daniel

    2017-03-01

    Hello Sunday Morning is an online health promotion organisation that began in 2009. Hello Sunday Morning asks participants to stop consuming alcohol for a period of time, set a goal and document their progress on a personal blog. Hello Sunday Morning is a unique health intervention for three interrelated reasons: (1) it was generated outside a clinical setting, (2) it uses new media technologies to create structured forms of participation in an iterative and open-ended way and (3) participants generate a written record of their progress along with demographic, behavioural and engagement data. This article presents a text analysis of the blog posts of Hello Sunday Morning participants using the software program Leximancer. Analysis of blogs illustrates how participants' expressions change over time. In the first month, participants tended to set goals, describe their current drinking practices in individual and cultural terms, express hopes and anxieties and report on early efforts to change. After month 1, participants continued to report on efforts to change and associated challenges and reflect on their place as individuals in a drinking culture. In addition to this, participants evaluated their efforts to change and presented their 'findings' and 'theorised' them to provide advice for others. We contextualise this text analysis with respect to Hello Sunday Morning's development of more structured forms of online participation. We offer a critical appraisal of the value of text analytics in the development of online health interventions.

  7. Analytical Validation of Accelerator Mass Spectrometry for Pharmaceutical Development: the Measurement of Carbon-14 Isotope Ratio.

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

    Keck, B D; Ognibene, T; Vogel, J S

    2010-02-05

    Accelerator mass spectrometry (AMS) is an isotope based measurement technology that utilizes carbon-14 labeled compounds in the pharmaceutical development process to measure compounds at very low concentrations, empowers microdosing as an investigational tool, and extends the utility of {sup 14}C labeled compounds to dramatically lower levels. It is a form of isotope ratio mass spectrometry that can provide either measurements of total compound equivalents or, when coupled to separation technology such as chromatography, quantitation of specific compounds. The properties of AMS as a measurement technique are investigated here, and the parameters of method validation are shown. AMS, independent of anymore » separation technique to which it may be coupled, is shown to be accurate, linear, precise, and robust. As the sensitivity and universality of AMS is constantly being explored and expanded, this work underpins many areas of pharmaceutical development including drug metabolism as well as absorption, distribution and excretion of pharmaceutical compounds as a fundamental step in drug development. The validation parameters for pharmaceutical analyses were examined for the accelerator mass spectrometry measurement of {sup 14}C/C ratio, independent of chemical separation procedures. The isotope ratio measurement was specific (owing to the {sup 14}C label), stable across samples storage conditions for at least one year, linear over 4 orders of magnitude with an analytical range from one tenth Modern to at least 2000 Modern (instrument specific). Further, accuracy was excellent between 1 and 3 percent while precision expressed as coefficient of variation is between 1 and 6% determined primarily by radiocarbon content and the time spent analyzing a sample. Sensitivity, expressed as LOD and LLOQ was 1 and 10 attomoles of carbon-14 (which can be expressed as compound equivalents) and for a typical small molecule labeled at 10% incorporated with {sup 14}C corresponds to 30

  8. Unified analytic representation of physical sputtering yield

    NASA Astrophysics Data System (ADS)

    Janev, R. K.; Ralchenko, Yu. V.; Kenmotsu, T.; Hosaka, K.

    2001-03-01

    Generalized energy parameter η= η( ɛ, δ) and normalized sputtering yield Ỹ(η) , where ɛ= E/ ETF and δ= Eth/ ETF, are introduced to achieve a unified representation of all available experimental and sputtering data at normal ion incidence. The sputtering data in the new Ỹ(η) representation retain their original uncertainties. The Ỹ(η) data can be fitted to a simple three-parameter analytic expression with an rms deviation of 32%, well within the uncertainties of original data. Both η and Ỹ(η) have correct physical behavior in the threshold and high-energy regions. The available theoretical data produced by the TRIM.SP code can also be represented by the same single analytic function Ỹ(η) with a similar accuracy.

  9. Analytic continuation of quantum Monte Carlo data by stochastic analytical inference.

    PubMed

    Fuchs, Sebastian; Pruschke, Thomas; Jarrell, Mark

    2010-05-01

    We present an algorithm for the analytic continuation of imaginary-time quantum Monte Carlo data which is strictly based on principles of Bayesian statistical inference. Within this framework we are able to obtain an explicit expression for the calculation of a weighted average over possible energy spectra, which can be evaluated by standard Monte Carlo simulations, yielding as by-product also the distribution function as function of the regularization parameter. Our algorithm thus avoids the usual ad hoc assumptions introduced in similar algorithms to fix the regularization parameter. We apply the algorithm to imaginary-time quantum Monte Carlo data and compare the resulting energy spectra with those from a standard maximum-entropy calculation.

  10. MODFLOW equipped with a new method for the accurate simulation of axisymmetric flow

    NASA Astrophysics Data System (ADS)

    Samani, N.; Kompani-Zare, M.; Barry, D. A.

    2004-01-01

    Axisymmetric flow to a well is an important topic of groundwater hydraulics, the simulation of which depends on accurate computation of head gradients. Groundwater numerical models with conventional rectilinear grid geometry such as MODFLOW (in contrast to analytical models) generally have not been used to simulate aquifer test results at a pumping well because they are not designed or expected to closely simulate the head gradient near the well. A scaling method is proposed based on mapping the governing flow equation from cylindrical to Cartesian coordinates, and vice versa. A set of relationships and scales is derived to implement the conversion. The proposed scaling method is then embedded in MODFLOW 2000. To verify the accuracy of the method steady and unsteady flows in confined and unconfined aquifers with fully or partially penetrating pumping wells are simulated and compared with the corresponding analytical solutions. In all cases a high degree of accuracy is achieved.

  11. Analytic reflected light curves for exoplanets

    NASA Astrophysics Data System (ADS)

    Haggard, Hal M.; Cowan, Nicolas B.

    2018-07-01

    The disc-integrated reflected brightness of an exoplanet changes as a function of time due to orbital and rotational motions coupled with an inhomogeneous albedo map. We have previously derived analytic reflected light curves for spherical harmonic albedo maps in the special case of a synchronously rotating planet on an edge-on orbit (Cowan, Fuentes & Haggard). In this paper, we present analytic reflected light curves for the general case of a planet on an inclined orbit, with arbitrary spin period and non-zero obliquity. We do so for two different albedo basis maps: bright points (δ-maps), and spherical harmonics (Y_ l^m-maps). In particular, we use Wigner D-matrices to express an harmonic light curve for an arbitrary viewing geometry as a non-linear combination of harmonic light curves for the simpler edge-on, synchronously rotating geometry. These solutions will enable future exploration of the degeneracies and information content of reflected light curves, as well as fast calculation of light curves for mapping exoplanets based on time-resolved photometry. To these ends, we make available Exoplanet Analytic Reflected Lightcurves, a simple open-source code that allows rapid computation of reflected light curves.

  12. A Computational Framework for Analyzing Stochasticity in Gene Expression

    PubMed Central

    Sherman, Marc S.; Cohen, Barak A.

    2014-01-01

    Stochastic fluctuations in gene expression give rise to distributions of protein levels across cell populations. Despite a mounting number of theoretical models explaining stochasticity in protein expression, we lack a robust, efficient, assumption-free approach for inferring the molecular mechanisms that underlie the shape of protein distributions. Here we propose a method for inferring sets of biochemical rate constants that govern chromatin modification, transcription, translation, and RNA and protein degradation from stochasticity in protein expression. We asked whether the rates of these underlying processes can be estimated accurately from protein expression distributions, in the absence of any limiting assumptions. To do this, we (1) derived analytical solutions for the first four moments of the protein distribution, (2) found that these four moments completely capture the shape of protein distributions, and (3) developed an efficient algorithm for inferring gene expression rate constants from the moments of protein distributions. Using this algorithm we find that most protein distributions are consistent with a large number of different biochemical rate constant sets. Despite this degeneracy, the solution space of rate constants almost always informs on underlying mechanism. For example, we distinguish between regimes where transcriptional bursting occurs from regimes reflecting constitutive transcript production. Our method agrees with the current standard approach, and in the restrictive regime where the standard method operates, also identifies rate constants not previously obtainable. Even without making any assumptions we obtain estimates of individual biochemical rate constants, or meaningful ratios of rate constants, in 91% of tested cases. In some cases our method identified all of the underlying rate constants. The framework developed here will be a powerful tool for deducing the contributions of particular molecular mechanisms to specific patterns

  13. Accurate quantitation for in vitro refolding of single domain antibody fragments expressed as inclusion bodies by referring the concomitant expression of a soluble form in the periplasms of Escherichia coli.

    PubMed

    Noguchi, Tomoaki; Nishida, Yuichi; Takizawa, Keiji; Cui, Yue; Tsutsumi, Koki; Hamada, Takashi; Nishi, Yoshisuke

    2017-03-01

    Single domain antibody fragments from two species, a camel V H H (PM1) and a shark V NAR (A6), were derived from inclusion bodies of E. coli and refolded in vitro following three refolding recipes for comparing refolding efficiencies: three-step cold dialysis refolding (TCDR), one-step hot dialysis refolding (OHDR), and one-step cold dialysis refolding (OCDR), as these fragments were expressed as 'a soluble form' either in cytoplasm or periplasm, but the amount were much less than those expressed as 'an insoluble form (inclusion body)' in cytoplasm and periplasm. In order to verify the refolding efficiencies from inclusion bodies correctly, proteins purified from periplasmic soluble fractions were used as reference samples. These samples showed far-UV spectra of a typical β-sheet-dominant structure in circular dichroism (CD) spectroscopy and so did the refolded samples as well. As the maximal magnitude of ellipticity in millidegrees (θ max ) observed at a given wave length was proportional to the concentrations of the respective reference samples, we could draw linear regression lines for the magnitudes vs. sample concentrations. By using these lines, we measured the concentrations for the refolded PM1 and A6 samples purified from solubilized cytoplasmic insoluble fractions. The refolding efficiency of PM1 was almost 50% following TCDR and 40% and 30% following OHDR and OCDR, respectively, whereas the value of A6 was around 30% following TCDR, and out of bound for quantitation following the other two recipes. The ELISA curves, which were derived from the refolded samples, coincided better with those obtained from the reference samples after converting the values from the protein-concentrations at recovery to the ones of refolded proteins using recovery ratios, indicating that such a correction gives better results for the accurate measure of the ELISA curves than those without correction. Our method require constructing a dual expression system, expressed both in

  14. Discordance between net analyte signal theory and practical multivariate calibration.

    PubMed

    Brown, Christopher D

    2004-08-01

    Lorber's concept of net analyte signal is reviewed in the context of classical and inverse least-squares approaches to multivariate calibration. It is shown that, in the presence of device measurement error, the classical and inverse calibration procedures have radically different theoretical prediction objectives, and the assertion that the popular inverse least-squares procedures (including partial least squares, principal components regression) approximate Lorber's net analyte signal vector in the limit is disproved. Exact theoretical expressions for the prediction error bias, variance, and mean-squared error are given under general measurement error conditions, which reinforce the very discrepant behavior between these two predictive approaches, and Lorber's net analyte signal theory. Implications for multivariate figures of merit and numerous recently proposed preprocessing treatments involving orthogonal projections are also discussed.

  15. Dissociation between recognition and detection advantage for facial expressions: a meta-analysis.

    PubMed

    Nummenmaa, Lauri; Calvo, Manuel G

    2015-04-01

    Happy facial expressions are recognized faster and more accurately than other expressions in categorization tasks, whereas detection in visual search tasks is widely believed to be faster for angry than happy faces. We used meta-analytic techniques for resolving this categorization versus detection advantage discrepancy for positive versus negative facial expressions. Effect sizes were computed on the basis of the r statistic for a total of 34 recognition studies with 3,561 participants and 37 visual search studies with 2,455 participants, yielding a total of 41 effect sizes for recognition accuracy, 25 for recognition speed, and 125 for visual search speed. Random effects meta-analysis was conducted to estimate effect sizes at population level. For recognition tasks, an advantage in recognition accuracy and speed for happy expressions was found for all stimulus types. In contrast, for visual search tasks, moderator analysis revealed that a happy face detection advantage was restricted to photographic faces, whereas a clear angry face advantage was found for schematic and "smiley" faces. Robust detection advantage for nonhappy faces was observed even when stimulus emotionality was distorted by inversion or rearrangement of the facial features, suggesting that visual features primarily drive the search. We conclude that the recognition advantage for happy faces is a genuine phenomenon related to processing of facial expression category and affective valence. In contrast, detection advantages toward either happy (photographic stimuli) or nonhappy (schematic) faces is contingent on visual stimulus features rather than facial expression, and may not involve categorical or affective processing. (c) 2015 APA, all rights reserved).

  16. Analytic double product integrals for all-frequency relighting.

    PubMed

    Wang, Rui; Pan, Minghao; Chen, Weifeng; Ren, Zhong; Zhou, Kun; Hua, Wei; Bao, Hujun

    2013-07-01

    This paper presents a new technique for real-time relighting of static scenes with all-frequency shadows from complex lighting and highly specular reflections from spatially varying BRDFs. The key idea is to depict the boundaries of visible regions using piecewise linear functions, and convert the shading computation into double product integrals—the integral of the product of lighting and BRDF on visible regions. By representing lighting and BRDF with spherical Gaussians and approximating their product using Legendre polynomials locally in visible regions, we show that such double product integrals can be evaluated in an analytic form. Given the precomputed visibility, our technique computes the visibility boundaries on the fly at each shading point, and performs the analytic integral to evaluate the shading color. The result is a real-time all-frequency relighting technique for static scenes with dynamic, spatially varying BRDFs, which can generate more accurate shadows than the state-of-the-art real-time PRT methods.

  17. Hybrid Analytical and Data-Driven Modeling for Feed-Forward Robot Control.

    PubMed

    Reinhart, René Felix; Shareef, Zeeshan; Steil, Jochen Jakob

    2017-02-08

    Feed-forward model-based control relies on models of the controlled plant, e.g., in robotics on accurate knowledge of manipulator kinematics or dynamics. However, mechanical and analytical models do not capture all aspects of a plant's intrinsic properties and there remain unmodeled dynamics due to varying parameters, unmodeled friction or soft materials. In this context, machine learning is an alternative suitable technique to extract non-linear plant models from data. However, fully data-based models suffer from inaccuracies as well and are inefficient if they include learning of well known analytical models. This paper thus argues that feed-forward control based on hybrid models comprising an analytical model and a learned error model can significantly improve modeling accuracy. Hybrid modeling here serves the purpose to combine the best of the two modeling worlds. The hybrid modeling methodology is described and the approach is demonstrated for two typical problems in robotics, i.e., inverse kinematics control and computed torque control. The former is performed for a redundant soft robot and the latter for a rigid industrial robot with redundant degrees of freedom, where a complete analytical model is not available for any of the platforms.

  18. Calibrant-Free Analyte Quantitation via a Variable Velocity Flow Cell.

    PubMed

    Beck, Jason G; Skuratovsky, Aleksander; Granger, Michael C; Porter, Marc D

    2017-01-17

    In this paper, we describe a novel method for analyte quantitation that does not rely on calibrants, internal standards, or calibration curves but, rather, leverages the relationship between disparate and predictable surface-directed analyte flux to an array of sensing addresses and a measured resultant signal. To reduce this concept to practice, we fabricated two flow cells such that the mean linear fluid velocity, U, was varied systematically over an array of electrodes positioned along the flow axis. This resulted in a predictable variation of the address-directed flux of a redox analyte, ferrocenedimethanol (FDM). The resultant limiting currents measured at a series of these electrodes, and accurately described by a convective-diffusive transport model, provided a means to calculate an "unknown" concentration without the use of calibrants, internal standards, or a calibration curve. Furthermore, the experiment and concentration calculation only takes minutes to perform. Deviation in calculated FDM concentrations from true values was minimized to less than 0.5% when empirically derived values of U were employed.

  19. Assessment of methicillin resistant Staphylococcus Aureus detection methods: analytical comparative study.

    PubMed

    Ibrahim, Omer Mohammed Ali; Bilal, Naser Eldin; Osman, Omran Fadl; Magzoub, Magzoub Abbas

    2017-01-01

    The heterogeneous expression of methicillin resistance in Staphylococcus aureus (MRSA) affects the efficiency of tests available to detect it. The objective of this study was to assess four phenotypic tests used to detect MRSA. This is an analytical comparative study conducted among sudanese patients during period from May 2012 to July 2014, Staphylococcus aureus strains were isolated and identified by conventional methods, and then confirmed by PCR detection of coagulase gene. PCR detection of mecA gene was used as a gold standard to assess oxacillin resistance screen agar base (ORSAB), oxacillin disc, cefoxitin disc (at different temperatures and incubation periods) and MRSA-latex agglutination test. S.aureus ATCC 25923 was used as control. Sensitivity and specificity were calculated. MRSA- latex agglutination was the most accurate test; it showed 100% of both sensitivity and specificity, followed by cefoxitin disc with sensitivity of 98.48% and specificity of 100%. However, both of oxacillin disc and oxacillin resistance screen agar base showed less accurate results, and were affected by incubation periods. Oxacillin disc after 24 h incubation both at 30°C and 35°C showed sensitivity and specificity values of 87.88% and 96.23%, respectively. However, after 48h incubation the test at 30°C showed sensitivity and specificity values of 89.39%, and 94.34%, respectively. At 35°C (48h) it showed values of 89.39%, 92.45% respectively. Specificity of ORSAB was more than oxacillin disc at 35°C after 24h incubation 98.11% and 96.23%, respectively. MRSA- latex agglutination and cefoxitin disc diffusion tests are recommended for routine detection of MRSA.

  20. Predictive Analytical Model for Isolator Shock-Train Location in a Mach 2.2 Direct-Connect Supersonic Combustion Tunnel

    NASA Astrophysics Data System (ADS)

    Lingren, Joe; Vanstone, Leon; Hashemi, Kelley; Gogineni, Sivaram; Donbar, Jeffrey; Akella, Maruthi; Clemens, Noel

    2016-11-01

    This study develops an analytical model for predicting the leading shock of a shock-train in the constant area isolator section in a Mach 2.2 direct-connect scramjet simulation tunnel. The effective geometry of the isolator is assumed to be a weakly converging duct owing to boundary-layer growth. For some given pressure rise across the isolator, quasi-1D equations relating to isentropic or normal shock flows can be used to predict the normal shock location in the isolator. The surface pressure distribution through the isolator was measured during experiments and both the actual and predicted locations can be calculated. Three methods of finding the shock-train location are examined, one based on the measured pressure rise, one using a non-physics-based control model, and one using the physics-based analytical model. It is shown that the analytical model performs better than the non-physics-based model in all cases. The analytic model is less accurate than the pressure threshold method but requires significantly less information to compute. In contrast to other methods for predicting shock-train location, this method is relatively accurate and requires as little as a single pressure measurement. This makes this method potentially useful for unstart control applications.

  1. Carbene footprinting accurately maps binding sites in protein-ligand and protein-protein interactions

    NASA Astrophysics Data System (ADS)

    Manzi, Lucio; Barrow, Andrew S.; Scott, Daniel; Layfield, Robert; Wright, Timothy G.; Moses, John E.; Oldham, Neil J.

    2016-11-01

    Specific interactions between proteins and their binding partners are fundamental to life processes. The ability to detect protein complexes, and map their sites of binding, is crucial to understanding basic biology at the molecular level. Methods that employ sensitive analytical techniques such as mass spectrometry have the potential to provide valuable insights with very little material and on short time scales. Here we present a differential protein footprinting technique employing an efficient photo-activated probe for use with mass spectrometry. Using this methodology the location of a carbohydrate substrate was accurately mapped to the binding cleft of lysozyme, and in a more complex example, the interactions between a 100 kDa, multi-domain deubiquitinating enzyme, USP5 and a diubiquitin substrate were located to different functional domains. The much improved properties of this probe make carbene footprinting a viable method for rapid and accurate identification of protein binding sites utilizing benign, near-UV photoactivation.

  2. Analytic gradient for second order Møller-Plesset perturbation theory with the polarizable continuum model based on the fragment molecular orbital method.

    PubMed

    Nagata, Takeshi; Fedorov, Dmitri G; Li, Hui; Kitaura, Kazuo

    2012-05-28

    A new energy expression is proposed for the fragment molecular orbital method interfaced with the polarizable continuum model (FMO/PCM). The solvation free energy is shown to be more accurate on a set of representative polypeptides with neutral and charged residues, in comparison to the original formulation at the same level of the many-body expansion of the electrostatic potential determining the apparent surface charges. The analytic first derivative of the energy with respect to nuclear coordinates is formulated at the second-order Møller-Plesset (MP2) perturbation theory level combined with PCM, for which we derived coupled perturbed Hartree-Fock equations. The accuracy of the analytic gradient is demonstrated on test calculations in comparison to numeric gradient. Geometry optimization of the small Trp-cage protein (PDB: 1L2Y) is performed with FMO/PCM/6-31(+)G(d) at the MP2 and restricted Hartree-Fock with empirical dispersion (RHF/D). The root mean square deviations between the FMO optimized and NMR experimental structure are found to be 0.414 and 0.426 Å for RHF/D and MP2, respectively. The details of the hydrogen bond network in the Trp-cage protein are revealed.

  3. Analytic gradient for second order Møller-Plesset perturbation theory with the polarizable continuum model based on the fragment molecular orbital method

    NASA Astrophysics Data System (ADS)

    Nagata, Takeshi; Fedorov, Dmitri G.; Li, Hui; Kitaura, Kazuo

    2012-05-01

    A new energy expression is proposed for the fragment molecular orbital method interfaced with the polarizable continuum model (FMO/PCM). The solvation free energy is shown to be more accurate on a set of representative polypeptides with neutral and charged residues, in comparison to the original formulation at the same level of the many-body expansion of the electrostatic potential determining the apparent surface charges. The analytic first derivative of the energy with respect to nuclear coordinates is formulated at the second-order Møller-Plesset (MP2) perturbation theory level combined with PCM, for which we derived coupled perturbed Hartree-Fock equations. The accuracy of the analytic gradient is demonstrated on test calculations in comparison to numeric gradient. Geometry optimization of the small Trp-cage protein (PDB: 1L2Y) is performed with FMO/PCM/6-31(+)G(d) at the MP2 and restricted Hartree-Fock with empirical dispersion (RHF/D). The root mean square deviations between the FMO optimized and NMR experimental structure are found to be 0.414 and 0.426 Å for RHF/D and MP2, respectively. The details of the hydrogen bond network in the Trp-cage protein are revealed.

  4. Biomarker Surrogates Do Not Accurately Predict Sputum Eosinophils and Neutrophils in Asthma

    PubMed Central

    Hastie, Annette T.; Moore, Wendy C.; Li, Huashi; Rector, Brian M.; Ortega, Victor E.; Pascual, Rodolfo M.; Peters, Stephen P.; Meyers, Deborah A.; Bleecker, Eugene R.

    2013-01-01

    Background Sputum eosinophils (Eos) are a strong predictor of airway inflammation, exacerbations, and aid asthma management, whereas sputum neutrophils (Neu) indicate a different severe asthma phenotype, potentially less responsive to TH2-targeted therapy. Variables such as blood Eos, total IgE, fractional exhaled nitric oxide (FeNO) or FEV1% predicted, may predict airway Eos, while age, FEV1%predicted, or blood Neu may predict sputum Neu. Availability and ease of measurement are useful characteristics, but accuracy in predicting airway Eos and Neu, individually or combined, is not established. Objectives To determine whether blood Eos, FeNO, and IgE accurately predict sputum eosinophils, and age, FEV1% predicted, and blood Neu accurately predict sputum neutrophils (Neu). Methods Subjects in the Wake Forest Severe Asthma Research Program (N=328) were characterized by blood and sputum cells, healthcare utilization, lung function, FeNO, and IgE. Multiple analytical techniques were utilized. Results Despite significant association with sputum Eos, blood Eos, FeNO and total IgE did not accurately predict sputum Eos, and combinations of these variables failed to improve prediction. Age, FEV1%predicted and blood Neu were similarly unsatisfactory for prediction of sputum Neu. Factor analysis and stepwise selection found FeNO, IgE and FEV1% predicted, but not blood Eos, correctly predicted 69% of sputum Eosaccurately assigned only 41% of samples. Conclusion Despite statistically significant associations FeNO, IgE, blood Eos and Neu, FEV1%predicted, and age are poor surrogates, separately and combined, for accurately predicting sputum eosinophils and neutrophils. PMID:23706399

  5. Validation of reference genes for accurate normalization of gene expression for real time-quantitative PCR in strawberry fruits using different cultivars and osmotic stresses.

    PubMed

    Galli, Vanessa; Borowski, Joyce Moura; Perin, Ellen Cristina; Messias, Rafael da Silva; Labonde, Julia; Pereira, Ivan dos Santos; Silva, Sérgio Delmar Dos Anjos; Rombaldi, Cesar Valmor

    2015-01-10

    The increasing demand of strawberry (Fragaria×ananassa Duch) fruits is associated mainly with their sensorial characteristics and the content of antioxidant compounds. Nevertheless, the strawberry production has been hampered due to its sensitivity to abiotic stresses. Therefore, to understand the molecular mechanisms highlighting stress response is of great importance to enable genetic engineering approaches aiming to improve strawberry tolerance. However, the study of expression of genes in strawberry requires the use of suitable reference genes. In the present study, seven traditional and novel candidate reference genes were evaluated for transcript normalization in fruits of ten strawberry cultivars and two abiotic stresses, using RefFinder, which integrates the four major currently available software programs: geNorm, NormFinder, BestKeeper and the comparative delta-Ct method. The results indicate that the expression stability is dependent on the experimental conditions. The candidate reference gene DBP (DNA binding protein) was considered the most suitable to normalize expression data in samples of strawberry cultivars and under drought stress condition, and the candidate reference gene HISTH4 (histone H4) was the most stable under osmotic stresses and salt stress. The traditional genes GAPDH (glyceraldehyde-3-phosphate dehydrogenase) and 18S (18S ribosomal RNA) were considered the most unstable genes in all conditions. The expression of phenylalanine ammonia lyase (PAL) and 9-cis epoxycarotenoid dioxygenase (NCED1) genes were used to further confirm the validated candidate reference genes, showing that the use of an inappropriate reference gene may induce erroneous results. This study is the first survey on the stability of reference genes in strawberry cultivars and osmotic stresses and provides guidelines to obtain more accurate RT-qPCR results for future breeding efforts. Copyright © 2014 Elsevier B.V. All rights reserved.

  6. Applying Pragmatics Principles for Interaction with Visual Analytics.

    PubMed

    Hoque, Enamul; Setlur, Vidya; Tory, Melanie; Dykeman, Isaac

    2018-01-01

    Interactive visual data analysis is most productive when users can focus on answering the questions they have about their data, rather than focusing on how to operate the interface to the analysis tool. One viable approach to engaging users in interactive conversations with their data is a natural language interface to visualizations. These interfaces have the potential to be both more expressive and more accessible than other interaction paradigms. We explore how principles from language pragmatics can be applied to the flow of visual analytical conversations, using natural language as an input modality. We evaluate the effectiveness of pragmatics support in our system Evizeon, and present design considerations for conversation interfaces to visual analytics tools.

  7. Efficient alignment-free DNA barcode analytics.

    PubMed

    Kuksa, Pavel; Pavlovic, Vladimir

    2009-11-10

    In this work we consider barcode DNA analysis problems and address them using alternative, alignment-free methods and representations which model sequences as collections of short sequence fragments (features). The methods use fixed-length representations (spectrum) for barcode sequences to measure similarities or dissimilarities between sequences coming from the same or different species. The spectrum-based representation not only allows for accurate and computationally efficient species classification, but also opens possibility for accurate clustering analysis of putative species barcodes and identification of critical within-barcode loci distinguishing barcodes of different sample groups. New alignment-free methods provide highly accurate and fast DNA barcode-based identification and classification of species with substantial improvements in accuracy and speed over state-of-the-art barcode analysis methods. We evaluate our methods on problems of species classification and identification using barcodes, important and relevant analytical tasks in many practical applications (adverse species movement monitoring, sampling surveys for unknown or pathogenic species identification, biodiversity assessment, etc.) On several benchmark barcode datasets, including ACG, Astraptes, Hesperiidae, Fish larvae, and Birds of North America, proposed alignment-free methods considerably improve prediction accuracy compared to prior results. We also observe significant running time improvements over the state-of-the-art methods. Our results show that newly developed alignment-free methods for DNA barcoding can efficiently and with high accuracy identify specimens by examining only few barcode features, resulting in increased scalability and interpretability of current computational approaches to barcoding.

  8. Efficient alignment-free DNA barcode analytics

    PubMed Central

    Kuksa, Pavel; Pavlovic, Vladimir

    2009-01-01

    Background In this work we consider barcode DNA analysis problems and address them using alternative, alignment-free methods and representations which model sequences as collections of short sequence fragments (features). The methods use fixed-length representations (spectrum) for barcode sequences to measure similarities or dissimilarities between sequences coming from the same or different species. The spectrum-based representation not only allows for accurate and computationally efficient species classification, but also opens possibility for accurate clustering analysis of putative species barcodes and identification of critical within-barcode loci distinguishing barcodes of different sample groups. Results New alignment-free methods provide highly accurate and fast DNA barcode-based identification and classification of species with substantial improvements in accuracy and speed over state-of-the-art barcode analysis methods. We evaluate our methods on problems of species classification and identification using barcodes, important and relevant analytical tasks in many practical applications (adverse species movement monitoring, sampling surveys for unknown or pathogenic species identification, biodiversity assessment, etc.) On several benchmark barcode datasets, including ACG, Astraptes, Hesperiidae, Fish larvae, and Birds of North America, proposed alignment-free methods considerably improve prediction accuracy compared to prior results. We also observe significant running time improvements over the state-of-the-art methods. Conclusion Our results show that newly developed alignment-free methods for DNA barcoding can efficiently and with high accuracy identify specimens by examining only few barcode features, resulting in increased scalability and interpretability of current computational approaches to barcoding. PMID:19900305

  9. Approximate analytical solution for induction heating of solid cylinders

    DOE PAGES

    Jankowski, Todd Andrew; Pawley, Norma Helen; Gonzales, Lindsey Michal; ...

    2015-10-20

    An approximate solution to the mathematical model for induction heating of a solid cylinder in a cylindrical induction coil is presented here. The coupled multiphysics model includes equations describing the electromagnetic field in the heated object, a heat transfer simulation to determine temperature of the heated object, and an AC circuit simulation of the induction heating power supply. A multiple-scale perturbation method is used to solve the multiphysics model. The approximate analytical solution yields simple closed-form expressions for the electromagnetic field and heat generation rate in the solid cylinder, for the equivalent impedance of the associated tank circuit, and formore » the frequency response of a variable frequency power supply driving the tank circuit. The solution developed here is validated by comparing predicted power supply frequency to both experimental measurements and calculated values from finite element analysis for heating of graphite cylinders in an induction furnace. The simple expressions from the analytical solution clearly show the functional dependence of the power supply frequency on the material properties of the load and the geometrical characteristics of the furnace installation. In conclusion, the expressions developed here provide physical insight into observations made during load signature analysis of induction heating.« less

  10. Analytical study of the critical behavior of the nonlinear pendulum

    NASA Astrophysics Data System (ADS)

    Lima, F. M. S.

    2010-11-01

    The dynamics of a simple pendulum consisting of a small bob and a massless rigid rod has three possible regimes depending on its total energy E: Oscillatory (when E is not enough for the pendulum to reach the top position), "perpetual ascent" when E is exactly the energy needed to reach the top, and nonoscillatory for greater energies. In the latter regime, the pendulum rotates periodically without velocity inversions. In contrast to the oscillatory regime, for which an exact analytic solution is known, the other two regimes are usually studied by solving the equation of motion numerically. By applying conservation of energy, I derive exact analytical solutions to both the perpetual ascent and nonoscillatory regimes and an exact expression for the pendulum period in the nonoscillatory regime. Based on Cromer's approximation for the large-angle pendulum period, I find a simple approximate expression for the decrease of the period with the initial velocity in the nonoscillatory regime, valid near the critical velocity. This expression is used to study the critical slowing down, which is observed near the transition between the oscillatory and nonoscillatory regimes.

  11. Fast and accurate calculation of dilute quantum gas using Uehling–Uhlenbeck model equation

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

    Yano, Ryosuke, E-mail: ryosuke.yano@tokiorisk.co.jp

    The Uehling–Uhlenbeck (U–U) model equation is studied for the fast and accurate calculation of a dilute quantum gas. In particular, the direct simulation Monte Carlo (DSMC) method is used to solve the U–U model equation. DSMC analysis based on the U–U model equation is expected to enable the thermalization to be accurately obtained using a small number of sample particles and the dilute quantum gas dynamics to be calculated in a practical time. Finally, the applicability of DSMC analysis based on the U–U model equation to the fast and accurate calculation of a dilute quantum gas is confirmed by calculatingmore » the viscosity coefficient of a Bose gas on the basis of the Green–Kubo expression and the shock layer of a dilute Bose gas around a cylinder.« less

  12. Semantic Interaction for Sensemaking: Inferring Analytical Reasoning for Model Steering.

    PubMed

    Endert, A; Fiaux, P; North, C

    2012-12-01

    Visual analytic tools aim to support the cognitively demanding task of sensemaking. Their success often depends on the ability to leverage capabilities of mathematical models, visualization, and human intuition through flexible, usable, and expressive interactions. Spatially clustering data is one effective metaphor for users to explore similarity and relationships between information, adjusting the weighting of dimensions or characteristics of the dataset to observe the change in the spatial layout. Semantic interaction is an approach to user interaction in such spatializations that couples these parametric modifications of the clustering model with users' analytic operations on the data (e.g., direct document movement in the spatialization, highlighting text, search, etc.). In this paper, we present results of a user study exploring the ability of semantic interaction in a visual analytic prototype, ForceSPIRE, to support sensemaking. We found that semantic interaction captures the analytical reasoning of the user through keyword weighting, and aids the user in co-creating a spatialization based on the user's reasoning and intuition.

  13. A simple analytical aerodynamic model of Langley Winged-Cone Aerospace Plane concept

    NASA Technical Reports Server (NTRS)

    Pamadi, Bandu N.

    1994-01-01

    A simple three DOF analytical aerodynamic model of the Langley Winged-Coned Aerospace Plane concept is presented in a form suitable for simulation, trajectory optimization, and guidance and control studies. The analytical model is especially suitable for methods based on variational calculus. Analytical expressions are presented for lift, drag, and pitching moment coefficients from subsonic to hypersonic Mach numbers and angles of attack up to +/- 20 deg. This analytical model has break points at Mach numbers of 1.0, 1.4, 4.0, and 6.0. Across these Mach number break points, the lift, drag, and pitching moment coefficients are made continuous but their derivatives are not. There are no break points in angle of attack. The effect of control surface deflection is not considered. The present analytical model compares well with the APAS calculations and wind tunnel test data for most angles of attack and Mach numbers.

  14. Analytical and Clinical Validation of a Digital Sequencing Panel for Quantitative, Highly Accurate Evaluation of Cell-Free Circulating Tumor DNA

    PubMed Central

    Zill, Oliver A.; Sebisanovic, Dragan; Lopez, Rene; Blau, Sibel; Collisson, Eric A.; Divers, Stephen G.; Hoon, Dave S. B.; Kopetz, E. Scott; Lee, Jeeyun; Nikolinakos, Petros G.; Baca, Arthur M.; Kermani, Bahram G.; Eltoukhy, Helmy; Talasaz, AmirAli

    2015-01-01

    Next-generation sequencing of cell-free circulating solid tumor DNA addresses two challenges in contemporary cancer care. First this method of massively parallel and deep sequencing enables assessment of a comprehensive panel of genomic targets from a single sample, and second, it obviates the need for repeat invasive tissue biopsies. Digital SequencingTM is a novel method for high-quality sequencing of circulating tumor DNA simultaneously across a comprehensive panel of over 50 cancer-related genes with a simple blood test. Here we report the analytic and clinical validation of the gene panel. Analytic sensitivity down to 0.1% mutant allele fraction is demonstrated via serial dilution studies of known samples. Near-perfect analytic specificity (> 99.9999%) enables complete coverage of many genes without the false positives typically seen with traditional sequencing assays at mutant allele frequencies or fractions below 5%. We compared digital sequencing of plasma-derived cell-free DNA to tissue-based sequencing on 165 consecutive matched samples from five outside centers in patients with stage III-IV solid tumor cancers. Clinical sensitivity of plasma-derived NGS was 85.0%, comparable to 80.7% sensitivity for tissue. The assay success rate on 1,000 consecutive samples in clinical practice was 99.8%. Digital sequencing of plasma-derived DNA is indicated in advanced cancer patients to prevent repeated invasive biopsies when the initial biopsy is inadequate, unobtainable for genomic testing, or uninformative, or when the patient’s cancer has progressed despite treatment. Its clinical utility is derived from reduction in the costs, complications and delays associated with invasive tissue biopsies for genomic testing. PMID:26474073

  15. A Multiscale Red Blood Cell Model with Accurate Mechanics, Rheology, and Dynamics

    PubMed Central

    Fedosov, Dmitry A.; Caswell, Bruce; Karniadakis, George Em

    2010-01-01

    Abstract Red blood cells (RBCs) have highly deformable viscoelastic membranes exhibiting complex rheological response and rich hydrodynamic behavior governed by special elastic and bending properties and by the external/internal fluid and membrane viscosities. We present a multiscale RBC model that is able to predict RBC mechanics, rheology, and dynamics in agreement with experiments. Based on an analytic theory, the modeled membrane properties can be uniquely related to the experimentally established RBC macroscopic properties without any adjustment of parameters. The RBC linear and nonlinear elastic deformations match those obtained in optical-tweezers experiments. The rheological properties of the membrane are compared with those obtained in optical magnetic twisting cytometry, membrane thermal fluctuations, and creep followed by cell recovery. The dynamics of RBCs in shear and Poiseuille flows is tested against experiments and theoretical predictions, and the applicability of the latter is discussed. Our findings clearly indicate that a purely elastic model for the membrane cannot accurately represent the RBC's rheological properties and its dynamics, and therefore accurate modeling of a viscoelastic membrane is necessary. PMID:20483330

  16. Satellite Orbit Under Influence of a Drag - Analytical Approach

    NASA Astrophysics Data System (ADS)

    Martinović, M. M.; Šegan, S. D.

    2017-12-01

    The report studies some changes in orbital elements of the artificial satellites of Earth under influence of atmospheric drag. In order to develop possibilities of applying the results in many future cases, an analytical interpretation of the orbital element perturbations is given via useful, but very long expressions. The development is based on the TD88 air density model, recently upgraded with some additional terms. Some expressions and formulae were developed by the computer algebra system Mathematica and tested in some hypothetical cases. The results have good agreement with iterative (numerical) approach.

  17. Semi-analytical Karhunen-Loeve representation of irregular waves based on the prolate spheroidal wave functions

    NASA Astrophysics Data System (ADS)

    Lee, Gibbeum; Cho, Yeunwoo

    2018-01-01

    A new semi-analytical approach is presented to solving the matrix eigenvalue problem or the integral equation in Karhunen-Loeve (K-L) representation of random data such as irregular ocean waves. Instead of direct numerical approach to this matrix eigenvalue problem, which may suffer from the computational inaccuracy for big data, a pair of integral and differential equations are considered, which are related to the so-called prolate spheroidal wave functions (PSWF). First, the PSWF is expressed as a summation of a small number of the analytical Legendre functions. After substituting them into the PSWF differential equation, a much smaller size matrix eigenvalue problem is obtained than the direct numerical K-L matrix eigenvalue problem. By solving this with a minimal numerical effort, the PSWF and the associated eigenvalue of the PSWF differential equation are obtained. Then, the eigenvalue of the PSWF integral equation is analytically expressed by the functional values of the PSWF and the eigenvalues obtained in the PSWF differential equation. Finally, the analytically expressed PSWFs and the eigenvalues in the PWSF integral equation are used to form the kernel matrix in the K-L integral equation for the representation of exemplary wave data such as ordinary irregular waves. It is found that, with the same accuracy, the required memory size of the present method is smaller than that of the direct numerical K-L representation and the computation time of the present method is shorter than that of the semi-analytical method based on the sinusoidal functions.

  18. Accurate prediction of secondary metabolite gene clusters in filamentous fungi.

    PubMed

    Andersen, Mikael R; Nielsen, Jakob B; Klitgaard, Andreas; Petersen, Lene M; Zachariasen, Mia; Hansen, Tilde J; Blicher, Lene H; Gotfredsen, Charlotte H; Larsen, Thomas O; Nielsen, Kristian F; Mortensen, Uffe H

    2013-01-02

    Biosynthetic pathways of secondary metabolites from fungi are currently subject to an intense effort to elucidate the genetic basis for these compounds due to their large potential within pharmaceutics and synthetic biochemistry. The preferred method is methodical gene deletions to identify supporting enzymes for key synthases one cluster at a time. In this study, we design and apply a DNA expression array for Aspergillus nidulans in combination with legacy data to form a comprehensive gene expression compendium. We apply a guilt-by-association-based analysis to predict the extent of the biosynthetic clusters for the 58 synthases active in our set of experimental conditions. A comparison with legacy data shows the method to be accurate in 13 of 16 known clusters and nearly accurate for the remaining 3 clusters. Furthermore, we apply a data clustering approach, which identifies cross-chemistry between physically separate gene clusters (superclusters), and validate this both with legacy data and experimentally by prediction and verification of a supercluster consisting of the synthase AN1242 and the prenyltransferase AN11080, as well as identification of the product compound nidulanin A. We have used A. nidulans for our method development and validation due to the wealth of available biochemical data, but the method can be applied to any fungus with a sequenced and assembled genome, thus supporting further secondary metabolite pathway elucidation in the fungal kingdom.

  19. Moving from Within The Maternal: The Choreography of Analytic Eroticism.

    PubMed

    Elise, Dianne

    2017-02-01

    With Kristeva's concept of maternal eroticism (2014) as starting point, the "multiverse" of mother/child erotic sensibilities-the dance of the semiotic chora-is explored and a parallel engagement proposed within the analytic dyad. The dance of psychoanalysis is not the creative product of the patient's mind alone. Clinical work invites, requires, a choreographic engagement by the clinician in interplay with the patient. The clinician's analytic activity is thus akin to choreography: the structuring of a dance, or of a session, expresses an inner impulse brought into narrative form. The embodied art of dance parallels the clinician's creative vitality in contributing to the shaping of the movement of a session. Through formulation of an analytic eroticism, the terrain of what traditionally has been viewed as erotic transference and countertransference can be expanded to clinical benefit.

  20. Evaluation of Suitable Reference Genes for Normalization of qPCR Gene Expression Studies in Brinjal (Solanum melongena L.) During Fruit Developmental Stages.

    PubMed

    Kanakachari, Mogilicherla; Solanke, Amolkumar U; Prabhakaran, Narayanasamy; Ahmad, Israr; Dhandapani, Gurusamy; Jayabalan, Narayanasamy; Kumar, Polumetla Ananda

    2016-02-01

    Brinjal/eggplant/aubergine is one of the major solanaceous vegetable crops. Recent availability of genome information greatly facilitates the fundamental research on brinjal. Gene expression patterns during different stages of fruit development can provide clues towards the understanding of its biological functions. Quantitative real-time PCR (qPCR) has become one of the most widely used methods for rapid and accurate quantification of gene expression. However, its success depends on the use of a suitable reference gene for data normalization. For qPCR analysis, a single reference gene is not universally suitable for all experiments. Therefore, reference gene validation is a crucial step. Suitable reference genes for qPCR analysis of brinjal fruit development have not been investigated so far. In this study, we have selected 21 candidate reference genes from the Brinjal (Solanum melongena) Plant Gene Indices database (compbio.dfci.harvard.edu/tgi/plant.html) and studied their expression profiles by qPCR during six different fruit developmental stages (0, 5, 10, 20, 30, and 50 days post anthesis) along with leaf samples of the Pusa Purple Long (PPL) variety. To evaluate the stability of gene expression, geNorm and NormFinder analytical softwares were used. geNorm identified SAND (SAND family protein) and TBP (TATA binding protein) as the best pairs of reference genes in brinjal fruit development. The results showed that for brinjal fruit development, individual or a combination of reference genes should be selected for data normalization. NormFinder identified Expressed gene (expressed sequence) as the best single reference gene in brinjal fruit development. In this study, we have identified and validated for the first time reference genes to provide accurate transcript normalization and quantification at various fruit developmental stages of brinjal which can also be useful for gene expression studies in other Solanaceae plant species.

  1. CAMELOT: Computational-Analytical Multi-fidElity Low-thrust Optimisation Toolbox

    NASA Astrophysics Data System (ADS)

    Di Carlo, Marilena; Romero Martin, Juan Manuel; Vasile, Massimiliano

    2018-03-01

    Computational-Analytical Multi-fidElity Low-thrust Optimisation Toolbox (CAMELOT) is a toolbox for the fast preliminary design and optimisation of low-thrust trajectories. It solves highly complex combinatorial problems to plan multi-target missions characterised by long spirals including different perturbations. To do so, CAMELOT implements a novel multi-fidelity approach combining analytical surrogate modelling and accurate computational estimations of the mission cost. Decisions are then made using two optimisation engines included in the toolbox, a single-objective global optimiser, and a combinatorial optimisation algorithm. CAMELOT has been applied to a variety of case studies: from the design of interplanetary trajectories to the optimal de-orbiting of space debris and from the deployment of constellations to on-orbit servicing. In this paper, the main elements of CAMELOT are described and two examples, solved using the toolbox, are presented.

  2. Process-Hardened, Multi-Analyte Sensor for Characterizing Rocket Plume Constituents

    NASA Technical Reports Server (NTRS)

    Goswami, Kisholoy

    2011-01-01

    A multi-analyte sensor was developed that enables simultaneous detection of rocket engine combustion-product molecules in a launch-vehicle ground test stand. The sensor was developed using a pin-printing method by incorporating multiple sensor elements on a single chip. It demonstrated accurate and sensitive detection of analytes such as carbon dioxide, carbon monoxide, kerosene, isopropanol, and ethylene from a single measurement. The use of pin-printing technology enables high-volume fabrication of the sensor chip, which will ultimately eliminate the need for individual sensor calibration since many identical sensors are made in one batch. Tests were performed using a single-sensor chip attached to a fiber-optic bundle. The use of a fiber bundle allows placement of the opto-electronic readout device at a place remote from the test stand. The sensors are rugged for operation in harsh environments.

  3. Analytical study on the self-healing property of Bessel beam

    NASA Astrophysics Data System (ADS)

    Chu, X.

    2012-10-01

    With the help of Babinet principle, an analytical expression for the self-healing of Bessel beam is derived by using the Gaussian absorption function to describe the obstacle. Based on the analytical expression, the self-healing properties of Bessel beam are studied. It shows that Bessel beam has the ability to reconstruct its beam shape disturbed by an obstacle. However, during the self-healing process, not only the intensity of the beam behind the obstacle but also the other part will be affected by the obstruction. Meanwhile, the highlight spot, which intensity is larger than that without the obstacle will appear, and the size and strength of the highlight spot is determined by the size of the obstacle. From the change of Poynting vector and Babinet principle, the physical interpretations for the self-healing ability, the effects of the obstruction on the other part and the appearance of highlight spot are given.

  4. Biological and analytical stability of a peripheral blood gene expression score for obstructive coronary artery disease in the PREDICT and COMPASS studies.

    PubMed

    Daniels, Susan E; Beineke, Philip; Rhees, Brian; McPherson, John A; Kraus, William E; Thomas, Gregory S; Rosenberg, Steven

    2014-10-01

    A gene expression score (GES) for obstructive coronary artery disease (CAD) has been validated in two multicenter studies. Receiver-operating characteristics (ROC) analysis of the GES on an expanded Personalized Risk Evaluation and Diagnosis in the Coronary Tree (PREDICT) cohort (NCT no. 00500617) with CAD defined by quantitative coronary angiography (QCA) or clinical reads yielded similar performance (area under the curve (AUC)=0.70, N=1,502) to the original validation cohort (AUC=0.70, N=526). Analysis of 138 non-Caucasian and 1,364 Caucasian patients showed very similar performance (AUCs=0.72 vs. 0.70). To assess analytic stability, stored samples of the original validation cohort (N=526) was re-tested after 5 years, and the mean score changed from 20.3 to 19.8 after 5 years (N=501, 95 %). To assess patient scores over time, GES was determined on samples from 173 Coronary Obstruction Detection by Molecular Personalized Gene Expression (COMPASS) study (NCT no. 01117506) patients at approximately 1 year post-enrollment. Mean scores increased slightly from 15.9 to 17.3, corresponding to a 2.5 % increase in obstructive CAD likelihood. Changes in cardiovascular medications did not show a significant change in GES.

  5. Choice as an engine of analytic thought.

    PubMed

    Savani, Krishna; Stephens, Nicole M; Markus, Hazel Rose

    2017-09-01

    Choice is a behavioral act that has a variety of well-documented motivational consequences-it fosters independence by allowing people to simultaneously express themselves and influence the environment. Given the link between independence and analytic thinking, the current research tested whether choice also leads people to think in a more analytic rather than holistic manner. Four experiments demonstrate that making choices, recalling choices, and viewing others make choices leads people to think more analytically, as indicated by their attitudes, perceptual judgments, categorization, and patterns of attention allocation. People who made choices scored higher on a subjective self-report measure of analytic cognition compared to whose did not make a choice (pilot study). Using an objective task-based measure, people who recalled choices rather than actions were less influenced by changes in the background when making judgments about focal objects (Experiment 1). People who thought of others' behaviors as choices rather than actions were more likely to group objects based on categories rather than relationships (Experiment 2). People who recalled choices rather than actions subsequently allocated more visual attention to focal objects in a scene (Experiment 3). Together, these experiments demonstrate that choice has important yet previously unexamined consequences for basic psychological processes such as attention and cognition. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

  6. Error analysis of analytic solutions for self-excited near-symmetric rigid bodies - A numerical study

    NASA Technical Reports Server (NTRS)

    Kia, T.; Longuski, J. M.

    1984-01-01

    Analytic error bounds are presented for the solutions of approximate models for self-excited near-symmetric rigid bodies. The error bounds are developed for analytic solutions to Euler's equations of motion. The results are applied to obtain a simplified analytic solution for Eulerian rates and angles. The results of a sample application of the range and error bound expressions for the case of the Galileo spacecraft experiencing transverse torques demonstrate the use of the bounds in analyses of rigid body spin change maneuvers.

  7. A general analytical platform and strategy in search for illegal drugs.

    PubMed

    Johansson, Monika; Fransson, Dick; Rundlöf, Torgny; Huynh, Ngoc-Hang; Arvidsson, Torbjörn

    2014-11-01

    An effective screening procedure to identify and quantify active pharmaceutical substances in suspected illegal medicinal products is described. The analytical platform, consisting of accurate mass determination with liquid chromatography time-of-flight mass spectrometry (LC-QTOF-MS) in combination with nuclear magnetic resonance (NMR) spectroscopy provides an excellent analytical tool to screen for unknowns in medicinal products, food supplements and herbal formulations. This analytical approach has been successfully applied to analyze thousands of samples. The general screening method usually starts with a methanol extraction of tablets/capsules followed by liquid chromatographic separation on a Halo Phenyl-Hexyl column (2.7μm; 100mm×2.1mm) using an acetonitrile/0.1% formic acid gradient as eluent. The accurate mass of peaks of interest was recorded and a search made against an in-house database containing approximately 4200 substances, mostly pharmaceutical compounds. The search could be general or tailored against different classes of compounds. Hits were confirmed by analyzing a reference substance and/or by NMR. Quantification was normally performed with quantitative NMR (qNMR) spectroscopy. Applications for weight-loss substances like sibutramine and orlistat, sexual potency enhancement (PDE-5 inhibitors), and analgesic drugs are presented in this study. We have also identified prostaglandin analogues in eyelash growth serum, exemplified by isopropyl cloprostenate and bimatoprost. For creams and ointments, matrix solid-phase dispersion (MSPD) was found to give a clean extracts with high recovery prior to LC-MS analyses. The structural elucidation of cetilistat, a new weight-loss substance recently found in illegal medicines purchased over the Internet, is also presented. Copyright © 2014 Elsevier B.V. All rights reserved.

  8. EXPRESS Rack Overview

    NASA Technical Reports Server (NTRS)

    Sledd, Annette M.; Mueller, Charles W.

    1999-01-01

    The EXpedite the PRocessing of Experiments to Space Station or EXPRESS Rack System, was developed to provide Space Station accommodations for small, subrack payloads. The EXPRESS Rack accepts Space Shuttle middeck locker type payloads and International Subrack Interface Standard (ISIS) Drawer payloads, allowing previously flown payloads an opportunity to transition to the International Space Station. The EXPRESS Rack provides power, data, command and control, video, water cooling, air cooling, vacuum exhaust, and Nitrogen supply to payloads. The EXPRESS Rack system also includes transportation racks to transport payloads to and from the Space Station, Suitcase Simulators to allow a payload developer to verify power and data interfaces at the development site, Functional Checkout Units to allow Payload checkout at KSC prior to launch, and trainer racks for the astronauts to learn how to operate the EXPRESS Racks prior to flight. Standard hardware and software interfaces provided by the EXPRESS Rack simplify the analytical and physical integration processes, and facilitates simpler ISS payload development. The EXPRESS Rack has also formed the basis for the U.S. Life Sciences payload racks on Space Station.

  9. Web Analytics

    EPA Pesticide Factsheets

    EPA’s Web Analytics Program collects, analyzes, and provides reports on traffic, quality assurance, and customer satisfaction metrics for EPA’s website. The program uses a variety of analytics tools, including Google Analytics and CrazyEgg.

  10. Hybrid Analytical and Data-Driven Modeling for Feed-Forward Robot Control †

    PubMed Central

    Reinhart, René Felix; Shareef, Zeeshan; Steil, Jochen Jakob

    2017-01-01

    Feed-forward model-based control relies on models of the controlled plant, e.g., in robotics on accurate knowledge of manipulator kinematics or dynamics. However, mechanical and analytical models do not capture all aspects of a plant’s intrinsic properties and there remain unmodeled dynamics due to varying parameters, unmodeled friction or soft materials. In this context, machine learning is an alternative suitable technique to extract non-linear plant models from data. However, fully data-based models suffer from inaccuracies as well and are inefficient if they include learning of well known analytical models. This paper thus argues that feed-forward control based on hybrid models comprising an analytical model and a learned error model can significantly improve modeling accuracy. Hybrid modeling here serves the purpose to combine the best of the two modeling worlds. The hybrid modeling methodology is described and the approach is demonstrated for two typical problems in robotics, i.e., inverse kinematics control and computed torque control. The former is performed for a redundant soft robot and the latter for a rigid industrial robot with redundant degrees of freedom, where a complete analytical model is not available for any of the platforms. PMID:28208697

  11. Big data analytics workflow management for eScience

    NASA Astrophysics Data System (ADS)

    Fiore, Sandro; D'Anca, Alessandro; Palazzo, Cosimo; Elia, Donatello; Mariello, Andrea; Nassisi, Paola; Aloisio, Giovanni

    2015-04-01

    In many domains such as climate and astrophysics, scientific data is often n-dimensional and requires tools that support specialized data types and primitives if it is to be properly stored, accessed, analysed and visualized. Currently, scientific data analytics relies on domain-specific software and libraries providing a huge set of operators and functionalities. However, most of these software fail at large scale since they: (i) are desktop based, rely on local computing capabilities and need the data locally; (ii) cannot benefit from available multicore/parallel machines since they are based on sequential codes; (iii) do not provide declarative languages to express scientific data analysis tasks, and (iv) do not provide newer or more scalable storage models to better support the data multidimensionality. Additionally, most of them: (v) are domain-specific, which also means they support a limited set of data formats, and (vi) do not provide a workflow support, to enable the construction, execution and monitoring of more complex "experiments". The Ophidia project aims at facing most of the challenges highlighted above by providing a big data analytics framework for eScience. Ophidia provides several parallel operators to manipulate large datasets. Some relevant examples include: (i) data sub-setting (slicing and dicing), (ii) data aggregation, (iii) array-based primitives (the same operator applies to all the implemented UDF extensions), (iv) data cube duplication, (v) data cube pivoting, (vi) NetCDF-import and export. Metadata operators are available too. Additionally, the Ophidia framework provides array-based primitives to perform data sub-setting, data aggregation (i.e. max, min, avg), array concatenation, algebraic expressions and predicate evaluation on large arrays of scientific data. Bit-oriented plugins have also been implemented to manage binary data cubes. Defining processing chains and workflows with tens, hundreds of data analytics operators is the

  12. Integrated signal probe based aptasensor for dual-analyte detection.

    PubMed

    Xiang, Juan; Pi, Xiaomei; Chen, Xiaoqing; Xiang, Lei; Yang, Minghui; Ren, Hao; Shen, Xiaojuan; Qi, Ning; Deng, Chunyan

    2017-10-15

    For the multi-analyte detection, although the sensitivity has commonly met the practical requirements, the reliability, reproducibility and stability need to be further improved. In this work, two different aptamer probes labeled with redox tags were used as signal probe1 (sP1) and signal probe2 (sP2), which were integrated into one unity DNA architecture to develop the integrated signal probe (ISP). Comparing with the conventional independent signal probes for the simultaneous multi-analyte detection, the proposed ISP was more reproducible and accurate. This can be due to that ISP in one DNA structure can ensure the completely same modification condition and an equal stoichiometric ratio between sP1 and sP2, and furthermore the cross interference between sP1 and sP2 can be successfully prevented by regulating the complementary position of sP1 and sP2. The ISP-based assay system would be a great progress for the dual-analyte detection. Combining with gold nanoparticles (AuNPs) signal amplification, the ISP/AuNPs-based aptasensor for the sensitive dual-analyte detection was explored. Based on DNA structural switching induced by targets binding to aptamer, the simultaneous dual-analyte detection was simply achieved by monitoring the electrochemical responses of methylene blue (MB) and ferrocene (Fc) This proposed detection system possesses such advantages as simplicity in design, easy operation, good reproducibility and accuracy, high sensitivity and selectivity, which indicates the excellent application of this aptasensor in the field of clinical diagnosis or other molecular sensors. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Analytical dose modeling for preclinical proton irradiation of millimetric targets.

    PubMed

    Vanstalle, Marie; Constanzo, Julie; Karakaya, Yusuf; Finck, Christian; Rousseau, Marc; Brasse, David

    2018-01-01

    Due to the considerable development of proton radiotherapy, several proton platforms have emerged to irradiate small animals in order to study the biological effectiveness of proton radiation. A dedicated analytical treatment planning tool was developed in this study to accurately calculate the delivered dose given the specific constraints imposed by the small dimensions of the irradiated areas. The treatment planning system (TPS) developed in this study is based on an analytical formulation of the Bragg peak and uses experimental range values of protons. The method was validated after comparison with experimental data from the literature and then compared to Monte Carlo simulations conducted using Geant4. Three examples of treatment planning, performed with phantoms made of water targets and bone-slab insert, were generated with the analytical formulation and Geant4. Each treatment planning was evaluated using dose-volume histograms and gamma index maps. We demonstrate the value of the analytical function for mouse irradiation, which requires a targeting accuracy of 0.1 mm. Using the appropriate database, the analytical modeling limits the errors caused by misestimating the stopping power. For example, 99% of a 1-mm tumor irradiated with a 24-MeV beam receives the prescribed dose. The analytical dose deviations from the prescribed dose remain within the dose tolerances stated by report 62 of the International Commission on Radiation Units and Measurements for all tested configurations. In addition, the gamma index maps show that the highly constrained targeting accuracy of 0.1 mm for mouse irradiation leads to a significant disagreement between Geant4 and the reference. This simulated treatment planning is nevertheless compatible with a targeting accuracy exceeding 0.2 mm, corresponding to rat and rabbit irradiations. Good dose accuracy for millimetric tumors is achieved with the analytical calculation used in this work. These volume sizes are typical in mouse

  14. Analytical approximations for spatial stochastic gene expression in single cells and tissues

    PubMed Central

    Smith, Stephen; Cianci, Claudia; Grima, Ramon

    2016-01-01

    Gene expression occurs in an environment in which both stochastic and diffusive effects are significant. Spatial stochastic simulations are computationally expensive compared with their deterministic counterparts, and hence little is currently known of the significance of intrinsic noise in a spatial setting. Starting from the reaction–diffusion master equation (RDME) describing stochastic reaction–diffusion processes, we here derive expressions for the approximate steady-state mean concentrations which are explicit functions of the dimensionality of space, rate constants and diffusion coefficients. The expressions have a simple closed form when the system consists of one effective species. These formulae show that, even for spatially homogeneous systems, mean concentrations can depend on diffusion coefficients: this contradicts the predictions of deterministic reaction–diffusion processes, thus highlighting the importance of intrinsic noise. We confirm our theory by comparison with stochastic simulations, using the RDME and Brownian dynamics, of two models of stochastic and spatial gene expression in single cells and tissues. PMID:27146686

  15. Aberrant Gene Expression in Humans

    PubMed Central

    Yang, Ence; Ji, Guoli; Brinkmeyer-Langford, Candice L.; Cai, James J.

    2015-01-01

    Gene expression as an intermediate molecular phenotype has been a focus of research interest. In particular, studies of expression quantitative trait loci (eQTL) have offered promise for understanding gene regulation through the discovery of genetic variants that explain variation in gene expression levels. Existing eQTL methods are designed for assessing the effects of common variants, but not rare variants. Here, we address the problem by establishing a novel analytical framework for evaluating the effects of rare or private variants on gene expression. Our method starts from the identification of outlier individuals that show markedly different gene expression from the majority of a population, and then reveals the contributions of private SNPs to the aberrant gene expression in these outliers. Using population-scale mRNA sequencing data, we identify outlier individuals using a multivariate approach. We find that outlier individuals are more readily detected with respect to gene sets that include genes involved in cellular regulation and signal transduction, and less likely to be detected with respect to the gene sets with genes involved in metabolic pathways and other fundamental molecular functions. Analysis of polymorphic data suggests that private SNPs of outlier individuals are enriched in the enhancer and promoter regions of corresponding aberrantly-expressed genes, suggesting a specific regulatory role of private SNPs, while the commonly-occurring regulatory genetic variants (i.e., eQTL SNPs) show little evidence of involvement. Additional data suggest that non-genetic factors may also underlie aberrant gene expression. Taken together, our findings advance a novel viewpoint relevant to situations wherein common eQTLs fail to predict gene expression when heritable, rare inter-individual variation exists. The analytical framework we describe, taking into consideration the reality of differential phenotypic robustness, may be valuable for investigating

  16. An Improved Analytical Model of the Local Interstellar Magnetic Field: The Extension to Compressibility

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

    Kleimann, Jens; Fichtner, Horst; Röken, Christian, E-mail: jk@tp4.rub.de, E-mail: hf@tp4.rub.de, E-mail: christian.roeken@mathematik.uni-regensburg.de

    A previously published analytical magnetohydrodynamic model for the local interstellar magnetic field in the vicinity of the heliopause (Röken et al. 2015) is extended from incompressible to compressible, yet predominantly subsonic flow, considering both isothermal and adiabatic equations of state. Exact expressions and suitable approximations for the density and the flow velocity are derived and discussed. In addition to the stationary induction equation, these expressions also satisfy the momentum balance equation along stream lines. The practical usefulness of the corresponding, still exact, analytical magnetic field solution is assessed by comparing it quantitatively to results from a fully self-consistent magnetohydrodynamic simulationmore » of the interstellar magnetic field draping around the heliopause.« less

  17. Multiclass cancer diagnosis using tumor gene expression signatures

    DOE PAGES

    Ramaswamy, S.; Tamayo, P.; Rifkin, R.; ...

    2001-12-11

    The optimal treatment of patients with cancer depends on establishing accurate diagnoses by using a complex combination of clinical and histopathological data. In some instances, this task is difficult or impossible because of atypical clinical presentation or histopathology. To determine whether the diagnosis of multiple common adult malignancies could be achieved purely by molecular classification, we subjected 218 tumor samples, spanning 14 common tumor types, and 90 normal tissue samples to oligonucleotide microarray gene expression analysis. The expression levels of 16,063 genes and expressed sequence tags were used to evaluate the accuracy of a multiclass classifier based on a supportmore » vector machine algorithm. Overall classification accuracy was 78%, far exceeding the accuracy of random classification (9%). Poorly differentiated cancers resulted in low-confidence predictions and could not be accurately classified according to their tissue of origin, indicating that they are molecularly distinct entities with dramatically different gene expression patterns compared with their well differentiated counterparts. Taken together, these results demonstrate the feasibility of accurate, multiclass molecular cancer classification and suggest a strategy for future clinical implementation of molecular cancer diagnostics.« less

  18. Accurate determination of Brillouin frequency based on cross recurrence plot analysis in Brillouin distributed fiber sensor

    NASA Astrophysics Data System (ADS)

    Haneef, Shahna M.; Srijith, K.; Venkitesh, D.; Srinivasan, B.

    2017-04-01

    We propose and demonstrate the use of cross recurrence plot analysis (CRPA) to accurately determine the Brillouin shift due to strain and temperature in a Brillouin distributed fiber sensor. This signal processing technique, which is implemented in Brillouin sensors for the first time relies on apriori data i.e, the lineshape of the Brillouin gain spectrum and its similarity with the spectral features measured at different locations along the fiber. Analytical and experimental investigation of the proposed scheme is presented in this paper.

  19. ANALYTICAL MODELING OF ELECTRON BACK-BOMBARDMENT INDUCED CURRENT INCREASE IN UN-GATED THERMIONIC CATHODE RF GUNS

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

    Edelen, J. P.; Sun, Y.; Harris, J. R.

    In this paper we derive analytical expressions for the output current of an un-gated thermionic cathode RF gun in the presence of back-bombardment heating. We provide a brief overview of back-bombardment theory and discuss comparisons between the analytical back-bombardment predictions and simulation models. We then derive an expression for the output current as a function of the RF repetition rate and discuss relationships between back-bombardment, fieldenhancement, and output current. We discuss in detail the relevant approximations and then provide predictions about how the output current should vary as a function of repetition rate for some given system configurations.

  20. How effective are expressive writing interventions for adolescents? A meta-analytic review.

    PubMed

    Travagin, Gabriele; Margola, Davide; Revenson, Tracey A

    2015-03-01

    This meta-analysis evaluated the effects of the expressive writing intervention (EW; Pennebaker & Beall, 1986) among adolescents. Twenty-one independent studies that assessed the efficacy of expressive writing on youth samples aged 10-18 ears were collected and analyzed. Results indicated an overall mean g-effect size that was positive in direction but relatively small (0.127), as well as significant g-effect sizes ranging from 0.107 to 0.246 for the outcome domains of Emotional Distress, Problem Behavior, Social Adjustment, and School Participation. Few significant effects were found within specific outcome domains for putative moderator variables that included characteristics of the participants, intervention instructions, or research design. Studies involving adolescents with high levels of emotional problems at baseline reported larger effects on school performance. Studies that implemented a higher dosage intervention (i.e., greater number and, to some extent, greater spacing of sessions) reported larger effects on somatic complaints. Overall, the findings suggest that expressive writing tends to produce small yet significant improvements on adolescents' well-being. The findings highlight the importance of modifying the traditional expressive writing protocol to enhance its efficacy and reduce potential detrimental effects. At this stage of research the evidence on expressive writing as a viable intervention for adolescents is promising but not decisive. Copyright © 2015 Elsevier Ltd. All rights reserved.

  1. Shape anomaly detection under strong measurement noise: An analytical approach to adaptive thresholding

    NASA Astrophysics Data System (ADS)

    Krasichkov, Alexander S.; Grigoriev, Eugene B.; Bogachev, Mikhail I.; Nifontov, Eugene M.

    2015-10-01

    We suggest an analytical approach to the adaptive thresholding in a shape anomaly detection problem. We find an analytical expression for the distribution of the cosine similarity score between a reference shape and an observational shape hindered by strong measurement noise that depends solely on the noise level and is independent of the particular shape analyzed. The analytical treatment is also confirmed by computer simulations and shows nearly perfect agreement. Using this analytical solution, we suggest an improved shape anomaly detection approach based on adaptive thresholding. We validate the noise robustness of our approach using typical shapes of normal and pathological electrocardiogram cycles hindered by additive white noise. We show explicitly that under high noise levels our approach considerably outperforms the conventional tactic that does not take into account variations in the noise level.

  2. An Accurate Absorption-Based Net Primary Production Model for the Global Ocean

    NASA Astrophysics Data System (ADS)

    Silsbe, G.; Westberry, T. K.; Behrenfeld, M. J.; Halsey, K.; Milligan, A.

    2016-02-01

    As a vital living link in the global carbon cycle, understanding how net primary production (NPP) varies through space, time, and across climatic oscillations (e.g. ENSO) is a key objective in oceanographic research. The continual improvement of ocean observing satellites and data analytics now present greater opportunities for advanced understanding and characterization of the factors regulating NPP. In particular, the emergence of spectral inversion algorithms now permits accurate retrievals of the phytoplankton absorption coefficient (aΦ) from space. As NPP is the efficiency in which absorbed energy is converted into carbon biomass, aΦ measurements circumvents chlorophyll-based empirical approaches by permitting direct and accurate measurements of phytoplankton energy absorption. It has long been recognized, and perhaps underappreciated, that NPP and phytoplankton growth rates display muted variability when normalized to aΦ rather than chlorophyll. Here we present a novel absorption-based NPP model that parameterizes the underlying physiological mechanisms behind this muted variability, and apply this physiological model to the global ocean. Through a comparison against field data from the Hawaii and Bermuda Ocean Time Series, we demonstrate how this approach yields more accurate NPP measurements than other published NPP models. By normalizing NPP to satellite estimates of phytoplankton carbon biomass, this presentation also explores the seasonality of phytoplankton growth rates across several oceanic regions. Finally, we discuss how future advances in remote-sensing (e.g. hyperspectral satellites, LIDAR, autonomous profilers) can be exploited to further improve absorption-based NPP models.

  3. Effect of coulomb spline on rotor dynamic response

    NASA Technical Reports Server (NTRS)

    Nataraj, C.; Nelson, H. D.; Arakere, N.

    1985-01-01

    A rigid rotor system coupled by a coulomb spline is modelled and analyzed by approximate analytical and numerical analytical methods. Expressions are derived for the variables of the resulting limit cycle and are shown to be quite accurate for a small departure from isotropy.

  4. Validation of reference genes aiming accurate normalization of qRT-PCR data in Dendrocalamus latiflorus Munro.

    PubMed

    Liu, Mingying; Jiang, Jing; Han, Xiaojiao; Qiao, Guirong; Zhuo, Renying

    2014-01-01

    Dendrocalamus latiflorus Munro distributes widely in subtropical areas and plays vital roles as valuable natural resources. The transcriptome sequencing for D. latiflorus Munro has been performed and numerous genes especially those predicted to be unique to D. latiflorus Munro were revealed. qRT-PCR has become a feasible approach to uncover gene expression profiling, and the accuracy and reliability of the results obtained depends upon the proper selection of stable reference genes for accurate normalization. Therefore, a set of suitable internal controls should be validated for D. latiflorus Munro. In this report, twelve candidate reference genes were selected and the assessment of gene expression stability was performed in ten tissue samples and four leaf samples from seedlings and anther-regenerated plants of different ploidy. The PCR amplification efficiency was estimated, and the candidate genes were ranked according to their expression stability using three software packages: geNorm, NormFinder and Bestkeeper. GAPDH and EF1α were characterized to be the most stable genes among different tissues or in all the sample pools, while CYP showed low expression stability. RPL3 had the optimal performance among four leaf samples. The application of verified reference genes was illustrated by analyzing ferritin and laccase expression profiles among different experimental sets. The analysis revealed the biological variation in ferritin and laccase transcript expression among the tissues studied and the individual plants. geNorm, NormFinder, and BestKeeper analyses recommended different suitable reference gene(s) for normalization according to the experimental sets. GAPDH and EF1α had the highest expression stability across different tissues and RPL3 for the other sample set. This study emphasizes the importance of validating superior reference genes for qRT-PCR analysis to accurately normalize gene expression of D. latiflorus Munro.

  5. An Extrapolation of a Radical Equation More Accurately Predicts Shelf Life of Frozen Biological Matrices.

    PubMed

    De Vore, Karl W; Fatahi, Nadia M; Sass, John E

    2016-08-01

    Arrhenius modeling of analyte recovery at increased temperatures to predict long-term colder storage stability of biological raw materials, reagents, calibrators, and controls is standard practice in the diagnostics industry. Predicting subzero temperature stability using the same practice is frequently criticized but nevertheless heavily relied upon. We compared the ability to predict analyte recovery during frozen storage using 3 separate strategies: traditional accelerated studies with Arrhenius modeling, and extrapolation of recovery at 20% of shelf life using either ordinary least squares or a radical equation y = B1x(0.5) + B0. Computer simulations were performed to establish equivalence of statistical power to discern the expected changes during frozen storage or accelerated stress. This was followed by actual predictive and follow-up confirmatory testing of 12 chemistry and immunoassay analytes. Linear extrapolations tended to be the most conservative in the predicted percent recovery, reducing customer and patient risk. However, the majority of analytes followed a rate of change that slowed over time, which was fit best to a radical equation of the form y = B1x(0.5) + B0. Other evidence strongly suggested that the slowing of the rate was not due to higher-order kinetics, but to changes in the matrix during storage. Predicting shelf life of frozen products through extrapolation of early initial real-time storage analyte recovery should be considered the most accurate method. Although in this study the time required for a prediction was longer than a typical accelerated testing protocol, there are less potential sources of error, reduced costs, and a lower expenditure of resources. © 2016 American Association for Clinical Chemistry.

  6. Negative chemical ionization gas chromatography coupled to hybrid quadrupole time-of-flight mass spectrometry and automated accurate mass data processing for determination of pesticides in fruit and vegetables.

    PubMed

    Besil, Natalia; Uclés, Samanta; Mezcúa, Milagros; Heinzen, Horacio; Fernández-Alba, Amadeo R

    2015-08-01

    Gas chromatography coupled to high resolution hybrid quadrupole time-of-flight mass spectrometry (GC-QTOF MS), operating in negative chemical ionization (NCI) mode and combining full scan with MSMS experiments using accurate mass analysis, has been explored for the automated determination of pesticide residues in fruit and vegetables. Seventy compounds were included in this approach where 50 % of them are not approved by the EU legislation. A global 76 % of the analytes could be identified at 1 μg kg(-1). Recovery studies were developed at three concentration levels (1, 5, and 10 μg kg(-1)). Seventy-seven percent of the detected pesticides at the lowest level yielded recoveries within the 70 %-120 % range, whereas 94 % could be quantified at 5 μg kg(-1), and the 100 % were determined at 10 μg kg(-1). Good repeatability, expressed as relative standard deviation (RSD <20 %), was obtained for all compounds. The main drawback of the method was the limited dynamic range that was observed for some analytes that can be overcome either diluting the sample or lowering the injection volume. A home-made database was developed and applied to an automatic accurate mass data processing. Measured mass accuracies of the generated ions were mainly less than 5 ppm for at least one diagnostic ion. When only one ion was obtained in the single-stage NCI-MS, a representative product ion from MSMS experiments was used as identification criterion. A total of 30 real samples were analyzed and 67 % of the samples were positive for 12 different pesticides in the range 1.0-1321.3 μg kg(-1).

  7. Expressions for the evaporation of sessile liquid droplets incorporating the evaporative cooling effect.

    PubMed

    Wang, Yilin; Ma, Liran; Xu, Xuefeng; Luo, Jianbin

    2016-12-15

    The evaporation along the surface of pinned, sessile droplets is investigated numerically by using the combined field approach. In the present model, the evaporative cooling at the droplet surface which leads to a reduction in the evaporation is taken into account. Simple, yet accurate analytical expressions for the local evaporation flux and for the total evaporation rate of sessile droplets are obtained. The theoretical analyses indicate that the reduction in the evaporation becomes more pronounced as the evaporative cooling number Ec increases. The results also reveal that the variation of total evaporation rate with contact angle will change its trend as the intensity of the evaporative cooling changes. For small values of Ec, the total evaporation rate increases with the contact angle, the same as predicted by Deegan et al. and by Hu and Larson in their isothermal models in which the evaporative cooling is neglected. Contrarily, when the evaporative cooling effect is strong enough, the total evaporation rate will decrease as the contact angle increases. The present theory is corroborated experimentally, and found in good agreement with the expressions proposed by Hu and Larson in the limiting isothermal case. Copyright © 2016 Elsevier Inc. All rights reserved.

  8. Non-Schwarzschild black-hole metric in four dimensional higher derivative gravity: Analytical approximation

    NASA Astrophysics Data System (ADS)

    Kokkotas, K. D.; Konoplya, R. A.; Zhidenko, A.

    2017-09-01

    Higher derivative extensions of Einstein gravity are important within the string theory approach to gravity and as alternative and effective theories of gravity. H. Lü, A. Perkins, C. Pope, and K. Stelle [Phys. Rev. Lett. 114, 171601 (2015), 10.1103/PhysRevLett.114.171601] found a numerical solution describing a spherically symmetric non-Schwarzschild asymptotically flat black hole in Einstein gravity with added higher derivative terms. Using the general and quickly convergent parametrization in terms of the continued fractions, we represent this numerical solution in the analytical form, which is accurate not only near the event horizon or far from the black hole, but in the whole space. Thereby, the obtained analytical form of the metric allows one to study easily all the further properties of the black hole, such as thermodynamics, Hawking radiation, particle motion, accretion, perturbations, stability, quasinormal spectrum, etc. Thus, the found analytical approximate representation can serve in the same way as an exact solution.

  9. Generalized analytic solutions and response characteristics of magnetotelluric fields on anisotropic infinite faults

    NASA Astrophysics Data System (ADS)

    Bing, Xue; Yicai, Ji

    2018-06-01

    In order to understand directly and analyze accurately the detected magnetotelluric (MT) data on anisotropic infinite faults, two-dimensional partial differential equations of MT fields are used to establish a model of anisotropic infinite faults using the Fourier transform method. A multi-fault model is developed to expand the one-fault model. The transverse electric mode and transverse magnetic mode analytic solutions are derived using two-infinite-fault models. The infinite integral terms of the quasi-analytic solutions are discussed. The dual-fault model is computed using the finite element method to verify the correctness of the solutions. The MT responses of isotropic and anisotropic media are calculated to analyze the response functions by different anisotropic conductivity structures. The thickness and conductivity of the media, influencing MT responses, are discussed. The analytic principles are also given. The analysis results are significant to how MT responses are perceived and to the data interpretation of the complex anisotropic infinite faults.

  10. Lung tumor diagnosis and subtype discovery by gene expression profiling.

    PubMed

    Wang, Lu-yong; Tu, Zhuowen

    2006-01-01

    The optimal treatment of patients with complex diseases, such as cancers, depends on the accurate diagnosis by using a combination of clinical and histopathological data. In many scenarios, it becomes tremendously difficult because of the limitations in clinical presentation and histopathology. To accurate diagnose complex diseases, the molecular classification based on gene or protein expression profiles are indispensable for modern medicine. Moreover, many heterogeneous diseases consist of various potential subtypes in molecular basis and differ remarkably in their response to therapies. It is critical to accurate predict subgroup on disease gene expression profiles. More fundamental knowledge of the molecular basis and classification of disease could aid in the prediction of patient outcome, the informed selection of therapies, and identification of novel molecular targets for therapy. In this paper, we propose a new disease diagnostic method, probabilistic boosting tree (PB tree) method, on gene expression profiles of lung tumors. It enables accurate disease classification and subtype discovery in disease. It automatically constructs a tree in which each node combines a number of weak classifiers into a strong classifier. Also, subtype discovery is naturally embedded in the learning process. Our algorithm achieves excellent diagnostic performance, and meanwhile it is capable of detecting the disease subtype based on gene expression profile.

  11. Recognition of Emotion from Facial Expressions with Direct or Averted Eye Gaze and Varying Expression Intensities in Children with Autism Disorder and Typically Developing Children

    PubMed Central

    Tell, Dina; Davidson, Denise; Camras, Linda A.

    2014-01-01

    Eye gaze direction and expression intensity effects on emotion recognition in children with autism disorder and typically developing children were investigated. Children with autism disorder and typically developing children identified happy and angry expressions equally well. Children with autism disorder, however, were less accurate in identifying fear expressions across intensities and eye gaze directions. Children with autism disorder rated expressions with direct eyes, and 50% expressions, as more intense than typically developing children. A trend was also found for sad expressions, as children with autism disorder were less accurate in recognizing sadness at 100% intensity with direct eyes than typically developing children. Although the present research showed that children with autism disorder are sensitive to eye gaze direction, impairments in the recognition of fear, and possibly sadness, exist. Furthermore, children with autism disorder and typically developing children perceive the intensity of emotional expressions differently. PMID:24804098

  12. Multimedia Analysis plus Visual Analytics = Multimedia Analytics

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

    Chinchor, Nancy; Thomas, James J.; Wong, Pak C.

    2010-10-01

    Multimedia analysis has focused on images, video, and to some extent audio and has made progress in single channels excluding text. Visual analytics has focused on the user interaction with data during the analytic process plus the fundamental mathematics and has continued to treat text as did its precursor, information visualization. The general problem we address in this tutorial is the combining of multimedia analysis and visual analytics to deal with multimedia information gathered from different sources, with different goals or objectives, and containing all media types and combinations in common usage.

  13. A multiscale red blood cell model with accurate mechanics, rheology, and dynamics.

    PubMed

    Fedosov, Dmitry A; Caswell, Bruce; Karniadakis, George Em

    2010-05-19

    Red blood cells (RBCs) have highly deformable viscoelastic membranes exhibiting complex rheological response and rich hydrodynamic behavior governed by special elastic and bending properties and by the external/internal fluid and membrane viscosities. We present a multiscale RBC model that is able to predict RBC mechanics, rheology, and dynamics in agreement with experiments. Based on an analytic theory, the modeled membrane properties can be uniquely related to the experimentally established RBC macroscopic properties without any adjustment of parameters. The RBC linear and nonlinear elastic deformations match those obtained in optical-tweezers experiments. The rheological properties of the membrane are compared with those obtained in optical magnetic twisting cytometry, membrane thermal fluctuations, and creep followed by cell recovery. The dynamics of RBCs in shear and Poiseuille flows is tested against experiments and theoretical predictions, and the applicability of the latter is discussed. Our findings clearly indicate that a purely elastic model for the membrane cannot accurately represent the RBC's rheological properties and its dynamics, and therefore accurate modeling of a viscoelastic membrane is necessary. Copyright 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  14. Collisional evolution - an analytical study for the nonsteady-state mass distribution

    NASA Astrophysics Data System (ADS)

    Martins, R. Vieira

    1999-05-01

    To study the collisional evolution of asteroidal groups we can use an analytical solutionfor the self-similar collision cascades. This solution is suitable to study the steady-state massdistribution of the collisional fragmentation. However, out of the steady-state conditions, thissolution is not satisfactory for some values of the collisional parameters. In fact, for some valuesfor the exponent of the mass distribution power law of an asteroidal group and its relation to theexponent of the function which describes how rocks break we arrive at singular points for theequation which describes the collisional evolution. These singularities appear since someapproximations are usually made in the laborious evaluation of many integrals that appear in theanalytical calculations. They concern the cutoff for the smallest and the largest bodies. Thesesingularities set some restrictions to the study of the analytical solution for the collisionalequation. To overcome these singularities we performed an algebraic computationconsidering the smallest and the largest bodies and we obtained the analytical expressions for theintegrals that describe the collisional evolution without restriction on the parameters. However,the new distribution is more sensitive to the values of the collisional parameters. In particular thesteady-state solution for the differential mass distribution has exponents slightly different from11⧸6 for the usual parameters in the Asteroid Belt. The sensitivity of this distribution with respectto the parameters is analyzed for the usual values in the asteroidal groups. With anexpression for the mass distribution without singularities, we can evaluate also its time evolution.We arrive at an analytical expression given by a power series of terms constituted by a smallparameter multiplied by the mass to an exponent, which depends on the initial power lawdistribution. This expression is a formal solution for the equation which describes the collisionalevolution

  15. Expressive facial animation synthesis by learning speech coarticulation and expression spaces.

    PubMed

    Deng, Zhigang; Neumann, Ulrich; Lewis, J P; Kim, Tae-Yong; Bulut, Murtaza; Narayanan, Shrikanth

    2006-01-01

    Synthesizing expressive facial animation is a very challenging topic within the graphics community. In this paper, we present an expressive facial animation synthesis system enabled by automated learning from facial motion capture data. Accurate 3D motions of the markers on the face of a human subject are captured while he/she recites a predesigned corpus, with specific spoken and visual expressions. We present a novel motion capture mining technique that "learns" speech coarticulation models for diphones and triphones from the recorded data. A Phoneme-Independent Expression Eigenspace (PIEES) that encloses the dynamic expression signals is constructed by motion signal processing (phoneme-based time-warping and subtraction) and Principal Component Analysis (PCA) reduction. New expressive facial animations are synthesized as follows: First, the learned coarticulation models are concatenated to synthesize neutral visual speech according to novel speech input, then a texture-synthesis-based approach is used to generate a novel dynamic expression signal from the PIEES model, and finally the synthesized expression signal is blended with the synthesized neutral visual speech to create the final expressive facial animation. Our experiments demonstrate that the system can effectively synthesize realistic expressive facial animation.

  16. PB-AM: An open-source, fully analytical linear poisson-boltzmann solver

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

    Felberg, Lisa E.; Brookes, David H.; Yap, Eng-Hui

    2016-11-02

    We present the open source distributed software package Poisson-Boltzmann Analytical Method (PB-AM), a fully analytical solution to the linearized Poisson Boltzmann equation. The PB-AM software package includes the generation of outputs files appropriate for visualization using VMD, a Brownian dynamics scheme that uses periodic boundary conditions to simulate dynamics, the ability to specify docking criteria, and offers two different kinetics schemes to evaluate biomolecular association rate constants. Given that PB-AM defines mutual polarization completely and accurately, it can be refactored as a many-body expansion to explore 2- and 3-body polarization. Additionally, the software has been integrated into the Adaptive Poisson-Boltzmannmore » Solver (APBS) software package to make it more accessible to a larger group of scientists, educators and students that are more familiar with the APBS framework.« less

  17. Accurate Encoding and Decoding by Single Cells: Amplitude Versus Frequency Modulation

    PubMed Central

    Micali, Gabriele; Aquino, Gerardo; Richards, David M.; Endres, Robert G.

    2015-01-01

    Cells sense external concentrations and, via biochemical signaling, respond by regulating the expression of target proteins. Both in signaling networks and gene regulation there are two main mechanisms by which the concentration can be encoded internally: amplitude modulation (AM), where the absolute concentration of an internal signaling molecule encodes the stimulus, and frequency modulation (FM), where the period between successive bursts represents the stimulus. Although both mechanisms have been observed in biological systems, the question of when it is beneficial for cells to use either AM or FM is largely unanswered. Here, we first consider a simple model for a single receptor (or ion channel), which can either signal continuously whenever a ligand is bound, or produce a burst in signaling molecule upon receptor binding. We find that bursty signaling is more accurate than continuous signaling only for sufficiently fast dynamics. This suggests that modulation based on bursts may be more common in signaling networks than in gene regulation. We then extend our model to multiple receptors, where continuous and bursty signaling are equivalent to AM and FM respectively, finding that AM is always more accurate. This implies that the reason some cells use FM is related to factors other than accuracy, such as the ability to coordinate expression of multiple genes or to implement threshold crossing mechanisms. PMID:26030820

  18. Progressive Visual Analytics: User-Driven Visual Exploration of In-Progress Analytics.

    PubMed

    Stolper, Charles D; Perer, Adam; Gotz, David

    2014-12-01

    As datasets grow and analytic algorithms become more complex, the typical workflow of analysts launching an analytic, waiting for it to complete, inspecting the results, and then re-Iaunching the computation with adjusted parameters is not realistic for many real-world tasks. This paper presents an alternative workflow, progressive visual analytics, which enables an analyst to inspect partial results of an algorithm as they become available and interact with the algorithm to prioritize subspaces of interest. Progressive visual analytics depends on adapting analytical algorithms to produce meaningful partial results and enable analyst intervention without sacrificing computational speed. The paradigm also depends on adapting information visualization techniques to incorporate the constantly refining results without overwhelming analysts and provide interactions to support an analyst directing the analytic. The contributions of this paper include: a description of the progressive visual analytics paradigm; design goals for both the algorithms and visualizations in progressive visual analytics systems; an example progressive visual analytics system (Progressive Insights) for analyzing common patterns in a collection of event sequences; and an evaluation of Progressive Insights and the progressive visual analytics paradigm by clinical researchers analyzing electronic medical records.

  19. Approximate Analytical Solutions for Hypersonic Flow Over Slender Power Law Bodies

    NASA Technical Reports Server (NTRS)

    Mirels, Harold

    1959-01-01

    Approximate analytical solutions are presented for two-dimensional and axisymmetric hypersonic flow over slender power law bodies. Both zero order (M approaches infinity) and first order (small but nonvanishing values of 1/(M(Delta)(sup 2) solutions are presented, where M is free-stream Mach number and Delta is a characteristic slope. These solutions are compared with exact numerical integration of the equations of motion and appear to be accurate particularly when the shock is relatively close to the body.

  20. Efficient and accurate causal inference with hidden confounders from genome-transcriptome variation data

    PubMed Central

    2017-01-01

    Mapping gene expression as a quantitative trait using whole genome-sequencing and transcriptome analysis allows to discover the functional consequences of genetic variation. We developed a novel method and ultra-fast software Findr for higly accurate causal inference between gene expression traits using cis-regulatory DNA variations as causal anchors, which improves current methods by taking into consideration hidden confounders and weak regulations. Findr outperformed existing methods on the DREAM5 Systems Genetics challenge and on the prediction of microRNA and transcription factor targets in human lymphoblastoid cells, while being nearly a million times faster. Findr is publicly available at https://github.com/lingfeiwang/findr. PMID:28821014

  1. Smartphone-based portable wireless optical system for the detection of target analytes.

    PubMed

    Gautam, Shreedhar; Batule, Bhagwan S; Kim, Hyo Yong; Park, Ki Soo; Park, Hyun Gyu

    2017-02-01

    Rapid and accurate on-site wireless measurement of hazardous molecules or biomarkers is one of the biggest challenges in nanobiotechnology. A novel smartphone-based Portable and Wireless Optical System (PAWS) for rapid, quantitative, and on-site analysis of target analytes is described. As a proof-of-concept, we employed gold nanoparticles (GNP) and an enzyme, horse radish peroxidase (HRP), to generate colorimetric signals in response to two model target molecules, melamine and hydrogen peroxide, respectively. The colorimetric signal produced by the presence of the target molecules is converted to an electrical signal by the inbuilt electronic circuit of the device. The converted electrical signal is then measured wirelessly via multimeter in the smartphone which processes the data and displays the results, including the concentration of analytes and its significance. This handheld device has great potential as a programmable and miniaturized platform to achieve rapid and on-site detection of various analytes in a point-of-care testing (POCT) manner. Copyright © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. A new method for constructing analytic elements for groundwater flow.

    NASA Astrophysics Data System (ADS)

    Strack, O. D.

    2007-12-01

    The analytic element method is based upon the superposition of analytic functions that are defined throughout the infinite domain, and can be used to meet a variety of boundary conditions. Analytic elements have been use successfully for a number of problems, mainly dealing with the Poisson equation (see, e.g., Theory and Applications of the Analytic Element Method, Reviews of Geophysics, 41,2/1005 2003 by O.D.L. Strack). The majority of these analytic elements consists of functions that exhibit jumps along lines or curves. Such linear analytic elements have been developed also for other partial differential equations, e.g., the modified Helmholz equation and the heat equation, and were constructed by integrating elementary solutions, the point sink and the point doublet, along a line. This approach is limiting for two reasons. First, the existence is required of the elementary solutions, and, second, the integration tends to limit the range of solutions that can be obtained. We present a procedure for generating analytic elements that requires merely the existence of a harmonic function with the desired properties; such functions exist in abundance. The procedure to be presented is used to generalize this harmonic function in such a way that the resulting expression satisfies the applicable differential equation. The approach will be applied, along with numerical examples, for the modified Helmholz equation and for the heat equation, while it is noted that the method is in no way restricted to these equations. The procedure is carried out entirely in terms of complex variables, using Wirtinger calculus.

  3. Sample Preparation of Corn Seed Tissue to Prevent Analyte Relocations for Mass Spectrometry Imaging

    NASA Astrophysics Data System (ADS)

    Kim, Shin Hye; Kim, Jeongkwon; Lee, Young Jin; Lee, Tae Geol; Yoon, Sohee

    2017-08-01

    Corn seed tissue sections were prepared by the tape support method using an adhesive tape, and mass spectrometry imaging (MSI) was performed. The effect of heat generated during sample preparation was investigated by time-of-flight secondary mass spectrometry (TOF-SIMS) imaging of corn seed tissue prepared by the tape support and the thaw-mounted methods. Unlike thaw-mounted sample preparation, the tape support method does not cause imaging distortion because of the absence of heat, which can cause migration of the analytes on the sample. By applying the tape-support method, the corn seed tissue was prepared without structural damage and MSI with accurate spatial information of analytes was successfully performed.

  4. An analytic cosmology solution of Poincaré gauge gravity

    NASA Astrophysics Data System (ADS)

    Lu, Jianbo; Chee, Guoying

    2016-06-01

    A cosmology of Poincaré gauge theory is developed. An analytic solution is obtained. The calculation results agree with observation data and can be compared with the ΛCDM model. The cosmological constant puzzle is the coincidence and fine tuning problem are solved naturally at the same time. The cosmological constant turns out to be the intrinsic torsion and curvature of the vacuum universe, and is derived from the theory naturally rather than added artificially. The dark energy originates from geometry, includes the cosmological constant but differs from it. The analytic expression of the state equations of the dark energy and the density parameters of the matter and the geometric dark energy are derived. The full equations of linear cosmological perturbations and the solutions are obtained.

  5. Let's Talk... Analytics

    ERIC Educational Resources Information Center

    Oblinger, Diana G.

    2012-01-01

    Talk about analytics seems to be everywhere. Everyone is talking about analytics. Yet even with all the talk, many in higher education have questions about--and objections to--using analytics in colleges and universities. In this article, the author explores the use of analytics in, and all around, higher education. (Contains 1 note.)

  6. Analytical Description of the H/D Exchange Kinetic of Macromolecule.

    PubMed

    Kostyukevich, Yury; Kononikhin, Alexey; Popov, Igor; Nikolaev, Eugene

    2018-04-17

    We present the accurate analytical solution obtained for the system of rate equations describing the isotope exchange process for molecules containing an arbitrary number of equivalent labile atoms. The exact solution was obtained using Mathematica 7.0 software, and this solution has the form of the time-dependent Gaussian distribution. For the case when forward exchange considerably overlaps the back exchange, it is possible to estimate the activation energy of the reaction by obtaining a temperature dependence of the reaction degree. Using a previously developed approach for performing H/D exchange directly in the ESI source, we have estimated the activation energies for ions with different functional groups and they were found to be in a range 0.04-0.3 eV. Since the value of the activation energy depends on the type of functional group, the developed approach can have potential analytical applications for determining types of functional groups in complex mixtures, such as petroleum, humic substances, bio-oil, and so on.

  7. Accurate Modeling Method for Cu Interconnect

    NASA Astrophysics Data System (ADS)

    Yamada, Kenta; Kitahara, Hiroshi; Asai, Yoshihiko; Sakamoto, Hideo; Okada, Norio; Yasuda, Makoto; Oda, Noriaki; Sakurai, Michio; Hiroi, Masayuki; Takewaki, Toshiyuki; Ohnishi, Sadayuki; Iguchi, Manabu; Minda, Hiroyasu; Suzuki, Mieko

    This paper proposes an accurate modeling method of the copper interconnect cross-section in which the width and thickness dependence on layout patterns and density caused by processes (CMP, etching, sputtering, lithography, and so on) are fully, incorporated and universally expressed. In addition, we have developed specific test patterns for the model parameters extraction, and an efficient extraction flow. We have extracted the model parameters for 0.15μm CMOS using this method and confirmed that 10%τpd error normally observed with conventional LPE (Layout Parameters Extraction) was completely dissolved. Moreover, it is verified that the model can be applied to more advanced technologies (90nm, 65nm and 55nm CMOS). Since the interconnect delay variations due to the processes constitute a significant part of what have conventionally been treated as random variations, use of the proposed model could enable one to greatly narrow the guardbands required to guarantee a desired yield, thereby facilitating design closure.

  8. Analytics for Education

    ERIC Educational Resources Information Center

    MacNeill, Sheila; Campbell, Lorna M.; Hawksey, Martin

    2014-01-01

    This article presents an overview of the development and use of analytics in the context of education. Using Buckingham Shum's three levels of analytics, the authors present a critical analysis of current developments in the domain of learning analytics, and contrast the potential value of analytics research and development with real world…

  9. Gummel Symmetry Test on charge based drain current expression using modified first-order hyperbolic velocity-field expression

    NASA Astrophysics Data System (ADS)

    Singh, Kirmender; Bhattacharyya, A. B.

    2017-03-01

    Gummel Symmetry Test (GST) has been a benchmark industry standard for MOSFET models and is considered as one of important tests by the modeling community. BSIM4 MOSFET model fails to pass GST as the drain current equation is not symmetrical because drain and source potentials are not referenced to bulk. BSIM6 MOSFET model overcomes this limitation by taking all terminal biases with reference to bulk and using proper velocity saturation (v -E) model. The drain current equation in BSIM6 is charge based and continuous in all regions of operation. It, however, adopts a complicated method to compute source and drain charges. In this work we propose to use conventional charge based method formulated by Enz for obtaining simpler analytical drain current expression that passes GST. For this purpose we adopt two steps: (i) In the first step we use a modified first-order hyperbolic v -E model with adjustable coefficients which is integrable, simple and accurate, and (ii) In the second we use a multiplying factor in the modified first-order hyperbolic v -E expression to obtain correct monotonic asymptotic behavior around the origin of lateral electric field. This factor is of empirical form, which is a function of drain voltage (vd) and source voltage (vs) . After considering both the above steps we obtain drain current expression whose accuracy is similar to that obtained from second-order hyperbolic v -E model. In modified first-order hyperbolic v -E expression if vd and vs is replaced by smoothing functions for the effective drain voltage (vdeff) and effective source voltage (vseff), it will as well take care of discontinuity between linear to saturation regions of operation. The condition of symmetry is shown to be satisfied by drain current and its higher order derivatives, as both of them are odd functions and their even order derivatives smoothly pass through the origin. In strong inversion region and technology node of 22 nm the GST is shown to pass till sixth

  10. The "Journal of Learning Analytics": Supporting and Promoting Learning Analytics Research

    ERIC Educational Resources Information Center

    Siemens, George

    2014-01-01

    The paper gives a brief overview of the main activities for the development of the emerging field of learning analytics led by the Society for Learning Analytics Research (SoLAR). The place of the "Journal of Learning Analytics" is identified. Analytics is the most significant new initiative of SoLAR.

  11. An Economical Semi-Analytical Orbit Theory for Retarded Satellite Motion About an Oblate Planet

    NASA Technical Reports Server (NTRS)

    Gordon, R. A.

    1980-01-01

    Brouwer and Brouwer-Lyddanes' use of the Von Zeipel-Delaunay method is employed to develop an efficient analytical orbit theory suitable for microcomputers. A succinctly simple pseudo-phenomenologically conceptualized algorithm is introduced which accurately and economically synthesizes modeling of drag effects. The method epitomizes and manifests effortless efficient computer mechanization. Simulated trajectory data is employed to illustrate the theory's ability to accurately accommodate oblateness and drag effects for microcomputer ground based or onboard predicted orbital representation. Real tracking data is used to demonstrate that the theory's orbit determination and orbit prediction capabilities are favorably adaptable to and are comparable with results obtained utilizing complex definitive Cowell method solutions on satellites experiencing significant drag effects.

  12. Targeted analyte detection by standard addition improves detection limits in matrix-assisted laser desorption/ionization mass spectrometry.

    PubMed

    Toghi Eshghi, Shadi; Li, Xingde; Zhang, Hui

    2012-09-18

    Matrix-assisted laser desorption/ionization (MALDI) has proven an effective tool for fast and accurate determination of many molecules. However, the detector sensitivity and chemical noise compromise the detection of many invaluable low-abundance molecules from biological and clinical samples. To challenge this limitation, we developed a targeted analyte detection (TAD) technique. In TAD, the target analyte is selectively elevated by spiking a known amount of that analyte into the sample, thereby raising its concentration above the noise level, where we take advantage of the improved sensitivity to detect the presence of the endogenous analyte in the sample. We assessed TAD on three peptides in simple and complex background solutions with various exogenous analyte concentrations in two MALDI matrices. TAD successfully improved the limit of detection (LOD) of target analytes when the target peptides were added to the sample in a concentration close to optimum concentration. The optimum exogenous concentration was estimated through a quantitative method to be approximately equal to the original LOD for each target. Also, we showed that TAD could achieve LOD improvements on an average of 3-fold in a simple and 2-fold in a complex sample. TAD provides a straightforward assay to improve the LOD of generic target analytes without the need for costly hardware modifications.

  13. Analytical approximation for the Einstein-dilaton-Gauss-Bonnet black hole metric

    NASA Astrophysics Data System (ADS)

    Kokkotas, K. D.; Konoplya, R. A.; Zhidenko, A.

    2017-09-01

    We construct an analytical approximation for the numerical black hole metric of P. Kanti et al. [Phys. Rev. D 54, 5049 (1996), 10.1103/PhysRevD.54.5049] in the four-dimensional Einstein-dilaton-Gauss-Bonnet (EdGB) theory. The continued fraction expansion in terms of a compactified radial coordinate, used here, converges slowly when the dilaton coupling approaches its extremal values, but for a black hole far from the extremal state, the analytical formula has a maximal relative error of a fraction of one percent already within the third order of the continued fraction expansion. The suggested analytical representation of the numerical black hole metric is relatively compact and a good approximation in the whole space outside the black hole event horizon. Therefore, it can serve in the same way as an exact solution when analyzing particles' motion, perturbations, quasinormal modes, Hawking radiation, accreting disks, and many other problems in the vicinity of a black hole. In addition, we construct the approximate analytical expression for the dilaton field.

  14. Accurate and reproducible measurements of RhoA activation in small samples of primary cells.

    PubMed

    Nini, Lylia; Dagnino, Lina

    2010-03-01

    Rho GTPase activation is essential in a wide variety of cellular processes. Measurement of Rho GTPase activation is difficult with limited material, such as tissues or primary cells that exhibit stringent culture requirements for growth and survival. We defined parameters to accurately and reproducibly measure RhoA activation (i.e., RhoA-GTP) in cultured primary keratinocytes in response to serum and growth factor stimulation using enzyme-linked immunosorbent assay (ELISA)-based G-LISA assays. We also established conditions that minimize RhoA-GTP in unstimulated cells without affecting viability, allowing accurate measurements of RhoA activation on stimulation or induction of exogenous GTPase expression. Copyright 2009 Elsevier Inc. All rights reserved.

  15. Influence of Pre-Analytical Factors on Thymus- and Activation-Regulated Chemokine Quantitation in Plasma

    PubMed Central

    Zhao, Xuemei; Delgado, Liliana; Weiner, Russell; Laterza, Omar F.

    2015-01-01

    Thymus- and activation-regulated chemokine (TARC) in serum/plasma associates with the disease activity of atopic dermatitis (AD), and is a promising tool for assessing the response to the treatment of the disease. TARC also exists within platelets, with elevated levels detectable in AD patients. We examined the effects of pre-analytical factors on the quantitation of TARC in human EDTA plasma. TARC levels in platelet-free plasma were significantly lower than those in platelet-containing plasma. After freeze-thaw, TARC levels increased in platelet-containing plasma, but remained unchanged in platelet-free plasma, suggesting TARC was released from the platelets during the freeze-thaw process. In contrast, TARC levels were stable in serum independent of freeze-thaw. These findings underscore the importance of pre-analytical factors to TARC quantitation. Plasma TARC levels should be measured in platelet-free plasma for accurate quantitation. Pre-analytical factors influence the quantitation, interpretation, and implementation of circulating TARC as a biomarker for the development of AD therapeutics. PMID:28936246

  16. Analytical halo model of galactic conformity

    NASA Astrophysics Data System (ADS)

    Pahwa, Isha; Paranjape, Aseem

    2017-09-01

    We present a fully analytical halo model of colour-dependent clustering that incorporates the effects of galactic conformity in a halo occupation distribution framework. The model, based on our previous numerical work, describes conformity through a correlation between the colour of a galaxy and the concentration of its parent halo, leading to a correlation between central and satellite galaxy colours at fixed halo mass. The strength of the correlation is set by a tunable 'group quenching efficiency', and the model can separately describe group-level correlations between galaxy colour (1-halo conformity) and large-scale correlations induced by assembly bias (2-halo conformity). We validate our analytical results using clustering measurements in mock galaxy catalogues, finding that the model is accurate at the 10-20 per cent level for a wide range of luminosities and length-scales. We apply the formalism to interpret the colour-dependent clustering of galaxies in the Sloan Digital Sky Survey (SDSS). We find good overall agreement between the data and a model that has 1-halo conformity at a level consistent with previous results based on an SDSS group catalogue, although the clustering data require satellites to be redder than suggested by the group catalogue. Within our modelling uncertainties, however, we do not find strong evidence of 2-halo conformity driven by assembly bias in SDSS clustering.

  17. Mayday - integrative analytics for expression data

    PubMed Central

    2010-01-01

    Background DNA Microarrays have become the standard method for large scale analyses of gene expression and epigenomics. The increasing complexity and inherent noisiness of the generated data makes visual data exploration ever more important. Fast deployment of new methods as well as a combination of predefined, easy to apply methods with programmer's access to the data are important requirements for any analysis framework. Mayday is an open source platform with emphasis on visual data exploration and analysis. Many built-in methods for clustering, machine learning and classification are provided for dissecting complex datasets. Plugins can easily be written to extend Mayday's functionality in a large number of ways. As Java program, Mayday is platform-independent and can be used as Java WebStart application without any installation. Mayday can import data from several file formats, database connectivity is included for efficient data organization. Numerous interactive visualization tools, including box plots, profile plots, principal component plots and a heatmap are available, can be enhanced with metadata and exported as publication quality vector files. Results We have rewritten large parts of Mayday's core to make it more efficient and ready for future developments. Among the large number of new plugins are an automated processing framework, dynamic filtering, new and efficient clustering methods, a machine learning module and database connectivity. Extensive manual data analysis can be done using an inbuilt R terminal and an integrated SQL querying interface. Our visualization framework has become more powerful, new plot types have been added and existing plots improved. Conclusions We present a major extension of Mayday, a very versatile open-source framework for efficient micro array data analysis designed for biologists and bioinformaticians. Most everyday tasks are already covered. The large number of available plugins as well as the extension

  18. Fast and accurate focusing analysis of large photon sieve using pinhole ring diffraction model.

    PubMed

    Liu, Tao; Zhang, Xin; Wang, Lingjie; Wu, Yanxiong; Zhang, Jizhen; Qu, Hemeng

    2015-06-10

    In this paper, we developed a pinhole ring diffraction model for the focusing analysis of a large photon sieve. Instead of analyzing individual pinholes, we discuss the focusing of all of the pinholes in a single ring. An explicit equation for the diffracted field of individual pinhole ring has been proposed. We investigated the validity range of this generalized model and analytically describe the sufficient conditions for the validity of this pinhole ring diffraction model. A practical example and investigation reveals the high accuracy of the pinhole ring diffraction model. This simulation method could be used for fast and accurate focusing analysis of a large photon sieve.

  19. Analytical phase diagrams for colloids and non-adsorbing polymer.

    PubMed

    Fleer, Gerard J; Tuinier, Remco

    2008-11-04

    We review the free-volume theory (FVT) of Lekkerkerker et al. [Europhys. Lett. 20 (1992) 559] for the phase behavior of colloids in the presence of non-adsorbing polymer and we extend this theory in several aspects: (i) We take the solvent into account as a separate component and show that the natural thermodynamic parameter for the polymer properties is the insertion work Pi(v), where Pi is the osmotic pressure of the (external) polymer solution and v the volume of a colloid particle. (ii) Curvature effects are included along the lines of Aarts et al. [J. Phys.: Condens. Matt. 14 (2002) 7551] but we find accurate simple power laws which simplify the mathematical procedure considerably. (iii) We find analytical forms for the first, second, and third derivatives of the grand potential, needed for the calculation of the colloid chemical potential, the pressure, gas-liquid critical points and the critical endpoint (cep), where the (stable) critical line ends and then coincides with the triple point. This cep determines the boundary condition for a stable liquid. We first apply these modifications to the so-called colloid limit, where the size ratio q(R)=R/a between the radius of gyration R of the polymer and the particle radius a is small. In this limit the binodal polymer concentrations are below overlap: the depletion thickness delta is nearly equal to R, and Pi can be approximated by the ideal (van't Hoff) law Pi=Pi(0)=phi/N, where phi is the polymer volume fraction and N the number of segments per chain. The results are close to those of the original Lekkerkerker theory. However, our analysis enables very simple analytical expressions for the polymer and colloid concentrations in the critical and triple points and along the binodals as a function of q(R). Also the position of the cep is found analytically. In order to make the model applicable to higher size ratio's q(R) (including the so-called protein limit where q(R)>1) further extensions are needed. We

  20. Accurate determination of selected pesticides in soya beans by liquid chromatography coupled to isotope dilution mass spectrometry.

    PubMed

    Huertas Pérez, J F; Sejerøe-Olsen, B; Fernández Alba, A R; Schimmel, H; Dabrio, M

    2015-05-01

    A sensitive, accurate and simple liquid chromatography coupled with mass spectrometry method for the determination of 10 selected pesticides in soya beans has been developed and validated. The method is intended for use during the characterization of selected pesticides in a reference material. In this process, high accuracy and appropriate uncertainty levels associated to the analytical measurements are of utmost importance. The analytical procedure is based on sample extraction by the use of a modified QuEChERS (quick, easy, cheap, effective, rugged, safe) extraction and subsequent clean-up of the extract with C18, PSA and Florisil. Analytes were separated on a C18 column using gradient elution with water-methanol/2.5 mM ammonium acetate mobile phase, and finally identified and quantified by triple quadrupole mass spectrometry in the multiple reaction monitoring mode (MRM). Reliable and accurate quantification of the analytes was achieved by means of stable isotope-labelled analogues employed as internal standards (IS) and calibration with pure substance solutions containing both, the isotopically labelled and native compounds. Exceptions were made for thiodicarb and malaoxon where the isotopically labelled congeners were not commercially available at the time of analysis. For the quantification of those compounds methomyl-(13)C2(15)N and malathion-D10 were used respectively. The method was validated according to the general principles covered by DG SANCO guidelines. However, validation criteria were set more stringently. Mean recoveries were in the range of 86-103% with RSDs lower than 8.1%. Repeatability and intermediate precision were in the range of 3.9-7.6% and 1.9-8.7% respectively. LODs were theoretically estimated and experimentally confirmed to be in the range 0.001-0.005 mg kg(-1) in the matrix, while LOQs established as the lowest spiking mass fractionation level were in the range 0.01-0.05 mg kg(-1). The method reliably identifies and quantifies the

  1. Analytic solution of magnetic induction distribution of ideal hollow spherical field sources

    NASA Astrophysics Data System (ADS)

    Xu, Xiaonong; Lu, Dingwei; Xu, Xibin; Yu, Yang; Gu, Min

    2017-12-01

    The Halbach type hollow spherical permanent magnet arrays (HSPMA) are volume compacted, energy efficient field sources, and capable of producing multi-Tesla field in the cavity of the array, which have attracted intense interests in many practical applications. Here, we present analytical solutions of magnetic induction to the ideal HSPMA in entire space, outside of array, within the cavity of array, and in the interior of the magnet. We obtain solutions using concept of magnetic charge to solve the Poisson's and Laplace's equations for the HSPMA. Using these analytical field expressions inside the material, a scalar demagnetization function is defined to approximately indicate the regions of magnetization reversal, partial demagnetization, and inverse magnetic saturation. The analytical field solution provides deeper insight into the nature of HSPMA and offer guidance in designing optimized one.

  2. An UPLC-MS/MS method for separation and accurate quantification of tamoxifen and its metabolites isomers.

    PubMed

    Arellano, Cécile; Allal, Ben; Goubaa, Anwar; Roché, Henri; Chatelut, Etienne

    2014-11-01

    A selective and accurate analytical method is needed to quantify tamoxifen and its phase I metabolites in a prospective clinical protocol, for evaluation of pharmacokinetic parameters of tamoxifen and its metabolites in adjuvant treatment of breast cancer. The selectivity of the analytical method is a fundamental criteria to allow the quantification of the main active metabolites (Z)-isomers from (Z)'-isomers. An UPLC-MS/MS method was developed and validated for the quantification of (Z)-tamoxifen, (Z)-endoxifen, (E)-endoxifen, Z'-endoxifen, (Z)'-endoxifen, (Z)-4-hydroxytamoxifen, (Z)-4'-hydroxytamoxifen, N-desmethyl tamoxifen, and tamoxifen-N-oxide. The validation range was set between 0.5ng/mL and 125ng/mL for 4-hydroxytamoxifen and endoxifen isomers, and between 12.5ng/mL and 300ng/mL for tamoxifen, tamoxifen N-desmethyl and tamoxifen-N-oxide. The application to patient plasma samples was performed. Copyright © 2014 Elsevier B.V. All rights reserved.

  3. A globally convergent and closed analytical solution of the Blasius equation with beneficial applications

    NASA Astrophysics Data System (ADS)

    Zheng, Jun; Han, Xinyue; Wang, ZhenTao; Li, Changfeng; Zhang, Jiazhong

    2017-06-01

    For about a century, people have been trying to seek for a globally convergent and closed analytical solution (CAS) of the Blasius Equation (BE). In this paper, we proposed a formally satisfied solution which could be parametrically expressed by two power series. Some analytical results of the laminar boundary layer of a flat plate, that were not analytically given in former studies, e.g. the thickness of the boundary layer and higher order derivatives, could be obtained based on the solution. Besides, the heat transfer in the laminar boundary layer of a flat plate with constant temperature could also be analytically formulated. Especially, the solution of the singular situation with Prandtl number Pr=0, which seems impossible to be analyzed in prior studies, could be given analytically. The method for finding the CAS of Blasius equation was also utilized in the problem of the boundary layer regulation through wall injection and slip velocity on the wall surface.

  4. Analytical Calculation of Mutual Information between Weakly Coupled Poisson-Spiking Neurons in Models of Dynamically Gated Communication.

    PubMed

    Cannon, Jonathan

    2017-01-01

    Mutual information is a commonly used measure of communication between neurons, but little theory exists describing the relationship between mutual information and the parameters of the underlying neuronal interaction. Such a theory could help us understand how specific physiological changes affect the capacity of neurons to synaptically communicate, and, in particular, they could help us characterize the mechanisms by which neuronal dynamics gate the flow of information in the brain. Here we study a pair of linear-nonlinear-Poisson neurons coupled by a weak synapse. We derive an analytical expression describing the mutual information between their spike trains in terms of synapse strength, neuronal activation function, the time course of postsynaptic currents, and the time course of the background input received by the two neurons. This expression allows mutual information calculations that would otherwise be computationally intractable. We use this expression to analytically explore the interaction of excitation, information transmission, and the convexity of the activation function. Then, using this expression to quantify mutual information in simulations, we illustrate the information-gating effects of neural oscillations and oscillatory coherence, which may either increase or decrease the mutual information across the synapse depending on parameters. Finally, we show analytically that our results can quantitatively describe the selection of one information pathway over another when multiple sending neurons project weakly to a single receiving neuron.

  5. Evaluation of New Reference Genes in Papaya for Accurate Transcript Normalization under Different Experimental Conditions

    PubMed Central

    Chen, Weixin; Chen, Jianye; Lu, Wangjin; Chen, Lei; Fu, Danwen

    2012-01-01

    Real-time reverse transcription PCR (RT-qPCR) is a preferred method for rapid and accurate quantification of gene expression studies. Appropriate application of RT-qPCR requires accurate normalization though the use of reference genes. As no single reference gene is universally suitable for all experiments, thus reference gene(s) validation under different experimental conditions is crucial for RT-qPCR analysis. To date, only a few studies on reference genes have been done in other plants but none in papaya. In the present work, we selected 21 candidate reference genes, and evaluated their expression stability in 246 papaya fruit samples using three algorithms, geNorm, NormFinder and RefFinder. The samples consisted of 13 sets collected under different experimental conditions, including various tissues, different storage temperatures, different cultivars, developmental stages, postharvest ripening, modified atmosphere packaging, 1-methylcyclopropene (1-MCP) treatment, hot water treatment, biotic stress and hormone treatment. Our results demonstrated that expression stability varied greatly between reference genes and that different suitable reference gene(s) or combination of reference genes for normalization should be validated according to the experimental conditions. In general, the internal reference genes EIF (Eukaryotic initiation factor 4A), TBP1 (TATA binding protein 1) and TBP2 (TATA binding protein 2) genes had a good performance under most experimental conditions, whereas the most widely present used reference genes, ACTIN (Actin 2), 18S rRNA (18S ribosomal RNA) and GAPDH (Glyceraldehyde-3-phosphate dehydrogenase) were not suitable in many experimental conditions. In addition, two commonly used programs, geNorm and Normfinder, were proved sufficient for the validation. This work provides the first systematic analysis for the selection of superior reference genes for accurate transcript normalization in papaya under different experimental conditions. PMID

  6. Analytical study of the reflection and transmission coefficient of the submarine interface

    NASA Astrophysics Data System (ADS)

    Zhang, Guangli; Hao, Chongtao; Yao, Chen

    2018-05-01

    The analytical study of the reflection and transmission coefficient of the seafloor interface is essential for the characterization of the ocean bottom in marine seismic exploration. Based on the boundary conditions of the seafloor interface, the analytical expression of the reflection and transmission coefficient at the submarine interface is derived in this study by using the steady-state wave solution of the elastic wave in a homogeneous, isotropic medium. With this analytical expression, the characteristics of the reflection and transmission coefficient at the submarine interface are analysed and discussed using critical angles. The results show that the change in the reflection and transmission coefficient with the incidence angle presents a "segmented" characteristic, in which the critical angle is the dividing point. The amplitude value and phase angle of the coefficient at the submarine interface change dramatically at the critical angle, which is related to the P- and S-wave velocities in the seabed layer. Compared with the stiff seabed, the soft seabed has a larger P-wave critical angle and an absence of the converted S-wave critical angle, owing to the low P- and S-wave velocities in the solid seabed layer. By analysing and discussing the special changes that occur in the coefficient values at the critical angle, the reflection and transmission characteristics of the different incident angles are obtained. Synthetic models of both stiff and soft seafloors are provided in this study to verify the analytical results. Finally, we compared our synthetic results with real data from the Gulf of Mexico, which enabled the validation of our conclusions.

  7. Spherical indentation of a freestanding circular membrane revisited: Analytical solutions and experiments

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

    Jin, Congrui; Davoodabadi, Ali; Li, Jianlin

    Because of the development of novel micro-fabrication techniques to produce ultra-thin materials and increasing interest in thin biological membranes, in recent years, the mechanical characterization of thin films has received a significant amount of attention. To provide a more accurate solution for the relationship among contact radius, load and deflection, the fundamental and widely applicable problem of spherical indentation of a freestanding circular membrane have been revisited. The work presented here significantly extends the previous contributions by providing an exact analytical solution to the governing equations of Föppl–Hecky membrane indented by a frictionless spherical indenter. In this study, experiments ofmore » spherical indentation has been performed, and the exact analytical solution presented in this article is compared against experimental data from existing literature as well as our own experimental results.« less

  8. Analytic score distributions for a spatially continuous tridirectional Monte Carol transport problem

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

    Booth, T.E.

    1996-01-01

    The interpretation of the statistical error estimates produced by Monte Carlo transport codes is still somewhat of an art. Empirically, there are variance reduction techniques whose error estimates are almost always reliable, and there are variance reduction techniques whose error estimates are often unreliable. Unreliable error estimates usually result from inadequate large-score sampling from the score distribution`s tail. Statisticians believe that more accurate confidence interval statements are possible if the general nature of the score distribution can be characterized. Here, the analytic score distribution for the exponential transform applied to a simple, spatially continuous Monte Carlo transport problem is provided.more » Anisotropic scattering and implicit capture are included in the theory. In large part, the analytic score distributions that are derived provide the basis for the ten new statistical quality checks in MCNP.« less

  9. Spherical indentation of a freestanding circular membrane revisited: Analytical solutions and experiments

    DOE PAGES

    Jin, Congrui; Davoodabadi, Ali; Li, Jianlin; ...

    2017-01-11

    Because of the development of novel micro-fabrication techniques to produce ultra-thin materials and increasing interest in thin biological membranes, in recent years, the mechanical characterization of thin films has received a significant amount of attention. To provide a more accurate solution for the relationship among contact radius, load and deflection, the fundamental and widely applicable problem of spherical indentation of a freestanding circular membrane have been revisited. The work presented here significantly extends the previous contributions by providing an exact analytical solution to the governing equations of Föppl–Hecky membrane indented by a frictionless spherical indenter. In this study, experiments ofmore » spherical indentation has been performed, and the exact analytical solution presented in this article is compared against experimental data from existing literature as well as our own experimental results.« less

  10. GeneAnalytics: An Integrative Gene Set Analysis Tool for Next Generation Sequencing, RNAseq and Microarray Data.

    PubMed

    Ben-Ari Fuchs, Shani; Lieder, Iris; Stelzer, Gil; Mazor, Yaron; Buzhor, Ella; Kaplan, Sergey; Bogoch, Yoel; Plaschkes, Inbar; Shitrit, Alina; Rappaport, Noa; Kohn, Asher; Edgar, Ron; Shenhav, Liraz; Safran, Marilyn; Lancet, Doron; Guan-Golan, Yaron; Warshawsky, David; Shtrichman, Ronit

    2016-03-01

    Postgenomics data are produced in large volumes by life sciences and clinical applications of novel omics diagnostics and therapeutics for precision medicine. To move from "data-to-knowledge-to-innovation," a crucial missing step in the current era is, however, our limited understanding of biological and clinical contexts associated with data. Prominent among the emerging remedies to this challenge are the gene set enrichment tools. This study reports on GeneAnalytics™ ( geneanalytics.genecards.org ), a comprehensive and easy-to-apply gene set analysis tool for rapid contextualization of expression patterns and functional signatures embedded in the postgenomics Big Data domains, such as Next Generation Sequencing (NGS), RNAseq, and microarray experiments. GeneAnalytics' differentiating features include in-depth evidence-based scoring algorithms, an intuitive user interface and proprietary unified data. GeneAnalytics employs the LifeMap Science's GeneCards suite, including the GeneCards®--the human gene database; the MalaCards-the human diseases database; and the PathCards--the biological pathways database. Expression-based analysis in GeneAnalytics relies on the LifeMap Discovery®--the embryonic development and stem cells database, which includes manually curated expression data for normal and diseased tissues, enabling advanced matching algorithm for gene-tissue association. This assists in evaluating differentiation protocols and discovering biomarkers for tissues and cells. Results are directly linked to gene, disease, or cell "cards" in the GeneCards suite. Future developments aim to enhance the GeneAnalytics algorithm as well as visualizations, employing varied graphical display items. Such attributes make GeneAnalytics a broadly applicable postgenomics data analyses and interpretation tool for translation of data to knowledge-based innovation in various Big Data fields such as precision medicine, ecogenomics, nutrigenomics, pharmacogenomics, vaccinomics

  11. New hybrid voxelized/analytical primitive in Monte Carlo simulations for medical applications

    NASA Astrophysics Data System (ADS)

    Bert, Julien; Lemaréchal, Yannick; Visvikis, Dimitris

    2016-05-01

    Monte Carlo simulations (MCS) applied in particle physics play a key role in medical imaging and particle therapy. In such simulations, particles are transported through voxelized phantoms derived from predominantly patient CT images. However, such voxelized object representation limits the incorporation of fine elements, such as artificial implants from CAD modeling or anatomical and functional details extracted from other imaging modalities. In this work we propose a new hYbrid Voxelized/ANalytical primitive (YVAN) that combines both voxelized and analytical object descriptions within the same MCS, without the need to simultaneously run two parallel simulations, which is the current gold standard methodology. Given that YVAN is simply a new primitive object, it does not require any modifications on the underlying MC navigation code. The new proposed primitive was assessed through a first simple MCS. Results from the YVAN primitive were compared against an MCS using a pure analytical geometry and the layer mass geometry concept. A perfect agreement was found between these simulations, leading to the conclusion that the new hybrid primitive is able to accurately and efficiently handle phantoms defined by a mixture of voxelized and analytical objects. In addition, two application-based evaluation studies in coronary angiography and intra-operative radiotherapy showed that the use of YVAN was 6.5% and 12.2% faster than the layered mass geometry method, respectively, without any associated loss of accuracy. However, the simplification advantages and differences in computational time improvements obtained with YVAN depend on the relative proportion of the analytical and voxelized structures used in the simulation as well as the size and number of triangles used in the description of the analytical object meshes.

  12. A hybrid analytical model for open-circuit field calculation of multilayer interior permanent magnet machines

    NASA Astrophysics Data System (ADS)

    Zhang, Zhen; Xia, Changliang; Yan, Yan; Geng, Qiang; Shi, Tingna

    2017-08-01

    Due to the complicated rotor structure and nonlinear saturation of rotor bridges, it is difficult to build a fast and accurate analytical field calculation model for multilayer interior permanent magnet (IPM) machines. In this paper, a hybrid analytical model suitable for the open-circuit field calculation of multilayer IPM machines is proposed by coupling the magnetic equivalent circuit (MEC) method and the subdomain technique. In the proposed analytical model, the rotor magnetic field is calculated by the MEC method based on the Kirchhoff's law, while the field in the stator slot, slot opening and air-gap is calculated by subdomain technique based on the Maxwell's equation. To solve the whole field distribution of the multilayer IPM machines, the coupled boundary conditions on the rotor surface are deduced for the coupling of the rotor MEC and the analytical field distribution of the stator slot, slot opening and air-gap. The hybrid analytical model can be used to calculate the open-circuit air-gap field distribution, back electromotive force (EMF) and cogging torque of multilayer IPM machines. Compared with finite element analysis (FEA), it has the advantages of faster modeling, less computation source occupying and shorter time consuming, and meanwhile achieves the approximate accuracy. The analytical model is helpful and applicable for the open-circuit field calculation of multilayer IPM machines with any size and pole/slot number combination.

  13. Analytical expressions for the closure probability of a stiff wormlike chain for finite capture radius.

    PubMed

    Guérin, T

    2017-08-01

    Estimating the probability that two monomers of the same polymer chain are close together is a key ingredient to characterize intramolecular reactions and polymer looping. In the case of stiff wormlike polymers (rigid fluctuating elastic rods), for which end-to-end encounters are rare events, we derive an explicit analytical formula for the probability η(r_{c}) that the distance between the chain extremities is smaller than some capture radius r_{c}. The formula is asymptotically exact in the limit of stiff chains, and it leads to the identification of two distinct scaling regimes for the closure factor, originating from a strong variation of the fluctuations of the chain orientation at closure. Our theory is compatible with existing analytical results from the literature that cover the cases of a vanishing capture radius and of nearly fully extended chains.

  14. Generalized model of electromigration with 1:1 (analyte:selector) complexation stoichiometry: part I. Theory.

    PubMed

    Dubský, Pavel; Müllerová, Ludmila; Dvořák, Martin; Gaš, Bohuslav

    2015-03-06

    The model of electromigration of a multivalent weak acidic/basic/amphoteric analyte that undergoes complexation with a mixture of selectors is introduced. The model provides an extension of the series of models starting with the single-selector model without dissociation by Wren and Rowe in 1992, continuing with the monovalent weak analyte/single-selector model by Rawjee, Williams and Vigh in 1993 and that by Lelièvre in 1994, and ending with the multi-selector overall model without dissociation developed by our group in 2008. The new multivalent analyte multi-selector model shows that the effective mobility of the analyte obeys the original Wren and Row's formula. The overall complexation constant, mobility of the free analyte and mobility of complex can be measured and used in a standard way. The mathematical expressions for the overall parameters are provided. We further demonstrate mathematically that the pH dependent parameters for weak analytes can be simply used as an input into the multi-selector overall model and, in reverse, the multi-selector overall parameters can serve as an input into the pH-dependent models for the weak analytes. These findings can greatly simplify the rationale method development in analytical electrophoresis, specifically enantioseparations. Copyright © 2015 Elsevier B.V. All rights reserved.

  15. xQuake: A Modern Approach to Seismic Network Analytics

    NASA Astrophysics Data System (ADS)

    Johnson, C. E.; Aikin, K. E.

    2017-12-01

    While seismic networks have expanded over the past few decades, and social needs for accurate and timely information has increased dramatically, approaches to the operational needs of both global and regional seismic observatories have been slow to adopt new technologies. This presentation presents the xQuake system that provides a fresh approach to seismic network analytics based on complexity theory and an adaptive architecture of streaming connected microservices as diverse data (picks, beams, and other data) flow into a final, curated catalog of events. The foundation for xQuake is the xGraph (executable graph) framework that is essentially a self-organizing graph database. An xGraph instance provides both the analytics as well as the data storage capabilities at the same time. Much of the analytics, such as synthetic annealing in the detection process and an evolutionary programing approach for event evolution, draws from the recent GLASS 3.0 seismic associator developed by and for the USGS National Earthquake Information Center (NEIC). In some respects xQuake is reminiscent of the Earthworm system, in that it comprises processes interacting through store and forward rings; not surprising as the first author was the lead architect of the original Earthworm project when it was known as "Rings and Things". While Earthworm components can easily be integrated into the xGraph processing framework, the architecture and analytics are more current (e.g. using a Kafka Broker for store and forward rings). The xQuake system is being released under an unrestricted open source license to encourage and enable sthe eismic community support in further development of its capabilities.

  16. Linking family cohesion and flexibility with expressed emotion, family burden and psychological distress in caregivers of patients with psychosis: A path analytic model.

    PubMed

    Koutra, Katerina; Simos, Panagiotis; Triliva, Sofia; Lionis, Christos; Vgontzas, Alexandros N

    2016-06-30

    The present study aimed to evaluate a path analytic model accounting for caregivers' psychological distress that takes into account perceived family cohesion and flexibility, expressed emotion and caregiver's burden associated with the presence of mental illness in the family. 50 first-episode and 50 chronic patients diagnosed with schizophrenia or bipolar disorder (most recent episode manic severe with psychotic features) recruited from the Inpatient Psychiatric Unit of the University Hospital of Heraklion, Crete, Greece, and their family caregivers participated in the study. Family functioning was assessed in terms of cohesion and flexibility (FACES-IV), expressed emotion (FQ), family burden (FBS) and caregivers' psychological distress (GHQ-28). Structural equation modelling was used to evaluate the direct and indirect effects of family dynamics on caregivers' psychological distress. The results showed that neither family cohesion nor family flexibility exerted significant direct effects on caregivers' psychological distress. Instead, the effect of flexibility was mediated by caregivers' criticism and family burden indicating an indirect effect on caregivers' psychological distress. These results apply equally to caregivers of first episode and chronic patients. Family interventions aiming to improve dysfunctional family interactions by promoting awareness of family dynamics could reduce the burden and improve the emotional well-being of family caregivers. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  17. Analytic integration of real-virtual counterterms in NNLO jet cross sections II

    NASA Astrophysics Data System (ADS)

    Bolzoni, Paolo; Moch, Sven-Olaf; Somogyi, Gábor; Trócsányi, Zoltán

    2009-08-01

    We present analytic expressions of all integrals required to complete the explicit evaluation of the real-virtual integrated counterterms needed to define a recently proposed subtraction scheme for jet cross sections at next-to-next-to-leading order in QCD. We use the Mellin-Barnes representation of these integrals in 4 - 2epsilon dimensions to obtain the coefficients of their Laurent expansions around epsilon = 0. These coefficients are given by linear combinations of multidimensional Mellin-Barnes integrals. We compute the coefficients of such expansions in epsilon both numerically and analytically by complex integration over the Mellin-Barnes contours.

  18. Analytical quality by design: a tool for regulatory flexibility and robust analytics.

    PubMed

    Peraman, Ramalingam; Bhadraya, Kalva; Padmanabha Reddy, Yiragamreddy

    2015-01-01

    Very recently, Food and Drug Administration (FDA) has approved a few new drug applications (NDA) with regulatory flexibility for quality by design (QbD) based analytical approach. The concept of QbD applied to analytical method development is known now as AQbD (analytical quality by design). It allows the analytical method for movement within method operable design region (MODR). Unlike current methods, analytical method developed using analytical quality by design (AQbD) approach reduces the number of out-of-trend (OOT) results and out-of-specification (OOS) results due to the robustness of the method within the region. It is a current trend among pharmaceutical industry to implement analytical quality by design (AQbD) in method development process as a part of risk management, pharmaceutical development, and pharmaceutical quality system (ICH Q10). Owing to the lack explanatory reviews, this paper has been communicated to discuss different views of analytical scientists about implementation of AQbD in pharmaceutical quality system and also to correlate with product quality by design and pharmaceutical analytical technology (PAT).

  19. Analytical Quality by Design: A Tool for Regulatory Flexibility and Robust Analytics

    PubMed Central

    Bhadraya, Kalva; Padmanabha Reddy, Yiragamreddy

    2015-01-01

    Very recently, Food and Drug Administration (FDA) has approved a few new drug applications (NDA) with regulatory flexibility for quality by design (QbD) based analytical approach. The concept of QbD applied to analytical method development is known now as AQbD (analytical quality by design). It allows the analytical method for movement within method operable design region (MODR). Unlike current methods, analytical method developed using analytical quality by design (AQbD) approach reduces the number of out-of-trend (OOT) results and out-of-specification (OOS) results due to the robustness of the method within the region. It is a current trend among pharmaceutical industry to implement analytical quality by design (AQbD) in method development process as a part of risk management, pharmaceutical development, and pharmaceutical quality system (ICH Q10). Owing to the lack explanatory reviews, this paper has been communicated to discuss different views of analytical scientists about implementation of AQbD in pharmaceutical quality system and also to correlate with product quality by design and pharmaceutical analytical technology (PAT). PMID:25722723

  20. Quantitative 1H NMR: Development and Potential of an Analytical Method – an Update

    PubMed Central

    Pauli, Guido F.; Gödecke, Tanja; Jaki, Birgit U.; Lankin, David C.

    2012-01-01

    Covering the literature from mid-2004 until the end of 2011, this review continues a previous literature overview on quantitative 1H NMR (qHNMR) methodology and its applications in the analysis of natural products (NPs). Among the foremost advantages of qHNMR is its accurate function with external calibration, the lack of any requirement for identical reference materials, a high precision and accuracy when properly validated, and an ability to quantitate multiple analytes simultaneously. As a result of the inclusion of over 170 new references, this updated review summarizes a wealth of detailed experiential evidence and newly developed methodology that supports qHNMR as a valuable and unbiased analytical tool for natural product and other areas of research. PMID:22482996

  1. The Direct Effect of Toroidal Magnetic Fields on Stellar Oscillations: An Analytical Expression for the General Matrix Element

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

    Kiefer, René; Schad, Ariane; Roth, Markus

    2017-09-10

    Where is the solar dynamo located and what is its modus operandi? These are still open questions in solar physics. Helio- and asteroseismology can help answer them by enabling us to study solar and stellar internal structures through global oscillations. The properties of solar and stellar acoustic modes are changing with the level of magnetic activity. However, until now, the inference on subsurface magnetic fields with seismic measures has been very limited. The aim of this paper is to develop a formalism to calculate the effect of large-scale toroidal magnetic fields on solar and stellar global oscillation eigenfunctions and eigenfrequencies.more » If the Lorentz force is added to the equilibrium equation of motion, stellar eigenmodes can couple. In quasi-degenerate perturbation theory, this coupling, also known as the direct effect, can be quantified by the general matrix element. We present the analytical expression of the matrix element for a superposition of subsurface zonal toroidal magnetic field configurations. The matrix element is important for forward calculations of perturbed solar and stellar eigenfunctions and frequency perturbations. The results presented here will help to ascertain solar and stellar large-scale subsurface magnetic fields, and their geometric configuration, strength, and change over the course of activity cycles.« less

  2. The Direct Effect of Toroidal Magnetic Fields on Stellar Oscillations: An Analytical Expression for the General Matrix Element

    NASA Astrophysics Data System (ADS)

    Kiefer, René; Schad, Ariane; Roth, Markus

    2017-09-01

    Where is the solar dynamo located and what is its modus operandi? These are still open questions in solar physics. Helio- and asteroseismology can help answer them by enabling us to study solar and stellar internal structures through global oscillations. The properties of solar and stellar acoustic modes are changing with the level of magnetic activity. However, until now, the inference on subsurface magnetic fields with seismic measures has been very limited. The aim of this paper is to develop a formalism to calculate the effect of large-scale toroidal magnetic fields on solar and stellar global oscillation eigenfunctions and eigenfrequencies. If the Lorentz force is added to the equilibrium equation of motion, stellar eigenmodes can couple. In quasi-degenerate perturbation theory, this coupling, also known as the direct effect, can be quantified by the general matrix element. We present the analytical expression of the matrix element for a superposition of subsurface zonal toroidal magnetic field configurations. The matrix element is important for forward calculations of perturbed solar and stellar eigenfunctions and frequency perturbations. The results presented here will help to ascertain solar and stellar large-scale subsurface magnetic fields, and their geometric configuration, strength, and change over the course of activity cycles.

  3. Evaluation of one dimensional analytical models for vegetation canopies

    NASA Technical Reports Server (NTRS)

    Goel, Narendra S.; Kuusk, Andres

    1992-01-01

    The SAIL model for one-dimensional homogeneous vegetation canopies has been modified to include the specular reflectance and hot spot effects. This modified model and the Nilson-Kuusk model are evaluated by comparing the reflectances given by them against those given by a radiosity-based computer model, Diana, for a set of canopies, characterized by different leaf area index (LAI) and leaf angle distribution (LAD). It is shown that for homogeneous canopies, the analytical models are generally quite accurate in the visible region, but not in the infrared region. For architecturally realistic heterogeneous canopies of the type found in nature, these models fall short. These shortcomings are quantified.

  4. HPAEC-PAD for oligosaccharide analysis-novel insights into analyte sensitivity and response stability.

    PubMed

    Mechelke, Matthias; Herlet, Jonathan; Benz, J Philipp; Schwarz, Wolfgang H; Zverlov, Vladimir V; Liebl, Wolfgang; Kornberger, Petra

    2017-12-01

    The rising importance of accurately detecting oligosaccharides in biomass hydrolyzates or as ingredients in food, such as in beverages and infant milk products, demands for the availability of tools to sensitively analyze the broad range of available oligosaccharides. Over the last decades, HPAEC-PAD has been developed into one of the major technologies for this task and represents a popular alternative to state-of-the-art LC-MS oligosaccharide analysis. This work presents the first comprehensive study which gives an overview of the separation of 38 analytes as well as enzymatic hydrolyzates of six different polysaccharides focusing on oligosaccharides. The high sensitivity of the PAD comes at cost of its stability due to recession of the gold electrode. By an in-depth analysis of the sensitivity drop over time for 35 analytes, including xylo- (XOS), arabinoxylo- (AXOS), laminari- (LOS), manno- (MOS), glucomanno- (GMOS), and cellooligosaccharides (COS), we developed an analyte-specific one-phase decay model for this effect over time. Using this model resulted in significantly improved data normalization when using an internal standard. Our results thereby allow a quantification approach which takes the inevitable and analyte-specific PAD response drop into account. Graphical abstract HPAEC-PAD analysis of oligosaccharides and determination of PAD response drop leading to an improved data normalization.

  5. Accurate analytical periodic solution of the elliptical Kepler equation using the Adomian decomposition method

    NASA Astrophysics Data System (ADS)

    Alshaery, Aisha; Ebaid, Abdelhalim

    2017-11-01

    Kepler's equation is one of the fundamental equations in orbital mechanics. It is a transcendental equation in terms of the eccentric anomaly of a planet which orbits the Sun. Determining the position of a planet in its orbit around the Sun at a given time depends upon the solution of Kepler's equation, which we will solve in this paper by the Adomian decomposition method (ADM). Several properties of the periodicity of the obtained approximate solutions have been proved in lemmas. Our calculations demonstrated a rapid convergence of the obtained approximate solutions which are displayed in tables and graphs. Also, it has been shown in this paper that only a few terms of the Adomian decomposition series are sufficient to achieve highly accurate numerical results for any number of revolutions of the Earth around the Sun as a consequence of the periodicity property. Numerically, the four-term approximate solution coincides with the Bessel-Fourier series solution in the literature up to seven decimal places at some values of the time parameter and nine decimal places at other values. Moreover, the absolute error approaches zero using the nine term approximate Adomian solution. In addition, the approximate Adomian solutions for the eccentric anomaly have been used to show the convergence of the approximate radial distances of the Earth from the Sun for any number of revolutions. The minimal distance (perihelion) and maximal distance (aphelion) approach 147 million kilometers and 152.505 million kilometers, respectively, and these coincide with the well known results in astronomical physics. Therefore, the Adomian decomposition method is validated as an effective tool to solve Kepler's equation for elliptical orbits.

  6. A novel dual-marker expression panel for easy and accurate risk stratification of patients with gastric cancer.

    PubMed

    Kanda, Mitsuro; Murotani, Kenta; Tanaka, Haruyoshi; Miwa, Takashi; Umeda, Shinichi; Tanaka, Chie; Kobayashi, Daisuke; Hayashi, Masamichi; Hattori, Norifumi; Suenaga, Masaya; Yamada, Suguru; Nakayama, Goro; Fujiwara, Michitaka; Kodera, Yasuhiro

    2018-05-07

    Development of specific biomarkers is necessary for individualized management of patients with gastric cancer. The aim of this study was to design a simple expression panel comprising novel molecular markers for precise risk stratification. Patients (n = 200) who underwent gastrectomy for gastric cancer were randomly assigned into learning and validation sets. Tissue mRNA expression levels of 15 candidate molecular markers were determined using quantitative PCR analysis. A dual-marker expression panel was created according to concordance index (C-index) values of overall survival for all 105 combinations of two markers in the learning set. The reproducibility and clinical significance of the dual-marker expression panel were evaluated in the validation set. The patient characteristics of the learning and validation sets were well balanced. The C-index values of combinations were significantly higher compared with those of single markers. The panel with the highest C-index (0.718) of the learning set comprised SYT8 and MAGED2, which clearly stratified patients into low-, intermediate-, and high-risk groups. The reproducibility of the panel was demonstrated in the validation set. High expression scores were significantly associated with larger tumor size, vascular invasion, lymph node metastasis, peritoneal metastasis, and advanced disease. The dual-marker expression panel provides a simple tool that clearly stratifies patients with gastric cancer into low-, intermediate-, and high risk after gastrectomy. © 2018 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.

  7. Recent α decay half-lives and analytic expression predictions including superheavy nuclei

    NASA Astrophysics Data System (ADS)

    Royer, G.; Zhang, H. F.

    2008-03-01

    New recent experimental α decay half-lives have been compared with the results obtained from previously proposed formulas depending only on the mass and charge numbers of the α emitter and the Qα value. For the heaviest nuclei they are also compared with calculations using the Density-Dependent M3Y (DDM3Y) effective interaction and the Viola-Seaborg-Sobiczewski (VSS) formulas. The correct agreement allows us to make predictions for the α decay half-lives of other still unknown superheavy nuclei from these analytic formulas using the extrapolated Qα of G. Audi, A. H. Wapstra, and C. Thibault [Nucl. Phys. A729, 337 (2003)].

  8. Recent {alpha} decay half-lives and analytic expression predictions including superheavy nuclei

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

    Royer, G.; Zhang, H. F.

    New recent experimental {alpha} decay half-lives have been compared with the results obtained from previously proposed formulas depending only on the mass and charge numbers of the {alpha} emitter and the Q{sub {alpha}} value. For the heaviest nuclei they are also compared with calculations using the Density-Dependent M3Y (DDM3Y) effective interaction and the Viola-Seaborg-Sobiczewski (VSS) formulas. The correct agreement allows us to make predictions for the {alpha} decay half-lives of other still unknown superheavy nuclei from these analytic formulas using the extrapolated Q{sub {alpha}} of G. Audi, A. H. Wapstra, and C. Thibault [Nucl. Phys. A729, 337 (2003)].

  9. Accurate Bit Error Rate Calculation for Asynchronous Chaos-Based DS-CDMA over Multipath Channel

    NASA Astrophysics Data System (ADS)

    Kaddoum, Georges; Roviras, Daniel; Chargé, Pascal; Fournier-Prunaret, Daniele

    2009-12-01

    An accurate approach to compute the bit error rate expression for multiuser chaosbased DS-CDMA system is presented in this paper. For more realistic communication system a slow fading multipath channel is considered. A simple RAKE receiver structure is considered. Based on the bit energy distribution, this approach compared to others computation methods existing in literature gives accurate results with low computation charge. Perfect estimation of the channel coefficients with the associated delays and chaos synchronization is assumed. The bit error rate is derived in terms of the bit energy distribution, the number of paths, the noise variance, and the number of users. Results are illustrated by theoretical calculations and numerical simulations which point out the accuracy of our approach.

  10. Analytical approximations for effective relative permeability in the capillary limit

    NASA Astrophysics Data System (ADS)

    Rabinovich, Avinoam; Li, Boxiao; Durlofsky, Louis J.

    2016-10-01

    We present an analytical method for calculating two-phase effective relative permeability, krjeff, where j designates phase (here CO2 and water), under steady state and capillary-limit assumptions. These effective relative permeabilities may be applied in experimental settings and for upscaling in the context of numerical flow simulations, e.g., for CO2 storage. An exact solution for effective absolute permeability, keff, in two-dimensional log-normally distributed isotropic permeability (k) fields is the geometric mean. We show that this does not hold for krjeff since log normality is not maintained in the capillary-limit phase permeability field (Kj=k·krj) when capillary pressure, and thus the saturation field, is varied. Nevertheless, the geometric mean is still shown to be suitable for approximating krjeff when the variance of ln⁡k is low. For high-variance cases, we apply a correction to the geometric average gas effective relative permeability using a Winsorized mean, which neglects large and small Kj values symmetrically. The analytical method is extended to anisotropically correlated log-normal permeability fields using power law averaging. In these cases, the Winsorized mean treatment is applied to the gas curves for cases described by negative power law exponents (flow across incomplete layers). The accuracy of our analytical expressions for krjeff is demonstrated through extensive numerical tests, using low-variance and high-variance permeability realizations with a range of correlation structures. We also present integral expressions for geometric-mean and power law average krjeff for the systems considered, which enable derivation of closed-form series solutions for krjeff without generating permeability realizations.

  11. Development and analytical performance evaluation of FREND-SAA and FREND-Hp

    NASA Astrophysics Data System (ADS)

    Choi, Eunha; Seong, Jihyun; Lee, Seiyoung; Han, Sunmi

    2017-07-01

    The FREND System is a portable cartridge reader, quantifying analytes by measuring laser-induced fluorescence in a single-use reagent cartridge. The objective of this study was to evaluate FREND-SAA and FREND-Hp assays. The FREND-SAA and Hp assays were standardized to the WHO and IFCC reference materials. Analytical performance studies of Precision, Linearity, Limits of Detections, Interferences, and Method Comparisons for both assays were performed according to the CLSI guidelines. Both assays demonstrated acceptable imprecision of %CV in three different levels of samples. The linearity of the assays was found to be acceptable (SAA 5 150 mg/L, Hp 30 400 mg/dL). The detection limits were 3.8 mg/L (SAA) and 10.2 mg/dL (Hp). No significant interference and no significant deviation from linearity was found in the both comparison studies. In conclusion, NanoEnTek's FREND-SAA and Hp assays represent rapid, accurate and convenient means to quantify SAA and Hp in human serum on FREND system.

  12. PB-AM: An open-source, fully analytical linear poisson-boltzmann solver.

    PubMed

    Felberg, Lisa E; Brookes, David H; Yap, Eng-Hui; Jurrus, Elizabeth; Baker, Nathan A; Head-Gordon, Teresa

    2017-06-05

    We present the open source distributed software package Poisson-Boltzmann Analytical Method (PB-AM), a fully analytical solution to the linearized PB equation, for molecules represented as non-overlapping spherical cavities. The PB-AM software package includes the generation of outputs files appropriate for visualization using visual molecular dynamics, a Brownian dynamics scheme that uses periodic boundary conditions to simulate dynamics, the ability to specify docking criteria, and offers two different kinetics schemes to evaluate biomolecular association rate constants. Given that PB-AM defines mutual polarization completely and accurately, it can be refactored as a many-body expansion to explore 2- and 3-body polarization. Additionally, the software has been integrated into the Adaptive Poisson-Boltzmann Solver (APBS) software package to make it more accessible to a larger group of scientists, educators, and students that are more familiar with the APBS framework. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  13. Accurate potentiometric determination of lipid membrane-water partition coefficients and apparent dissociation constants of ionizable drugs: electrostatic corrections.

    PubMed

    Elsayed, Mustafa M A; Vierl, Ulrich; Cevc, Gregor

    2009-06-01

    Potentiometric lipid membrane-water partition coefficient studies neglect electrostatic interactions to date; this leads to incorrect results. We herein show how to account properly for such interactions in potentiometric data analysis. We conducted potentiometric titration experiments to determine lipid membrane-water partition coefficients of four illustrative drugs, bupivacaine, diclofenac, ketoprofen and terbinafine. We then analyzed the results conventionally and with an improved analytical approach that considers Coulombic electrostatic interactions. The new analytical approach delivers robust partition coefficient values. In contrast, the conventional data analysis yields apparent partition coefficients of the ionized drug forms that depend on experimental conditions (mainly the lipid-drug ratio and the bulk ionic strength). This is due to changing electrostatic effects originating either from bound drug and/or lipid charges. A membrane comprising 10 mol-% mono-charged molecules in a 150 mM (monovalent) electrolyte solution yields results that differ by a factor of 4 from uncharged membranes results. Allowance for the Coulombic electrostatic interactions is a prerequisite for accurate and reliable determination of lipid membrane-water partition coefficients of ionizable drugs from potentiometric titration data. The same conclusion applies to all analytical methods involving drug binding to a surface.

  14. Understanding Business Analytics

    DTIC Science & Technology

    2015-01-05

    analytics have been used in organizations for a variety of reasons for quite some time; ranging from the simple (generating and understanding business analytics...process. understanding business analytics 3 How well these two components are orchestrated will determine the level of success an organization has in

  15. Edge detection of magnetic anomalies using analytic signal of tilt angle (ASTA)

    NASA Astrophysics Data System (ADS)

    Alamdar, K.; Ansari, A. H.; Ghorbani, A.

    2009-04-01

    Magnetic is a commonly used geophysical technique to identify and image potential subsurface targets. Interpretation of magnetic anomalies is a complex process due to the superposition of multiple magnetic sources, presence of geologic and cultural noise and acquisition and positioning error. Both the vertical and horizontal derivatives of potential field data are useful; horizontal derivative, enhance edges whereas vertical derivative narrow the width of anomaly and so locate source bodies more accurately. We can combine vertical and horizontal derivative of magnetic field to achieve analytic signal which is independent to body magnetization direction and maximum value of this lies over edges of body directly. Tilt angle filter is phased-base filter and is defined as angle between vertical derivative and total horizontal derivative. Tilt angle value differ from +90 degree to -90 degree and its zero value lies over body edge. One of disadvantage of this filter is when encountering with deep sources the detected edge is blurred. For overcome this problem many authors introduced new filters such as total horizontal derivative of tilt angle or vertical derivative of tilt angle which Because of using high-order derivative in these filters results may be too noisy. If we combine analytic signal and tilt angle, a new filter termed (ASTA) is produced which its maximum value lies directly over body edge and is easer than tilt angle to delineate body edge and no complicity of tilt angle. In this work new filter has been demonstrated on magnetic data from an area in Sar- Cheshme region in Iran. This area is located in 55 degree longitude and 32 degree latitude and is a copper potential region. The main formation in this area is Andesith and Trachyandezite. Magnetic surveying was employed to separate the boundaries of Andezite and Trachyandezite from adjacent area. In this regard a variety of filters such as analytic signal, tilt angle and ASTA filter have been applied which

  16. Expressions Module for the Satellite Orbit Analysis Program

    NASA Technical Reports Server (NTRS)

    Edmonds, Karina

    2008-01-01

    The Expressions Module is a software module that has been incorporated into the Satellite Orbit Analysis Program (SOAP). The module includes an expressions- parser submodule built on top of an analytical system, enabling the user to define logical and numerical variables and constants. The variables can capture output from SOAP orbital-prediction and geometric-engine computations. The module can combine variables and constants with built-in logical operators (such as Boolean AND, OR, and NOT), relational operators (such as >, <, or =), and mathematical operators (such as addition, subtraction, multiplication, division, modulus, exponentiation, differentiation, and integration). Parentheses can be used to specify precedence of operations. The module contains a library of mathematical functions and operations, including logarithms, trigonometric functions, Bessel functions, minimum/ maximum operations, and floating- point-to-integer conversions. The module supports combinations of time, distance, and angular units and has a dimensional- analysis component that checks for correct usage of units. A parser based on the Flex language and the Bison program looks for and indicates errors in syntax. SOAP expressions can be built using other expressions as arguments, thus enabling the user to build analytical trees. A graphical user interface facilitates use.

  17. Analyticity without Differentiability

    ERIC Educational Resources Information Center

    Kirillova, Evgenia; Spindler, Karlheinz

    2008-01-01

    In this article we derive all salient properties of analytic functions, including the analytic version of the inverse function theorem, using only the most elementary convergence properties of series. Not even the notion of differentiability is required to do so. Instead, analytical arguments are replaced by combinatorial arguments exhibiting…

  18. Method for accurate determination of dissociation constants of optical ratiometric systems: chemical probes, genetically encoded sensors, and interacting molecules.

    PubMed

    Pomorski, Adam; Kochańczyk, Tomasz; Miłoch, Anna; Krężel, Artur

    2013-12-03

    Ratiometric chemical probes and genetically encoded sensors are of high interest for both analytical chemists and molecular biologists. Their high sensitivity toward the target ligand and ability to obtain quantitative results without a known sensor concentration have made them a very useful tool in both in vitro and in vivo assays. Although ratiometric sensors are widely used in many applications, their successful and accurate usage depends on how they are characterized in terms of sensing target molecules. The most important feature of probes and sensors besides their optical parameters is an affinity constant toward analyzed molecules. The literature shows that different analytical approaches are used to determine the stability constants, with the ratio approach being most popular. However, oversimplification and lack of attention to detail results in inaccurate determination of stability constants, which in turn affects the results obtained using these sensors. Here, we present a new method where ratio signal is calibrated for borderline values of intensities of both wavelengths, instead of borderline ratio values that generate errors in many studies. At the same time, the equation takes into account the cooperativity factor or fluorescence artifacts and therefore can be used to characterize systems with various stoichiometries and experimental conditions. Accurate determination of stability constants is demonstrated utilizing four known optical ratiometric probes and sensors, together with a discussion regarding other, currently used methods.

  19. An accurate boundary element method for the exterior elastic scattering problem in two dimensions

    NASA Astrophysics Data System (ADS)

    Bao, Gang; Xu, Liwei; Yin, Tao

    2017-11-01

    This paper is concerned with a Galerkin boundary element method solving the two dimensional exterior elastic wave scattering problem. The original problem is first reduced to the so-called Burton-Miller [1] boundary integral formulation, and essential mathematical features of its variational form are discussed. In numerical implementations, a newly-derived and analytically accurate regularization formula [2] is employed for the numerical evaluation of hyper-singular boundary integral operator. A new computational approach is employed based on the series expansions of Hankel functions for the computation of weakly-singular boundary integral operators during the reduction of corresponding Galerkin equations into a discrete linear system. The effectiveness of proposed numerical methods is demonstrated using several numerical examples.

  20. Identification of stable reference genes for gene expression analysis of three-dimensional cultivated human bone marrow-derived mesenchymal stromal cells for bone tissue engineering.

    PubMed

    Rauh, Juliane; Jacobi, Angela; Stiehler, Maik

    2015-02-01

    The principles of tissue engineering (TE) are widely used for bone regeneration concepts. Three-dimensional (3D) cultivation of autologous human mesenchymal stromal cells (MSCs) on porous scaffolds is the basic prerequisite to generate newly formed bone tissue. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is a specific and sensitive analytical tool for the measurement of mRNA-levels in cells or tissues. For an accurate quantification of gene expression levels, stably expressed reference genes (RGs) are essential to obtain reliable results. Since the 3D environment can affect a cell's morphology, proliferation, and gene expression profile compared with two-dimensional (2D) cultivation, there is a need to identify robust RGs for the quantification of gene expression. So far, this issue has not been adequately investigated. The aim of this study was to identify the most stably expressed RGs for gene expression analysis of 3D-cultivated human bone marrow-derived MSCs (BM-MSCs). For this, we analyzed the gene expression levels of n=31 RGs in 3D-cultivated human BM-MSCs from six different donors compared with conventional 2D cultivation using qRT-PCR. MSCs isolated from bone marrow aspirates were cultivated on human cancellous bone cube scaffolds for 14 days. Osteogenic differentiation was assessed by cell-specific alkaline phosphatase (ALP) activity and expression of osteogenic marker genes. Expression levels of potential reference and target genes were quantified using commercially available TaqMan(®) assays. mRNA expression stability of RGs was determined by calculating the coefficient of variation (CV) and using the algorithms of geNorm and NormFinder. Using both algorithms, we identified TATA box binding protein (TBP), transferrin receptor (p90, CD71) (TFRC), and hypoxanthine phosphoribosyltransferase 1 (HPRT1) as the most stably expressed RGs in 3D-cultivated BM-MSCs. Notably, genes that are routinely used as RGs, for example, beta actin

  1. Identification of Stable Reference Genes for Gene Expression Analysis of Three-Dimensional Cultivated Human Bone Marrow-Derived Mesenchymal Stromal Cells for Bone Tissue Engineering

    PubMed Central

    Rauh, Juliane; Jacobi, Angela

    2015-01-01

    The principles of tissue engineering (TE) are widely used for bone regeneration concepts. Three-dimensional (3D) cultivation of autologous human mesenchymal stromal cells (MSCs) on porous scaffolds is the basic prerequisite to generate newly formed bone tissue. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) is a specific and sensitive analytical tool for the measurement of mRNA-levels in cells or tissues. For an accurate quantification of gene expression levels, stably expressed reference genes (RGs) are essential to obtain reliable results. Since the 3D environment can affect a cell's morphology, proliferation, and gene expression profile compared with two-dimensional (2D) cultivation, there is a need to identify robust RGs for the quantification of gene expression. So far, this issue has not been adequately investigated. The aim of this study was to identify the most stably expressed RGs for gene expression analysis of 3D-cultivated human bone marrow-derived MSCs (BM-MSCs). For this, we analyzed the gene expression levels of n=31 RGs in 3D-cultivated human BM-MSCs from six different donors compared with conventional 2D cultivation using qRT-PCR. MSCs isolated from bone marrow aspirates were cultivated on human cancellous bone cube scaffolds for 14 days. Osteogenic differentiation was assessed by cell-specific alkaline phosphatase (ALP) activity and expression of osteogenic marker genes. Expression levels of potential reference and target genes were quantified using commercially available TaqMan® assays. mRNA expression stability of RGs was determined by calculating the coefficient of variation (CV) and using the algorithms of geNorm and NormFinder. Using both algorithms, we identified TATA box binding protein (TBP), transferrin receptor (p90, CD71) (TFRC), and hypoxanthine phosphoribosyltransferase 1 (HPRT1) as the most stably expressed RGs in 3D-cultivated BM-MSCs. Notably, genes that are routinely used as RGs, for example, beta actin

  2. Usefulness of Analytical Research: Rethinking Analytical R&D&T Strategies.

    PubMed

    Valcárcel, Miguel

    2017-11-07

    This Perspective is intended to help foster true innovation in Research & Development & Transfer (R&D&T) in Analytical Chemistry in the form of advances that are primarily useful for analytical purposes rather than solely for publishing. Devising effective means to strengthen the crucial contribution of Analytical Chemistry to progress in Chemistry, Science & Technology, and Society requires carefully examining the present status of our discipline and also identifying internal and external driving forces with a potential adverse impact on its development. The diagnostic process should be followed by administration of an effective therapy and supported by adoption of a theragnostic strategy if Analytical Chemistry is to enjoy a better future.

  3. Implicit/explicit memory versus analytic/nonanalytic processing: rethinking the mere exposure effect.

    PubMed

    Whittlesea, B W; Price, J R

    2001-03-01

    In studies of the mere exposure effect, rapid presentation of items can increase liking without accurate recognition. The effect on liking has been explained as a misattribution of fluency caused by prior presentation. However, fluency is also a source of feelings of familiarity. It is, therefore, surprising that prior experience can enhance liking without also causing familiarity-based recognition. We suggest that when study opportunities are minimal and test items are perceptually similar, people adopt an analytic approach, attempting to recognize distinctive features. That strategy fails because rapid presentation prevents effective encoding of such features; it also prevents people from experiencing fluency and a consequent feeling of familiarity. We suggest that the liking-without-recognition effect results from using an effective (nonanalytic) strategy in judging pleasantness, but an ineffective (analytic) strategy in recognition. Explanations of the mere exposure effect based on a distinction between implicit and explicit memory are unnecessary.

  4. Analytic calculation of 1-jettiness in DIS at O (α s)

    DOE PAGES

    Kang, Daekyoung; Lee, Christopher; Stewart, Iain W.

    2014-11-01

    We present an analytic O(α s) calculation of cross sections in deep inelastic scattering (DIS) dependent on an event shape, 1-jettiness, that probes final states with one jet plus initial state radiation. This is the first entirely analytic calculation for a DIS event shape cross section at this order. We present results for the differential and cumulative 1-jettiness cross sections, and express both in terms of structure functions dependent not only on the usual DIS variables x, Q 2 but also on the 1-jettiness τ. Combined with previous results for log resummation, predictions are obtained over the entire range ofmore » the 1-jettiness distribution.« less

  5. Analytical characterization of wine and its precursors by capillary electrophoresis.

    PubMed

    Gomez, Federico J V; Monasterio, Romina P; Vargas, Verónica Carolina Soto; Silva, María F

    2012-08-01

    The accurate determination of marker chemical species in grape, musts, and wines presents a unique analytical challenge with high impact on diverse areas of knowledge such as health, plant physiology, and economy. Capillary electromigration techniques have emerged as a powerful tool, allowing the separation and identification of highly polar compounds that cannot be easily separated by traditional HPLC methods, providing complementary information and permitting the simultaneous analysis of analytes with different nature in a single run. The main advantage of CE over traditional methods for wine analysis is that in most cases samples require no treatment other than filtration. The purpose of this article is to present a revision on capillary electromigration methods applied to the analysis of wine and its precursors over the last decade. The current state of the art of the topic is evaluated, with special emphasis on the natural compounds that have allowed wine to be considered as a functional food. The most representative revised compounds are phenolic compounds, amino acids, proteins, elemental species, mycotoxins, and organic acids. Finally, a discussion on future trends of the role of capillary electrophoresis in the field of analytical characterization of wines for routine analysis, wine classification, as well as multidisciplinary aspects of the so-called "from soil to glass" chain is presented. © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  6. NNLOPS accurate associated HW production

    NASA Astrophysics Data System (ADS)

    Astill, William; Bizon, Wojciech; Re, Emanuele; Zanderighi, Giulia

    2016-06-01

    We present a next-to-next-to-leading order accurate description of associated HW production consistently matched to a parton shower. The method is based on reweighting events obtained with the HW plus one jet NLO accurate calculation implemented in POWHEG, extended with the MiNLO procedure, to reproduce NNLO accurate Born distributions. Since the Born kinematics is more complex than the cases treated before, we use a parametrization of the Collins-Soper angles to reduce the number of variables required for the reweighting. We present phenomenological results at 13 TeV, with cuts suggested by the Higgs Cross section Working Group.

  7. Almost analytical Karhunen-Loeve representation of irregular waves based on the prolate spheroidal wave functions

    NASA Astrophysics Data System (ADS)

    Lee, Gibbeum; Cho, Yeunwoo

    2017-11-01

    We present an almost analytical new approach to solving the matrix eigenvalue problem or the integral equation in Karhunen-Loeve (K-L) representation of random data such as irregular ocean waves. Instead of solving this matrix eigenvalue problem purely numerically, which may suffer from the computational inaccuracy for big data, first, we consider a pair of integral and differential equations, which are related to the so-called prolate spheroidal wave functions (PSWF). For the PSWF differential equation, the pair of the eigenvectors (PSWF) and eigenvalues can be obtained from a relatively small number of analytical Legendre functions. Then, the eigenvalues in the PSWF integral equation are expressed in terms of functional values of the PSWF and the eigenvalues of the PSWF differential equation. Finally, the analytically expressed PSWFs and the eigenvalues in the PWSF integral equation are used to form the kernel matrix in the K-L integral equation for the representation of exemplary wave data; ordinary irregular waves and rogue waves. We found that the present almost analytical method is better than the conventional data-independent Fourier representation and, also, the conventional direct numerical K-L representation in terms of both accuracy and computational cost. This work was supported by the National Research Foundation of Korea (NRF). (NRF-2017R1D1A1B03028299).

  8. New analytic results for speciation times in neutral models.

    PubMed

    Gernhard, Tanja

    2008-05-01

    In this paper, we investigate the standard Yule model, and a recently studied model of speciation and extinction, the "critical branching process." We develop an analytic way-as opposed to the common simulation approach-for calculating the speciation times in a reconstructed phylogenetic tree. Simple expressions for the density and the moments of the speciation times are obtained. Methods for dating a speciation event become valuable, if for the reconstructed phylogenetic trees, no time scale is available. A missing time scale could be due to supertree methods, morphological data, or molecular data which violates the molecular clock. Our analytic approach is, in particular, useful for the model with extinction, since simulations of birth-death processes which are conditioned on obtaining n extant species today are quite delicate. Further, simulations are very time consuming for big n under both models.

  9. Toward Hamiltonian Adaptive QM/MM: Accurate Solvent Structures Using Many-Body Potentials.

    PubMed

    Boereboom, Jelle M; Potestio, Raffaello; Donadio, Davide; Bulo, Rosa E

    2016-08-09

    Adaptive quantum mechanical (QM)/molecular mechanical (MM) methods enable efficient molecular simulations of chemistry in solution. Reactive subregions are modeled with an accurate QM potential energy expression while the rest of the system is described in a more approximate manner (MM). As solvent molecules diffuse in and out of the reactive region, they are gradually included into (and excluded from) the QM expression. It would be desirable to model such a system with a single adaptive Hamiltonian, but thus far this has resulted in distorted structures at the boundary between the two regions. Solving this long outstanding problem will allow microcanonical adaptive QM/MM simulations that can be used to obtain vibrational spectra and dynamical properties. The difficulty lies in the complex QM potential energy expression, with a many-body expansion that contains higher order terms. Here, we outline a Hamiltonian adaptive multiscale scheme within the framework of many-body potentials. The adaptive expressions are entirely general, and complementary to all standard (nonadaptive) QM/MM embedding schemes available. We demonstrate the merit of our approach on a molecular system defined by two different MM potentials (MM/MM'). For the long-range interactions a numerical scheme is used (particle mesh Ewald), which yields energy expressions that are many-body in nature. Our Hamiltonian approach is the first to provide both energy conservation and the correct solvent structure everywhere in this system.

  10. Heparin removal by ecteola-cellulose pre-treatment enables the use of plasma samples for accurate measurement of anti-Yellow fever virus neutralizing antibodies.

    PubMed

    Campi-Azevedo, Ana Carolina; Peruhype-Magalhães, Vanessa; Coelho-Dos-Reis, Jordana Grazziela; Costa-Pereira, Christiane; Yamamura, Anna Yoshida; Lima, Sheila Maria Barbosa de; Simões, Marisol; Campos, Fernanda Magalhães Freire; de Castro Zacche Tonini, Aline; Lemos, Elenice Moreira; Brum, Ricardo Cristiano; de Noronha, Tatiana Guimarães; Freire, Marcos Silva; Maia, Maria de Lourdes Sousa; Camacho, Luiz Antônio Bastos; Rios, Maria; Chancey, Caren; Romano, Alessandro; Domingues, Carla Magda; Teixeira-Carvalho, Andréa; Martins-Filho, Olindo Assis

    2017-09-01

    Technological innovations in vaccinology have recently contributed to bring about novel insights for the vaccine-induced immune response. While the current protocols that use peripheral blood samples may provide abundant data, a range of distinct components of whole blood samples are required and the different anticoagulant systems employed may impair some properties of the biological sample and interfere with functional assays. Although the interference of heparin in functional assays for viral neutralizing antibodies such as the functional plaque-reduction neutralization test (PRNT), considered the gold-standard method to assess and monitor the protective immunity induced by the Yellow fever virus (YFV) vaccine, has been well characterized, the development of pre-analytical treatments is still required for the establishment of optimized protocols. The present study intended to optimize and evaluate the performance of pre-analytical treatment of heparin-collected blood samples with ecteola-cellulose (ECT) to provide accurate measurement of anti-YFV neutralizing antibodies, by PRNT. The study was designed in three steps, including: I. Problem statement; II. Pre-analytical steps; III. Analytical steps. Data confirmed the interference of heparin on PRNT reactivity in a dose-responsive fashion. Distinct sets of conditions for ECT pre-treatment were tested to optimize the heparin removal. The optimized protocol was pre-validated to determine the effectiveness of heparin plasma:ECT treatment to restore the PRNT titers as compared to serum samples. The validation and comparative performance was carried out by using a large range of serum vs heparin plasma:ECT 1:2 paired samples obtained from unvaccinated and 17DD-YFV primary vaccinated subjects. Altogether, the findings support the use of heparin plasma:ECT samples for accurate measurement of anti-YFV neutralizing antibodies. Copyright © 2017 Elsevier B.V. All rights reserved.

  11. Analytical performances of the Diazyme ADA assay on the Cobas® 6000 system.

    PubMed

    Delacour, Hervé; Sauvanet, Christophe; Ceppa, Franck; Burnat, Pascal

    2010-12-01

    To evaluate the analytical performance of the Diazyme ADA assay on the Cobas® 6000 system for pleural fluid samples analysis. Imprecision, linearity, calibration curve stability, interference, and correlation studies were completed. The Diazyme ADA assay demonstrated excellent precision (CV<4%) over the analytical measurement range (0.5-117 U/L). Bilirubin above 50 μmol/L and haemoglobin above 177 μmol/L interfered with the test, inducing a negative and a positive interference respectively. The Diazyme ADA assay correlated well with the Giusti method (r(2)=0.93) but exhibited a negative bias (~ -30%). The Diazyme ADA assay on the Cobas® 6000 system represents a rapid, accurate, precise and reliable method for determination of ADA activity in pleural fluid samples. Copyright © 2010 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

  12. Analytical Optimization of the Net Residual Dispersion in SPM-Limited Dispersion-Managed Systems

    NASA Astrophysics Data System (ADS)

    Xiao, Xiaosheng; Gao, Shiming; Tian, Yu; Yang, Changxi

    2006-05-01

    Dispersion management is an effective technique to suppress the nonlinear impairment in fiber transmission systems, which includes tuning the amounts of precompensation, residual dispersion per span (RDPS), and net residual dispersion (NRD) of the systems. For self-phase modulation (SPM)-limited systems, optimizing the NRD is necessary because it can greatly improve the system performance. In this paper, an analytical method is presented to optimize NRD for SPM-limited dispersion-managed systems. The method is based on the correlation between the nonlinear impairment and the output pulse broadening of SPM-limited systems; therefore, dispersion-managed systems can be optimized through minimizing the output single-pulse broadening. A set of expressions is derived to calculate the output pulse broadening of the SPM-limited dispersion-managed system, from which the analytical result of optimal NRD is obtained. Furthermore, with the expressions of pulse broadening, how the nonlinear impairment depends on the amounts of precompensation and RDPS can be revealed conveniently.

  13. Relative motion using analytical differential gravity

    NASA Technical Reports Server (NTRS)

    Gottlieb, Robert G.

    1988-01-01

    This paper presents a new approach to the computation of the motion of one satellite relative to another. The trajectory of the reference satellite is computed accurately subject to geopotential perturbations. This precise trajectory is used as a reference in computing the position of a nearby body, or bodies. The problem that arises in this approach is differencing nearly equal terms in the geopotential model, especially as the separation of the reference and nearby bodies approaches zero. By developing closed form expressions for differences in higher order and degree geopotential terms, the numerical problem inherent in the differencing approach is eliminated.

  14. Suitable Reference Genes for Accurate Gene Expression Analysis in Parsley (Petroselinum crispum) for Abiotic Stresses and Hormone Stimuli

    PubMed Central

    Li, Meng-Yao; Song, Xiong; Wang, Feng; Xiong, Ai-Sheng

    2016-01-01

    Parsley, one of the most important vegetables in the Apiaceae family, is widely used in the food, medicinal, and cosmetic industries. Recent studies on parsley mainly focus on its chemical composition, and further research involving the analysis of the plant's gene functions and expressions is required. qPCR is a powerful method for detecting very low quantities of target transcript levels and is widely used to study gene expression. To ensure the accuracy of results, a suitable reference gene is necessary for expression normalization. In this study, four software, namely geNorm, NormFinder, BestKeeper, and RefFinder were used to evaluate the expression stabilities of eight candidate reference genes of parsley (GAPDH, ACTIN, eIF-4α, SAND, UBC, TIP41, EF-1α, and TUB) under various conditions, including abiotic stresses (heat, cold, salt, and drought) and hormone stimuli treatments (GA, SA, MeJA, and ABA). Results showed that EF-1α and TUB were the most stable genes for abiotic stresses, whereas EF-1α, GAPDH, and TUB were the top three choices for hormone stimuli treatments. Moreover, EF-1α and TUB were the most stable reference genes among all tested samples, and UBC was the least stable one. Expression analysis of PcDREB1 and PcDREB2 further verified that the selected stable reference genes were suitable for gene expression normalization. This study can guide the selection of suitable reference genes in gene expression in parsley. PMID:27746803

  15. Suitable Reference Genes for Accurate Gene Expression Analysis in Parsley (Petroselinum crispum) for Abiotic Stresses and Hormone Stimuli.

    PubMed

    Li, Meng-Yao; Song, Xiong; Wang, Feng; Xiong, Ai-Sheng

    2016-01-01

    Parsley, one of the most important vegetables in the Apiaceae family, is widely used in the food, medicinal, and cosmetic industries. Recent studies on parsley mainly focus on its chemical composition, and further research involving the analysis of the plant's gene functions and expressions is required. qPCR is a powerful method for detecting very low quantities of target transcript levels and is widely used to study gene expression. To ensure the accuracy of results, a suitable reference gene is necessary for expression normalization. In this study, four software, namely geNorm, NormFinder, BestKeeper, and RefFinder were used to evaluate the expression stabilities of eight candidate reference genes of parsley ( GAPDH, ACTIN, eIF-4 α, SAND, UBC, TIP41, EF-1 α, and TUB ) under various conditions, including abiotic stresses (heat, cold, salt, and drought) and hormone stimuli treatments (GA, SA, MeJA, and ABA). Results showed that EF-1 α and TUB were the most stable genes for abiotic stresses, whereas EF-1 α, GAPDH , and TUB were the top three choices for hormone stimuli treatments. Moreover, EF-1 α and TUB were the most stable reference genes among all tested samples, and UBC was the least stable one. Expression analysis of PcDREB1 and PcDREB2 further verified that the selected stable reference genes were suitable for gene expression normalization. This study can guide the selection of suitable reference genes in gene expression in parsley.

  16. TimeBench: a data model and software library for visual analytics of time-oriented data.

    PubMed

    Rind, Alexander; Lammarsch, Tim; Aigner, Wolfgang; Alsallakh, Bilal; Miksch, Silvia

    2013-12-01

    Time-oriented data play an essential role in many Visual Analytics scenarios such as extracting medical insights from collections of electronic health records or identifying emerging problems and vulnerabilities in network traffic. However, many software libraries for Visual Analytics treat time as a flat numerical data type and insufficiently tackle the complexity of the time domain such as calendar granularities and intervals. Therefore, developers of advanced Visual Analytics designs need to implement temporal foundations in their application code over and over again. We present TimeBench, a software library that provides foundational data structures and algorithms for time-oriented data in Visual Analytics. Its expressiveness and developer accessibility have been evaluated through application examples demonstrating a variety of challenges with time-oriented data and long-term developer studies conducted in the scope of research and student projects.

  17. Analytic few-photon scattering in waveguide QED

    NASA Astrophysics Data System (ADS)

    Hurst, David L.; Kok, Pieter

    2018-04-01

    We develop an approach to light-matter coupling in waveguide QED based upon scattering amplitudes evaluated via Dyson series. For optical states containing more than single photons, terms in this series become increasingly complex, and we provide a diagrammatic recipe for their evaluation, which is capable of yielding analytic results. Our method fully specifies a combined emitter-optical state that permits investigation of light-matter entanglement generation protocols. We use our expressions to study two-photon scattering from a Λ -system and find that the pole structure of the transition amplitude is dramatically altered as the two ground states are tuned from degeneracy.

  18. Accurate Arabic Script Language/Dialect Classification

    DTIC Science & Technology

    2014-01-01

    Army Research Laboratory Accurate Arabic Script Language/Dialect Classification by Stephen C. Tratz ARL-TR-6761 January 2014 Approved for public...1197 ARL-TR-6761 January 2014 Accurate Arabic Script Language/Dialect Classification Stephen C. Tratz Computational and Information Sciences...Include area code) Standard Form 298 (Rev. 8/98) Prescribed by ANSI Std. Z39.18 January 2014 Final Accurate Arabic Script Language/Dialect Classification

  19. Transforming Lepidopteran Insect Cells for Improved Protein Processing and Expression

    USDA-ARS?s Scientific Manuscript database

    The lepidopteran insect cells used with the baculovirus expression vector system (BEVS) are capable of synthesizing and accurately processing foreign proteins. However, proteins expressed in baculovirus-infected cells often fail to be completely processed, or are not processed in a manner that meet...

  20. Prevalence of Pre-Analytical Errors in Clinical Chemistry Diagnostic Labs in Sulaimani City of Iraqi Kurdistan.

    PubMed

    Najat, Dereen

    2017-01-01

    hospitals focus only on the analytical phase, and none of the pre-analytical errors were recorded. Interestingly, none of the labs were internationally accredited; therefore, corrective actions are needed at these hospitals to ensure better health outcomes. Internal and External Quality Assessment Schemes (EQAS) for the pre-analytical phase at Sulaimani clinical laboratories should be implemented at public hospitals. Furthermore, lab personnel, particularly phlebotomists, need continuous training on the importance of sample quality to obtain accurate test results.

  1. Absorption of infrared radiation by electrons in the field of a neutral hydrogen atom

    NASA Technical Reports Server (NTRS)

    Stallcop, J. R.

    1974-01-01

    An analytical expression for the absorption coefficient is developed from a relationship between the cross-section for inverse bremsstrahlung absorption and the cross-section for electron-atom momentum transfer; it is accurate for those photon frequencies v and temperatures such that hv/kT is small. The determination of the absorption of infrared radiation by free-free transitions of the negative hydrogen ion has been extended to higher temperatures. A simple analytical expression for the absorption coefficient has been derived.

  2. Analytical Characterisation of Nanoscale Zero-Valent Iron: A ...

    EPA Pesticide Factsheets

    Zero-valent iron nanoparticles (nZVI) have been widely tested as they are showing significant promise for environmental remediation. However, many recent studies have demonstrated that their mobility and reactivity in subsurface environments are significantly affected by their tendency to aggregate. Both the mobility and reactivity of nZVI mainly depends on properties such as particle size, surface chemistry and bulk composition. In order to ensure efficient remediation, it is crucial to accurately assess and understand the implications of these properties before deploying these materials into contaminated environments. Many analytical techniques are now available to determine these parameters and this paper provides a critical review of their usefulness and limitations for nZVI characterisation. These analytical techniques include microscopy and light scattering techniques for the determination of particle size, size distribution and aggregation state, and X-ray techniques for the characterisation of surface chemistry and bulk composition. Example characterisation data derived from commercial nZVI materials is used to further illustrate method strengths and limitations. Finally, some important challenges with respect to the characterisation of nZVI in groundwater samples are discussed. In recent years, manufactured nanoparticles (MNPs) have attracted increasing interest for their potential applications in the treatment of contaminated soil and water. In compar

  3. Proactive Supply Chain Performance Management with Predictive Analytics

    PubMed Central

    Stefanovic, Nenad

    2014-01-01

    Today's business climate requires supply chains to be proactive rather than reactive, which demands a new approach that incorporates data mining predictive analytics. This paper introduces a predictive supply chain performance management model which combines process modelling, performance measurement, data mining models, and web portal technologies into a unique model. It presents the supply chain modelling approach based on the specialized metamodel which allows modelling of any supply chain configuration and at different level of details. The paper also presents the supply chain semantic business intelligence (BI) model which encapsulates data sources and business rules and includes the data warehouse model with specific supply chain dimensions, measures, and KPIs (key performance indicators). Next, the paper describes two generic approaches for designing the KPI predictive data mining models based on the BI semantic model. KPI predictive models were trained and tested with a real-world data set. Finally, a specialized analytical web portal which offers collaborative performance monitoring and decision making is presented. The results show that these models give very accurate KPI projections and provide valuable insights into newly emerging trends, opportunities, and problems. This should lead to more intelligent, predictive, and responsive supply chains capable of adapting to future business environment. PMID:25386605

  4. Proactive supply chain performance management with predictive analytics.

    PubMed

    Stefanovic, Nenad

    2014-01-01

    Today's business climate requires supply chains to be proactive rather than reactive, which demands a new approach that incorporates data mining predictive analytics. This paper introduces a predictive supply chain performance management model which combines process modelling, performance measurement, data mining models, and web portal technologies into a unique model. It presents the supply chain modelling approach based on the specialized metamodel which allows modelling of any supply chain configuration and at different level of details. The paper also presents the supply chain semantic business intelligence (BI) model which encapsulates data sources and business rules and includes the data warehouse model with specific supply chain dimensions, measures, and KPIs (key performance indicators). Next, the paper describes two generic approaches for designing the KPI predictive data mining models based on the BI semantic model. KPI predictive models were trained and tested with a real-world data set. Finally, a specialized analytical web portal which offers collaborative performance monitoring and decision making is presented. The results show that these models give very accurate KPI projections and provide valuable insights into newly emerging trends, opportunities, and problems. This should lead to more intelligent, predictive, and responsive supply chains capable of adapting to future business environment.

  5. On readout of vibrational qubits using quantum beats

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

    Shyshlov, Dmytro; Babikov, Dmitri, E-mail: Dmitri.Babikov@mu.edu; Berrios, Eduardo

    2014-12-14

    Readout of the final states of qubits is a crucial step towards implementing quantum computation in experiment. Although not scalable to large numbers of qubits per molecule, computational studies show that molecular vibrations could provide a significant (factor 2–5 in the literature) increase in the number of qubits compared to two-level systems. In this theoretical work, we explore the process of readout from vibrational qubits in thiophosgene molecule, SCCl{sub 2}, using quantum beat oscillations. The quantum beats are measured by first exciting the superposition of the qubit-encoding vibrational states to the electronically excited readout state with variable time-delay pulses. Themore » resulting oscillation of population of the readout state is then detected as a function of time delay. In principle, fitting the quantum beat signal by an analytical expression should allow extracting the values of probability amplitudes and the relative phases of the vibrational qubit states. However, we found that if this procedure is implemented using the standard analytic expression for quantum beats, a non-negligible phase error is obtained. We discuss the origin and properties of this phase error, and propose a new analytical expression to correct the phase error. The corrected expression fits the quantum beat signal very accurately, which may permit reading out the final state of vibrational qubits in experiments by combining the analytic fitting expression with numerical modelling of the readout process. The new expression is also useful as a simple model for fitting any quantum beat experiments where more accurate phase information is desired.« less

  6. Hybrid experimental/analytical models of structural dynamics - Creation and use for predictions

    NASA Technical Reports Server (NTRS)

    Balmes, Etienne

    1993-01-01

    An original complete methodology for the construction of predictive models of damped structural vibrations is introduced. A consistent definition of normal and complex modes is given which leads to an original method to accurately identify non-proportionally damped normal mode models. A new method to create predictive hybrid experimental/analytical models of damped structures is introduced, and the ability of hybrid models to predict the response to system configuration changes is discussed. Finally a critical review of the overall methodology is made by application to the case of the MIT/SERC interferometer testbed.

  7. AN ANALYTIC RADIATIVE-CONVECTIVE MODEL FOR PLANETARY ATMOSPHERES

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

    Robinson, Tyler D.; Catling, David C., E-mail: robinson@astro.washington.edu

    2012-09-20

    We present an analytic one-dimensional radiative-convective model of the thermal structure of planetary atmospheres. Our model assumes that thermal radiative transfer is gray and can be represented by the two-stream approximation. Model atmospheres are assumed to be in hydrostatic equilibrium, with a power-law scaling between the atmospheric pressure and the gray thermal optical depth. The convective portions of our models are taken to follow adiabats that account for condensation of volatiles through a scaling parameter to the dry adiabat. By combining these assumptions, we produce simple, analytic expressions that allow calculations of the atmospheric-pressure-temperature profile, as well as expressions formore » the profiles of thermal radiative flux and convective flux. We explore the general behaviors of our model. These investigations encompass (1) worlds where atmospheric attenuation of sunlight is weak, which we show tend to have relatively high radiative-convective boundaries; (2) worlds with some attenuation of sunlight throughout the atmosphere, which we show can produce either shallow or deep radiative-convective boundaries, depending on the strength of sunlight attenuation; and (3) strongly irradiated giant planets (including hot Jupiters), where we explore the conditions under which these worlds acquire detached convective regions in their mid-tropospheres. Finally, we validate our model and demonstrate its utility through comparisons to the average observed thermal structure of Venus, Jupiter, and Titan, and by comparing computed flux profiles to more complex models.« less

  8. Two-dimensional analytical model of double-gate tunnel FETs with interface trapped charges including effects of channel mobile charge carriers

    NASA Astrophysics Data System (ADS)

    Xu, Huifang; Dai, Yuehua

    2017-02-01

    A two-dimensional analytical model of double-gate (DG) tunneling field-effect transistors (TFETs) with interface trapped charges is proposed in this paper. The influence of the channel mobile charges on the potential profile is also taken into account in order to improve the accuracy of the models. On the basis of potential profile, the electric field is derived and the expression for the drain current is obtained by integrating the BTBT generation rate. The model can be used to study the impact of interface trapped charges on the surface potential, the shortest tunneling length, the drain current and the threshold voltage for varying interface trapped charge densities, length of damaged region as well as the structural parameters of the DG TFET and can also be utilized to design the charge trapped memory devices based on TFET. The biggest advantage of this model is that it is more accurate, and in its expression there are no fitting parameters with small calculating amount. Very good agreements for both the potential, drain current and threshold voltage are observed between the model calculations and the simulated results. Project supported by the National Natural Science Foundation of China (No. 61376106), the University Natural Science Research Key Project of Anhui Province (No. KJ2016A169), and the Introduced Talents Project of Anhui Science and Technology University.

  9. Analytic descriptions of cylindrical electromagnetic waves in a nonlinear medium

    PubMed Central

    Xiong, Hao; Si, Liu-Gang; Yang, Xiaoxue; Wu, Ying

    2015-01-01

    A simple but highly efficient approach for dealing with the problem of cylindrical electromagnetic waves propagation in a nonlinear medium is proposed based on an exact solution proposed recently. We derive an analytical explicit formula, which exhibiting rich interesting nonlinear effects, to describe the propagation of any amount of cylindrical electromagnetic waves in a nonlinear medium. The results obtained by using the present method are accurately concordant with the results of using traditional coupled-wave equations. As an example of application, we discuss how a third wave affects the sum- and difference-frequency generation of two waves propagation in the nonlinear medium. PMID:26073066

  10. A results-based process for evaluation of diverse visual analytics tools

    NASA Astrophysics Data System (ADS)

    Rubin, Gary; Berger, David H.

    2013-05-01

    With the pervasiveness of still and full-motion imagery in commercial and military applications, the need to ingest and analyze these media has grown rapidly in recent years. Additionally, video hosting and live camera websites provide a near real-time view of our changing world with unprecedented spatial coverage. To take advantage of these controlled and crowd-sourced opportunities, sophisticated visual analytics (VA) tools are required to accurately and efficiently convert raw imagery into usable information. Whether investing in VA products or evaluating algorithms for potential development, it is important for stakeholders to understand the capabilities and limitations of visual analytics tools. Visual analytics algorithms are being applied to problems related to Intelligence, Surveillance, and Reconnaissance (ISR), facility security, and public safety monitoring, to name a few. The diversity of requirements means that a onesize- fits-all approach to performance assessment will not work. We present a process for evaluating the efficacy of algorithms in real-world conditions, thereby allowing users and developers of video analytics software to understand software capabilities and identify potential shortcomings. The results-based approach described in this paper uses an analysis of end-user requirements and Concept of Operations (CONOPS) to define Measures of Effectiveness (MOEs), test data requirements, and evaluation strategies. We define metrics that individually do not fully characterize a system, but when used together, are a powerful way to reveal both strengths and weaknesses. We provide examples of data products, such as heatmaps, performance maps, detection timelines, and rank-based probability-of-detection curves.

  11. Addressing the Analytic Challenges of Cross-Sectional Pediatric Pneumonia Etiology Data

    PubMed Central

    Feikin, Daniel R.; Scott, J. Anthony G.; Zeger, Scott L.; Murdoch, David R.; O’Brien, Katherine L.; Deloria Knoll, Maria

    2017-01-01

    Abstract Despite tremendous advances in diagnostic laboratory technology, identifying the pathogen(s) causing pneumonia remains challenging because the infected lung tissue cannot usually be sampled for testing. Consequently, to obtain information about pneumonia etiology, clinicians and researchers test specimens distant to the site of infection. These tests may lack sensitivity (eg, blood culture, which is only positive in a small proportion of children with pneumonia) and/or specificity (eg, detection of pathogens in upper respiratory tract specimens, which may indicate asymptomatic carriage or a less severe syndrome, such as upper respiratory infection). While highly sensitive nucleic acid detection methods and testing of multiple specimens improve sensitivity, multiple pathogens are often detected and this adds complexity to the interpretation as the etiologic significance of results may be unclear (ie, the pneumonia may be caused by none, one, some, or all of the pathogens detected). Some of these challenges can be addressed by adjusting positivity rates to account for poor sensitivity or incorporating test results from controls without pneumonia to account for poor specificity. However, no classical analytic methods can account for measurement error (ie, sensitivity and specificity) for multiple specimen types and integrate the results of measurements for multiple pathogens to produce an accurate understanding of etiology. We describe the major analytic challenges in determining pneumonia etiology and review how the common analytical approaches (eg, descriptive, case-control, attributable fraction, latent class analysis) address some but not all challenges. We demonstrate how these limitations necessitate a new, integrated analytical approach to pneumonia etiology data. PMID:28575372

  12. An accurate metric for the spacetime around rotating neutron stars

    NASA Astrophysics Data System (ADS)

    Pappas, George

    2017-04-01

    The problem of having an accurate description of the spacetime around rotating neutron stars is of great astrophysical interest. For astrophysical applications, one needs to have a metric that captures all the properties of the spacetime around a rotating neutron star. Furthermore, an accurate appropriately parametrized metric, I.e. a metric that is given in terms of parameters that are directly related to the physical structure of the neutron star, could be used to solve the inverse problem, which is to infer the properties of the structure of a neutron star from astrophysical observations. In this work, we present such an approximate stationary and axisymmetric metric for the exterior of rotating neutron stars, which is constructed using the Ernst formalism and is parametrized by the relativistic multipole moments of the central object. This metric is given in terms of an expansion on the Weyl-Papapetrou coordinates with the multipole moments as free parameters and is shown to be extremely accurate in capturing the physical properties of a neutron star spacetime as they are calculated numerically in general relativity. Because the metric is given in terms of an expansion, the expressions are much simpler and easier to implement, in contrast to previous approaches. For the parametrization of the metric in general relativity, the recently discovered universal 3-hair relations are used to produce a three-parameter metric. Finally, a straightforward extension of this metric is given for scalar-tensor theories with a massless scalar field, which also admit a formulation in terms of an Ernst potential.

  13. Evaluation of the availability of bound analyte for passive sampling in the presence of mobile binding matrix.

    PubMed

    Xu, Jianqiao; Huang, Shuyao; Jiang, Ruifen; Cui, Shufen; Luan, Tiangang; Chen, Guosheng; Qiu, Junlang; Cao, Chenyang; Zhu, Fang; Ouyang, Gangfeng

    2016-04-21

    Elucidating the availability of the bound analytes for the mass transfer through the diffusion boundary layers (DBLs) adjacent to passive samplers is important for understanding the passive sampling kinetics in complex samples, in which the lability factor of the bound analyte in the DBL is an important parameter. In this study, the mathematical expression of lability factor was deduced by assuming a pseudo-steady state during passive sampling, and the equation indicated that the lability factor was equal to the ratio of normalized concentration gradients between the bound and free analytes. Through the introduction of the mathematical expression of lability factor, the modified effective average diffusion coefficient was proven to be more suitable for describing the passive sampling kinetics in the presence of mobile binding matrixes. Thereafter, the lability factors of the bound polycyclic aromatic hydrocarbons (PAHs) with sodium dodecylsulphate (SDS) micelles as the binding matrixes were figured out according to the improved theory. The lability factors were observed to decrease with larger binding ratios and smaller micelle sizes, and were successfully used to predict the mass transfer efficiencies of PAHs through DBLs. This study would promote the understanding of the availability of bound analytes for passive sampling based on the theoretical improvements and experimental assessments. Copyright © 2016 Elsevier B.V. All rights reserved.

  14. Investigation of the "true" extraction recovery of analytes from multiple types of tissues and its impact on tissue bioanalysis using two model compounds.

    PubMed

    Yuan, Long; Ma, Li; Dillon, Lisa; Fancher, R Marcus; Sun, Huadong; Zhu, Mingshe; Lehman-McKeeman, Lois; Aubry, Anne-Françoise; Ji, Qin C

    2016-11-16

    LC-MS/MS has been widely applied to the quantitative analysis of tissue samples. However, one key remaining issue is that the extraction recovery of analyte from spiked tissue calibration standard and quality control samples (QCs) may not accurately represent the "true" recovery of analyte from incurred tissue samples. This may affect the accuracy of LC-MS/MS tissue bioanalysis. Here, we investigated whether the recovery determined using tissue QCs by LC-MS/MS can accurately represent the "true" recovery from incurred tissue samples using two model compounds: BMS-986104, a S1P 1 receptor modulator drug candidate, and its phosphate metabolite, BMS-986104-P. We first developed a novel acid and surfactant assisted protein precipitation method for the extraction of BMS-986104 and BMS-986104-P from rat tissues, and determined their recoveries using tissue QCs by LC-MS/MS. We then used radioactive incurred samples from rats dosed with 3 H-labeled BMS-986104 to determine the absolute total radioactivity recovery in six different tissues. The recoveries determined using tissue QCs and incurred samples matched with each other very well. The results demonstrated that, in this assay, tissue QCs accurately represented the incurred tissue samples to determine the "true" recovery, and LC-MS/MS assay was accurate for tissue bioanalysis. Another aspect we investigated is how the tissue QCs should be prepared to better represent the incurred tissue samples. We compared two different QC preparation methods (analyte spiked in tissue homogenates or in intact tissues) and demonstrated that the two methods had no significant difference when a good sample preparation was in place. The developed assay showed excellent accuracy and precision, and was successfully applied to the quantitative determination of BMS-986104 and BMS-986104-P in tissues in a rat toxicology study. Copyright © 2016 Elsevier B.V. All rights reserved.

  15. Semi-analytical solution for the generalized absorbing boundary condition in molecular dynamics simulations

    NASA Astrophysics Data System (ADS)

    Lee, Chung-Shuo; Chen, Yan-Yu; Yu, Chi-Hua; Hsu, Yu-Chuan; Chen, Chuin-Shan

    2017-07-01

    We present a semi-analytical solution of a time-history kernel for the generalized absorbing boundary condition in molecular dynamics (MD) simulations. To facilitate the kernel derivation, the concept of virtual atoms in real space that can conform with an arbitrary boundary in an arbitrary lattice is adopted. The generalized Langevin equation is regularized using eigenvalue decomposition and, consequently, an analytical expression of an inverse Laplace transform is obtained. With construction of dynamical matrices in the virtual domain, a semi-analytical form of the time-history kernel functions for an arbitrary boundary in an arbitrary lattice can be found. The time-history kernel functions for different crystal lattices are derived to show the generality of the proposed method. Non-equilibrium MD simulations in a triangular lattice with and without the absorbing boundary condition are conducted to demonstrate the validity of the solution.

  16. The areal reduction factor: A new analytical expression for the Lazio Region in central Italy

    NASA Astrophysics Data System (ADS)

    Mineo, C.; Ridolfi, E.; Napolitano, F.; Russo, F.

    2018-05-01

    For the study and modeling of hydrological phenomena, both in urban and rural areas, a proper estimation of the areal reduction factor (ARF) is crucial. In this paper, we estimated the ARF from observed rainfall data as the ratio between the average rainfall occurring in a specific area and the point rainfall. Then, we compared the obtained ARF values with some of the most widespread empirical approaches in literature which are used when rainfall observations are not available. Results highlight that the literature formulations can lead to a substantial over- or underestimation of the ARF estimated from observed data. These findings can have severe consequences, especially in the design of hydraulic structures where empirical formulations are extensively applied. The aim of this paper is to present a new analytical relationship with an explicit dependence on the rainfall duration and area that can better represent the ARF-area trend over the area case of study. The analytical curve presented here can find an important application to estimate the ARF values for design purposes. The test study area is the Lazio Region (central Italy).

  17. BIOACCESSIBILITY TESTS ACCURATELY ESTIMATE ...

    EPA Pesticide Factsheets

    Hazards of soil-borne Pb to wild birds may be more accurately quantified if the bioavailability of that Pb is known. To better understand the bioavailability of Pb to birds, we measured blood Pb concentrations in Japanese quail (Coturnix japonica) fed diets containing Pb-contaminated soils. Relative bioavailabilities were expressed by comparison with blood Pb concentrations in quail fed a Pb acetate reference diet. Diets containing soil from five Pb-contaminated Superfund sites had relative bioavailabilities from 33%-63%, with a mean of about 50%. Treatment of two of the soils with P significantly reduced the bioavailability of Pb. The bioaccessibility of the Pb in the test soils was then measured in six in vitro tests and regressed on bioavailability. They were: the “Relative Bioavailability Leaching Procedure” (RBALP) at pH 1.5, the same test conducted at pH 2.5, the “Ohio State University In vitro Gastrointestinal” method (OSU IVG), the “Urban Soil Bioaccessible Lead Test”, the modified “Physiologically Based Extraction Test” and the “Waterfowl Physiologically Based Extraction Test.” All regressions had positive slopes. Based on criteria of slope and coefficient of determination, the RBALP pH 2.5 and OSU IVG tests performed very well. Speciation by X-ray absorption spectroscopy demonstrated that, on average, most of the Pb in the sampled soils was sorbed to minerals (30%), bound to organic matter 24%, or present as Pb sulfate 18%. Ad

  18. Analytical model for the radio-frequency sheath

    NASA Astrophysics Data System (ADS)

    Czarnetzki, Uwe

    2013-12-01

    A simple analytical model for the planar radio-frequency (rf) sheath in capacitive discharges is developed that is based on the assumptions of a step profile for the electron front, charge exchange collisions with constant cross sections, negligible ionization within the sheath, and negligible ion dynamics. The continuity, momentum conservation, and Poisson equations are combined in a single integro-differential equation for the square of the ion drift velocity, the so called sheath equation. Starting from the kinetic Boltzmann equation, special attention is paid to the derivation and the validity of the approximate fluid equation for momentum balance. The integrals in the sheath equation appear in the screening function which considers the relative contribution of the temporal mean of the electron density to the space charge in the sheath. It is shown that the screening function is quite insensitive to variations of the effective sheath parameters. The two parameters defining the solution are the ratios of the maximum sheath extension to the ion mean free path and the Debye length, respectively. A simple general analytic expression for the screening function is introduced. By means of this expression approximate analytical solutions are obtained for the collisionless as well as the highly collisional case that compare well with the exact numerical solution. A simple transition formula allows application to all degrees of collisionality. In addition, the solutions are used to calculate all static and dynamic quantities of the sheath, e.g., the ion density, fields, and currents. Further, the rf Child-Langmuir laws for the collisionless as well as the collisional case are derived. An essential part of the model is the a priori knowledge of the wave form of the sheath voltage. This wave form is derived on the basis of a cubic charge-voltage relation for individual sheaths, considering both sheaths and the self-consistent self-bias in a discharge with arbitrary

  19. Analytical model for the radio-frequency sheath.

    PubMed

    Czarnetzki, Uwe

    2013-12-01

    A simple analytical model for the planar radio-frequency (rf) sheath in capacitive discharges is developed that is based on the assumptions of a step profile for the electron front, charge exchange collisions with constant cross sections, negligible ionization within the sheath, and negligible ion dynamics. The continuity, momentum conservation, and Poisson equations are combined in a single integro-differential equation for the square of the ion drift velocity, the so called sheath equation. Starting from the kinetic Boltzmann equation, special attention is paid to the derivation and the validity of the approximate fluid equation for momentum balance. The integrals in the sheath equation appear in the screening function which considers the relative contribution of the temporal mean of the electron density to the space charge in the sheath. It is shown that the screening function is quite insensitive to variations of the effective sheath parameters. The two parameters defining the solution are the ratios of the maximum sheath extension to the ion mean free path and the Debye length, respectively. A simple general analytic expression for the screening function is introduced. By means of this expression approximate analytical solutions are obtained for the collisionless as well as the highly collisional case that compare well with the exact numerical solution. A simple transition formula allows application to all degrees of collisionality. In addition, the solutions are used to calculate all static and dynamic quantities of the sheath, e.g., the ion density, fields, and currents. Further, the rf Child-Langmuir laws for the collisionless as well as the collisional case are derived. An essential part of the model is the a priori knowledge of the wave form of the sheath voltage. This wave form is derived on the basis of a cubic charge-voltage relation for individual sheaths, considering both sheaths and the self-consistent self-bias in a discharge with arbitrary

  20. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate... indispensable in examinations conducted within the Department of Veterans Affairs. Muscle atrophy must also be...

  1. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate... indispensable in examinations conducted within the Department of Veterans Affairs. Muscle atrophy must also be...

  2. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate... indispensable in examinations conducted within the Department of Veterans Affairs. Muscle atrophy must also be...

  3. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate... indispensable in examinations conducted within the Department of Veterans Affairs. Muscle atrophy must also be...

  4. 38 CFR 4.46 - Accurate measurement.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... RATING DISABILITIES Disability Ratings The Musculoskeletal System § 4.46 Accurate measurement. Accurate... indispensable in examinations conducted within the Department of Veterans Affairs. Muscle atrophy must also be...

  5. Feedback about More Accurate versus Less Accurate Trials: Differential Effects on Self-Confidence and Activation

    ERIC Educational Resources Information Center

    Badami, Rokhsareh; VaezMousavi, Mohammad; Wulf, Gabriele; Namazizadeh, Mahdi

    2012-01-01

    One purpose of the present study was to examine whether self-confidence or anxiety would be differentially affected by feedback from more accurate rather than less accurate trials. The second purpose was to determine whether arousal variations (activation) would predict performance. On Day 1, participants performed a golf putting task under one of…

  6. Quality Assurance of RNA Expression Profiling in Clinical Laboratories

    PubMed Central

    Tang, Weihua; Hu, Zhiyuan; Muallem, Hind; Gulley, Margaret L.

    2012-01-01

    RNA expression profiles are increasingly used to diagnose and classify disease, based on expression patterns of as many as several thousand RNAs. To ensure quality of expression profiling services in clinical settings, a standard operating procedure incorporates multiple quality indicators and controls, beginning with preanalytic specimen preparation and proceeding thorough analysis, interpretation, and reporting. Before testing, histopathological examination of each cellular specimen, along with optional cell enrichment procedures, ensures adequacy of the input tissue. Other tactics include endogenous controls to evaluate adequacy of RNA and exogenous or spiked controls to evaluate run- and patient-specific performance of the test system, respectively. Unique aspects of quality assurance for array-based tests include controls for the pertinent outcome signatures that often supersede controls for each individual analyte, built-in redundancy for critical analytes or biochemical pathways, and software-supported scrutiny of abundant data by a laboratory physician who interprets the findings in a manner facilitating appropriate medical intervention. Access to high-quality reagents, instruments, and software from commercial sources promotes standardization and adoption in clinical settings, once an assay is vetted in validation studies as being analytically sound and clinically useful. Careful attention to the well-honed principles of laboratory medicine, along with guidance from government and professional groups on strategies to preserve RNA and manage large data sets, promotes clinical-grade assay performance. PMID:22020152

  7. Analytical ground state for the Jaynes-Cummings model with ultrastrong coupling

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

    Zhang Yuanwei; Institute of Theoretical Physics, Shanxi University, Taiyuan 030006; Chen Gang

    2011-06-15

    We present a generalized variational method to analytically obtain the ground-state properties of the Jaynes-Cummings model with the ultrastrong coupling. An explicit expression for the ground-state energy, which agrees well with the numerical simulation in a wide range of the experimental parameters, is given. In particular, the introduced method can successfully solve this Jaynes-Cummings model with the positive detuning (the atomic resonant level is larger than the photon frequency), which cannot be treated in the adiabatical approximation and the generalized rotating-wave approximation. Finally, we also demonstrate analytically how to control the mean photon number by means of the current experimentalmore » parameters including the photon frequency, the coupling strength, and especially the atomic resonant level.« less

  8. Post-analytical stability of 23 common chemistry and immunochemistry analytes in incurred samples.

    PubMed

    Nielsen, Betina Klint; Frederiksen, Tina; Friis-Hansen, Lennart; Larsen, Pia Bükmann

    2017-12-01

    Storage of blood samples after centrifugation, decapping and initial sampling allows ordering of additional blood tests. The pre-analytic stability of biochemistry and immunochemistry analytes has been studied in detail, but little is known about the post-analytical stability in incurred samples. We examined the stability of 23 routine analytes on the Dimension Vista® (Siemens Healthineers, Denmark): 42-60 routine samples in lithium-heparin gel tubes (Vacutainer, BD, USA) were centrifuged at 3000×g for 10min. Immediately after centrifugation, initial concentration of analytes were measured in duplicate (t=0). The tubes were stored decapped at room temperature and re-analyzed after 2, 4, 6, 8 and 10h in singletons. The concentration from reanalysis were normalized to initial concentration (t=0). Internal acceptance criteria for bias and total error were used to determine stability of each analyte. Additionally, evaporation from the decapped blood collection tubes and the residual platelet count in the plasma after centrifugation were quantified. We report a post-analytical stability of most routine analytes of ≥8h and do therefore - with few exceptions - suggest a standard 8hour-time limit for reordering and reanalysis of analytes in incurred samples. Copyright © 2017 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

  9. Identification of chemical modulators of the constitutive activated receptor (CAR) in a gene expression compendium

    PubMed Central

    Oshida, Keiyu; Vasani, Naresh; Jones, Carlton; Moore, Tanya; Hester, Susan; Nesnow, Stephen; Auerbach, Scott; Geter, David R.; Aleksunes, Lauren M.; Thomas, Russell S.; Applegate, Dawn; Klaassen, Curtis D.; Corton, J. Christopher

    2015-01-01

    inflammation including acetaminophen, concanavalin A, lipopolysaccharide, and 300 nm silica particles. In conclusion, we have shown that a CAR biomarker signature coupled with a rank-based similarity method accurately predicts CAR activation. This analytical approach, when applied to a gene expression compendium, increased the universe of known chemicals that directly or indirectly activate CAR, highlighting the promiscuous nature of CAR activation and signaling through activation of other xenobiotic-activated receptors. PMID:25949234

  10. A Semi-Analytical Solution to Time Dependent Groundwater Flow Equation Incorporating Stream-Wetland-Aquifer Interactions

    NASA Astrophysics Data System (ADS)

    Boyraz, Uǧur; Melek Kazezyılmaz-Alhan, Cevza

    2017-04-01

    Groundwater is a vital element of hydrologic cycle and the analytical & numerical solutions of different forms of groundwater flow equations play an important role in understanding the hydrological behavior of subsurface water. The interaction between groundwater and surface water bodies can be determined using these solutions. In this study, new hypothetical approaches are implemented to groundwater flow system in order to contribute to the studies on surface water/groundwater interactions. A time dependent problem is considered in a 2-dimensional stream-wetland-aquifer system. The sloped stream boundary is used to represent the interaction between stream and aquifer. The rest of the aquifer boundaries are assumed as no-flux boundary. In addition, a wetland is considered as a surface water body which lies over the whole aquifer. The effect of the interaction between the wetland and the aquifer is taken into account with a source/sink term in the groundwater flow equation and the interaction flow is calculated by using Darcy's approach. A semi-analytical solution is developed for the 2-dimensional groundwater flow equation in 5 steps. First, Laplace and Fourier cosine transforms are employed to obtain the general solution in Fourier and Laplace domain. Then, the initial and boundary conditions are applied to obtain the particular solution. Finally, inverse Fourier transform is carried out analytically and inverse Laplace transform is carried out numerically to obtain the final solution in space and time domain, respectively. In order to verify the semi-analytical solution, an explicit finite difference algorithm is developed and analytical and numerical solutions are compared for synthetic examples. The comparison of the analytical and numerical solutions shows that the analytical solution gives accurate results.

  11. Compensation method for obtaining accurate, sub-micrometer displacement measurements of immersed specimens using electronic speckle interferometry.

    PubMed

    Fazio, Massimo A; Bruno, Luigi; Reynaud, Juan F; Poggialini, Andrea; Downs, J Crawford

    2012-03-01

    We proposed and validated a compensation method that accounts for the optical distortion inherent in measuring displacements on specimens immersed in aqueous solution. A spherically-shaped rubber specimen was mounted and pressurized on a custom apparatus, with the resulting surface displacements recorded using electronic speckle pattern interferometry (ESPI). Point-to-point light direction computation is achieved by a ray-tracing strategy coupled with customized B-spline-based analytical representation of the specimen shape. The compensation method reduced the mean magnitude of the displacement error induced by the optical distortion from 35% to 3%, and ESPI displacement measurement repeatability showed a mean variance of 16 nm at the 95% confidence level for immersed specimens. The ESPI interferometer and numerical data analysis procedure presented herein provide reliable, accurate, and repeatable measurement of sub-micrometer deformations obtained from pressurization tests of spherically-shaped specimens immersed in aqueous salt solution. This method can be used to quantify small deformations in biological tissue samples under load, while maintaining the hydration necessary to ensure accurate material property assessment.

  12. Efficient statistically accurate algorithms for the Fokker-Planck equation in large dimensions

    NASA Astrophysics Data System (ADS)

    Chen, Nan; Majda, Andrew J.

    2018-02-01

    Solving the Fokker-Planck equation for high-dimensional complex turbulent dynamical systems is an important and practical issue. However, most traditional methods suffer from the curse of dimensionality and have difficulties in capturing the fat tailed highly intermittent probability density functions (PDFs) of complex systems in turbulence, neuroscience and excitable media. In this article, efficient statistically accurate algorithms are developed for solving both the transient and the equilibrium solutions of Fokker-Planck equations associated with high-dimensional nonlinear turbulent dynamical systems with conditional Gaussian structures. The algorithms involve a hybrid strategy that requires only a small number of ensembles. Here, a conditional Gaussian mixture in a high-dimensional subspace via an extremely efficient parametric method is combined with a judicious non-parametric Gaussian kernel density estimation in the remaining low-dimensional subspace. Particularly, the parametric method provides closed analytical formulae for determining the conditional Gaussian distributions in the high-dimensional subspace and is therefore computationally efficient and accurate. The full non-Gaussian PDF of the system is then given by a Gaussian mixture. Different from traditional particle methods, each conditional Gaussian distribution here covers a significant portion of the high-dimensional PDF. Therefore a small number of ensembles is sufficient to recover the full PDF, which overcomes the curse of dimensionality. Notably, the mixture distribution has significant skill in capturing the transient behavior with fat tails of the high-dimensional non-Gaussian PDFs, and this facilitates the algorithms in accurately describing the intermittency and extreme events in complex turbulent systems. It is shown in a stringent set of test problems that the method only requires an order of O (100) ensembles to successfully recover the highly non-Gaussian transient PDFs in up to 6

  13. Efficient Statistically Accurate Algorithms for the Fokker-Planck Equation in Large Dimensions

    NASA Astrophysics Data System (ADS)

    Chen, N.; Majda, A.

    2017-12-01

    Solving the Fokker-Planck equation for high-dimensional complex turbulent dynamical systems is an important and practical issue. However, most traditional methods suffer from the curse of dimensionality and have difficulties in capturing the fat tailed highly intermittent probability density functions (PDFs) of complex systems in turbulence, neuroscience and excitable media. In this article, efficient statistically accurate algorithms are developed for solving both the transient and the equilibrium solutions of Fokker-Planck equations associated with high-dimensional nonlinear turbulent dynamical systems with conditional Gaussian structures. The algorithms involve a hybrid strategy that requires only a small number of ensembles. Here, a conditional Gaussian mixture in a high-dimensional subspace via an extremely efficient parametric method is combined with a judicious non-parametric Gaussian kernel density estimation in the remaining low-dimensional subspace. Particularly, the parametric method, which is based on an effective data assimilation framework, provides closed analytical formulae for determining the conditional Gaussian distributions in the high-dimensional subspace. Therefore, it is computationally efficient and accurate. The full non-Gaussian PDF of the system is then given by a Gaussian mixture. Different from the traditional particle methods, each conditional Gaussian distribution here covers a significant portion of the high-dimensional PDF. Therefore a small number of ensembles is sufficient to recover the full PDF, which overcomes the curse of dimensionality. Notably, the mixture distribution has a significant skill in capturing the transient behavior with fat tails of the high-dimensional non-Gaussian PDFs, and this facilitates the algorithms in accurately describing the intermittency and extreme events in complex turbulent systems. It is shown in a stringent set of test problems that the method only requires an order of O(100) ensembles to

  14. Clustering in analytical chemistry.

    PubMed

    Drab, Klaudia; Daszykowski, Michal

    2014-01-01

    Data clustering plays an important role in the exploratory analysis of analytical data, and the use of clustering methods has been acknowledged in different fields of science. In this paper, principles of data clustering are presented with a direct focus on clustering of analytical data. The role of the clustering process in the analytical workflow is underlined, and its potential impact on the analytical workflow is emphasized.

  15. Analytical Ferrography Standardization.

    DTIC Science & Technology

    1982-01-01

    AD-AII6 508 MECHANICAL TECHNOLOGY INC LATHAM NY RESEARCH AND 0EV--ETC F/6 7/4 ANALYTICAL FERROGRAPHY STANDARDIZATION. (U) JAN 82 P A SENHOLZI, A S...ii Mwl jutio7 Unimte SMechanical Technology Incorporated Research and Development Division ReerhadDvlpetDvso I FINAL REPORT ANALYTICAL FERROGRAPHY ...Final Report MTI Technical Report No. 82TRS6 ANALYTICAL FERROGRAPHY STANDARDIZATION P. B. Senholzi A. S. Maciejewski Applications Engineering Mechanical

  16. Steady-state protein focusing in carrier ampholyte based isoelectric focusing: Part I-Analytical solution.

    PubMed

    Shim, Jaesool; Yoo, Kisoo; Dutta, Prashanta

    2017-03-01

    The determination of an analytical solution to find the steady-state protein concentration distribution in IEF is very challenging due to the nonlinear coupling between mass and charge conservation equations. In this study, approximate analytical solutions are obtained for steady-state protein distribution in carrier ampholyte based IEF. Similar to the work of Svensson, the final concentration profile for proteins is assumed to be Gaussian, but appropriate expressions are presented in order to obtain the effective electric field and pH gradient in the focused protein band region. Analytical results are found from iterative solutions of a system of coupled algebraic equations using only several iterations for IEF separation of three plasma proteins: albumin, cardiac troponin I, and hemoglobin. The analytical results are compared with numerically predicted results for IEF, showing excellent agreement. Analytically obtained electric field and ionic conductivity distributions show significant deviation from their nominal values, which is essential in finding the protein focusing behavior at isoelectric points. These analytical solutions can be used to determine steady-state protein concentration distribution for experiment design of IEF considering any number of proteins and ampholytes. Moreover, the model presented herein can be used to find the conductivity, electric field, and pH field. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Influence of Analyte Concentration on Stability Constant Values Determined by Capillary Electrophoresis.

    PubMed

    Sursyakova, Viktoria V; Burmakina, Galina V; Rubaylo, Anatoly I

    2016-08-01

    The influence of analyte concentration when compared with the concentration of a charged ligand in background electrolyte (BGE) on the measured values of electrophoretic mobilities and stability constants (association, binding or formation constants) is studied using capillary electrophoresis (CE) and a dynamic mathematical simulator of CE. The study is performed using labile complexes (with fast kinetics) of iron (III) and 5-sulfosalicylate ions (ISC) as an example. It is shown that because the ligand concentration in the analyte zone is not equal to that in BGE, considerable changes in the migration times and electrophoretic mobilities are observed, resulting in systematic errors in the stability constant values. Of crucial significance is the slope of the dependence of the electrophoretic mobility decrease on the ligand equilibrium concentration. Without prior information on this dependence to accurately evaluate the stability constants for similar systems, the total ligand concentration must be at least >50-100 times higher than the total concentration of analyte. Experimental ISC peak fronting and the difference between the direction of the experimental pH dependence of the electrophoretic mobility decrease and the mathematical simulation allow assuming the presence of capillary wall interaction. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

  18. An analytic, approximate method for modeling steady, three-dimensional flow to partially penetrating wells

    NASA Astrophysics Data System (ADS)

    Bakker, Mark

    2001-05-01

    An analytic, approximate solution is derived for the modeling of three-dimensional flow to partially penetrating wells. The solution is written in terms of a correction on the solution for a fully penetrating well and is obtained by dividing the aquifer up, locally, in a number of aquifer layers. The resulting system of differential equations is solved by application of the theory for multiaquifer flow. The presented approach has three major benefits. First, the solution may be applied to any groundwater model that can simulate flow to a fully penetrating well; the solution may be superimposed onto the solution for the fully penetrating well to simulate the local three-dimensional drawdown and flow field. Second, the approach is applicable to isotropic, anisotropic, and stratified aquifers and to both confined and unconfined flow. Third, the solution extends over a small area around the well only; outside this area the three-dimensional effect of the partially penetrating well is negligible, and no correction to the fully penetrating well is needed. A number of comparisons are made to existing three-dimensional, analytic solutions, including radial confined and unconfined flow and a well in a uniform flow field. It is shown that a subdivision in three layers is accurate for many practical cases; very accurate solutions are obtained with more layers.

  19. Characterization of Compton-scatter imaging with an analytical simulation method

    PubMed Central

    Jones, Kevin C; Redler, Gage; Templeton, Alistair; Bernard, Damian; Turian, Julius V; Chu, James C H

    2018-01-01

    By collimating the photons scattered when a megavoltage therapy beam interacts with the patient, a Compton-scatter image may be formed without the delivery of an extra dose. To characterize and assess the potential of the technique, an analytical model for simulating scatter images was developed and validated against Monte Carlo (MC). For three phantoms, the scatter images collected during irradiation with a 6 MV flattening-filter-free therapy beam were simulated. Images, profiles, and spectra were compared for different phantoms and different irradiation angles. The proposed analytical method simulates accurate scatter images up to 1000 times faster than MC. Minor differences between MC and analytical simulated images are attributed to limitations in the isotropic superposition/convolution algorithm used to analytically model multiple-order scattering. For a detector placed at 90° relative to the treatment beam, the simulated scattered photon energy spectrum peaks at 140–220 keV, and 40–50% of the photons are the result of multiple scattering. The high energy photons originate at the beam entrance. Increasing the angle between source and detector increases the average energy of the collected photons and decreases the relative contribution of multiple scattered photons. Multiple scattered photons cause blurring in the image. For an ideal 5 mm diameter pinhole collimator placed 18.5 cm from the isocenter, 10 cGy of deposited dose (2 Hz imaging rate for 1200 MU min−1 treatment delivery) is expected to generate an average 1000 photons per mm2 at the detector. For the considered lung tumor CT phantom, the contrast is high enough to clearly identify the lung tumor in the scatter image. Increasing the treatment beam size perpendicular to the detector plane decreases the contrast, although the scatter subject contrast is expected to be greater than the megavoltage transmission image contrast. With the analytical method, real-time tumor tracking may be possible

  20. Characterization of Compton-scatter imaging with an analytical simulation method

    NASA Astrophysics Data System (ADS)

    Jones, Kevin C.; Redler, Gage; Templeton, Alistair; Bernard, Damian; Turian, Julius V.; Chu, James C. H.

    2018-01-01

    By collimating the photons scattered when a megavoltage therapy beam interacts with the patient, a Compton-scatter image may be formed without the delivery of an extra dose. To characterize and assess the potential of the technique, an analytical model for simulating scatter images was developed and validated against Monte Carlo (MC). For three phantoms, the scatter images collected during irradiation with a 6 MV flattening-filter-free therapy beam were simulated. Images, profiles, and spectra were compared for different phantoms and different irradiation angles. The proposed analytical method simulates accurate scatter images up to 1000 times faster than MC. Minor differences between MC and analytical simulated images are attributed to limitations in the isotropic superposition/convolution algorithm used to analytically model multiple-order scattering. For a detector placed at 90° relative to the treatment beam, the simulated scattered photon energy spectrum peaks at 140-220 keV, and 40-50% of the photons are the result of multiple scattering. The high energy photons originate at the beam entrance. Increasing the angle between source and detector increases the average energy of the collected photons and decreases the relative contribution of multiple scattered photons. Multiple scattered photons cause blurring in the image. For an ideal 5 mm diameter pinhole collimator placed 18.5 cm from the isocenter, 10 cGy of deposited dose (2 Hz imaging rate for 1200 MU min-1 treatment delivery) is expected to generate an average 1000 photons per mm2 at the detector. For the considered lung tumor CT phantom, the contrast is high enough to clearly identify the lung tumor in the scatter image. Increasing the treatment beam size perpendicular to the detector plane decreases the contrast, although the scatter subject contrast is expected to be greater than the megavoltage transmission image contrast. With the analytical method, real-time tumor tracking may be possible

  1. Exact analytical thermodynamic expressions for a Brownian heat engine

    NASA Astrophysics Data System (ADS)

    Taye, Mesfin Asfaw

    2015-09-01

    The nonequilibrium thermodynamics feature of a Brownian motor operating between two different heat baths is explored as a function of time t . Using the Gibbs entropy and Schnakenberg microscopic stochastic approach, we find exact closed form expressions for the free energy, the rate of entropy production, and the rate of entropy flow from the system to the outside. We show that when the system is out of equilibrium, it constantly produces entropy and at the same time extracts entropy out of the system. Its entropy production and extraction rates decrease in time and saturate to a constant value. In the long time limit, the rate of entropy production balances the rate of entropy extraction, and at equilibrium both entropy production and extraction rates become zero. Furthermore, via the present model, many thermodynamic theories can be checked.

  2. Exact analytical thermodynamic expressions for a Brownian heat engine.

    PubMed

    Taye, Mesfin Asfaw

    2015-09-01

    The nonequilibrium thermodynamics feature of a Brownian motor operating between two different heat baths is explored as a function of time t. Using the Gibbs entropy and Schnakenberg microscopic stochastic approach, we find exact closed form expressions for the free energy, the rate of entropy production, and the rate of entropy flow from the system to the outside. We show that when the system is out of equilibrium, it constantly produces entropy and at the same time extracts entropy out of the system. Its entropy production and extraction rates decrease in time and saturate to a constant value. In the long time limit, the rate of entropy production balances the rate of entropy extraction, and at equilibrium both entropy production and extraction rates become zero. Furthermore, via the present model, many thermodynamic theories can be checked.

  3. ODF Maxima Extraction in Spherical Harmonic Representation via Analytical Search Space Reduction

    PubMed Central

    Aganj, Iman; Lenglet, Christophe; Sapiro, Guillermo

    2015-01-01

    By revealing complex fiber structure through the orientation distribution function (ODF), q-ball imaging has recently become a popular reconstruction technique in diffusion-weighted MRI. In this paper, we propose an analytical dimension reduction approach to ODF maxima extraction. We show that by expressing the ODF, or any antipodally symmetric spherical function, in the common fourth order real and symmetric spherical harmonic basis, the maxima of the two-dimensional ODF lie on an analytically derived one-dimensional space, from which we can detect the ODF maxima. This method reduces the computational complexity of the maxima detection, without compromising the accuracy. We demonstrate the performance of our technique on both artificial and human brain data. PMID:20879302

  4. A Mathematica program for the approximate analytical solution to a nonlinear undamped Duffing equation by a new approximate approach

    NASA Astrophysics Data System (ADS)

    Wu, Dongmei; Wang, Zhongcheng

    2006-03-01

    , we present a new iteration algorithm to calculate the coefficients of the Fourier series. By using this new method, the iteration procedure starts with a(x)cos(ωx)+b(x)sin(ωx), and the accuracy may be improved gradually by determining new coefficients a,a,… will be produced automatically in an one-by-one manner. In all the stage of calculation, we need only to solve a cubic equation. Using this new algorithm, we develop a Mathematica program, which demonstrates following main advantages over the previous HB method: (1) it avoids solving a set of associate nonlinear equations; (2) it is easier to be implemented into a computer program, and produces a highly accurate solution with analytical expression efficiently. It is interesting to find that, generally, for a given set of parameters, a nonlinear Duffing equation can have three independent oscillation modes. For some sets of the parameters, it can have two modes with complex displacement and one with real displacement. But in some cases, it can have three modes, all of them having real displacement. Therefore, we can divide the parameters into two classes, according to the solution property: there is only one mode with real displacement and there are three modes with real displacement. This program should be useful to study the dynamically periodic behavior of a Duffing oscillator and can provide an approximate analytical solution with high-accuracy for testing the error behavior of newly developed numerical methods with a wide range of parameters. Program summaryTitle of program:AnalyDuffing.nb Catalogue identifier:ADWR_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADWR_v1_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Licensing provisions:none Computer for which the program is designed and others on which it has been tested:the program has been designed for a microcomputer and been tested on the microcomputer. Computers:IBM PC Installations:the address

  5. Analytical Solution for the Anisotropic Rabi Model: Effects of Counter-Rotating Terms

    NASA Astrophysics Data System (ADS)

    Zhang, Guofeng; Zhu, Hanjie

    2015-03-01

    The anisotropic Rabi model, which was proposed recently, differs from the original Rabi model: the rotating and counter-rotating terms are governed by two different coupling constants. This feature allows us to vary the counter-rotating interaction independently and explore the effects of it on some quantum properties. In this paper, we eliminate the counter-rotating terms approximately and obtain the analytical energy spectrums and wavefunctions. These analytical results agree well with the numerical calculations in a wide range of the parameters including the ultrastrong coupling regime. In the weak counter-rotating coupling limit we find out that the counter-rotating terms can be considered as the shifts to the parameters of the Jaynes-Cummings model. This modification shows the validness of the rotating-wave approximation on the assumption of near-resonance and relatively weak coupling. Moreover, the analytical expressions of several physics quantities are also derived, and the results show the break-down of the U(1)-symmetry and the deviation from the Jaynes-Cummings model.

  6. Analytical solution for the anisotropic Rabi model: effects of counter-rotating terms.

    PubMed

    Zhang, Guofeng; Zhu, Hanjie

    2015-03-04

    The anisotropic Rabi model, which was proposed recently, differs from the original Rabi model: the rotating and counter-rotating terms are governed by two different coupling constants. This feature allows us to vary the counter-rotating interaction independently and explore the effects of it on some quantum properties. In this paper, we eliminate the counter-rotating terms approximately and obtain the analytical energy spectrums and wavefunctions. These analytical results agree well with the numerical calculations in a wide range of the parameters including the ultrastrong coupling regime. In the weak counter-rotating coupling limit we find out that the counter-rotating terms can be considered as the shifts to the parameters of the Jaynes-Cummings model. This modification shows the validness of the rotating-wave approximation on the assumption of near-resonance and relatively weak coupling. Moreover, the analytical expressions of several physics quantities are also derived, and the results show the break-down of the U(1)-symmetry and the deviation from the Jaynes-Cummings model.

  7. Extended internal standard method for quantitative 1H NMR assisted by chromatography (EIC) for analyte overlapping impurity on 1H NMR spectra.

    PubMed

    Saito, Naoki; Kitamaki, Yuko; Otsuka, Satoko; Yamanaka, Noriko; Nishizaki, Yuzo; Sugimoto, Naoki; Imura, Hisanori; Ihara, Toshihide

    2018-07-01

    We devised a novel extended internal standard method of quantitative 1 H NMR (qNMR) assisted by chromatography (EIC) that accurately quantifies 1 H signal areas of analytes, even when the chemical shifts of the impurity and analyte signals overlap completely. When impurity and analyte signals overlap in the 1 H NMR spectrum but can be separated in a chromatogram, the response ratio of the impurity and an internal standard (IS) can be obtained from the chromatogram. If the response ratio can be converted into the 1 H signal area ratio of the impurity and the IS, the 1 H signal area of the analyte can be evaluated accurately by mathematically correcting the contributions of the 1 H signal area of the impurity overlapping the analyte in the 1 H NMR spectrum. In this study, gas chromatography and liquid chromatography were used. We used 2-chlorophenol and 4-chlorophenol containing phenol as an impurity as examples in which impurity and analyte signals overlap to validate and demonstrate the EIC, respectively. Because the 1 H signals of 2-chlorophenol and phenol can be separated in specific alkaline solutions, 2-chlorophenol is suitable to validate the EIC by comparing analytical value obtained by the EIC with that by only qNMR under the alkaline condition. By the EIC, the purity of 2-chlorophenol was obtained with a relative expanded uncertainty (k = 2) of 0.24%. The purity matched that obtained under the alkaline condition. Furthermore, the EIC was also validated by evaluating the phenol content with the absolute calibration curve method by gas chromatography. Finally, we demonstrated that the EIC was possible to evaluate the purity of 4-chlorophenol, with a relative expanded uncertainty (k = 2) of 0.22%, which was not able to be separated from the 1 H signal of phenol under any condition. Copyright © 2018 Elsevier B.V. All rights reserved.

  8. Analytical solutions of one-dimensional multispecies reactive transport in a permeable reactive barrier-aquifer system

    NASA Astrophysics Data System (ADS)

    Mieles, John; Zhan, Hongbin

    2012-06-01

    The permeable reactive barrier (PRB) remediation technology has proven to be more cost-effective than conventional pump-and-treat systems, and has demonstrated the ability to rapidly reduce the concentrations of specific chemicals of concern (COCs) by up to several orders of magnitude in some scenarios. This study derives new steady-state analytical solutions to multispecies reactive transport in a PRB-aquifer (dual domain) system. The advantage of the dual domain model is that it can account for the potential existence of natural degradation in the aquifer, when designing the required PRB thickness. The study focuses primarily on the steady-state analytical solutions of the tetrachloroethene (PCE) serial degradation pathway and secondly on the analytical solutions of the parallel degradation pathway. The solutions in this study can also be applied to other types of dual domain systems with distinct flow and transport properties. The steady-state analytical solutions are shown to be accurate and the numerical program RT3D is selected for comparison. The results of this study are novel in that the solutions provide improved modeling flexibility including: 1) every species can have unique first-order reaction rates and unique retardation factors, and 2) daughter species can be modeled with their individual input concentrations or solely as byproducts of the parent species. The steady-state analytical solutions exhibit a limitation that occurs when interspecies reaction rate factors equal each other, which result in undefined solutions. Excel spreadsheet programs were created to facilitate prompt application of the steady-state analytical solutions, for both the serial and parallel degradation pathways.

  9. Analytical model for fast reconnection in large guide field plasma configurations

    NASA Astrophysics Data System (ADS)

    Simakov, A. N.; Chacón, L.; Grasso, D.; Borgogno, D.; Zocco, A.

    2009-11-01

    Significant progress in understanding magnetic reconnection without a guide field was made recently by deriving quantitatively accurate analytical models for reconnection in electron [1] and Hall [2] MHD. However, no such analytical model is available for reconnection with a guide field. Here, we derive such an analytical model for the large-guide-field, low-β, cold-ion fluid model [3] with electron inertia, ion viscosity μ, and resistivity η. We find that the reconnection is Sweet-Parker-like when the Sweet-Parker layer thickness δSP> (ρs^4 + de^4)^1/4, with ρs and de the sound Larmor radius and electron inertial length. However, reconnection changes character otherwise, resulting in reconnection rates Ez/Bx^2 √2 η/μ (ρs^2 + de^2)/(ρsw) with Bx the upstream magnetic field and w the diffusion region length. Unlike the zero-guide-field case, μ plays crucial role in manifesting fast reconnection rates. If it represents the perpendicular viscosity [3], √η/μ ˜&-1circ;√(me/mi)(Ti/Te) and Ez becomes dissipation independent and therefore potentially fast.[0pt] [1] L. Chac'on, A. N. Simakov, and A. Zocco, PRL 99, 235001 (2007).[0pt] [2] A. N. Simakov and L. Chac'on, PRL 101, 105003 (2008).[0pt] [3] D. Biskamp, Magnetic reconnection in plasmas, Cambridge University Press, 2000.

  10. An efficient method for the calculation of mean extinction. I - The analyticity of the complex extinction efficiency of homogeneous spheres

    NASA Astrophysics Data System (ADS)

    Xing, Zhang-Fan; Greenberg, J. M.

    1992-11-01

    Results of an investigation of the analyticity of the complex extinction efficiency Q-tilde(ext) in different parameter domains are presented. In the size parameter domain, x = omega(a/c), numerical Hilbert transforms are used to study the analyticity properties of Q-tilde(ext) for homogeneous spheres. Q-tilde(ext) is found to be analytic in the entire lower complex x-tilde-plane when the refractive index, m, is fixed as a real constant (pure scattering) or infinity (perfect conductor); poles, however, appear in the left side of the lower complex x-tilde-plane as m becomes complex. The computation of the mean extinction produced by an extended size distribution of particles may be conveniently and accurately approximated using only a few values of the complex extinction evaluated in the complex plane.

  11. Hydraulic modeling of riverbank filtration systems with curved boundaries using analytic elements and series solutions

    NASA Astrophysics Data System (ADS)

    Bakker, Mark

    2010-08-01

    A new analytic solution approach is presented for the modeling of steady flow to pumping wells near rivers in strip aquifers; all boundaries of the river and strip aquifer may be curved. The river penetrates the aquifer only partially and has a leaky stream bed. The water level in the river may vary spatially. Flow in the aquifer below the river is semi-confined while flow in the aquifer adjacent to the river is confined or unconfined and may be subject to areal recharge. Analytic solutions are obtained through superposition of analytic elements and Fourier series. Boundary conditions are specified at collocation points along the boundaries. The number of collocation points is larger than the number of coefficients in the Fourier series and a solution is obtained in the least squares sense. The solution is analytic while boundary conditions are met approximately. Very accurate solutions are obtained when enough terms are used in the series. Several examples are presented for domains with straight and curved boundaries, including a well pumping near a meandering river with a varying water level. The area of the river bottom where water infiltrates into the aquifer is delineated and the fraction of river water in the well water is computed for several cases.

  12. Comprehensive identification and structural characterization of target components from Gelsemium elegans by high-performance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry based on accurate mass databases combined with MS/MS spectra.

    PubMed

    Liu, Yan-Chun; Xiao, Sa; Yang, Kun; Ling, Li; Sun, Zhi-Liang; Liu, Zhao-Ying

    2017-06-01

    This study reports an applicable analytical strategy of comprehensive identification and structure characterization of target components from Gelsemium elegans by using high-performance liquid chromatography quadrupole time-of-flight mass spectrometry (LC-QqTOF MS) based on the use of accurate mass databases combined with MS/MS spectra. The databases created included accurate masses and elemental compositions of 204 components from Gelsemium and their structural data. The accurate MS and MS/MS spectra were acquired through data-dependent auto MS/MS mode followed by an extraction of the potential compounds from the LC-QqTOF MS raw data of the sample. The same was matched using the databases to search for targeted components in the sample. The structures for detected components were tentatively characterized by manually interpreting the accurate MS/MS spectra for the first time. A total of 57 components have been successfully detected and structurally characterized from the crude extracts of G. elegans, but has failed to differentiate some isomers. This analytical strategy is generic and efficient, avoids isolation and purification procedures, enables a comprehensive structure characterization of target components of Gelsemium and would be widely applicable for complicated mixtures that are derived from Gelsemium preparations. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

  13. Gene Expression Ratios Lead to Accurate and Translatable Predictors of DR5 Agonism across Multiple Tumor Lineages.

    PubMed

    Reddy, Anupama; Growney, Joseph D; Wilson, Nick S; Emery, Caroline M; Johnson, Jennifer A; Ward, Rebecca; Monaco, Kelli A; Korn, Joshua; Monahan, John E; Stump, Mark D; Mapa, Felipa A; Wilson, Christopher J; Steiger, Janine; Ledell, Jebediah; Rickles, Richard J; Myer, Vic E; Ettenberg, Seth A; Schlegel, Robert; Sellers, William R; Huet, Heather A; Lehár, Joseph

    2015-01-01

    Death Receptor 5 (DR5) agonists demonstrate anti-tumor activity in preclinical models but have yet to demonstrate robust clinical responses. A key limitation may be the lack of patient selection strategies to identify those most likely to respond to treatment. To overcome this limitation, we screened a DR5 agonist Nanobody across >600 cell lines representing 21 tumor lineages and assessed molecular features associated with response. High expression of DR5 and Casp8 were significantly associated with sensitivity, but their expression thresholds were difficult to translate due to low dynamic ranges. To address the translational challenge of establishing thresholds of gene expression, we developed a classifier based on ratios of genes that predicted response across lineages. The ratio classifier outperformed the DR5+Casp8 classifier, as well as standard approaches for feature selection and classification using genes, instead of ratios. This classifier was independently validated using 11 primary patient-derived pancreatic xenograft models showing perfect predictions as well as a striking linearity between prediction probability and anti-tumor response. A network analysis of the genes in the ratio classifier captured important biological relationships mediating drug response, specifically identifying key positive and negative regulators of DR5 mediated apoptosis, including DR5, CASP8, BID, cFLIP, XIAP and PEA15. Importantly, the ratio classifier shows translatability across gene expression platforms (from Affymetrix microarrays to RNA-seq) and across model systems (in vitro to in vivo). Our approach of using gene expression ratios presents a robust and novel method for constructing translatable biomarkers of compound response, which can also probe the underlying biology of treatment response.

  14. Gene Expression Ratios Lead to Accurate and Translatable Predictors of DR5 Agonism across Multiple Tumor Lineages

    PubMed Central

    Reddy, Anupama; Growney, Joseph D.; Wilson, Nick S.; Emery, Caroline M.; Johnson, Jennifer A.; Ward, Rebecca; Monaco, Kelli A.; Korn, Joshua; Monahan, John E.; Stump, Mark D.; Mapa, Felipa A.; Wilson, Christopher J.; Steiger, Janine; Ledell, Jebediah; Rickles, Richard J.; Myer, Vic E.; Ettenberg, Seth A.; Schlegel, Robert; Sellers, William R.

    2015-01-01

    Death Receptor 5 (DR5) agonists demonstrate anti-tumor activity in preclinical models but have yet to demonstrate robust clinical responses. A key limitation may be the lack of patient selection strategies to identify those most likely to respond to treatment. To overcome this limitation, we screened a DR5 agonist Nanobody across >600 cell lines representing 21 tumor lineages and assessed molecular features associated with response. High expression of DR5 and Casp8 were significantly associated with sensitivity, but their expression thresholds were difficult to translate due to low dynamic ranges. To address the translational challenge of establishing thresholds of gene expression, we developed a classifier based on ratios of genes that predicted response across lineages. The ratio classifier outperformed the DR5+Casp8 classifier, as well as standard approaches for feature selection and classification using genes, instead of ratios. This classifier was independently validated using 11 primary patient-derived pancreatic xenograft models showing perfect predictions as well as a striking linearity between prediction probability and anti-tumor response. A network analysis of the genes in the ratio classifier captured important biological relationships mediating drug response, specifically identifying key positive and negative regulators of DR5 mediated apoptosis, including DR5, CASP8, BID, cFLIP, XIAP and PEA15. Importantly, the ratio classifier shows translatability across gene expression platforms (from Affymetrix microarrays to RNA-seq) and across model systems (in vitro to in vivo). Our approach of using gene expression ratios presents a robust and novel method for constructing translatable biomarkers of compound response, which can also probe the underlying biology of treatment response. PMID:26378449

  15. An analytical approach for the calculation of stress-intensity factors in transformation-toughened ceramics

    NASA Astrophysics Data System (ADS)

    Müller, W. H.

    1990-12-01

    Stress-induced transformation toughening in Zirconia-containing ceramics is described analytically by means of a quantitative model: A Griffith crack which interacts with a transformed, circular Zirconia inclusion. Due to its volume expansion, a ZrO2-particle compresses its flanks, whereas a particle in front of the crack opens the flanks such that the crack will be attracted and finally absorbed. Erdogan's integral equation technique is applied to calculate the dislocation functions and the stress-intensity-factors which correspond to these situations. In order to derive analytical expressions, the elastic constants of the inclusion and the matrix are assumed to be equal.

  16. Robust TLR4-induced gene expression patterns are not an accurate indicator of human immunity

    PubMed Central

    2010-01-01

    Background Activation of Toll-like receptors (TLRs) is widely accepted as an essential event for defence against infection. Many TLRs utilize a common signalling pathway that relies on activation of the kinase IRAK4 and the transcription factor NFκB for the rapid expression of immunity genes. Methods 21 K DNA microarray technology was used to evaluate LPS-induced (TLR4) gene responses in blood monocytes from a child with an IRAK4-deficiency. In vitro responsiveness to LPS was confirmed by real-time PCR and ELISA and compared to the clinical predisposition of the child and IRAK4-deficient mice to Gram negative infection. Results We demonstrated that the vast majority of LPS-responsive genes in IRAK4-deficient monocytes were greatly suppressed, an observation that is consistent with the described role for IRAK4 as an essential component of TLR4 signalling. The severely impaired response to LPS, however, is inconsistent with a remarkably low incidence of Gram negative infections observed in this child and other children with IRAK4-deficiency. This unpredicted clinical phenotype was validated by demonstrating that IRAK4-deficient mice had a similar resistance to infection with Gram negative S. typhimurium as wildtype mice. A number of immunity genes, such as chemokines, were expressed at normal levels in human IRAK4-deficient monocytes, indicating that particular IRAK4-independent elements within the repertoire of TLR4-induced responses are expressed. Conclusions Sufficient defence to Gram negative immunity does not require IRAK4 or a robust, 'classic' inflammatory and immune response. PMID:20105294

  17. The predictive accuracy of analytical formulas and semiclassical approaches for α decay half-lives of superheavy nuclei

    NASA Astrophysics Data System (ADS)

    Zhao, T. L.; Bao, X. J.; Guo, S. Q.

    2018-02-01

    Systematic calculations on the α decay half-lives are performed by using three analytical formulas and two semiclassical approaches. For the three analytical formulas, the experimental α decay half-lives and {Q}α values of the 66 reference nuclei have been used to obtain the coefficients. We get only four adjustable parameters to describe α decay half-lives for even-even, odd-A, and odd-odd nuclei. By comparison between the calculated values from ten analytical formulas and experimental data, it is shown that the new universal decay law (NUDL) foumula is the most accurate one to reproduce the experimental α decay half-lives of the superheavy nuclei (SHN). Meanwhile it is found that the experimental α decay half-lives of SHN are well reproduced by the Royer formula although many parameters are contained. The results show that the NUDL formula and the generalized liquid drop model (GLDM2) with consideration of the preformation factor can give fairly equivalent results for the superheavy nuclei.

  18. Microfluidic paper-based analytical devices for potential use in quantitative and direct detection of disease biomarkers in clinical analysis.

    PubMed

    Lim, Wei Yin; Goh, Boon Tong; Khor, Sook Mei

    2017-08-15

    Clinicians, working in the health-care diagnostic systems of developing countries, currently face the challenges of rising costs, increased number of patient visits, and limited resources. A significant trend is using low-cost substrates to develop microfluidic devices for diagnostic purposes. Various fabrication techniques, materials, and detection methods have been explored to develop these devices. Microfluidic paper-based analytical devices (μPADs) have gained attention for sensing multiplex analytes, confirming diagnostic test results, rapid sample analysis, and reducing the volume of samples and analytical reagents. μPADs, which can provide accurate and reliable direct measurement without sample pretreatment, can reduce patient medical burden and yield rapid test results, aiding physicians in choosing appropriate treatment. The objectives of this review are to provide an overview of the strategies used for developing paper-based sensors with enhanced analytical performances and to discuss the current challenges, limitations, advantages, disadvantages, and future prospects of paper-based microfluidic platforms in clinical diagnostics. μPADs, with validated and justified analytical performances, can potentially improve the quality of life by providing inexpensive, rapid, portable, biodegradable, and reliable diagnostics. Copyright © 2017 Elsevier B.V. All rights reserved.

  19. A complete analytical solution for the inverse instantaneous kinematics of a spherical-revolute-spherical (7R) redundant manipulator

    NASA Technical Reports Server (NTRS)

    Podhorodeski, R. P.; Fenton, R. G.; Goldenberg, A. A.

    1989-01-01

    Using a method based upon resolving joint velocities using reciprocal screw quantities, compact analytical expressions are generated for the inverse solution of the joint rates of a seven revolute (spherical-revolute-spherical) manipulator. The method uses a sequential decomposition of screw coordinates to identify reciprocal screw quantities used in the resolution of a particular joint rate solution, and also to identify a Jacobian null-space basis used for the direct solution of optimal joint rates. The results of the screw decomposition are used to study special configurations of the manipulator, generating expressions for the inverse velocity solution for all non-singular configurations of the manipulator, and identifying singular configurations and their characteristics. Two functions are therefore served: a new general method for the solution of the inverse velocity problem is presented; and complete analytical expressions are derived for the resolution of the joint rates of a seven degree of freedom manipulator useful for telerobotic and industrial robotic application.

  20. Accurate analysis of parabens in human urine using isotope-dilution ultrahigh-performance liquid chromatography-high resolution mass spectrometry.

    PubMed

    Zhou, Hui-Ting; Chen, Hsin-Chang; Ding, Wang-Hsien

    2018-02-20

    An analytical method that utilizes isotope-dilution ultrahigh-performance liquid chromatography coupled with hybrid quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-MS or called UHPLC-HRMS) was developed, and validated to be highly precise and accurate for the detection of nine parabens (methyl-, ethyl-, propyl-, isopropyl-, butyl-, isobutyl-, pentyl-, hexyl-, and benzyl-parabens) in human urine samples. After sample preparation by ultrasound-assisted emulsification microextraction (USAEME), the extract was directly injected into UHPLC-HRMS. By using negative electrospray ionization in the multiple reaction monitoring (MRM) mode and measuring the peak area ratios of both the natural and the labeled-analogues in the samples and calibration standards, the target analytes could be accurately identified and quantified. Another use for the labeled-analogues was to correct for systematic errors associated with the analysis, such as the matrix effect and other variations. The limits of quantitation (LOQs) were ranging from 0.3 to 0.6 ng/mL. High precisions for both repeatability and reproducibility were obtained ranging from 1 to 8%. High trueness (mean extraction recovery, or called accuracy) ranged from 93 to 107% on two concentration levels. According to preliminary results, the total concentrations of four most detected parabens (methyl-, ethyl-, propyl- and butyl-) ranged from 0.5 to 79.1 ng/mL in male urine samples, and from 17 to 237 ng/mL in female urine samples. Interestingly, two infrequently detected pentyl- and hexyl-parabens were found in one of the male samples in this study. Copyright © 2017 Elsevier B.V. All rights reserved.

  1. Decoding Children's Expressions of Affect.

    ERIC Educational Resources Information Center

    Feinman, Joel A.; Feldman, Robert S.

    Mothers' ability to decode the emotional expressions of their male and female children was compared to the decoding ability of non-mothers. Happiness, sadness, fear and anger were induced in children in situations that varied in terms of spontaneous and role-played encoding modes. It was hypothesized that mothers would be more accurate decoders of…

  2. Comparing numerical and analytic approximate gravitational waveforms

    NASA Astrophysics Data System (ADS)

    Afshari, Nousha; Lovelace, Geoffrey; SXS Collaboration

    2016-03-01

    A direct observation of gravitational waves will test Einstein's theory of general relativity under the most extreme conditions. The Laser Interferometer Gravitational-Wave Observatory, or LIGO, began searching for gravitational waves in September 2015 with three times the sensitivity of initial LIGO. To help Advanced LIGO detect as many gravitational waves as possible, a major research effort is underway to accurately predict the expected waves. In this poster, I will explore how the gravitational waveform produced by a long binary-black-hole inspiral, merger, and ringdown is affected by how fast the larger black hole spins. In particular, I will present results from simulations of merging black holes, completed using the Spectral Einstein Code (black-holes.org/SpEC.html), including some new, long simulations designed to mimic black hole-neutron star mergers. I will present comparisons of the numerical waveforms with analytic approximations.

  3. Towards accurate cosmological predictions for rapidly oscillating scalar fields as dark matter

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

    Ureña-López, L. Arturo; Gonzalez-Morales, Alma X., E-mail: lurena@ugto.mx, E-mail: alma.gonzalez@fisica.ugto.mx

    2016-07-01

    As we are entering the era of precision cosmology, it is necessary to count on accurate cosmological predictions from any proposed model of dark matter. In this paper we present a novel approach to the cosmological evolution of scalar fields that eases their analytic and numerical analysis at the background and at the linear order of perturbations. The new method makes use of appropriate angular variables that simplify the writing of the equations of motion, and which also show that the usual field variables play a secondary role in the cosmological dynamics. We apply the method to a scalar fieldmore » endowed with a quadratic potential and revisit its properties as dark matter. Some of the results known in the literature are recovered, and a better understanding of the physical properties of the model is provided. It is confirmed that there exists a Jeans wavenumber k {sub J} , directly related to the suppression of linear perturbations at wavenumbers k > k {sub J} , and which is verified to be k {sub J} = a √ mH . We also discuss some semi-analytical results that are well satisfied by the full numerical solutions obtained from an amended version of the CMB code CLASS. Finally we draw some of the implications that this new treatment of the equations of motion may have in the prediction of cosmological observables from scalar field dark matter models.« less

  4. Prevalence of Pre-Analytical Errors in Clinical Chemistry Diagnostic Labs in Sulaimani City of Iraqi Kurdistan

    PubMed Central

    2017-01-01

    %). Most quality control schemes at Sulaimani hospitals focus only on the analytical phase, and none of the pre-analytical errors were recorded. Interestingly, none of the labs were internationally accredited; therefore, corrective actions are needed at these hospitals to ensure better health outcomes. Internal and External Quality Assessment Schemes (EQAS) for the pre-analytical phase at Sulaimani clinical laboratories should be implemented at public hospitals. Furthermore, lab personnel, particularly phlebotomists, need continuous training on the importance of sample quality to obtain accurate test results. PMID:28107395

  5. Broadening of Analyte Streams due to a Transverse Pressure Gradient in Free-Flow Isoelectric Focusing

    PubMed Central

    Dutta, Debashis

    2017-01-01

    Pressure-driven cross-flows can arise in free-flow isoelectric focusing systems (FFIEF) due to a non-uniform electroosmotic flow velocity along the channel width induced by the pH gradient in this direction. In addition, variations in the channel cross-section as well as unwanted differences in hydrostatic heads at the buffer/sample inlet ports can also lead to such pressure-gradients which besides altering the equilibrium position of the sample zones have a tendency to substantially broaden their widths deteriorating the separations. In this situation, a thorough assessment of stream broadening due to transverse pressure-gradients in FFIEF devices is necessary in order to establish accurate design rules for the assay. The present article describes a mathematical framework to estimate the noted zone dispersion in FFIEF separations based on the method-of-moments approach under laminar flow conditions. A closed-form expression has been derived for the spatial variance of the analyte streams at their equilibrium positions as a function of the various operating parameters governing the assay performance. This expression predicts the normalized stream variance under the chosen conditions to be determined by two dimensionless Péclet numbers evaluated based on the transverse pressure-driven and electrophoretic solute velocities in the separation chamber, respectively. Moreover, the analysis shows that while the stream width can be expected to increase with an increase in the value of the first Péclet number, the opposite trend will be followed with respect to the latter. The noted results have been validated using Monte Carlo simulations that also establish a time/length scale over which the predicted equilibrium stream width is attained in the system. PMID:28081900

  6. Addressing the Analytic Challenges of Cross-Sectional Pediatric Pneumonia Etiology Data.

    PubMed

    Hammitt, Laura L; Feikin, Daniel R; Scott, J Anthony G; Zeger, Scott L; Murdoch, David R; O'Brien, Katherine L; Deloria Knoll, Maria

    2017-06-15

    Despite tremendous advances in diagnostic laboratory technology, identifying the pathogen(s) causing pneumonia remains challenging because the infected lung tissue cannot usually be sampled for testing. Consequently, to obtain information about pneumonia etiology, clinicians and researchers test specimens distant to the site of infection. These tests may lack sensitivity (eg, blood culture, which is only positive in a small proportion of children with pneumonia) and/or specificity (eg, detection of pathogens in upper respiratory tract specimens, which may indicate asymptomatic carriage or a less severe syndrome, such as upper respiratory infection). While highly sensitive nucleic acid detection methods and testing of multiple specimens improve sensitivity, multiple pathogens are often detected and this adds complexity to the interpretation as the etiologic significance of results may be unclear (ie, the pneumonia may be caused by none, one, some, or all of the pathogens detected). Some of these challenges can be addressed by adjusting positivity rates to account for poor sensitivity or incorporating test results from controls without pneumonia to account for poor specificity. However, no classical analytic methods can account for measurement error (ie, sensitivity and specificity) for multiple specimen types and integrate the results of measurements for multiple pathogens to produce an accurate understanding of etiology. We describe the major analytic challenges in determining pneumonia etiology and review how the common analytical approaches (eg, descriptive, case-control, attributable fraction, latent class analysis) address some but not all challenges. We demonstrate how these limitations necessitate a new, integrated analytical approach to pneumonia etiology data. © The Author 2017. Published by Oxford University Press for the Infectious Diseases Society of America.

  7. Common cues to emotion in the dynamic facial expressions of speech and song

    PubMed Central

    Livingstone, Steven R.; Thompson, William F.; Wanderley, Marcelo M.; Palmer, Caroline

    2015-01-01

    Speech and song are universal forms of vocalization that may share aspects of emotional expression. Research has focused on parallels in acoustic features, overlooking facial cues to emotion. In three experiments, we compared moving facial expressions in speech and song. In Experiment 1, vocalists spoke and sang statements each with five emotions. Vocalists exhibited emotion-dependent movements of the eyebrows and lip corners that transcended speech–song differences. Vocalists’ jaw movements were coupled to their acoustic intensity, exhibiting differences across emotion and speech–song. Vocalists’ emotional movements extended beyond vocal sound to include large sustained expressions, suggesting a communicative function. In Experiment 2, viewers judged silent videos of vocalists’ facial expressions prior to, during, and following vocalization. Emotional intentions were identified accurately for movements during and after vocalization, suggesting that these movements support the acoustic message. Experiment 3 compared emotional identification in voice-only, face-only, and face-and-voice recordings. Emotion judgements for voice-only singing were poorly identified, yet were accurate for all other conditions, confirming that facial expressions conveyed emotion more accurately than the voice in song, yet were equivalent in speech. Collectively, these findings highlight broad commonalities in the facial cues to emotion in speech and song, yet highlight differences in perception and acoustic-motor production. PMID:25424388

  8. Common cues to emotion in the dynamic facial expressions of speech and song.

    PubMed

    Livingstone, Steven R; Thompson, William F; Wanderley, Marcelo M; Palmer, Caroline

    2015-01-01

    Speech and song are universal forms of vocalization that may share aspects of emotional expression. Research has focused on parallels in acoustic features, overlooking facial cues to emotion. In three experiments, we compared moving facial expressions in speech and song. In Experiment 1, vocalists spoke and sang statements each with five emotions. Vocalists exhibited emotion-dependent movements of the eyebrows and lip corners that transcended speech-song differences. Vocalists' jaw movements were coupled to their acoustic intensity, exhibiting differences across emotion and speech-song. Vocalists' emotional movements extended beyond vocal sound to include large sustained expressions, suggesting a communicative function. In Experiment 2, viewers judged silent videos of vocalists' facial expressions prior to, during, and following vocalization. Emotional intentions were identified accurately for movements during and after vocalization, suggesting that these movements support the acoustic message. Experiment 3 compared emotional identification in voice-only, face-only, and face-and-voice recordings. Emotion judgements for voice-only singing were poorly identified, yet were accurate for all other conditions, confirming that facial expressions conveyed emotion more accurately than the voice in song, yet were equivalent in speech. Collectively, these findings highlight broad commonalities in the facial cues to emotion in speech and song, yet highlight differences in perception and acoustic-motor production.

  9. Dependence of yield of nuclear track-biosensors on track radius and analyte concentration

    NASA Astrophysics Data System (ADS)

    García-Arellano, H.; Muñoz H., G.; Fink, D.; Vacik, J.; Hnatowicz, V.; Alfonta, L.; Kiv, A.

    2018-04-01

    In swift heavy ion track-based polymeric biosensor foils with incorporated enzymes one exploits the correlation between the analyte concentration and the sensor current, via the enrichment of charged enzymatic reaction products in the track's confinement. Here we study the influence of the etched track radius on the biosensor's efficiency. These sensors are analyte-specific only if both the track radii and the analyte concentration exceed certain threshold values of ∼15 nm and ∼10-6 M (for glucose sensing), respectively. Below these limits the sensor signal stems un-specifically from any charge carrier. In its proper working regime, the inner track walls are smoothly covered by enzymes and the efficiency is practically radius independent. Theory shows that the measured current should be slightly sub-proportional to the analyte concentration; the measurements roughly reconfirm this. Narrower tracks (∼5-15 nm radius) with reduced enzyme coverage lead to decreasing efficiency. Tiny signals visible when the tracks are etched to effective radii between 0 and ∼5 nm are tentatively ascribed to enzymes bonded to surface-near nano-cracks in the polymer foil, resulting from its degradation due to aging, rather than to the tracks. Precondition for this study was the accurate determination of the etched track radii, which is possible only by a nanofluidic approach. This holds to some extent even for enzyme-covered tracks, though in this case most of the wall charges are compensated by enzyme bonding.

  10. Electron-cyclotron absorption in high-temperature plasmas: quasi-exact analytical evaluation and comparative numerical analysis

    NASA Astrophysics Data System (ADS)

    Albajar, F.; Bertelli, N.; Bornatici, M.; Engelmann, F.

    2007-01-01

    On the basis of the electromagnetic energy balance equation, a quasi-exact analytical evaluation of the electron-cyclotron (EC) absorption coefficient is performed for arbitrary propagation (with respect to the magnetic field) in a (Maxwellian) magneto-plasma for the temperature range of interest for fusion reactors (in which EC radiation losses tend to be important in the plasma power balance). The calculation makes use of Bateman's expansion for the product of two Bessel functions, retaining the lowest-order contribution. The integration over electron momentum can then be carried out analytically, fully accounting for finite Larmor radius effects in this approximation. On the basis of the analytical expressions for the EC absorption coefficients of both the extraordinary and ordinary modes thus obtained, (i) for the case of perpendicular propagation simple formulae are derived for both modes and (ii) a numerical analysis of the angular distribution of EC absorption is carried out. An assessment of the accuracy of asymptotic expressions that have been given earlier is also performed, showing that these approximations can be usefully applied for calculating EC power losses from reactor-grade plasmas. Presented in part at the 14th Joint Workshop on Electron Cyclotron Emission and Electron Cyclotron Resonance Heating, Santorini, Greece, 9-12 May 2006.

  11. Empirical and semi-analytical models for predicting peak outflows caused by embankment dam failures

    NASA Astrophysics Data System (ADS)

    Wang, Bo; Chen, Yunliang; Wu, Chao; Peng, Yong; Song, Jiajun; Liu, Wenjun; Liu, Xin

    2018-07-01

    Prediction of peak discharge of floods has attracted great attention for researchers and engineers. In present study, nine typical nonlinear mathematical models are established based on database of 40 historical dam failures. The first eight models that were developed with a series of regression analyses are purely empirical, while the last one is a semi-analytical approach that was derived from an analytical solution of dam-break floods in a trapezoidal channel. Water depth above breach invert (Hw), volume of water stored above breach invert (Vw), embankment length (El), and average embankment width (Ew) are used as independent variables to develop empirical formulas of estimating the peak outflow from breached embankment dams. It is indicated from the multiple regression analysis that a function using the former two variables (i.e., Hw and Vw) produce considerably more accurate results than that using latter two variables (i.e., El and Ew). It is shown that the semi-analytical approach works best in terms of both prediction accuracy and uncertainty, and the established empirical models produce considerably reasonable results except the model only using El. Moreover, present models have been compared with other models available in literature for estimating peak discharge.

  12. Non-degenerate two-photon absorption in silicon waveguides. Analytical and experimental study

    DOE PAGES

    Zhang, Yanbing; Husko, Chad; Lefrancois, Simon; ...

    2015-06-22

    We theoretically and experimentally investigate the nonlinear evolution of two optical pulses in a silicon waveguide. We provide an analytic solution for the weak probe wave undergoing non-degenerate two-photon absorption (TPA) from the strong pump. At larger pump intensities, we employ a numerical solution to study the interplay between TPA and photo-generated free carriers. We develop a simple and powerful approach to extract and separate out the distinct loss contributions of TPA and free-carrier absorption from readily available experimental data. Our analysis accounts accurately for experimental results in silicon photonic crystal waveguides.

  13. On analytic modeling of lunar perturbations of artificial satellites of the earth

    NASA Astrophysics Data System (ADS)

    Lane, M. T.

    1989-06-01

    Two different procedures for analytically modeling the effects of the moon's direct gravitational force on artificial earth satellites are discussed from theoretical and numerical viewpoints. One is developed using classical series expansions of inclination and eccentricity for both the satellite and the moon, and the other employs the method of averaging. Both solutions are seen to have advantages, but it is shown that while the former is more accurate in special situations, the latter is quicker and more practical for the general orbit determination problem where observed data are used to correct the orbit in near real time.

  14. Pre-analytical issues in the haemostasis laboratory: guidance for the clinical laboratories.

    PubMed

    Magnette, A; Chatelain, M; Chatelain, B; Ten Cate, H; Mullier, F

    2016-01-01

    Ensuring quality has become a daily requirement in laboratories. In haemostasis, even more than in other disciplines of biology, quality is determined by a pre-analytical step that encompasses all procedures, starting with the formulation of the medical question, and includes patient preparation, sample collection, handling, transportation, processing, and storage until time of analysis. This step, based on a variety of manual activities, is the most vulnerable part of the total testing process and is a major component of the reliability and validity of results in haemostasis and constitutes the most important source of erroneous or un-interpretable results. Pre-analytical errors may occur throughout the testing process and arise from unsuitable, inappropriate or wrongly handled procedures. Problems may arise during the collection of blood specimens such as misidentification of the sample, use of inadequate devices or needles, incorrect order of draw, prolonged tourniquet placing, unsuccessful attempts to locate the vein, incorrect use of additive tubes, collection of unsuitable samples for quality or quantity, inappropriate mixing of a sample, etc. Some factors can alter the result of a sample constituent after collection during transportation, preparation and storage. Laboratory errors can often have serious adverse consequences. Lack of standardized procedures for sample collection accounts for most of the errors encountered within the total testing process. They can also have clinical consequences as well as a significant impact on patient care, especially those related to specialized tests as these are often considered as "diagnostic". Controlling pre-analytical variables is critical since this has a direct influence on the quality of results and on their clinical reliability. The accurate standardization of the pre-analytical phase is of pivotal importance for achieving reliable results of coagulation tests and should reduce the side effects of the influence

  15. An Accurate New Potential Function for Ground-State X{e}_2 from UV and Virial Coefficient Data

    NASA Astrophysics Data System (ADS)

    Le Roy, Robert J.; Mackie, J. Cameron; Chandrasekhar, Pragna

    2011-06-01

    Determining accurate analytic pair potentials for rare gas dimers has been a longstanding goal in molecular physics. However, most potential energy functions reported to date fail to optimally represent the available spectroscopic data, in spite of the fact that such data provide constraints of unparalleled precision on the attractive potential energy wells of these species. A recent study of ArXe showed that it is a straightforward matter to combine multi-isotopologue spectroscopic data (in that case, microwave, and high resolution UV measurements) and virial coefficients in a direct fit to obtain a flexible analytic potential function that incorporates the theoretically predicted damped inverse-power long-range behaviour. The present work reports the application of this approach to Xe_2, with a direct fit to high resolution rotationally resolved UV emission data for v''=0 and 1, band head data for v''=0-9, and virial coefficient data for T=165-950 K being used to obtain an accurate new potential energy function for the ground state of this Van der Waals molecule. Analogous results for other rare-gas pairs will also be presented, as time permits. L. Piticco, F. Merkt, A.A. Cholewinski, F.R. McCourt and R.J. Le Roy, J. Mol. Spectrosc. 264, 83 (2010). A. Wüest and K.G. Bruin and F. Merkt, Can. J. Chem. 82, 750 (2004). D.E. Freeman, K. Yoshino, and Y. Tanaka, J. Chem. Phys. 61, 4880 (1974). J.H. Dymond, K.N. Marsh, R.C. Wilhoit and K.C. Wong, in Landold-Börnstein, New Series, Group IV, edited by M. Frenkel and K.N. Marsh, Vol. 21 (2003).

  16. Adjustment of pesticide concentrations for temporal changes in analytical recovery, 1992–2010

    USGS Publications Warehouse

    Martin, Jeffrey D.; Eberle, Michael

    2011-01-01

    Recovery is the proportion of a target analyte that is quantified by an analytical method and is a primary indicator of the analytical bias of a measurement. Recovery is measured by analysis of quality-control (QC) water samples that have known amounts of target analytes added ("spiked" QC samples). For pesticides, recovery is the measured amount of pesticide in the spiked QC sample expressed as a percentage of the amount spiked, ideally 100 percent. Temporal changes in recovery have the potential to adversely affect time-trend analysis of pesticide concentrations by introducing trends in apparent environmental concentrations that are caused by trends in performance of the analytical method rather than by trends in pesticide use or other environmental conditions. This report presents data and models related to the recovery of 44 pesticides and 8 pesticide degradates (hereafter referred to as "pesticides") that were selected for a national analysis of time trends in pesticide concentrations in streams. Water samples were analyzed for these pesticides from 1992 through 2010 by gas chromatography/mass spectrometry. Recovery was measured by analysis of pesticide-spiked QC water samples. Models of recovery, based on robust, locally weighted scatterplot smooths (lowess smooths) of matrix spikes, were developed separately for groundwater and stream-water samples. The models of recovery can be used to adjust concentrations of pesticides measured in groundwater or stream-water samples to 100 percent recovery to compensate for temporal changes in the performance (bias) of the analytical method.

  17. Quantitative evaluation of analyte transport on microfluidic paper-based analytical devices (μPADs).

    PubMed

    Ota, Riki; Yamada, Kentaro; Suzuki, Koji; Citterio, Daniel

    2018-02-07

    The transport efficiency during capillary flow-driven sample transport on microfluidic paper-based analytical devices (μPADs) made from filter paper has been investigated for a selection of model analytes (Ni 2+ , Zn 2+ , Cu 2+ , PO 4 3- , bovine serum albumin, sulforhodamine B, amaranth) representing metal cations, complex anions, proteins and anionic molecules. For the first time, the transport of the analytical target compounds rather than the sample liquid, has been quantitatively evaluated by means of colorimetry and absorption spectrometry-based methods. The experiments have revealed that small paperfluidic channel dimensions, additional user operation steps (e.g. control of sample volume, sample dilution, washing step) as well as the introduction of sample liquid wicking areas allow to increase analyte transport efficiency. It is also shown that the interaction of analytes with the negatively charged cellulosic paper substrate surface is strongly influenced by the physico-chemical properties of the model analyte and can in some cases (Cu 2+ ) result in nearly complete analyte depletion during sample transport. The quantitative information gained through these experiments is expected to contribute to the development of more sensitive μPADs.

  18. A Semi-Analytical Model for Dispersion Modelling Studies in the Atmospheric Boundary Layer

    NASA Astrophysics Data System (ADS)

    Gupta, A.; Sharan, M.

    2017-12-01

    The severe impact of harmful air pollutants has always been a cause of concern for a wide variety of air quality analysis. The analytical models based on the solution of the advection-diffusion equation have been the first and remain the convenient way for modeling air pollutant dispersion as it is easy to handle the dispersion parameters and related physics in it. A mathematical model describing the crosswind integrated concentration is presented. The analytical solution to the resulting advection-diffusion equation is limited to a constant and simple profiles of eddy diffusivity and wind speed. In practice, the wind speed depends on the vertical height above the ground and eddy diffusivity profiles on the downwind distance from the source as well as the vertical height. In the present model, a method of eigen-function expansion is used to solve the resulting partial differential equation with the appropriate boundary conditions. This leads to a system of first order ordinary differential equations with a coefficient matrix depending on the downwind distance. The solution of this system, in general, can be expressed in terms of Peano-baker series which is not easy to compute, particularly when the coefficient matrix becomes non-commutative (Martin et al., 1967). An approach based on Taylor's series expansion is introduced to find the numerical solution of first order system. The method is applied to various profiles of wind speed and eddy diffusivities. The solution computed from the proposed methodology is found to be efficient and accurate in comparison to those available in the literature. The performance of the model is evaluated with the diffusion datasets from Copenhagen (Gryning et al., 1987) and Hanford (Doran et al., 1985). In addition, the proposed method is used to deduce three dimensional concentrations by considering the Gaussian distribution in crosswind direction, which is also evaluated with diffusion data corresponding to a continuous point source.

  19. Children's Knowledge of Display Rules for Emotional Expression and Control.

    ERIC Educational Resources Information Center

    Doubleday, Catherine; And Others

    An important task for children is to acquire their culture's rules for emotional display. Accurate knowledge of display rules prescribing, for example, safe targets for anger or indelicate situations for excitement helps regulate expressive behavior and mediate the impact of emotional expression on the self and others. In this study, children's…

  20. Accurate evaluation for the biofilm-activated sludge reactor using graphical techniques

    NASA Astrophysics Data System (ADS)

    Fouad, Moharram; Bhargava, Renu

    2018-05-01

    A complete graphical solution is obtained for the completely mixed biofilm-activated sludge reactor (hybrid reactor). The solution consists of a series of curves deduced from the principal equations of the hybrid system after converting them in dimensionless form. The curves estimate the basic parameters of the hybrid system such as suspended biomass concentration, sludge residence time, wasted mass of sludge, and food to biomass ratio. All of these parameters can be expressed as functions of hydraulic retention time, influent substrate concentration, substrate concentration in the bulk, stagnant liquid layer thickness, and the minimum substrate concentration which can maintain the biofilm growth in addition to the basic kinetics of the activated sludge process in which all these variables are expressed in a dimensionless form. Compared to other solutions of such system these curves are simple, easy to use, and provide an accurate tool for analyzing such system based on fundamental principles. Further, these curves may be used as a quick tool to get the effect of variables change on the other parameters and the whole system.