Science.gov

Sample records for derived interaction parameters

  1. Derived Interaction Parameters for the Tsai-Wu Tensor Polynomial Theory of Strength for Composite Materials

    SciTech Connect

    DeTeresa, S J; Larsen, G J

    2001-08-03

    It is shown that the two interactive strength parameters in the Tsai-Wu tensor polynomial strength criterion for fiber composites can be derived in terms of the uniaxial or non-interacting strength parameters if the composite does not fail under practical levels of hydrostatic pressure or equal transverse compression. Thus the required number of parameters is reduced from seven to five and all five of the remaining strength terms are easily determined using standard test methods. The derived interactive parameters fall within the stability limits of the theory, yet they lead to open failure surfaces in the compressive stress quadrant. The assumptions used to derive the interactive parameters were supported by measurements for the effect of hydrostatic pressure and unequal transverse compression on the behavior of a typical carbon fiber composite.

  2. Derivation of Pitzer Interaction Parameters for an Aqueous Species Pair of FeCitrate- and Mg2+

    NASA Astrophysics Data System (ADS)

    Jang, J.; Olivas, T.; Nemer, M.

    2013-12-01

    The Waste Isolation Pilot Plant (WIPP) is a deep underground repository for the disposal of transuranic (TRU) radioactive waste developed by the U.S. Department of Energy (DOE). The WIPP is located within the bedded salts of the Permian Salado Formation, which consists of interbedded halite and anhydrite layers overlaying the Castile Formation. The waste includes, but is not limited to, the salts of citric acid and iron. To calculate the solution chemistry for brines of WIPP-relevance, WIPP Performance Assessment (PA) employs the Pitzer formulation to determine the activity coefficients of aqueous species in brine. The current WIPP thermodynamic database, however, does not include iron species and their Pitzer parameters, in spite of the fact that there will be a large amount of iron in the WIPP. Iron would be emplaced as part of the waste, as well as the containers for the waste. The objective of this analysis is to derive the Pitzer binary interaction parameters for the pair of Mg2+ and FeCitrate-. Briefly, an aqueous model for dissolution of Fe(OH)2(s) in MgNa2Citrate solution was fitted to the experimentally measured solubility data. The aqueous model consists of several chemical reactions and related Pitzer interaction parameters. Specifically, Pitzer binary interaction parameters for the Mg2+ and FeCitrate- pair (β(0), β(1), and Cφ) were fitted to the experimental data. Anoxic gloveboxes were used to keep the oxygen level low (less than 6 ppm) throughout the experiments. Aging time was more than 800 days to ensure equilibrium. EQ3NR packaged in EQ3/6 v.8.0a calculates the aqueous speciation and saturation index using an aqueous model addressed in EQ3/6's database. The saturation index indicates how far the system is from equilibrium with respect to the solid of interest. Thus, the smaller the sum of squared saturation indices that the aqueous model calculates for the given number of experiments, the more closely the model attributes equilibrium to each

  3. Derivation of Pitzer Interaction Parameters for an Aqueous Species Pair of Sodium and Iron(II)-Citrate Complex

    NASA Astrophysics Data System (ADS)

    Jang, J. H.; Nemer, M.

    2015-12-01

    The U.S. DOE Waste Isolation Pilot Plant (WIPP) is a deep underground repository for the permanent disposal of transuranic (TRU) radioactive waste. The WIPP is located in the Permian Delaware Basin near Carlsbad, New Mexico, U.S.A. The TRU waste includes, but is not limited to, iron-based alloys and the complexing agent, citric acid. Iron is also present from the steel used in the waste containers. The objective of this analysis is to derive the Pitzer activity coefficients for the pair of Na+ and FeCit- complex to expand current WIPP thermodynamic database. An aqueous model for the dissolution of Fe(OH)2(s) in a Na3Cit solution was fitted to the experimentally measured solubility data. The aqueous model consists of several chemical reactions and related Pitzer interaction parameters. Specifically, Pitzer interaction parameters for the Na+ and FeCit- pair (β(0), β(1), and Cφ) plus the stability constant for species of FeCit- were fitted to the experimental data. Anoxic gloveboxes were used to keep the oxygen level low (<1 ppm) throughout the experiments due to redox sensitivity. EQ3NR, a computer program for geochemical aqueous speciation-solubility calculations, packaged in EQ3/6 v.8.0a, calculates the aqueous speciation and saturation index using an aqueous model addressed in EQ3/6's database. The saturation index indicates how far the system is from equilibrium with respect to the solid of interest. Thus, the smaller the sum of squared saturation indices that the aqueous model calculates for the given number of experiments, the more closely the model attributes equilibrium to each individual experiment with respect to the solid of interest. The calculation of aqueous speciation and saturation indices was repeated by adjusting stability constant of FeCit-, β(0), β(1), and Cφ in the database until the values are found that make the sum of squared saturation indices the smallest for the given number of experiments. Results will be presented at the time of

  4. Hexagonal boron nitride and water interaction parameters.

    PubMed

    Wu, Yanbin; Wagner, Lucas K; Aluru, Narayana R

    2016-04-28

    The study of hexagonal boron nitride (hBN) in microfluidic and nanofluidic applications at the atomic level requires accurate force field parameters to describe the water-hBN interaction. In this work, we begin with benchmark quality first principles quantum Monte Carlo calculations on the interaction energy between water and hBN, which are used to validate random phase approximation (RPA) calculations. We then proceed with RPA to derive force field parameters, which are used to simulate water contact angle on bulk hBN, attaining a value within the experimental uncertainties. This paper demonstrates that end-to-end multiscale modeling, starting at detailed many-body quantum mechanics and ending with macroscopic properties, with the approximations controlled along the way, is feasible for these systems. PMID:27131542

  5. Hexagonal boron nitride and water interaction parameters.

    PubMed

    Wu, Yanbin; Wagner, Lucas K; Aluru, Narayana R

    2016-04-28

    The study of hexagonal boron nitride (hBN) in microfluidic and nanofluidic applications at the atomic level requires accurate force field parameters to describe the water-hBN interaction. In this work, we begin with benchmark quality first principles quantum Monte Carlo calculations on the interaction energy between water and hBN, which are used to validate random phase approximation (RPA) calculations. We then proceed with RPA to derive force field parameters, which are used to simulate water contact angle on bulk hBN, attaining a value within the experimental uncertainties. This paper demonstrates that end-to-end multiscale modeling, starting at detailed many-body quantum mechanics and ending with macroscopic properties, with the approximations controlled along the way, is feasible for these systems.

  6. Topological order parameters for interacting topological insulators.

    PubMed

    Wang, Zhong; Qi, Xiao-Liang; Zhang, Shou-Cheng

    2010-12-17

    We propose a topological order parameter for interacting topological insulators, expressed in terms of the full Green's functions of the interacting system. We show that it is exactly quantized for a time-reversal invariant topological insulator, and it can be experimentally measured through the topological magneto-electric effect. This topological order parameter can be applied to both interacting and disordered systems, and used for determining their phase diagrams. PMID:21231609

  7. Dissipative Particle Dynamics interaction parameters from ab initio calculations

    NASA Astrophysics Data System (ADS)

    Sepehr, Fatemeh; Paddison, Stephen J.

    2016-02-01

    Dissipative Particle Dynamics (DPD) is a commonly employed coarse-grained method to model complex systems. Presented here is a pragmatic approach to connect atomic-scale information to the meso-scale interactions defined between the DPD particles or beads. Specifically, electronic structure calculations were utilized for the calculation of the DPD pair-wise interaction parameters. An implicit treatment of the electrostatic interactions for charged beads is introduced. The method is successfully applied to derive the parameters for a hydrated perfluorosulfonic acid ionomer with absorbed vanadium cations.

  8. DCE-MRI-Derived Parameters in Evaluating Abraxane-Induced Early Vascular Response and the Effectiveness of Its Synergistic Interaction with Cisplatin.

    PubMed

    Sun, Xilin; Yang, Lili; Yan, Xuefeng; Sun, Yingying; Zhao, Dongliang; Ji, Yang; Wang, Kai; Chen, Xiaoyuan; Shen, Baozhong

    2016-01-01

    Our previous studies revealed molecular alterations of tumor vessels, varying from immature to mature alterations, resulting from Abraxane, and demonstrated that the integrin-specific PET tracer 18F-FPPRGD2 can be used to noninvasively monitor such changes. However, changes in the tumor vasculature at functional levels such as perfusion and permeability are also important for monitoring Abraxane treatment outcomes in patients with cancer. The purpose of this study is to further investigate the vascular response during Abraxane therapy and the effectiveness of its synergistic interaction with cisplatin using Dynamic contrast enhanced-magnetic resonance imaging (DCE-MRI). Thirty MDA-MB-435 tumor mice were randomized into three groups: PBS control (C group), Abraxane only (A group), and sequential treatment with Abraxane followed by cisplatin (A-P group). Tumor volume was monitored based on caliper measurements. A DCE-MRI protocol was performed at baseline and day 3. The Ktrans, Kep and Ve were calculated and compared with CD31, α-SMA, and Ki67 histology data. Sequential treatment with Abraxane followed by cisplatin produced a significantly greater inhibition of tumor growth during the three weeks of the observation period. Decreases in Ktrans and Kep for the A and A-P groups were observed on day 3. Immunohistological staining suggested vascular remodeling during the Abraxane therapy. The changes in Ktrans and Kep values were correlated with alterations in the permeability of the tumor vasculature induced by the Abraxane treatment. In conclusion, Abraxane-mediated permeability variations in tumor vasculature can be quantitatively visualized by DCE-MRI, making this a useful method for studying the effects of early cancer treatment, especially the early vascular response. Vascular remodeling by Abraxane improves the efficiency of cisplatin delivery and thus results in a favorable treatment outcome. PMID:27632532

  9. DCE-MRI-Derived Parameters in Evaluating Abraxane-Induced Early Vascular Response and the Effectiveness of Its Synergistic Interaction with Cisplatin

    PubMed Central

    Sun, Xilin; Yang, Lili; Yan, Xuefeng; Sun, Yingying; Zhao, Dongliang; Ji, Yang; Wang, Kai; Chen, Xiaoyuan; Shen, Baozhong

    2016-01-01

    Our previous studies revealed molecular alterations of tumor vessels, varying from immature to mature alterations, resulting from Abraxane, and demonstrated that the integrin-specific PET tracer 18F-FPPRGD2 can be used to noninvasively monitor such changes. However, changes in the tumor vasculature at functional levels such as perfusion and permeability are also important for monitoring Abraxane treatment outcomes in patients with cancer. The purpose of this study is to further investigate the vascular response during Abraxane therapy and the effectiveness of its synergistic interaction with cisplatin using Dynamic contrast enhanced-magnetic resonance imaging (DCE-MRI). Thirty MDA-MB-435 tumor mice were randomized into three groups: PBS control (C group), Abraxane only (A group), and sequential treatment with Abraxane followed by cisplatin (A-P group). Tumor volume was monitored based on caliper measurements. A DCE-MRI protocol was performed at baseline and day 3. The Ktrans, Kep and Ve were calculated and compared with CD31, α-SMA, and Ki67 histology data. Sequential treatment with Abraxane followed by cisplatin produced a significantly greater inhibition of tumor growth during the three weeks of the observation period. Decreases in Ktrans and Kep for the A and A-P groups were observed on day 3. Immunohistological staining suggested vascular remodeling during the Abraxane therapy. The changes in Ktrans and Kep values were correlated with alterations in the permeability of the tumor vasculature induced by the Abraxane treatment. In conclusion, Abraxane-mediated permeability variations in tumor vasculature can be quantitatively visualized by DCE-MRI, making this a useful method for studying the effects of early cancer treatment, especially the early vascular response. Vascular remodeling by Abraxane improves the efficiency of cisplatin delivery and thus results in a favorable treatment outcome. PMID:27632532

  10. Application of Statistically Derived CPAS Parachute Parameters

    NASA Technical Reports Server (NTRS)

    Romero, Leah M.; Ray, Eric S.

    2013-01-01

    The Capsule Parachute Assembly System (CPAS) Analysis Team is responsible for determining parachute inflation parameters and dispersions that are ultimately used in verifying system requirements. A model memo is internally released semi-annually documenting parachute inflation and other key parameters reconstructed from flight test data. Dispersion probability distributions published in previous versions of the model memo were uniform because insufficient data were available for determination of statistical based distributions. Uniform distributions do not accurately represent the expected distributions since extreme parameter values are just as likely to occur as the nominal value. CPAS has taken incremental steps to move away from uniform distributions. Model Memo version 9 (MMv9) made the first use of non-uniform dispersions, but only for the reefing cutter timing, for which a large number of sample was available. In order to maximize the utility of the available flight test data, clusters of parachutes were reconstructed individually starting with Model Memo version 10. This allowed for statistical assessment for steady-state drag area (CDS) and parachute inflation parameters such as the canopy fill distance (n), profile shape exponent (expopen), over-inflation factor (C(sub k)), and ramp-down time (t(sub k)) distributions. Built-in MATLAB distributions were applied to the histograms, and parameters such as scale (sigma) and location (mu) were output. Engineering judgment was used to determine the "best fit" distribution based on the test data. Results include normal, log normal, and uniform (where available data remains insufficient) fits of nominal and failure (loss of parachute and skipped stage) cases for all CPAS parachutes. This paper discusses the uniform methodology that was previously used, the process and result of the statistical assessment, how the dispersions were incorporated into Monte Carlo analyses, and the application of the distributions in

  11. A new fifth parameter for transverse isotropy II: partial derivatives

    NASA Astrophysics Data System (ADS)

    Kawakatsu, Hitoshi

    2016-07-01

    Kawakatsu et al. and Kawakatsu introduced a new fifth parameter, ηκ, to describe transverse isotropy (TI). Considering that ηκ characterizes the incidence angle dependence of body wave phase velocities for TI models, its relevance for body wave seismology is obvious. Here, we derive expressions for partial derivatives (sensitivity kernels) of surface wave phase velocity and normal mode eigenfrequency for the new set of five parameters. The partial derivative for ηκ is about twice as large as that for the conventional η, indicating that ηκ should be more readily resolved. While partial derivatives for S velocities are not so changed, those for P velocities are significantly modified; the sensitivity for anisotropic P velocities is greatly reduced. In contrary to the suggestion by Dziewonski & Anderson and Anderson & Dziewonski, there is not much control on the anisotropic P velocities. On the other hand, the significance of ηκ for long-period seismology has become clear.

  12. System for Predicting Pitzer Ion-Interaction Model Parameters

    NASA Astrophysics Data System (ADS)

    Schreiber, D. R.; Obias, T.

    2002-12-01

    Pitzer's Ion-Interaction Model has been widely utilized for the prediction of non-ideal solution behavior. The Pitzer model does an excellent job of predicting the solubility of minerals over a wide range of conditions for natural water systems. While Pitzer's equations have been successful in modeling systems when there are parameters available, there are still some systems that can't be modeled because parameters aren't available for all of the salts of interest. For example, there is little to no data for aluminum salts yet in acidified natural waters it may be present at significant concentrations. In addition, aluminum chemistry will also be important in the remediation of acidified High-level waste. Given the quantity of work involved in generating the needed parameters it would be advantageous to be able to predict Pitzer parameters for salt systems when there is no data available. Recently we began work on modeling High-level waste systems where Pitzer parameters are not available for some of the constituents of interest. We will discuss a set of relations we have developed for the prediction of Pitzer's binary ion-interaction parameters. In the binary parameter case, we reformulated the Pitzer's equations by replacing the parameters, β(0), β(1), β(2), and C, with expressions in ionic radii. Equations have been developed for salts of a particular anion with cations of similar charge. For example, there is a single equation for the 1:1 chloride salts. Relations for acids were developed separately. Also we have developed a separate set of equations for all salts of a particular charge type independent of the anion. While the latter set of equations are of lesser predictive value, they can be used in cases where we don't have a relation for a particular anion. Since any system used to predict parameters would result in a loss of accuracy, experimentally determined parameters should be used when available. The ability of parameters derived from our model

  13. FUNDPAR: A program for Deriving Fundamental Parameters from Equivalent Widths

    NASA Astrophysics Data System (ADS)

    Saffe, C.

    2011-04-01

    We implemented a Fortran code that determines fundamental parameters of solar type stars from a list of Fe line equivalent widths. The solution should verify three conditions in the standard method: ionization equilibrium, excitation equilibrium and independence between metallicity and equivalent widths. Solar-scaled Kurucz model atmospheres with NEWODF opacities are calculated with an independent program. Parameter files control different details, such as the mixing-length parameter and the overshooting. FUNDPAR derives the uncertainties following two methods: the criterion of Gonzalez & Vanture (1998) and the dispersion using the χ2 function. The code uses the 2009 version of the MOOG program. The results derived with FUNDPAR are in agreement with previous determinations in the literature. The program is freely available from the web.

  14. A Comparison of Flare Forecasting Parameters Derived From Photospheric Magnetograms

    NASA Astrophysics Data System (ADS)

    Barnes, G.; Leka, K.

    2007-12-01

    A variety of researchers have proposed parameters for use in forecasting of solar flares. However, the parameters have been calculated from different data sources, and their performance has been judged based on various different criteria. We present here a systematic comparison of a small number of parameters which can be derived from the photospheric magnetic field, some of which characterize the photospheric field itself, and some which characterize the coronal magnetic topology. We compute the parameters for a collection of over 1200 vector magnetograms from the Imaging Vector Magnetograph at Haleakala, and judge their ability to forecast flares based on discriminant analysis, climatological skill scores, and the ability to provide an "all-clear" forecast.

  15. Parameters, limits and higher derivative type II string corrections

    NASA Astrophysics Data System (ADS)

    Gubay, Finn; West, Peter

    2012-11-01

    String theory in d dimensions has n + 1 = 11 - d parameters that may be thought of as being inherited from the geometry of an n + 1 torus which may be used to construct the theory using dimensional reduction from eleven dimensions. We give the precise relationship between these parameters and the expectation values of the scalar fields that parameterise the E n+1 coset of the d dimensional theory. This allows us to examine all possible limits of the automorphic forms which occur as the coefficient functions of the higher derivative corrections to the d dimensional type II string effective action.

  16. Deriving sea-state parameters using RISAT-1 SAR data

    NASA Astrophysics Data System (ADS)

    Ganguly, Debojyoti; Mishra, Manoj K.; Chauhan, Prakash

    2015-01-01

    A technique has been demonstrated for deriving various sea-wave parameters such as peak wavelength, peak direction, and significant wave height from two-dimensional synthetic aperture radar (SAR) data acquired by Indian active microwave remote-sensing satellite RISAT-1 (Radar Imaging Satellite 1). The significant wave height is obtained using the method of azimuth cutoff wavelength, which is the minimum wavelength that can be imaged in the azimuth direction and results due to the roll-off of the SAR image spectra at higher wave numbers. In the present paper, RISAT-1 SAR fine-resolution scan mode intensity image data are used for deriving various wave parameters at a high spatial resolution of 300 m. The changes in wavelength, wave height, and wave direction of sea waves are studied for a coastal wave system using high-resolution sea-wave spectral information. The SAR-derived coastal wave parameters are then compared with JASON-2 altimeter Geophysical Data Record (GDR) products and The European Center for Medium-Range Weather Forecasts (ECMWF)-modeled values, and are found to be in reasonable agreement.

  17. Evaluation of hail suppression programme effectiveness using radar derived parameters

    NASA Astrophysics Data System (ADS)

    Tani, Satyanarayana; Paulitsch, Helmut; Teschl, Reinhard; Süsser-Rechberger, Barbara

    2016-04-01

    The objective of this study is evaluating "the operational hail suppression programme" in the province of Styria, Austria "for the year 2015". For the evaluation purpose the HAILSYS software tool was developed by integrating single polarization C-band weather radar data, aircraft trajectory, radiosonde freezing level data, hail events and crop damages information from the ground. The hail related radar derived parameters are: hail mass aloft, hail mass flux, probability of hail, vertical integrated hail mass, hail kinetic energy flux, and storm severity index. The spatial maps of hail kinetic energy and hail mass were developed to evaluate the seeding effect. The time history plots of vertical integrated hail mass, hail mass aloft and the probability of hail are drawn over an entire cell lifetime. The sensitivity and variation of radar hail parameters over time and associated changes due to cloud seeding will be presented.

  18. Relationship between Cole-Cole model parameters and spectral decomposition parameters derived from SIP data

    NASA Astrophysics Data System (ADS)

    Weigand, M.; Kemna, A.

    2016-06-01

    Spectral induced polarization (SIP) data are commonly analysed using phenomenological models. Among these models the Cole-Cole (CC) model is the most popular choice to describe the strength and frequency dependence of distinct polarization peaks in the data. More flexibility regarding the shape of the spectrum is provided by decomposition schemes. Here the spectral response is decomposed into individual responses of a chosen elementary relaxation model, mathematically acting as kernel in the involved integral, based on a broad range of relaxation times. A frequently used kernel function is the Debye model, but also the CC model with some other a priorly specified frequency dispersion (e.g. Warburg model) has been proposed as kernel in the decomposition. The different decomposition approaches in use, also including conductivity and resistivity formulations, pose the question to which degree the integral spectral parameters typically derived from the obtained relaxation time distribution are biased by the approach itself. Based on synthetic SIP data sampled from an ideal CC response, we here investigate how the two most important integral output parameters deviate from the corresponding CC input parameters. We find that the total chargeability may be underestimated by up to 80 per cent and the mean relaxation time may be off by up to three orders of magnitude relative to the original values, depending on the frequency dispersion of the analysed spectrum and the proximity of its peak to the frequency range limits considered in the decomposition. We conclude that a quantitative comparison of SIP parameters across different studies, or the adoption of parameter relationships from other studies, for example when transferring laboratory results to the field, is only possible on the basis of a consistent spectral analysis procedure. This is particularly important when comparing effective CC parameters with spectral parameters derived from decomposition results.

  19. Comparison of HRV parameters derived from photoplethysmography and electrocardiography signals.

    PubMed

    Jeyhani, Vala; Mahdiani, Shadi; Peltokangas, Mikko; Vehkaoja, Antti

    2015-01-01

    Heart rate variability (HRV) has become a useful tool in analysis of cardiovascular system in both research and clinical fields. HRV has been also used in other applications such as stress level estimation in wearable devices. HRV is normally obtained from ECG as the time interval of two successive R waves. Recently PPG has been proposed as an alternative for ECG in HRV analysis to overcome some difficulties in measurement of ECG. In addition, PPG-HRV is also used in some commercial devices such as modern optical wrist-worn heart rate monitors. However, some researches have shown that PPG is not a surrogate for heart rate variability analysis. In this work, HRV analysis was applied on beat-to-beat intervals obtained from ECG and PPG in 19 healthy male subjects. Some important HRV parameters were calculated from PPG-HRV and ECG-HRV. Maximum of PPG and its second derivative were considered as two methods for obtaining the beat-to-beat signals from PPG and the results were compared with those achieved from ECG-HRV. Our results show that the smallest error happens in SDNN and SD2 with relative error of 2.46% and 2%, respectively. The most affected parameter is pNN50 with relative error of 29.89%. In addition, in our trial, using the maximum of PPG gave better results than its second derivative.

  20. VLBI-derived troposphere parameters during CONT08

    NASA Astrophysics Data System (ADS)

    Heinkelmann, R.; Böhm, J.; Bolotin, S.; Engelhardt, G.; Haas, R.; Lanotte, R.; MacMillan, D. S.; Negusini, M.; Skurikhina, E.; Titov, O.; Schuh, H.

    2011-07-01

    Time-series of zenith wet and total troposphere delays as well as north and east gradients are compared, and zenith total delays ( ZTD) are combined on the level of parameter estimates. Input data sets are provided by ten Analysis Centers (ACs) of the International VLBI Service for Geodesy and Astrometry (IVS) for the CONT08 campaign (12-26 August 2008). The inconsistent usage of meteorological data and models, such as mapping functions, causes systematics among the ACs, and differing parameterizations and constraints add noise to the troposphere parameter estimates. The empirical standard deviation of ZTD among the ACs with regard to an unweighted mean is 4.6 mm. The ratio of the analysis noise to the observation noise assessed by the operator/software impact (OSI) model is about 2.5. These and other effects have to be accounted for to improve the intra-technique combination of VLBI-derived troposphere parameters. While the largest systematics caused by inconsistent usage of meteorological data can be avoided and the application of different mapping functions can be considered by applying empirical corrections, the noise has to be modeled in the stochastic model of intra-technique combination. The application of different stochastic models shows no significant effects on the combined parameters but results in different mean formal errors: the mean formal errors of the combined ZTD are 2.3 mm (unweighted), 4.4 mm (diagonal), 8.6 mm [variance component (VC) estimation], and 8.6 mm (operator/software impact, OSI). On the one hand, the OSI model, i.e. the inclusion of off-diagonal elements in the cofactor-matrix, considers the reapplication of observations yielding a factor of about two for mean formal errors as compared to the diagonal approach. On the other hand, the combination based on VC estimation shows large differences among the VCs and exhibits a comparable scaling of formal errors. Thus, for the combination of troposphere parameters a combination of the two

  1. Effect of plasma surface interactions on PLT plasma parameters

    SciTech Connect

    Meservey, E.B.; Arunasalam, V.; Barnes, C.

    1980-07-01

    This paper gives a brief description of the geometry and parameters of the PLT tokamak, reviews some of the last four years' results that are particularly relevant to plasma-boundary interactions, and then concentrates on two specific problems.

  2. Derivation of Delaware Bay tidal parameters from space shuttle photography

    SciTech Connect

    Zheng, Quanan; Yan, Xiaohai; Klemas, V. )

    1993-06-01

    The tide-related parameters of the Delaware Bay are derived from space shuttle time-series photographs. The water areas in the bay are measured from interpretation maps of the photographs with a CALCOMP 9100 digitizer and ERDAS Image Processing System. The corresponding tidal levels are calculated using the exposure time annotated on the photographs. From these data, an approximate function relating the water area to the tidal level at a reference point is determined. Based on the function, the water areas of the Delaware Bay at mean high water (MHW) and mean low water (MLW), below 0 m, and for the tidal zone are inferred. With MHW and MLW areas and the mean tidal range, the authors calculate the tidal influx of the Delaware Bay, which is 2.76 x 1O[sup 9] m[sup 3]. Furthermore, the velocity of flood tide at the bay mouth is determined using the tidal flux and an integral of the velocity distribution function at the cross section between Cape Henlopen and Cape May. The result is 132 cm/s, which compares well with the data on tidal current charts.

  3. Interacting Dark Fluid in Anisotropic Universe with Dynamical Deceleration Parameter

    NASA Astrophysics Data System (ADS)

    Adhav, K. S.; Bokey, V. D.; Bansod, A. S.; Munde, S. L.

    2016-10-01

    In this paper we have studied the anisotropic and homogeneous Bianchi Type-I and V universe filled with Interacting Dark Matter and Holographic Dark Energy. The solutions of field equations are obtained for both models under the assumption of linearly varying deceleration parameter which yields dynamical deceleration parameter. It has been observed that the anisotropy of expansion dies out very quickly (soon after inflation) in both models (B-I, B-V). The physical and geometrical parameters for the both models have been obtained and discussed in details.

  4. Interacting Dark Fluid in Anisotropic Universe with Dynamical Deceleration Parameter

    NASA Astrophysics Data System (ADS)

    Adhav, K. S.; Bokey, V. D.; Bansod, A. S.; Munde, S. L.

    2016-06-01

    In this paper we have studied the anisotropic and homogeneous Bianchi Type-I and V universe filled with Interacting Dark Matter and Holographic Dark Energy. The solutions of field equations are obtained for both models under the assumption of linearly varying deceleration parameter which yields dynamical deceleration parameter. It has been observed that the anisotropy of expansion dies out very quickly (soon after inflation) in both models (B-I, B-V). The physical and geometrical parameters for the both models have been obtained and discussed in details.

  5. Toward the Computational Prediction of Muon Sites and Interaction Parameters

    NASA Astrophysics Data System (ADS)

    Bonfà, Pietro; De Renzi, Roberto

    2016-09-01

    The rapid developments of computational quantum chemistry methods and supercomputing facilities motivate the renewed interest in the analysis of the muon/electron interactions in μSR experiments with ab initio approaches. Modern simulation methods seem to be able to provide the answers to the frequently asked questions of many μSR experiments: where is the muon? Is it a passive probe? What are the interaction parameters governing the muon-sample interaction? In this review we describe some of the approaches used to provide quantitative estimations of the aforementioned quantities and we provide the reader with a short discussion on the current developments in this field.

  6. Validating a large geophysical data set: Experiences with satellite-derived cloud parameters

    NASA Technical Reports Server (NTRS)

    Kahn, Ralph; Haskins, Robert D.; Knighton, James E.; Pursch, Andrew; Granger-Gallegos, Stephanie

    1992-01-01

    We are validating the global cloud parameters derived from the satellite-borne HIRS2 and MSU atmospheric sounding instrument measurements, and are using the analysis of these data as one prototype for studying large geophysical data sets in general. The HIRS2/MSU data set contains a total of 40 physical parameters, filling 25 MB/day; raw HIRS2/MSU data are available for a period exceeding 10 years. Validation involves developing a quantitative sense for the physical meaning of the derived parameters over the range of environmental conditions sampled. This is accomplished by comparing the spatial and temporal distributions of the derived quantities with similar measurements made using other techniques, and with model results. The data handling needed for this work is possible only with the help of a suite of interactive graphical and numerical analysis tools. Level 3 (gridded) data is the common form in which large data sets of this type are distributed for scientific analysis. We find that Level 3 data is inadequate for the data comparisons required for validation. Level 2 data (individual measurements in geophysical units) is needed. A sampling problem arises when individual measurements, which are not uniformly distributed in space or time, are used for the comparisons. Standard 'interpolation' methods involve fitting the measurements for each data set to surfaces, which are then compared. We are experimenting with formal criteria for selecting geographical regions, based upon the spatial frequency and variability of measurements, that allow us to quantify the uncertainty due to sampling. As part of this project, we are also dealing with ways to keep track of constraints placed on the output by assumptions made in the computer code. The need to work with Level 2 data introduces a number of other data handling issues, such as accessing data files across machine types, meeting large data storage requirements, accessing other validated data sets, processing speed

  7. Bulk Surface Momentum Parameters for Satellite-Derived Vegetation Fields

    NASA Technical Reports Server (NTRS)

    Jasinski, Michael F.; Borak, Jordan; Crago, Richard

    2005-01-01

    The bulk aerodynamic parameters associated with the absorption of surface momentum by vegetated landscapes are theoretically estimated within the context of Raupach's roughness sublayer formulation. The parameters include the bulk plant drag coefficient, maximum u*/U(sub h), sheltering coefficient, and canopy area density at onset of sheltering. Parameters are estimated for the four principal IGBP land cover classes within the U.S. Southern Great Plains: evergreen needleleaf forests, grasslands, croplands, and open shrublands. The estimation approach applies the Method of Moments to roughness data from several international field experiments and other published sources. The results provide the necessary land surface parameters for satellite-based estimation of momentum aerodynamic roughness length and zero-plane displacement height for seasonally variable vegetation fields employed in most terrestrial and atmospheric simulation models used today. Construction of sample displacement and roughness maps over the Southern United States using MODIS land products demonstrates the potential of this approach for regional to global applications.

  8. Interactions of Isophorone Derivatives with DNA: Spectroscopic Studies

    PubMed Central

    Deiana, Marco; Matczyszyn, Katarzyna; Massin, Julien; Olesiak-Banska, Joanna; Andraud, Chantal; Samoc, Marek

    2015-01-01

    Interactions of three new isophorone derivatives, Isoa Isob and Isoc with salmon testes DNA have been investigated using UV-Vis, fluorescence and circular dichroism spectroscopic methods. All the studied compounds interact with DNA through intercalative binding mode. The stoichiometry of the isophorone/DNA adducts was found to be 1:1. The fluorescence quenching data revealed a binding interaction with the base pairs of DNA. The CD data indicate that all the investigated isophorones induce DNA modifications. PMID:26069963

  9. Derivative self-interactions for a massive vector field

    NASA Astrophysics Data System (ADS)

    Beltrán Jiménez, Jose; Heisenberg, Lavinia

    2016-06-01

    In this work we revisit the construction of theories for a massive vector field with derivative self-interactions such that only the 3 desired polarizations corresponding to a Proca field propagate. We start from the decoupling limit by constructing healthy interactions containing second derivatives of the Stueckelberg field with itself and also with the transverse modes. The resulting interactions can then be straightforwardly generalized beyond the decoupling limit. We then proceed to a systematic construction of the interactions by using the Levi-Civita tensors. Both approaches lead to a finite family of allowed derivative self-interactions for the Proca field. This construction allows us to show that some higher order terms recently introduced as new interactions trivialize in 4 dimensions by virtue of the Cayley-Hamilton theorem. Moreover, we discuss how the resulting derivative interactions can be written in a compact determinantal form, which can also be regarded as a generalization of the Born-Infeld lagrangian for electromagnetism. Finally, we generalize our results for a curved background and give the necessary non-minimal couplings guaranteeing that no additional polarizations propagate even in the presence of gravity.

  10. Study of some cosmological parameters for interacting new holographic dark energy model in f(T) gravity

    NASA Astrophysics Data System (ADS)

    Ranjit, Chayan; Rudra, Prabir

    2016-10-01

    The present work is based on the idea of an interacting framework of new holographic dark energy (HDE) with cold dark matter in the background of f(T) gravity. Here, we have considered the flat modified Friedmann universe for f(T) gravity which is filled with new HDE and dark matter. We have derived some cosmological parameters like deceleration parameter, equation of state (EoS) parameter, state-finder parameters, cosmographic parameters, Om parameter and graphically investigated the nature of these parameters for the above mentioned interacting scenario. The results are found to be consistent with the accelerating universe. Also, we have graphically investigated the trajectories in ω-ω‧ plane for different values of the interacting parameter and explored the freezing region and thawing region in ω-ω‧ plane. Finally, we have analyzed the stability of this model.

  11. Density functional theory studies of Pb (II) interaction with chitosan and its derivatives.

    PubMed

    Hassan, Basila; Muraleedharan, K; Abdul Mujeeb, V M

    2015-03-01

    Density functional theory (DFT) studies of Pb (II) ions interaction with biopolymer chitosan and its derivatives are presented. Schiff bases and N-alkylated/arylated derivatives of chitosan were characterized as adsorbents of lead ions and are studied at monomer level. Natural bond orbital (NBO) analysis was carried out for chitosan and derivatives to understand the donor-acceptor interactions. Molecular electrostatic potential (MEP) maps of the adsorbents were plotted with color code. Global reactivity parameters of adsorbents were calculated on the basis of frontier molecular orbital (FMO) energies. Structure of complexes formed between chitosan and derivatives with Pb (II) ion were examined at B3LYP/LanL2DZ level of DFT. The stability of the complexes are discussed based on the values of Eads. We observed that the N-reduced pyridine carboxaldehyde derivative of chitosan (RPC) forms more stable complex with Pb (II) ions than with other derivatves. PMID:25583020

  12. Interaction between subdaily Earth rotation parameters and GPS orbits

    NASA Astrophysics Data System (ADS)

    Panafidina, Natalia; Seitz, Manuela; Hugentobler, Urs

    2013-04-01

    In processing GPS observations the geodetic parameters like station coordinates and ERPs (Earth rotation parameters) are estimated w.r.t. the celestial reference system realized by the satellite orbits. The interactions/correlations between estimated GPS orbis and other parameters may lead to numerical problems with the solution and introduce systematic errors in the computed values: the well known correlations comprise 1) the correlation between the orbital parameters determining the orientation of the orbital plane in inertial space and the nutation and 2) in the case of estimating ERPs with subdaily resolution the correlation between retrograde diurnal polar motion and nutation (and so the respective orbital elements). In this contribution we study the interaction between the GPS orbits and subdaily model for the ERPs. Existing subdaily ERP model recommended by the IERS comprises ~100 terms in polar motion and ~70 terms in Universal Time at diurnal and semidiurnal tidal periods. We use a long time series of daily normal equation systems (NEQ) obtaine from GPS observations from 1994 till 2007 where the ERPs with 1-hour resolution are transformed into tidal terms and the influence of the tidal terms with different frequencies on the estimated orbital parameters is considered. We found that although there is no algebraic correlation in the NEQ between the individual orbital parameters and the tidal terms, the changes in the amplitudes of tidal terms with periods close to 24 hours can be better accmodated by systematic changes in the orbital parameters than for tidal terms with other periods. Since the variation in Earth rotation with the period of siderial day (23.93h, tide K1) in terrestrial frame has in inertial space the same period as the period of revolution of GPS satellites, the K1 tidal term in polar motion is seen by the satellites as a permanent shift. The tidal terms with close periods (from ~24.13h to ~23.80h) are seen as a slow rotation of the

  13. Natural Rubber-Filler Interactions: What Are the Parameters?

    PubMed

    Chan, Alan Jenkin; Steenkeste, Karine; Canette, Alexis; Eloy, Marie; Brosson, Damien; Gaboriaud, Fabien; Fontaine-Aupart, Marie-Pierre

    2015-11-17

    Reinforcement of a polymer matrix through the incorporation of nanoparticles (fillers) is a common industrial practice that greatly enhances the mechanical properties of the composite material. The origin of such mechanical reinforcement has been linked to the interaction between the polymer and filler as well as the homogeneous dispersion of the filler within the polymer matrix. In natural rubber (NR) technology, knowledge of the conditions necessary to achieve more efficient NR-filler interactions is improving continuously. This study explores the important physicochemical parameters required to achieve NR-filler interactions under dilute aqueous conditions by varying both the properties of the filler (size, composition, surface activity, concentration) and the aqueous solution (ionic strength, ion valency). By combining fluorescence and electron microscopy methods, we show that NR and silica interact only in the presence of ions and that heteroaggregation is favored more than homoaggregation of silica-silica or NR-NR. The interaction kinetics increases with the ion valence, whereas the morphology of the heteroaggregates depends on the size of silica and the volume percent ratio (dry silica/dry NR). We observe dendritic structures using silica with a diameter (d) of 100 nm at a ∼20-50 vol % ratio, whereas we obtain raspberry-like structures using silica with d = 30 nm particles. We observe that in liquid the interaction is controlled by the hydrophilic bioshell, in contrast to dried conditions, where hydrophobic polymer dominates the interaction of NR with the fillers. A good correlation between the nanoscopic aggregation behavior and the macroscopic aggregation dynamics of the particles was observed. These results provide insight into improving the reinforcement of a polymer matrix using NR-filler films.

  14. Natural Rubber-Filler Interactions: What Are the Parameters?

    PubMed

    Chan, Alan Jenkin; Steenkeste, Karine; Canette, Alexis; Eloy, Marie; Brosson, Damien; Gaboriaud, Fabien; Fontaine-Aupart, Marie-Pierre

    2015-11-17

    Reinforcement of a polymer matrix through the incorporation of nanoparticles (fillers) is a common industrial practice that greatly enhances the mechanical properties of the composite material. The origin of such mechanical reinforcement has been linked to the interaction between the polymer and filler as well as the homogeneous dispersion of the filler within the polymer matrix. In natural rubber (NR) technology, knowledge of the conditions necessary to achieve more efficient NR-filler interactions is improving continuously. This study explores the important physicochemical parameters required to achieve NR-filler interactions under dilute aqueous conditions by varying both the properties of the filler (size, composition, surface activity, concentration) and the aqueous solution (ionic strength, ion valency). By combining fluorescence and electron microscopy methods, we show that NR and silica interact only in the presence of ions and that heteroaggregation is favored more than homoaggregation of silica-silica or NR-NR. The interaction kinetics increases with the ion valence, whereas the morphology of the heteroaggregates depends on the size of silica and the volume percent ratio (dry silica/dry NR). We observe dendritic structures using silica with a diameter (d) of 100 nm at a ∼20-50 vol % ratio, whereas we obtain raspberry-like structures using silica with d = 30 nm particles. We observe that in liquid the interaction is controlled by the hydrophilic bioshell, in contrast to dried conditions, where hydrophobic polymer dominates the interaction of NR with the fillers. A good correlation between the nanoscopic aggregation behavior and the macroscopic aggregation dynamics of the particles was observed. These results provide insight into improving the reinforcement of a polymer matrix using NR-filler films. PMID:26488560

  15. Neurocognitive derivation of protein surface property from protein aggregate parameters

    PubMed Central

    Mishra, Hrishikesh; Lahiri, Tapobrata

    2011-01-01

    Current work targeted to predicate parametric relationship between aggregate and individual property of a protein. In this approach, we considered individual property of a protein as its Surface Roughness Index (SRI) which was shown to have potential to classify SCOP protein families. The bulk property was however considered as Intensity Level based Multi-fractal Dimension (ILMFD) of ordinary microscopic images of heat denatured protein aggregates which was known to have potential to serve as protein marker. The protocol used multiple ILMFD inputs obtained for a protein to produce a set of mapped outputs as possible SRI candidates. The outputs were further clustered and largest cluster centre after normalization was found to be a close approximation of expected SRI that was calculated from known PDB structure. The outcome showed that faster derivation of individual protein’s surface property might be possible using its bulk form, heat denatured aggregates. PMID:21572883

  16. Linear elastic properties derivation from microstructures representative of transport parameters.

    PubMed

    Hoang, Minh Tan; Bonnet, Guy; Tuan Luu, Hoang; Perrot, Camille

    2014-06-01

    It is shown that three-dimensional periodic unit cells (3D PUC) representative of transport parameters involved in the description of long wavelength acoustic wave propagation and dissipation through real foam samples may also be used as a standpoint to estimate their macroscopic linear elastic properties. Application of the model yields quantitative agreement between numerical homogenization results, available literature data, and experiments. Key contributions of this work include recognizing the importance of membranes and properties of the base material for the physics of elasticity. The results of this paper demonstrate that a 3D PUC may be used to understand and predict not only the sound absorbing properties of porous materials but also their transmission loss, which is critical for sound insulation problems. PMID:24907783

  17. Characterizing tissue with acoustic parameters derived from ultrasound data

    NASA Astrophysics Data System (ADS)

    Littrup, Peter J.; Duric, Nebojsa; Leach, Richard, Jr.; Azevedo, Steve G.; Candy, James V.; Moore, Thomas; Chambers, David H.; Mast, Jeffrey E.; Holsapple, Earle

    2002-04-01

    In contrast to standard reflection ultrasound (US), transmission US holds the promise of more thorough tissue characterization by generating quantitative acoustic parameters. We compare results from a conventional US scanner with data acquired using an experimental circular scanner operating at frequencies of 0.3 - 1.5 MHz. Data were obtained on phantoms and a normal, formalin-fixed, excised breast. Both reflection and transmission-based algorithms were used to generate images of reflectivity, sound speed and attenuation.. Images of the phantoms demonstrate the ability to detect sub-mm features and quantify acoustic properties such as sound speed and attenuation. The human breast specimen showed full field evaluation, improved penetration and tissue definition. Comparison with conventional US indicates the potential for better margin definition and acoustic characterization of masses, particularly in the complex scattering environments of human breast tissue. The use of morphology, in the context of reflectivity, sound speed and attenuation, for characterizing tissue, is discussed.

  18. Characterizing Tissue with Acoustic Parameters Derived from Ultrasound Data

    SciTech Connect

    Littrup, P; Duric, N; Leach, R R; Azevedo, S G; Candy, J V; Moore, T; Chambers, D H; Mast, J E; Johnson, S A; Holsapple, E

    2002-01-23

    In contrast to standard reflection ultrasound (US), transmission US holds the promise of more thorough tissue characterization by generating quantitative acoustic parameters. We compare results from a conventional US scanner with data acquired using an experimental circular scanner operating at frequencies of 0.3 - 1.5 MHz. Data were obtained on phantoms and a normal, formalin-fixed, excised breast. Both reflection and transmission-based algorithms were used to generate images of reflectivity, sound speed and attenuation.. Images of the phantoms demonstrate the ability to detect sub-mm features and quantify acoustic properties such as sound speed and attenuation. The human breast specimen showed full field evaluation, improved penetration and tissue definition. Comparison with conventional US indicates the potential for better margin definition and acoustic characterization of masses, particularly in the complex scattering environments of human breast tissue. The use of morphology, in the context of reflectivity, sound speed and attenuation, for characterizing tissue, is discussed.

  19. Peptiderive server: derive peptide inhibitors from protein-protein interactions.

    PubMed

    Sedan, Yuval; Marcu, Orly; Lyskov, Sergey; Schueler-Furman, Ora

    2016-07-01

    The Rosetta Peptiderive protocol identifies, in a given structure of a protein-protein interaction, the linear polypeptide segment suggested to contribute most to binding energy. Interactions that feature a 'hot segment', a linear peptide with significant binding energy compared to that of the complex, may be amenable for inhibition and the peptide sequence and structure derived from the interaction provide a starting point for rational drug design. Here we present a web server for Peptiderive, which is incorporated within the ROSIE web interface for Rosetta protocols. A new feature of the protocol also evaluates whether derived peptides are good candidates for cyclization. Fast computation times and clear visualization allow users to quickly assess the interaction of interest. The Peptiderive server is available for free use at http://rosie.rosettacommons.org/peptiderive. PMID:27141963

  20. Peptiderive server: derive peptide inhibitors from protein–protein interactions

    PubMed Central

    Sedan, Yuval; Marcu, Orly; Lyskov, Sergey; Schueler-Furman, Ora

    2016-01-01

    The Rosetta Peptiderive protocol identifies, in a given structure of a protein–protein interaction, the linear polypeptide segment suggested to contribute most to binding energy. Interactions that feature a ‘hot segment’, a linear peptide with significant binding energy compared to that of the complex, may be amenable for inhibition and the peptide sequence and structure derived from the interaction provide a starting point for rational drug design. Here we present a web server for Peptiderive, which is incorporated within the ROSIE web interface for Rosetta protocols. A new feature of the protocol also evaluates whether derived peptides are good candidates for cyclization. Fast computation times and clear visualization allow users to quickly assess the interaction of interest. The Peptiderive server is available for free use at http://rosie.rosettacommons.org/peptiderive. PMID:27141963

  1. Source parameters derived from seismic spectrum in the Jalisco block

    NASA Astrophysics Data System (ADS)

    Gutierrez, Q. J.; Escudero, C. R.; Nunez-Cornu, F. J.

    2012-12-01

    The direct measure of the earthquake fault dimension represent a complicated task nevertheless a better approach is using the seismic waves spectrum. With this method we can estimate the dimensions of the fault, the stress drop and the seismic moment. The study area comprises the complex tectonic configuration of Jalisco block and the subduction of the Rivera plate beneath the North American plate; this causes that occur in Jalisco some of the most harmful earthquakes and other related natural disasters. Accordingly it is important to monitor and perform studies that helps to understand the physics of earthquake rupture mechanism in the area. The main proposue of this study is estimate earthquake seismic source parameters. The data was recorded by the MARS network (Mapping the Riviera Subduction Zone) and the RESAJ network. MARS had 51 stations and settled in the Jalisco block; that is delimited by the mesoamerican trench at the west, the Colima grabben to the south, and the Tepic-Zacoalco to the north; for a period of time, of January 1, 2006 until December 31, 2007 Of this network was taken 104 events, the magnitude range of these was between 3 to 6.5 MB. RESJAL has 10 stations and is within the state of Jalisco, began to record since October 2011 and continues to record. We firs remove the trend, the mean and the instrument response, then manually chosen the S wave, then the multitaper method was used to obtain the spectrum of this wave and so estimate the corner frequency and the spectra level. We substitude the obtained in the equations of the Brune model to calculate the source parameters. Doing this we obtained the following results; the source radius was between .1 to 2 km, the stress drop was between .1 to 2 MPa.

  2. Power Saving Optimization for Linear Collider Interaction Region Parameters

    SciTech Connect

    Seryi, Andrei; /SLAC

    2009-10-30

    Optimization of Interaction Region parameters of a TeV energy scale linear collider has to take into account constraints defined by phenomena such as beam-beam focusing forces, beamstrahlung radiation, and hour-glass effect. With those constraints, achieving a desired luminosity of about 2E34 would require use of e{sup +}e{sup -} beams with about 10 MW average power. Application of the 'travelling focus' regime may allow the required beam power to be reduced by at least a factor of two, helping reduce the cost of the collider, while keeping the beamstrahlung energy loss reasonably low. The technique is illustrated for the 500 GeV CM parameters of the International Linear Collider. This technique may also in principle allow recycling the e{sup +}e{sup -} beams and/or recuperation of their energy.

  3. Derived parameters for NGC 6791 from high-metallicity isochrones

    NASA Technical Reports Server (NTRS)

    Dorman, Ben; Hufnagel, Beth

    1995-01-01

    We have computed 8, 10, and 12 Gyr isochrones and physically consistent models of zero-age red horizontal branch stars for stellar masses between 0.55 and 1.3 solar mass, all at (fe/H) = +0.15. Comparison to the NGC 6791 BVI photometry of Kaluzny & Udalski (1992) and Montgomery et al. (1994) yields an age of 10.0 +/- 0.5 Gyr at an apparent distance modulus 13.49 less than (m-M)(sub V) less than 13.70. The color offsets required to fit the isochrones, combined with the spectroscopic results of Friel & Janes (1993), imply that the foreground reddening to NGC 6791 lies in the range 0.24 greater than E(B -V) greater than 0.19 with +0.27 less than (Fe/H) less than + 0.44. These results are derived using a technique by which we predict color shifts and apply these to the isochrones to simulate progressively higher metallicities. The zero-age horizontal branch model suggest that the red horizontal branch stars of NGC 6791 have masses approximately less than 0.7 solar mass. The masses are similar to those found for M67 red horizontal branch stars by Tripicco et al. (1993) and for globular cluster red horizontal branch stars, even though the M67 progenitors are approximately 0.2 solar-mass more massive, while the progenitors of globular cluster horizontal branch stars are similarly less massive. This suggests the presence of a mechanism, not strongly dependent on metallicity, which reduces stellar envelopes on the zero-age horizontal branch to a given mass rather than by a given amount.

  4. Technique for Calculating Solution Derivatives With Respect to Geometry Parameters in a CFD Code

    NASA Technical Reports Server (NTRS)

    Mathur, Sanjay

    2011-01-01

    A solution has been developed to the challenges of computation of derivatives with respect to geometry, which is not straightforward because these are not typically direct inputs to the computational fluid dynamics (CFD) solver. To overcome these issues, a procedure has been devised that can be used without having access to the mesh generator, while still being applicable to all types of meshes. The basic approach is inspired by the mesh motion algorithms used to deform the interior mesh nodes in a smooth manner when the surface nodes, for example, are in a fluid structure interaction problem. The general idea is to model the mesh edges and nodes as constituting a spring-mass system. Changes to boundary node locations are propagated to interior nodes by allowing them to assume their new equilibrium positions, for instance, one where the forces on each node are in balance. The main advantage of the technique is that it is independent of the volumetric mesh generator, and can be applied to structured, unstructured, single- and multi-block meshes. It essentially reduces the problem down to defining the surface mesh node derivatives with respect to the geometry parameters of interest. For analytical geometries, this is quite straightforward. In the more general case, one would need to be able to interrogate the underlying parametric CAD (computer aided design) model and to evaluate the derivatives either analytically, or by a finite difference technique. Because the technique is based on a partial differential equation (PDE), it is applicable not only to forward mode problems (where derivatives of all the output quantities are computed with respect to a single input), but it could also be extended to the adjoint problem, either by using an analytical adjoint of the PDE or a discrete analog.

  5. Ultlra-intense laser-matter interactions at extreme parameters

    SciTech Connect

    Hegellich, Bjorn M

    2010-11-24

    The field of shortpulse lasers has seen rapid growth in the recent years with the three major boundaries of energy, pulse duration and repetition rate being pushed in ever extremer regions. At peak powers, already exceeding 10{sup 22} W/cm{sup 2}, in virtually every experiment in relativistic laser physics, the laser pulse interacts with a more or less extended and heated plasma, due to prepulses and ASE-like pedestals on ps - ns time scales. By developing a new technique for ultrahigh contrast, we were able to initiate the next paradigm shift in relativistic laser-matter interactions, allowing us to interact ultrarelativistic pulses volumetrically with overdense targets. This becomes possible by using target and laser parameters that will turn the target relativistically transparent during the few 10s-100s femtoseconds fo the interaction. Specifically, we interact an ultraintese, ultrahigh contrast pulse with solid density, free standing, nanometer diamond target. This paradigm change towards a volumetric overdense interaction in turn enables new particle acceleration mechanisms for both electrons and ions, as well as forward directed relativistic surface harmonics. We report here on first experiments done on those topics at the 200 TW Trident laser at Los Alamos as well as at the Ti:Sapphire system at MBI. We will compare the experimental data to massive large scale 3D simulations done on the prototype of LANL's new Petafiop supercomputer Roadrunner, which is leading the current top 500 list. Specifically, we developed a shortpulse OPA based pulse cleaning technique. Fielding it at the Trident 200 TW laser at Los Alamos, we were able to improve the pulse contrast by 6 orders of magnitude to better than 2 x 10{sup -12} at less than a ps. This enabled for the first time the interaction of a 100J, 200TW laser pulse with a truly solid target with virtually no expansion before the main pulse - target interaction, making possible the use of very thin targets, The

  6. An interacting dark energy model with nonminimal derivative coupling

    NASA Astrophysics Data System (ADS)

    Nozari, Kourosh; Behrouz, Noushin

    2016-09-01

    We study cosmological dynamics of an extended gravitational theory that gravity is coupled non-minimally with derivatives of a dark energy component and there is also a phenomenological interaction between the dark energy and dark matter. Depending on the direction of energy flow between the dark sectors, the phenomenological interaction gets two different signs. We show that this feature affects the existence of attractor solution, the rate of growth of perturbations and stability of the solutions. By considering an exponential potential as a self-interaction potential of the scalar field, we obtain accelerated scaling solutions that are attractors and have the potential to alleviate the coincidence problem. While in the absence of the nonminimal derivative coupling there is no attractor solution for phantom field when energy transfers from dark matter to dark energy, we show an attractor solution exists if one considers an explicit nonminimal derivative coupling for phantom field in this case of energy transfer. We treat the cosmological perturbations in this setup with details to show that with phenomenological interaction, perturbations can grow faster than the minimal case.

  7. Recursion method for deriving an energy-independent effective interaction

    NASA Astrophysics Data System (ADS)

    Suzuki, Kenji; Kumagai, Hiroo; Okamoto, Ryoji; Matsuzaki, Masayuki

    2014-04-01

    The effective-interaction theory has been one of the useful and practical methods for solving nuclear many-body problems based on the shell model. Various approaches have been proposed which are constructed in terms of the so-called Q̂ box and its energy derivatives introduced by Kuo et al. In order to find out a method of calculating them we make a decomposition of a full Hilbert space into subspaces (the Krylov subspaces) and transform a Hamiltonian to a block-tridiagonal form. This transformation brings about much simplification of the calculation of the Q̂ box. In the previous work a recursion method was derived for calculating the Q̂ box analytically on the basis of such transformation of the Hamiltonian. In the present study, by extending the recursion method for the Q̂ box, we derive another recursion relation to calculate the derivatives of the Q̂ box of arbitrary order. With the Q̂ box and its derivatives thus determined we apply them to the calculation of the E-independent effective interaction given in the so-called Lee-Suzuki (LS) method for a system with a degenerate unperturbed energy. We show that the recursion method can also be applied to the generalized LS scheme for a system with nondegenerate unperturbed energies. If the Hilbert space is taken to be sufficiently large, the theory provides an exact way of calculating the Q̂ box and its derivatives. This approach enables us to perform recursive calculations for the effective interaction to arbitrary order for both systems with degenerate and nondegenerate unperturbed energies.

  8. Derivation of tree stem structural parameters from static terrestrial laser scanning data

    NASA Astrophysics Data System (ADS)

    Tian, Wei; Lin, Yi; Liu, Yajing; Niu, Zheng

    2014-11-01

    Accurate tree-level characteristic information is increasingly demanded for forest management and environment protection. The cutting-edge remote sensing technique of terrestrial laser scanning (TLS) shows the potential of filling this gap. This study focuses on exploring the methods for deriving various tree stem structural parameters, such as stem position, diameter at breast height (DBH), the degree of stem shrinkage, and the elevation angle and azimuth angle of stem inclination. The data for test was collected with a Leica HDS6100 TLS system in Seurasaari, Southern Finland in September 2010. In the field, the reference positions and DBHs of 100 trees were measured manually. The isolation of individual trees is based on interactive segmentation of point clouds. The estimation of stem position and DBH is based on the schematic of layering and then least-square-based circle fitting in each layer. The slope of robust fit line between the height of each layer and DBH is used to characterize the stem shrinkage. The elevation angle of stem inclination is described by the angle between the ground plane and the fitted stem axis. The angle between the north direction and the fitted stem axis gives the azimuth angle of stem inclination. The estimation of the DBHs performed with R square (R2) of 0.93 and root mean square error (RMSE) of 0.038m.The average angle corresponding to stem shrinkage is -1.86°. The elevation angles of stem inclinations are ranged from 31° to 88.3°. The results have basically validated TLS for deriving multiple structural parameters of stem, which help better grasp tree specialties.

  9. Derivation of Cinnamon Blocks Leukocyte Attachment by Interacting with Sialosides.

    PubMed

    Lin, Wei-Ling; Guu, Shih-Yun; Tsai, Chan-Chuan; Prakash, Ekambaranellore; Viswaraman, Mohan; Chen, Hsing-Bao; Chang, Chuan-Fa

    2015-01-01

    Molecules derived from cinnamon have demonstrated diverse pharmacological activities against infectious pathogens, diabetes and inflammatory diseases. This study aims to evaluate the effect of the cinnamon-derived molecule IND02 on the adhesion of leukocytes to host cells. The anti-inflammatory ability of IND02, a pentameric procyanidin type A polyphenol polymer isolated from cinnamon alcohol extract, was examined. Pretreatment with IND02 significantly reduced the attachment of THP-1 cells or neutrophils to TNF-α-activated HUVECs or E-selectin/ICAM-1, respectively. IND02 also reduced the binding of E-, L- and P-selectins with sialosides. Furthermore, IND02 could agglutinate human red blood cells (RBC), and the agglutination could be disrupted by sialylated glycoprotein. Our findings demonstrate that IND02, a cinnamon-derived compound, can interact with sialosides and block the binding of selectins and leukocytes with sialic acids.

  10. Derivation of Cinnamon Blocks Leukocyte Attachment by Interacting with Sialosides

    PubMed Central

    Lin, Wei-Ling; Guu, Shih-Yun; Tsai, Chan-Chuan; Prakash, Ekambaranellore; Viswaraman, Mohan; Chen, Hsing-Bao; Chang, Chuan-Fa

    2015-01-01

    Molecules derived from cinnamon have demonstrated diverse pharmacological activities against infectious pathogens, diabetes and inflammatory diseases. This study aims to evaluate the effect of the cinnamon-derived molecule IND02 on the adhesion of leukocytes to host cells. The anti-inflammatory ability of IND02, a pentameric procyanidin type A polyphenol polymer isolated from cinnamon alcohol extract, was examined. Pretreatment with IND02 significantly reduced the attachment of THP-1 cells or neutrophils to TNF-α-activated HUVECs or E-selectin/ICAM-1, respectively. IND02 also reduced the binding of E-, L- and P-selectins with sialosides. Furthermore, IND02 could agglutinate human red blood cells (RBC), and the agglutination could be disrupted by sialylated glycoprotein. Our findings demonstrate that IND02, a cinnamon-derived compound, can interact with sialosides and block the binding of selectins and leukocytes with sialic acids. PMID:26076445

  11. Period dependent short-term shortwave and longwave feedback parameters derived from CERES observation

    NASA Astrophysics Data System (ADS)

    Kato, S.; Loeb, N. G.

    2015-12-01

    Period dependent shortwave and longwave feedback parameters are derived from the CERES EBAF-TOA data from March 2000 through May 2014. The algorithm uses time series of top-of-atmosphere reflected shortwave and emitted longwave irradiances, as well as surface skin temperature monthly deseasonalized anomalies. The time series is converted to the period domain by Fourier transfer and feedback parameters are derived from the amplitude ratio of the reflected shortwave or emitted longwave anomalies to the surface skin temperature anomalies multiplied by the cosine of the phase shift (FFT approach). While feedback parameters vary significantly depending on the period, they appear to converge as the period increases. Once they are sorted into period bins with the width of 1 year and mean values from all bins are averaged, the global mean value agrees with that derived from a simple linear regression to their uncertainty. The FFT approach provides a method to screen feedback parameters with shorter periods (less than a year) that contribute to the variability significantly. While feedback parameters derived from current CERES observation of 15 years differ from climate feedback parameters, their relationship to climate feedback parameters can be tested with climate models. The advantage of the FFT approach as opposed to a linear regression is that it can derive time-scale dependent feedback parameters. In addition, period dependent feedback parameters can be used to assess a linear system assumption for shorter periods (less than 10 years) and provide a guide on the length of the data record needed to accurately infer climate feedback parameters.

  12. Redox interactions of nitric oxide with dopamine and its derivatives.

    PubMed

    Antunes, Fernando; Nunes, Carla; Laranjinha, João; Cadenas, Enrique

    2005-03-15

    Nitric oxide (*NO) is a ubiquitous diffusible messenger in the central nervous system. *NO and derived nitrogen species may interact with catecholamines, thus, modifying not only its regulatory actions but also producing oxidants and free radicals that are likely to trigger toxic pathways in the nervous system. Oxidative pathways and chain oxidation reactions triggered by catecholamines may be broken by ascorbate and glutathione, of which there is ample supply in the brain. At the subcellular level, mitochondria and cytosolic dopamine storage vesicles are likely to provide site-specific settings for *NO and catecholamines interactions. Thus, a complex picture emerges in which the steady- state levels of the individual reactants, the rate constants of the reactions involved, the oxygen tension, and the compartmentalization of reactions determine the biological significance of the redox interactions between *NO and dopamine metabolism in the brain. The physiological relevance of *NO-driven chemical modifications of dopamine and its derivatives and the ensuing free radical production are discussed in connection with the neurodegeneration inherent in Parkinson's disease.

  13. Desert megadunes: a product of interactions between various parameters?

    NASA Astrophysics Data System (ADS)

    Yang, Xiaoping; Liu, Tao; Zhu, Bingqi; Li, Hongwei; Liu, Ziting

    2010-05-01

    the dunes from later generations. The final size and form of dunes in this desert appear to be decided indeed by interactions of multiple parameters including direction and strength of winds, bedrock landforms, as well as climatic fluctuations related to local, regional and global systems.

  14. On consistent kinetic and derivative interactions for gravitons

    SciTech Connect

    Noller, Johannes

    2015-04-17

    The only known fully ghost-free and consistent Lorentz-invariant kinetic term for a graviton (or indeed for any spin-2 field) is the Einstein-Hilbert term. Here we propose and investigate a new candidate family of kinetic interactions and their extensions to derivative interactions involving several spin-2 fields. These new terms generically break diffeomorphism invariance(s) and as a result can lead to the propagation of 5 degrees of freedom for a single spin-2 field — analogous to ghost-free Massive Gravity. We discuss under what circumstances these new terms can be used to build healthy effective field theories and in the process establish the ‘Jordan’ and ‘Einstein’ frame pictures for Massive-, Bi- and Multi-Gravity.

  15. Tacrine derivatives-acetylcholinesterase interaction: 1H NMR relaxation study.

    PubMed

    Delfini, Maurizio; Di Cocco, Maria Enrica; Piccioni, Fabiana; Porcelli, Fernando; Borioni, Anna; Rodomonte, Andrea; Del Giudice, Maria Rosaria

    2007-06-01

    Two acetylcholinesterase (AChE) inhibitors structurally related to Tacrine, 6-methoxytacrine (1a) and 9-heptylamino-6-methoxytacrine (1b), and their interaction with Electrophorus Electricus AChE were investigated. The complete assignment of the 1H and 13C NMR spectra of 1a and 1b was performed by mono-dimensional and homo- and hetero-correlated two-dimensional NMR experiments. This study was undertaken to elucidate the interaction modes between AChE and 1a and 1b in solution, using NMR. The interaction between the two inhibitors and AChE was studied by the analysis of the motional parameters non-selective and selective spin-lattice relaxation times, thereby allowing the motional state of 1a and 1b, both free and bound with AChE, to be defined. The relaxation data pointed out the ligands molecular moiety most involved in the binding with AChE. The relevant ligand/enzyme interaction constants were also evaluated for both compounds and resulted to be 859 and 5412M(-1) for 1a and1b, respectively.

  16. Comparisons of the Earth Rotation Parameters derived from the IPMS and the BIH.

    NASA Astrophysics Data System (ADS)

    Ishii, H.; Goto, Y.; Ishikawa, T.

    The Earth Rotation Parameters (ERP) derived from the IPMS are compared with the BIH for the period from 1967 to 1987 and the IRIS from 1980 to 1987. Differences in the pole positions derived from the IRIS and the IPMS were about 0.002 and 0.007 for x and y, and differences of UT1 - TAI is about -0″02. The pole positions of the IPMS do not show secular variations relative to those of the IRIS.

  17. Determination of the interaction parameter and topological scaling features of symmetric star polymers in dilute solution.

    PubMed

    Rai, Durgesh K; Beaucage, Gregory; Ratkanthwar, Kedar; Beaucage, Peter; Ramachandran, Ramnath; Hadjichristidis, Nikos

    2015-07-01

    Star polymers provide model architectures to understand the dynamic and rheological effects of chain confinement for a range of complex topological structures like branched polymers, colloids, and micelles. It is important to describe the structure of such macromolecular topologies using small-angle neutron and x-ray scattering to facilitate understanding of their structure-property relationships. Modeling of scattering from linear, Gaussian polymers, such as in the melt, has applied the random phase approximation using the Debye polymer scattering function. The Flory-Huggins interaction parameter can be obtained using neutron scattering by this method. Gaussian scaling no longer applies for more complicated chain topologies or when chains are in good solvents. For symmetric star polymers, chain scaling can differ from ν=0.5(d(f)=2) due to excluded volume, steric interaction between arms, and enhanced density due to branching. Further, correlation between arms in a symmetric star leads to an interference term in the scattering function first described by Benoit for Gaussian chains. In this work, a scattering function is derived which accounts for interarm correlations in symmetric star polymers as well as the polymer-solvent interaction parameter for chains of arbitrary scaling dimension using a hybrid Unified scattering function. The approach is demonstrated for linear, four-arm and eight-arm polyisoprene stars in deuterated p-xylene.

  18. Interactions of salicylic acid derivatives with calcite crystals.

    PubMed

    Ukrainczyk, Marko; Gredičak, Matija; Jerić, Ivanka; Kralj, Damir

    2012-01-01

    Investigation of basic interactions between the active pharmaceutical compounds and calcium carbonates is of great importance because of the possibility to use the carbonates as a mineral carrier in drug delivery systems. In this study the mode and extent of interactions of salicylic acid and its amino acid derivates, chosen as pharmaceutically relevant model compounds, with calcite crystals are described. Therefore, the crystal growth kinetics of well defined rhombohedral calcite seed crystals in the systems containing salicylic acid (SA), 5-amino salicylic acid (5-ASA), N-salicyloil-l-aspartic acid (N-Sal-Asp) or N-salicyloil-l-glutamic acid (N-Sal-Glu), were investigated. The precipitation systems were of relatively low initial supersaturation and of apparently neutral pH. The data on the crystal growth rate reductions in the presence of the applied salicylate molecules were analyzed by means of Cabrera & Vermileya's, and Kubota & Mullin's models of interactions of the dissolved additives and crystal surfaces. The crystal growth kinetic experiments were additionally supported with the appropriate electrokinetic, spectroscopic and adsorption measurements. The Langmuir adsorption constants were determined and they were found to be in a good correlation with values obtained from crystal growth kinetic analyses. The results indicated that salicylate molecules preferentially adsorb along the steps on the growing calcite surfaces. The values of average spacing between the adjacent salicylate adsorption active sites and the average distance between the neighboring adsorbed salicylate molecules were also estimated. PMID:21963207

  19. Interactions of salicylic acid derivatives with calcite crystals.

    PubMed

    Ukrainczyk, Marko; Gredičak, Matija; Jerić, Ivanka; Kralj, Damir

    2012-01-01

    Investigation of basic interactions between the active pharmaceutical compounds and calcium carbonates is of great importance because of the possibility to use the carbonates as a mineral carrier in drug delivery systems. In this study the mode and extent of interactions of salicylic acid and its amino acid derivates, chosen as pharmaceutically relevant model compounds, with calcite crystals are described. Therefore, the crystal growth kinetics of well defined rhombohedral calcite seed crystals in the systems containing salicylic acid (SA), 5-amino salicylic acid (5-ASA), N-salicyloil-l-aspartic acid (N-Sal-Asp) or N-salicyloil-l-glutamic acid (N-Sal-Glu), were investigated. The precipitation systems were of relatively low initial supersaturation and of apparently neutral pH. The data on the crystal growth rate reductions in the presence of the applied salicylate molecules were analyzed by means of Cabrera & Vermileya's, and Kubota & Mullin's models of interactions of the dissolved additives and crystal surfaces. The crystal growth kinetic experiments were additionally supported with the appropriate electrokinetic, spectroscopic and adsorption measurements. The Langmuir adsorption constants were determined and they were found to be in a good correlation with values obtained from crystal growth kinetic analyses. The results indicated that salicylate molecules preferentially adsorb along the steps on the growing calcite surfaces. The values of average spacing between the adjacent salicylate adsorption active sites and the average distance between the neighboring adsorbed salicylate molecules were also estimated.

  20. Comprehensive derivation of bond-valence parameters for ion pairs involving oxygen

    PubMed Central

    Gagné, Olivier Charles; Hawthorne, Frank Christopher

    2015-01-01

    Published two-body bond-valence parameters for cation–oxygen bonds have been evaluated via the root mean-square deviation (RMSD) from the valence-sum rule for 128 cations, using 180 194 filtered bond lengths from 31 489 coordination polyhedra. Values of the RMSD range from 0.033–2.451 v.u. (1.1–40.9% per unit of charge) with a weighted mean of 0.174 v.u. (7.34% per unit of charge). The set of best published parameters has been determined for 128 ions and used as a benchmark for the determination of new bond-valence parameters in this paper. Two common methods for the derivation of bond-valence parameters have been evaluated: (1) fixing B and solving for R o; (2) the graphical method. On a subset of 90 ions observed in more than one coordination, fixing B at 0.37 Å leads to a mean weighted-RMSD of 0.139 v.u. (6.7% per unit of charge), while graphical derivation gives 0.161 v.u. (8.0% per unit of charge). The advantages and disadvantages of these (and other) methods of derivation have been considered, leading to the conclusion that current methods of derivation of bond-valence parameters are not satisfactory. A new method of derivation is introduced, the GRG (generalized reduced gradient) method, which leads to a mean weighted-RMSD of 0.128 v.u. (6.1% per unit of charge) over the same sample of 90 multiple-coordination ions. The evaluation of 19 two-parameter equations and 7 three-parameter equations to model the bond-valence–bond-length relation indicates that: (1) many equations can adequately describe the relation; (2) a plateau has been reached in the fit for two-parameter equations; (3) the equation of Brown & Altermatt (1985 ▸) is sufficiently good that use of any of the other equations tested is not warranted. Improved bond-valence parameters have been derived for 135 ions for the equation of Brown & Altermatt (1985 ▸) in terms of both the cation and anion bond-valence sums using the GRG method and our complete data set. PMID

  1. First-principles derivation of reactive transport modeling parameters for particle tracking and PDE approaches

    NASA Astrophysics Data System (ADS)

    Hansen, Scott K.; Scher, Harvey; Berkowitz, Brian

    2014-07-01

    Both Eulerian and Lagrangian reactive transport simulations in natural media require selection of a parameter that controls the “promiscuity” of the reacting particles. In Eulerian models, measurement of this parameter may be difficult because its value will generally differ between natural (diffusion-limited) systems and batch experiments, even though both are modeled by reaction terms of the same form. And in Lagrangian models, there previously has been no a priori way to compute this parameter. In both cases, then, selection is typically done by calibration, or ad hoc. This paper addresses the parameter selection problem for Fickian transport by deriving, from first principles and D (the diffusion constant) the reaction-rate-controlling parameters for particle tracking (PT) codes and for the diffusion-reaction equation (DRE). Using continuous time random walk analysis, exact reaction probabilities are derived for pairs of potentially reactive particles based on D and their probability of reaction provided that they collocate. Simultaneously, a second PT scheme directly employing collocation probabilities is derived. One-to-one correspondence between each of D, the reaction radius specified for a PT scheme, and the DRE decay constant are then developed. These results serve to ground reactive transport simulations in their underlying thermodynamics, and are confirmed by simulations.

  2. Phase equilibrium calculations of ternary liquid mixtures with binary interaction parameters and molecular size parameters determined from molecular dynamics.

    PubMed

    Oh, Suk Yung; Bae, Young Chan

    2010-07-15

    The method presented in this paper was developed to predict liquid-liquid equilibria in ternary liquid mixtures by using a combination of a thermodynamic model and molecular dynamics simulations. In general, common classical thermodynamic models have many parameters which are determined by fitting a model with experimental data. This proposed method, however, provides a simple procedure for calculating liquid-liquid equilibria utilizing binary interaction parameters and molecular size parameters determined from molecular dynamics simulations. This method was applied to mixtures containing water, hydrocarbons, alcohols, chlorides, ketones, acids, and other organic liquids over various temperature ranges. The predicted results agree well with the experimental data without the use of adjustable parameters.

  3. The evolution of MICOS: Ancestral and derived functions and interactions

    PubMed Central

    Muñoz-Gómez, Sergio A; Slamovits, Claudio H; Dacks, Joel B; Wideman, Jeremy G

    2015-01-01

    The MItochondrial Contact Site and Cristae Organizing System (MICOS) is required for the biogenesis and maintenance of mitochondrial cristae as well as the proper tethering of the mitochondrial inner and outer membranes. We recently demonstrated that the core components of MICOS, Mic10 and Mic60, are near-ubiquitous eukaryotic features inferred to have been present in the last eukaryote common ancestor. We also showed that Mic60 could be traced to α-proteobacteria, which suggests that mitochondrial cristae evolved from α-proteobacterial intracytoplasmic membranes. Here, we extend our evolutionary analysis to MICOS-interacting proteins (e.g., Sam50, Mia40, DNAJC11, DISC-1, QIL1, Aim24, and Cox17) and discuss the implications for both derived and ancestral functions of MICOS. PMID:27065250

  4. Nonperturbative overproduction of axionlike particles via derivative interactions

    NASA Astrophysics Data System (ADS)

    Mazumdar, Anupam; Qutub, Saleh

    2016-02-01

    Axionlike particles (ALPs) are quite generic in many scenarios for physics beyond the Standard Model. They are pseudoscalar Nambu-Goldstone bosons that appear once any global U (1 ) symmetry is broken spontaneously. The ALPs can gain mass from various nonperturbative quantum effects, such as anomalies or instantons. ALPs can couple to the matter sector including a scalar condensate such as inflaton or moduli field via derivative interactions, which are suppressed by the axion decay constant, fχ . Although weakly interacting, the ALPs can be produced abundantly from the coherent oscillations of a homogeneous condensate. In this paper we will study such a scenario where the ALPs can be produced abundantly, and in some cases can even overclose the Universe via odd- and even-dimensional operators, as long as fχ/ΦI≪1 , where ΦI denotes the initial amplitude of the coherent oscillations of the scalar condensate, ϕ . We will briefly mention how such dangerous overproduction would affect dark matter and dark radiation abundances in the Universe.

  5. Structural consequences of weak interactions in dispirooxindole derivatives.

    PubMed

    Ravikumar, Krishnan; Sridhar, Balasubramanian; Nanubolu, Jagadeesh Babu; Karthik, Govindaraju; Reddy, Basi Venkata Subba

    2015-11-01

    Spiro scaffolds are being increasingly utilized in drug discovery due to their inherent three-dimensionality and structural variations, resulting in new synthetic routes to introduce spiro building blocks into more pharmaceutically active molecules. Multicomponent cascade reactions, involving the in situ generation of carbonyl ylides from α-diazocarbonyl compounds and aldehydes, and 1,3-dipolar cycloadditon with 3-arylideneoxindoles gave a novel class of dispirooxindole derivatives, namely 1,1''-dibenzyl-5'-(4-chlorophenyl)-4'-phenyl-4',5'-dihydrodispiro[indoline-3,2'-furan-3',3''-indoline]-2,2''-dione, C44H33ClN2O3, (I), 1''-acetyl-1-benzyl-5'-(4-chlorophenyl)-4'-phenyl-4',5'-dihydrodispiro[indoline-3,2'-furan-3',3''-indoline]-2,2''-dione, C39H29ClN2O4, (II), 1''-acetyl-1-benzyl-4',5'-diphenyl-4',5'-dihydrodispiro[indoline-3,2'-furan-3',3''-indoline]-2,2''-dione, C39H30N2O4, (III), and 1''-acetyl-1-benzyl-4',5'-diphenyl-4',5'-dihydrodispiro[indoline-3,2'-furan-3',3''-indoline]-2,2''-dione acetonitrile hemisolvate, C39H30N2O4·0.5C2H3N, (IV). All four compounds exist as racemic mixtures of the SSSR and RRRS stereoisomers. In these structures, the two H atoms of the dihydrofuran ring and the two substituted oxindole rings are in a trans orientation, facilitating intramolecular C-H···O and π-π interactions. These weak interactions play a prominent role in the structural stability and aid the highly regio- and diastereoselective synthesis. In each of the four structures, the molecular assembly in the crystal is also governed by weak noncovalent interactions. Compound (IV) is the solvated analogue of (III) and the two compounds show similar structural features. PMID:26524175

  6. Validating a large geophysical data set - Experiences with satellite-derived cloud parameters

    NASA Technical Reports Server (NTRS)

    Kahn, Ralph; Haskins, Robert D.; Knighton, James E.; Pursch, Andrew; Granger-Gallegos, Stephanie

    1991-01-01

    The goal of this study is to validate the global cloud parameters derived from the satellite-borne HIRS2 and MSU atmospheric sounding instrument measurements, and to use the analysis of these data as one prototype for studying large geophysical data sets in general. The HIRS2/MSU data set contains a total of 40 physical parameters, filling 25 MB/day; raw HIRS2/MSU data are available for a period exceeding 10 years. Validation involves developing a quantitative sense for the physical meaning of the derived parameters over the range of environmental conditions sampled. This is accomplished by comparing the spatial and temporal distributions of the derived quantities with similar measurements made using other techniques, and with model results. The need to work with Level 2 (point) data, rather than Level 3 (gridded) data for validation purposes is discussed, and some techniques developed for charting the assumptions made in deriving an algorithm and generating a code to produce geophysical quantities from measured radiances are presented.

  7. An empirically-derived taxonomy of interaction primitives for interactive cartography and geovisualization.

    PubMed

    Roth, Robert E

    2013-12-01

    Proposals to establish a 'science of interaction' have been forwarded from Information Visualization and Visual Analytics, as well as Cartography, Geovisualization, and GIScience. This paper reports on two studies to contribute to this call for an interaction science, with the goal of developing a functional taxonomy of interaction primitives for map-based visualization. A semi-structured interview study first was conducted with 21 expert interactive map users to understand the way in which map-based visualizations currently are employed. The interviews were transcribed and coded to identify statements representative of either the task the user wished to accomplish (i.e., objective primitives) or the interactive functionality included in the visualization to achieve this task (i.e., operator primitives). A card sorting study then was conducted with 15 expert interactive map designers to organize these example statements into logical structures based on their experience translating client requests into interaction designs. Example statements were supplemented with primitive definitions in the literature and were separated into two sorting exercises: objectives and operators. The objective sort suggested five objectives that increase in cognitive sophistication (identify, compare, rank, associate, & delineate), but exhibited a large amount of variation across participants due to consideration of broader user goals (procure, predict, & prescribe) and interaction operands (space-alone, attributes-in-space, & space-in-time; elementary & general). The operator sort suggested five enabling operators (import, export, save, edit, & annotate) and twelve work operators (reexpress, arrange, sequence, resymbolize, overlay, pan, zoom, reproject, search, filter, retrieve, & calculate). This taxonomy offers an empirically-derived and ecologically-valid structure to inform future research and design on interaction.

  8. Optimal parameters of gyrotrons with weak electron-wave interaction

    NASA Astrophysics Data System (ADS)

    Glyavin, M. Yu.; Oparina, Yu. S.; Savilov, A. V.; Sedov, A. S.

    2016-09-01

    In low-power gyrotrons with weak electron-wave interaction, there is a problem of determining the optimal length of the operating cavity, which is found as a result of a tradeoff between the enhancement of the electron efficiency and the increase in the Ohmic loss share with increasing cavity length. In fact, this is the problem of an optimal ratio between the diffraction and Ohmic Q-factors of the operating gyrotron mode, which determines the share of the radiated rf power lost in the cavity wall. In this paper, this problem is studied on the basis of a universal set of equations, which are appropriate for a wide class of electron oscillators with low efficiencies of the electron-wave interaction.

  9. Drug-DNA Interaction Studies of Acridone-Based Derivatives.

    PubMed

    Thimmaiah, Kuntebomanahalli; Ugarkar, Apoorva G; Martis, Elvis F; Shaikh, Mushtaque S; Coutinho, Evans C; Yergeri, Mayur C

    2015-01-01

    N10-alkylated 2-bromoacridones are a novel series of potent antitumor compounds. DNA binding studies of these compounds were carried out using spectrophotometric titrations, Circular dichroism (CD) measurements using Calf Thymus DNA (CT DNA). The binding constants were identified at a range of K=0.3 to 3.9×10(5) M(-1) and the percentage of hypochromism from the spectral titrations at 28-54%. This study has identified a compound 9 with the good binding affinity of K=0.39768×10(5) M(-1) with CT DNA. Molecular dynamics (MD) simulations have investigated the changes in structural and dynamic features of native DNA on binding to the active compound 9. All the synthesized compounds have increased the uptake of Vinblastine in MDR KBChR-8-5 cells to an extent of 1.25- to1.9-fold than standard modulator Verapamil of similar concentration. These findings allowed us to draw preliminary conclusions about the structural features of 2-bromoacridones and further chemical enhancement will improve the binding affinity of the acridone derivatives to CT-DNA for better drug-DNA interaction. The molecular modeling studies have shown mechanism of action and the binding modes of the acridones to DNA.

  10. An investigation of using an RQP based method to calculate parameter sensitivity derivatives

    NASA Technical Reports Server (NTRS)

    Beltracchi, Todd J.; Gabriele, Gary A.

    1989-01-01

    Estimation of the sensitivity of problem functions with respect to problem variables forms the basis for many of our modern day algorithms for engineering optimization. The most common application of problem sensitivities has been in the calculation of objective function and constraint partial derivatives for determining search directions and optimality conditions. A second form of sensitivity analysis, parameter sensitivity, has also become an important topic in recent years. By parameter sensitivity, researchers refer to the estimation of changes in the modeling functions and current design point due to small changes in the fixed parameters of the formulation. Methods for calculating these derivatives have been proposed by several authors (Armacost and Fiacco 1974, Sobieski et al 1981, Schmit and Chang 1984, and Vanderplaats and Yoshida 1985). Two drawbacks to estimating parameter sensitivities by current methods have been: (1) the need for second order information about the Lagrangian at the current point, and (2) the estimates assume no change in the active set of constraints. The first of these two problems is addressed here and a new algorithm is proposed that does not require explicit calculation of second order information.

  11. Site-Specific Reference Person Parameters and Derived Concentration Standards for the Savannah River Site

    SciTech Connect

    Stone, Daniel K.; Higley, Kathryn A.; Jannik, G. Timothy

    2014-05-01

    The U.S. Department of Energy Order 458.1 states that the compliance with the 1 mSv annual dose constraint to a member of the public may be demonstrated by calculating dose to the maximally exposed individual (MEI) or to a representative person. Historically, the MEI concept was used for dose compliance at the Savannah River Site (SRS) using adult dose coefficients and adult male usage parameters. For future compliance, SRS plans to use the representative person concept for dose estimates to members of the public. The representative person dose will be based on the reference person dose coefficients from the U.S. DOE Derived Concentration Technical Standard and on usage parameters specific to SRS for the reference and typical person. Usage parameters and dose coefficients were determined for inhalation, ingestion and external exposure pathways. The parameters for the representative person were used to calculate and tabulate SRS-specific derived concentration standards (DCSs) for the pathways not included in DOE-STD-1196-2011.

  12. Site-Specific Reference Person Parameters and Derived Concentration Standards for the Savannah River Site

    DOE PAGES

    Stone, Daniel K.; Higley, Kathryn A.; Jannik, G. Timothy

    2014-05-01

    The U.S. Department of Energy Order 458.1 states that the compliance with the 1 mSv annual dose constraint to a member of the public may be demonstrated by calculating dose to the maximally exposed individual (MEI) or to a representative person. Historically, the MEI concept was used for dose compliance at the Savannah River Site (SRS) using adult dose coefficients and adult male usage parameters. For future compliance, SRS plans to use the representative person concept for dose estimates to members of the public. The representative person dose will be based on the reference person dose coefficients from the U.S.more » DOE Derived Concentration Technical Standard and on usage parameters specific to SRS for the reference and typical person. Usage parameters and dose coefficients were determined for inhalation, ingestion and external exposure pathways. The parameters for the representative person were used to calculate and tabulate SRS-specific derived concentration standards (DCSs) for the pathways not included in DOE-STD-1196-2011.« less

  13. Superconducting order parameter in NbSe2 derived from the specific heat

    NASA Astrophysics Data System (ADS)

    Lin, Jiunn-Yuan; Shen, H. Y.; Yang, H. D.; Huang, C. L.; Sun, C. P.; Lee, T. K.; Berger, H.

    2007-03-01

    To resolve the discrepancies on the superconducting order parameter of quasi-2D NbSe2, the comprehensive specific heat measurements have been carried out.The thermodynamic consistence requires more than one energy scale of the order parameters The zero field data and the results of the mixed states respectively with H//c and Hc conclude: (1) δL=1.26 meV and δS=0.73 meV; (2) NSe(0)/ N(0)=11%˜20%; (3) δS is 3-D and like on the Se derived Fermi surface. This present scenario largely removes the dispute over the order parameter existing in the previous literature. The alternative anisotropic s-wave model is also discussed.

  14. CONSTRAINING THE SYMMETRY PARAMETERS OF THE NUCLEAR INTERACTION

    SciTech Connect

    Lattimer, James M.; Lim, Yeunhwan E-mail: yeunhwan.lim@gmail.com

    2013-07-01

    One of the major uncertainties in the dense matter equation of state has been the nuclear symmetry energy. The density dependence of the symmetry energy is important in nuclear astrophysics, as it controls the neutronization of matter in core-collapse supernovae, the radii of neutron stars and the thicknesses of their crusts, the rate of cooling of neutron stars, and the properties of nuclei involved in r-process nucleosynthesis. We show that fits of nuclear masses to experimental masses, combined with other experimental information from neutron skins, heavy ion collisions, giant dipole resonances, and dipole polarizabilities, lead to stringent constraints on parameters that describe the symmetry energy near the nuclear saturation density. These constraints are remarkably consistent with inferences from theoretical calculations of pure neutron matter, and, furthermore, with astrophysical observations of neutron stars. The concordance of experimental, theoretical, and observational analyses suggests that the symmetry parameters S{sub v} and L are in the range 29.0-32.7 MeV and 40.5-61.9 MeV, respectively, and that the neutron star radius, for a 1.4 M{sub Sun} star, is in the narrow window 10.7 km

  15. SP_Ace: a new code to derive stellar parameters and elemental abundances

    NASA Astrophysics Data System (ADS)

    Boeche, C.; Grebel, E. K.

    2016-03-01

    Context. Ongoing and future massive spectroscopic surveys will collect large numbers (106-107) of stellar spectra that need to be analyzed. Highly automated software is needed to derive stellar parameters and chemical abundances from these spectra. Aims: We developed a new method of estimating the stellar parameters Teff, log g, [M/H], and elemental abundances. This method was implemented in a new code, SP_Ace (Stellar Parameters And Chemical abundances Estimator). This is a highly automated code suitable for analyzing the spectra of large spectroscopic surveys with low or medium spectral resolution (R = 2000-20 000). Methods: After the astrophysical calibration of the oscillator strengths of 4643 absorption lines covering the wavelength ranges 5212-6860 Å and 8400-8924 Å, we constructed a library that contains the equivalent widths (EW) of these lines for a grid of stellar parameters. The EWs of each line are fit by a polynomial function that describes the EW of the line as a function of the stellar parameters. The coefficients of these polynomial functions are stored in a library called the "GCOG library". SP_Ace, a code written in FORTRAN95, uses the GCOG library to compute the EWs of the lines, constructs models of spectra as a function of the stellar parameters and abundances, and searches for the model that minimizes the χ2 deviation when compared to the observed spectrum. The code has been tested on synthetic and real spectra for a wide range of signal-to-noise and spectral resolutions. Results: SP_Ace derives stellar parameters such as Teff, log g, [M/H], and chemical abundances of up to ten elements for low to medium resolution spectra of FGK-type stars with precision comparable to the one usually obtained with spectra of higher resolution. Systematic errors in stellar parameters and chemical abundances are presented and identified with tests on synthetic and real spectra. Stochastic errors are automatically estimated by the code for all the parameters

  16. Alkylating derivative of oxotremorine interacts irreversibly with the muscarinic receptor

    SciTech Connect

    Ehlert, F.J.; Jenden, D.J.; Ringdahl, B.

    1984-03-05

    A 2-chloroethylamine derivative of oxotremorine was studied in pharmacological experiments and muscarinic receptor binding assays. The compound, N-(4-(2-chloroethylmethylamino)-2-butynyl)-2-pyrrolidone (BM 123), forms an aziridinium ion in aqueous solution at neutral pH that stimulates contractions of guinea pig ileum with a potency similar to that of oxotremorine. Following the initial stimulation, there is a long lasting period of lack of sensitivity of the guinea pig ileum to muscarinic agonists. BM 123 also produces muscarinic effects in vivo. When homogenates of the rat cerebral cortex were incubated with BM 123 and assayed subsequently in muscarinic receptor binding assays, a loss of binding capacity for the muscarinic antagonist, (/sup 3/H)N-methylscopolamine ((/sup 3/H)NMS), was noted without a change in affinity. Similar observations were made in (/sup 3/H)1-3-quinuclidinyl benzilate ((/sup 3/H)-QNB) binding assays on the forebrains of mice that had been injected with BM 123 24 hr earlier. The loss in receptor capacity for both (/sup 3/H)NMS and (/sup 3/H)-QNB was prevented by atropine treatment. Kinetic studies of the interaction of BM 123 with homogenates of the rat cerebral cortex in vitro showed that the half-time for the loss of (/sup 3/H)-QNB binding sites increased from 10 to 45 min as the concentration of BM 123 decreased from 10 to 1 ..mu..M. In contrast to the aziridinium ion, the parent 2-chloroethylamine compound and the alcoholic hydrolysis product were largely devoid of pharmacological and binding activity.

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

    PubMed

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

    2015-05-01

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

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

    PubMed Central

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

    2015-01-01

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

  19. Usefulness of Derived Frank Lead Parameters in Screening for Coronary Artery Disease and Cardiomyopathy

    NASA Technical Reports Server (NTRS)

    DePalma, J. L.; Schlegel, T. T.; Arenare, B.; Greco, E. C.; Starc, V.; Rahman, M. A.; Delgado, R.

    2007-01-01

    We investigated the accuracy of several known as well as newly-introduced derived Frank-lead ECG parameters in differentiating healthy individuals from patients with obstructive coronary artery disease (CAD) and cardiomyopathy (CM). Advanced high-fidelity 12-lead ECG tests (approx. 5-min supine) were first performed on a "training set" of 99 individuals: 33 with ischemic or dilated CM and low ejection fraction (EF less than 40%); 33 with catheterization-proven obstructive CAD but normal EF; and 33 age-/gender-matched healthy controls. The following derived Frank lead parameters were studied for their accuracy in detecting CAD and CM: the spatial ventricular gradient (VG), including its beat-to-beat coefficient of variability (VG CV); the spatial mean QRS (SM-QRS) and T-waves (SM-T) and their beat-to-beat coefficients of variability; the spatial ventricular activation time (VAT); the mean and maximum spatial QRS-T angles; and standard late potentials parameters (RMS40, fQRSD and LAS). Several of these parameters were accurate in discriminating between the control group and both diseased groups at p less than 0.0001. For example the fQRSD, VG CV, mean spatial QRS-T angle and VG minus SM-QRS (which is similar to the SM-T) had retrospective areas under the ROC curve of 0.78, 0.78, 0.80, and 0.84 (CAD vs. controls) and 0.93, 0.88, 0.98 and 0.99 (CM vs. controls), respectively. The single most effective parameter in discriminating between the CAD and CM groups was the spatial VAT (44 plus or minus 5.8 vs. 53 plus or minus 9.9 ms, p less than 0.0001), with an area under the ROC curve of 0.80. Since subsequent prospective analyses using new groups of patients and healthy subjects have yielded only slightly less accurate results, we conclude that derived Frank-lead parameters show great promise for potentially contributing to the development of a rapid and inexpensive resting ECG-based screening test for heart disease.

  20. Geometric order parameters derived from the Voronoi tessellation show signatures of the jamming transition.

    PubMed

    Morse, Peter K; Corwin, Eric I

    2016-01-28

    A jammed packing of frictionless spheres at zero temperature is perfectly specified by the network of contact forces from which mechanical properties can be derived. However, we can alternatively consider a packing as a geometric structure, characterized by a Voronoi tessellation which encodes the local environment around each particle. We find that this local environment characterizes systems both above and below jamming and changes markedly at the transition. A variety of order parameters derived from this tessellation carry signatures of the jamming transition, complete with scaling exponents. Furthermore, we define a real space geometric correlation function which also displays a signature of jamming. Taken together, these results demonstrate the validity and usefulness of a purely geometric approach to jamming. PMID:26611105

  1. Effects of membrane physical parameters on hematoporphyrin-derivative binding to liposomes: a spectroscopic study

    SciTech Connect

    Gross, E.; Malik, Z.; Ehrenberg, B.

    1987-01-01

    Physical parameters of membrane bilayers were studied for their effect on the binding of hematoporphyrin derivative (Hpd), which is used as a sensitizer in photodynamic therapy of cancerous tissues. The purpose of this study was to clarify which parameters were relevant, under physiological conditions, to the selectivity of Hpd binding to cancer cells. Fluorescence spectroscopy was used to measure the relative partitioning of the dye between the lipid and aqueous media. Increasing the microviscosity of the liposomes' membranes by various bilayer additives results in a strong reduction of Hpd binding, to an extent independent of the specific additive. The effect of temperature near the physiological value as well as the effect of cross membrane potential are small. Surface potential does not affect the binding constant, indicating that the binding species does not carry a net electric charge.

  2. Morphology analysis of EKG R waves using wavelets with adaptive parameters derived from fuzzy logic

    NASA Astrophysics Data System (ADS)

    Caldwell, Max A.; Barrington, William W.; Miles, Richard R.

    1996-03-01

    Understanding of the EKG components P, QRS (R wave), and T is essential in recognizing cardiac disorders and arrhythmias. An estimation method is presented that models the R wave component of the EKG by adaptively computing wavelet parameters using fuzzy logic. The parameters are adaptively adjusted to minimize the difference between the original EKG waveform and the wavelet. The R wave estimate is derived from minimizing the combination of mean squared error (MSE), amplitude difference, spread difference, and shift difference. We show that the MSE in both non-noise and additive noise environment is less using an adaptive wavelet than a static wavelet. Research to date has focused on the R wave component of the EKG signal. Extensions of this method to model P and T waves are discussed.

  3. Site-specific reference person parameters and derived concentration standards for the Savannah River Site.

    PubMed

    Stone, Daniel K; Higley, Kathryn A; Jannik, G Timothy

    2014-05-01

    The U.S. Department of Energy Order 458.1 states that the compliance with the 1 mSv annual dose constraint to a member of the public may be demonstrated by calculating dose to the maximally exposed individual (MEI) or to a representative person. Historically, the MEI concept was used for dose compliance at the Savannah River Site (SRS) using adult dose coefficients and adult male usage parameters. For future compliance, SRS plans to use the representative person concept for dose estimates to members of the public. The representative person dose will be based on the reference person dose coefficients from the U.S. DOE Derived Concentration Technical Standard and on usage parameters specific to SRS for the reference and typical person. Usage parameters and dose coefficients were determined for inhalation, ingestion and external exposure pathways. The reference intake for air, water, meat, dairy, freshwater fish, saltwater invertebrates, produce (fruits and vegetables), and grains for the 95th percentile are 17.4 m d, 2.19 L d, 220.6 g d, 674 cm d, 66.4 g d, 23.0 g d, 633.4 g d (448.5 g dand 631.7 g d) and 251.3 g d, respectively. For the 50th percentile: 13.4 m d, 0.809 L d, 86.4 g d, 187 cm d, 8.97 g d, 3.04 g d, 169.5 g d (45.9 g d and 145.6 g d), 101.3 g d, respectively. These parameters for the representative person were used to calculate and tabulate SRS-specific derived concentration standards (DCSs) for the pathways not included in DOE-STD-1196-2011.

  4. The Atlas of Vesta Spectral Parameters derived from Dawn/VIR data

    NASA Astrophysics Data System (ADS)

    Frigeri, A.; De Sanctis, M. C.; Ammannito, E.; Tosi, F.; Zambon, F.; Capaccioni, F.; Capria, M. T.; Palomba, E.; Longobardo, A.; Fonte, S.; Giardino, M.; Magni, G.; Jaumann, R.; Raymond, C. A.; Russell, C. T.

    2013-09-01

    The Dawn mission mapped Vesta from three different orbital heights during Survey orbit (2700 km altitude), HAMO (High Altitude Mapping Orbit, 700 km altitude), and LAMO (Low Altitude Mapping Orbit, 210 km altitude) [1]. From these orbits the Dawn's Visible and Infrared Mapping Spectrometer (VIR) acquired infrared and visible spectra from 0.2 to 5 microns, sampled in 864 channels with a spatial resolution reaching about 150 m/pixel. Studies of the comparison of spectra from remote sensed data and spectra from laboratory allows to synthesize spectral parameters, which can be combined to identify specific physical and compositional states. VIR spectra of Vesta, stored in about 4300 Planetary Data System (PDS) cubes, have been analyzed to derive spectral parameters, each of which is diagnostic of the associated mineralogy on the surface of the asteroid being observed [2]. Maps of spectral parameters show terrain units compositions in their stratigraphic context. Band centers and band depths are among the most important diagnostic parameters of the mineralogy in a spectrum. In most pyroxenes and in the basaltic achondrites there is a strong correlation between the position of BI center and BII center and the associated mineralogy. For example, orthopyroxene bands shift towards longer wavelengths with increasing amounts of iron, whereas clinopyroxene bands shift towards longer wavelengths with increasing calcium content. Band depth is related to scattering effects, thus can be related to the physical state of the material.

  5. Using a scoop to derive soil mechanical parameters on the surface of Mars

    NASA Astrophysics Data System (ADS)

    Kargl, Günter; Poganski, Joshua; Kömle, Norbert I.; Schweiger, Helmut; Macher, Wolfgang

    2016-04-01

    We will report on the possibility of using the scoop attached to the instrument deployment arm to perform soil mechanical experiments directly on the surface of Mars. The Phoenix mission flown 2009 had an instrument deployment arm which was also used to sample surface material indo instruments mounted on the lander deck. The flight spare of this arm will again be flown to Mars on board the InSight mission. Although, the primary purpose of the arm and the attached scoop was not soil mechanical investigations it was already demonstrated by the Phoenix mission that the arm can be used to perform auxiliary investigations of the surface materials. We will report on modelling efforts using a Discrete Element Software package to demonstrate that simple soil mechanical experiments can be used to derive essential material parameters like e.g. angle of repose and others. This is of particular interest since it would be possible to implement experiments using the hardware of the InSight mission. PIC Cross section cut through a trench dug out by the scoop and the pile of the deposed material which both can be used to derive soil mechanical parameters.

  6. Shifts of neutrino oscillation parameters in reactor antineutrino experiments with non-standard interactions

    NASA Astrophysics Data System (ADS)

    Li, Yu-Feng; Zhou, Ye-Ling

    2014-11-01

    ,15]. They induce effective four-fermion interactions after integrating out some heavy particles beyond the SM, where the heavy particles can be scalars, pseudo-scalars, vectors, axial-vectors, or tensors [16]. For reactor antineutrino experiments NSIs may appear in the antineutrino production and detection processes, and can modify the neutrino oscillation probability. Therefore, the neutrino mixing angles and mass-squared differences can be shifted and the mass ordering (MO) measurement will be affected. There are some previous discussions on NSIs in reactor antineutrino experiments [17-19] and other types of oscillation experiments [20]. In this work, we study the NSI effect in reactor antineutrino oscillations in both specific models and also the most general case. Taking JUNO as an example, we apply our general framework to the medium baseline reactor antineutrino experiment. We discuss how NSIs influence the standard 3-generation neutrino oscillation measurements and to what extent we can constrain the NSI parameters.The remaining part of this work is organized as follows. Section 2 is to derive the analytical formalism. We develop a general framework on the NSI effect in reaction antineutrino oscillations, and calculate the neutrino survival probability in the presence of NSIs. In Section 3, we give the numerical analysis for the JUNO experiment. We analyze the NSI impacts on the precision measurement of mass-squared differences and the determination of the neutrino mass ordering, and present the JUNO sensitivity of the relevant NSI parameters. Finally, we conclude in Section 4.

  7. Derivation of Forest Inventory Parameters for Carbon Estimation Using Terrestrial LIDAR

    NASA Astrophysics Data System (ADS)

    Prasad Kalwar, Om Prakash; Hussin, Yousif A.; Weir, Michael J. C.; Karna, Yogendra K.

    2016-06-01

    This research was conducted to derive forest sample plot inventory parameters from terrestrial LiDAR (T-LiDAR) for estimating above ground biomass (AGB)/carbon stocks in primary tropical rain forest. Inventory parameters of all sampled trees within circular plots of 500 m2 were collected from field observations while T-LiDAR data were acquired through multiple scanning using Reigl VZ-400 scanner. Pre-processing and registration of multiple scans were done in RSCAN PRO software. Point cloud constructing individual sampled tree was extracted and tree inventory parameters (diameter at breast height-DBH and tree height) were measured manually. AGB/carbon stocks were estimated using Chave et al., (2005) allometric equation. An average 80 % of sampled trees were detected from point cloud of the plots. The average of plots values of R2 and RMSE for manually measured DBHs were 0.95, 2.7 cm respectively. Similarly, the average of plots values of R2 and RMSE for manually measured trees heights were 0.77, 2.96 m respectively. The average value of AGB/carbon stocks estimated from field measurements and T-LiDAR manually derived DBHs and trees heights were 286 Mg ha-1 and 134 Mg ha-1; and 278 M ha-1 and 130 Mg ha-1 respectively. The R2 values for the estimated AGB and AGC were both 0.93 and corresponding RMSE values were 42.4 Mg ha-1 and 19.9 Mg ha-1 respectively. AGB and AGC were estimated with 14.8 % accuracy.

  8. Sensor-derived physical activity parameters can predict future falls in people with dementia

    PubMed Central

    Schwenk, Michael; Hauer, Klaus; Zieschang, Tania; Englert, Stefan; Mohler, Jane; Najafi, Bijan

    2014-01-01

    Background There is a need for simple clinical tools that can objectively assess fall risk in people with dementia. Wearable sensors seem to have potential for fall prediction, however, there has been limited work performed in this important area. Objective To explore the validity of sensor-derived physical activity (PA) parameters for predicting future falls in people with dementia. To compare sensor-based fall risk assessment with conventional fall risk measures. Methods A cohort study of people with confirmed dementia discharged from a geriatric rehabilitation ward. PA was quantified using 24-hour motion-sensor monitoring at the beginning of the study. PA parameters (percentage of walking, standing, sitting, lying; duration of single walking, standing, and sitting bouts) were extracted using specific algorithms. Conventional assessment included performance-based tests (Timed-up-and-go test, Performance-Oriented-Mobility-Assessment, 5-chair stand) and questionnaires (cognition, ADL-status, fear of falling, depression, previous faller). Outcome measures were fallers (at least one fall in the 3-month follow-up period) versus non-fallers. Results Seventy-seven people were included in the study (age 81.8 ± 6.3; community dwelling 88%, institutionalized 12%). Surprisingly, fallers and non-fallers did not differ on any conventional assessment (p= 0.069–0.991), except for ‘previous faller’ (p= 0.006). Interestingly, several PA parameters discriminated between groups. The ‘walking bouts average duration’, ‘longest walking bout duration’ and ‘walking bouts duration variability’ were lower in fallers, compared to non-fallers (p= 0.008–0.027). The ‘standing bouts average duration’ was higher in fallers (p= 0.050). Two variables, ‘walking bouts average duration’ [odds ratio (OR) 0.79, p= 0.012] and ‘previous faller’ [OR 4.44, p= 0.007] were identified as independent predictors for falls. The OR for a ‘walking bouts average duration’ of

  9. SITE SPECIFIC REFERENCE PERSON PARAMETERS AND DERIVED CONCENTRATION STANDARDS FOR THE SAVANNAH RIVER SITE

    SciTech Connect

    Jannik, T.

    2013-03-14

    The purpose of this report is twofold. The first is to develop a set of behavioral parameters for a reference person specific for the Savannah River Site (SRS) such that the parameters can be used to determine dose to members of the public in compliance with Department of Energy (DOE) Order 458.1 “Radiation Protection of the Public and the Environment.” A reference person is a hypothetical, gender and age aggregation of human physical and physiological characteristics arrived at by international consensus for the purpose of standardizing radiation dose calculations. DOE O 458.1 states that compliance with the annual dose limit of 100 mrem (1 mSv) to a member of the public may be demonstrated by calculating the dose to the maximally exposed individual (MEI) or to a representative person. Historically, for dose compliance, SRS has used the MEI concept, which uses adult dose coefficients and adult male usage parameters. Beginning with the 2012 annual site environmental report, SRS will be using the representative person concept for dose compliance. The dose to a representative person will be based on 1) the SRS-specific reference person usage parameters at the 95th percentile of appropriate national or regional data, which are documented in this report, 2) the reference person (gender and age averaged) ingestion and inhalation dose coefficients provided in DOE Derived Concentration Technical Standard (DOE-STD-1196-2011), and 3) the external dose coefficients provided in the DC_PAK3 toolbox. The second purpose of this report is to develop SRS-specific derived concentration standards (DCSs) for all applicable food ingestion pathways, ground shine, and water submersion. The DCS is the concentration of a particular radionuclide in water, in air, or on the ground that results in a member of the public receiving 100 mrem (1 mSv) effective dose following continuous exposure for one year. In DOE-STD-1196-2011, DCSs were developed for the ingestion of water, inhalation of

  10. Regionalization of subsurface stormflow parameters of hydrologic models: Derivation from regional analysis of streamflow recession curves

    NASA Astrophysics Data System (ADS)

    Ye, Sheng; Li, Hong-Yi; Huang, Maoyi; Ali, Melkamu; Leng, Guoyong; Leung, L. Ruby; Wang, Shao-wen; Sivapalan, Murugesu

    2014-11-01

    Subsurface stormflow is an important component of the rainfall-runoff response, especially in steep terrain. Its contribution to total runoff is, however, poorly represented in the current generation of land surface models. The lack of physical basis of these common parameterizations precludes a priori estimation of the stormflow (i.e. without calibration), which is a major drawback for prediction in ungauged basins, or for use in global land surface models. This paper is aimed at deriving regionalized parameterizations of the storage-discharge relationship relating to subsurface stormflow from a top-down empirical data analysis of streamflow recession curves extracted from 50 eastern United States catchments. Detailed regression analyses were performed between parameters of the empirical storage-discharge relationships and the controlling climate, soil and topographic characteristics. The regression analyses performed on empirical recession curves at catchment scale indicated that the coefficient of the power-law form storage-discharge relationship is closely related to the catchment hydrologic characteristics, which is consistent with the hydraulic theory derived mainly at the hillslope scale. As for the exponent, besides the role of field scale soil hydraulic properties as suggested by hydraulic theory, it is found to be more strongly affected by climate (aridity) at the catchment scale. At a fundamental level these results point to the need for more detailed exploration of the co-dependence of soil, vegetation and topography with climate.

  11. Resolution dependence of petrophysical parameters derived from X-ray tomography of chalk

    SciTech Connect

    Müter, D.; Sørensen, H. O.; Jha, D.; Harti, R.; Dalby, K. N.; Stipp, S. L. S.; Suhonen, H.; Feidenhans'l, R.; Engstrøm, F.

    2014-07-28

    X-ray computed tomography data from chalk drill cuttings were taken over a series of voxel dimensions, ranging from 320 to 25 nm. From these data sets, standard petrophysical parameters (porosity, surface area, and permeability) were derived and we examined the effect of the voxel dimension (i.e., image resolution) on these properties. We found that for the higher voxel dimensions, they are severely over or underestimated, whereas for 50 and 25 nm voxel dimension, the resulting values (5%–30% porosity, 0.2–2 m{sup 2}/g specific surface area, and 0.06–0.34 mD permeability) are within the expected range for this type of rock. We compared our results to macroscopic measurements and in the case of surface area, also to measurements using the Brunauer-Emmett-Teller (BET) method and found that independent of the degree of compaction, the results from tomography amount to about 30% of the BET method. Finally, we concluded that at 25 nm voxel dimension, the essential features of the nanoscopic pore network in chalk are captured but better resolution is still needed to derive surface area.

  12. Stabilization of Satellite derived Gravity Field Coefficients by Earth Rotation Parameters

    NASA Astrophysics Data System (ADS)

    Heiker, A.; Kutterer, H.; Müller, J.

    2009-04-01

    Recent gravity field missions (e.g. GRACE) provide monthly solutions for the time-variable Earth gravity field. However, the low-degree harmonic coefficients are poorly resolved, especially those of degree 2. The Earth rotation parameters (ERP), consisting of polar motion and lod, and the gravity field coefficients (GFC) of degree 2 are linked by the Euler-Liouville Equation. Thus the consideration of ERP time series helps to improve the estimates of GFC2. Due to the covariances between the GFC of degree 2 and further low-degree gravity field coefficients (up to degree 10) the residuals of the first group of coefficients has to be propagated to the second group in order to guarantee an overall consistency. Previous work has shown a significant influence of ERP on GFC up to degree 4 with the results depending on the covariances assumed a priori. This presentation shows the result of a consistent joint analysis of GRACE derived GFC and ERP in an extended Gauss-Helmert model which includes a sophisticated variance-covariance component estimation (VCCE). As the covariances of the GRACE derived GFC are largely not known, some different variance-covariance structures are assumed and estimated with the VCCE. The results are compared and discussed.

  13. Regionalization of subsurface stormflow parameters of hydrologic models: Derivation from regional analysis of streamflow recession curves

    SciTech Connect

    Ye, Sheng; Li, Hongyi; Huang, Maoyi; Ali, Melkamu; Leng, Guoyong; Leung, Lai-Yung R.; Wang, Shaowen; Sivapalan, Murugesu

    2014-07-21

    Subsurface stormflow is an important component of the rainfall–runoff response, especially in steep terrain. Its contribution to total runoff is, however, poorly represented in the current generation of land surface models. The lack of physical basis of these common parameterizations precludes a priori estimation of the stormflow (i.e. without calibration), which is a major drawback for prediction in ungauged basins, or for use in global land surface models. This paper is aimed at deriving regionalized parameterizations of the storage–discharge relationship relating to subsurface stormflow from a top–down empirical data analysis of streamflow recession curves extracted from 50 eastern United States catchments. Detailed regression analyses were performed between parameters of the empirical storage–discharge relationships and the controlling climate, soil and topographic characteristics. The regression analyses performed on empirical recession curves at catchment scale indicated that the coefficient of the power-law form storage–discharge relationship is closely related to the catchment hydrologic characteristics, which is consistent with the hydraulic theory derived mainly at the hillslope scale. As for the exponent, besides the role of field scale soil hydraulic properties as suggested by hydraulic theory, it is found to be more strongly affected by climate (aridity) at the catchment scale. At a fundamental level these results point to the need for more detailed exploration of the co-dependence of soil, vegetation and topography with climate.

  14. Systematic Improvement of Potential-Derived Atomic Multipoles and Redundancy of the Electrostatic Parameter Space.

    PubMed

    Jakobsen, Sofie; Jensen, Frank

    2014-12-01

    We assess the accuracy of force field (FF) electrostatics at several levels of approximation from the standard model using fixed partial charges to conformational specific multipole fits including up to quadrupole moments. Potential-derived point charges and multipoles are calculated using least-squares methods for a total of ∼1000 different conformations of the 20 natural amino acids. Opposed to standard charge fitting schemes the procedure presented in the current work employs fitting points placed on a single isodensity surface, since the electrostatic potential (ESP) on such a surface determines the ESP at all points outside this surface. We find that the effect of multipoles beyond partial atomic charges is of the same magnitude as the effect due to neglecting conformational dependency (i.e., polarizability), suggesting that the two effects should be included at the same level in FF development. The redundancy at both the partial charge and multipole levels of approximation is quantified. We present an algorithm which stepwise reduces or increases the dimensionality of the charge or multipole parameter space and provides an upper limit of the ESP error that can be obtained at a given truncation level. Thereby, we can identify a reduced set of multipole moments corresponding to ∼40% of the total number of multipoles. This subset of parameters provides a significant improvement in the representation of the ESP compared to the simple point charge model and close to the accuracy obtained using the complete multipole parameter space. The selection of the ∼40% most important multipole sites is highly transferable among different conformations, and we find that quadrupoles are of high importance for atoms involved in π-bonding, since the anisotropic electric field generated in such regions requires a large degree of flexibility.

  15. Derivative interactions and perturbative UV contributions in N Higgs doublet models

    NASA Astrophysics Data System (ADS)

    Kikuta, Yohei; Yamamoto, Yasuhiro

    2016-05-01

    We study the Higgs derivative interactions on models including arbitrary number of the Higgs doublets. These interactions are generated by two ways. One is higher order corrections of composite Higgs models, and the other is integration of heavy scalars and vectors. In the latter case, three point couplings between the Higgs doublets and these heavy states are the sources of the derivative interactions. Their representations are constrained to couple with the doublets. We explicitly calculate all derivative interactions generated by integrating out. Their degrees of freedom and conditions to impose the custodial symmetry are discussed. We also study the vector boson scattering processes with a couple of two Higgs doublet models to see experimental signals of the derivative interactions. They are differently affected by each heavy field.

  16. Emergent Learning and Interactive Media Artworks: Parameters of Interaction for Novice Groups

    ERIC Educational Resources Information Center

    Kawka, Marta; Larkin, Kevin; Danaher, P. A.

    2011-01-01

    Emergent learning describes learning that occurs when participants interact and distribute knowledge, where learning is self-directed, and where the learning destination of the participants is largely unpredictable (Williams, Karousou, & Mackness, 2011). These notions of learning arise from the topologies of social networks and can be applied to…

  17. Intermolecular interaction of thiosemicarbazone derivatives to solvents and a potential Aedes aegypti target

    NASA Astrophysics Data System (ADS)

    da Silva, João Bosco P.; Hallwass, Fernando; da Silva, Aluizio G.; Moreira, Diogo Rodrigo; Ramos, Mozart N.; Espíndola, José Wanderlan P.; de Oliveira, Ana Daura T.; Brondani, Dalci José; Leite, Ana Cristina L.; Merz, Kenneth M.

    2015-08-01

    DFT calculations were used to access information about structure, energy and electronic properties of series of phenyl- and phenoxymethyl-(thio)semicarbazone derivatives with demonstrated activity against the larvae of Aedes aegypti in stage L4. The way as the thiosemicarbazone derivatives can interact with solvents like DMSO and water were analyzed from the comparison between calculated and experimental 1H NMR chemical shifts. The evidences of thiosemicarbazone derivatives making H-bond interaction to solvent have provide us insights on how they can interact with a potential A. aegypti's biological target, the Sterol Carrier Protein-2.

  18. Use of remote sensing derived parameters in a crop model for biomass prediction of hay crop

    NASA Astrophysics Data System (ADS)

    El Hajj, Mohammad; Baghdadi, Nicolas; Cheviron, Bruno; Belaud, Gilles; Zribi, Mehrez

    2016-04-01

    Pre-harvest yield forecasting is a critical challenge for producers, especially for large agricultural areas. During previous decades, numerous crop models were developed to predict crop growth and yield at daily time, most often for wheat or maize, and also for grasslands. Crop models require several input parameters that describe soil properties (e.g. field capacity), plant characteristics (e.g. maximal rooting depth) and management options (e.g. sowing dates, irrigation and harvest dates), which are referred to as the soil, plant and management families of parameters. Remote sensing technology has been extensively applied to identify spatially distributed values of some of the accessible parameters in the soil, plant and management families. The aim of this study was to address the feasibility, merits and limitations of forcing remote-sensing-derived parameters (LAI values, harvest and irrigation dates) in the PILOTE crop model, targeting the Total Dry Matter (TDM) of hay crops. Results show that optical images are suitable to feed PILOTE with LAI values without inducing significant errors on the predicted Total Dry Matter (TDM) values (Root Mean Square Error "RMSE" = 0.41 t/ha and Mean Absolute Percentage Error "MAPE" = 22%). Moreover, optical images with revisit times lower than 16 days are adequate to feed PILOTE with remotely sensed harvest dates (RMSE < 0.44 t/ha, MAPE < 10.8%). Finally, feeding PILOTE with noisy irrigation dates that were estimated from SAR images also enabled reliable model predictions, at least when attaching a random uncertainty of "only" 3 days to the real known irrigation dates. The case of one or several undetected irrigations has also been explored, with the expected conclusion that undetected irrigations significantly affect model predictions only in dry periods. For the tested soil properties and climatic conditions, a maximum underestimation of TDM of approximately 1.55 t/ha (reference TDM of 3.43 t/ha) was observed in the second

  19. Interatomic interactions and thermodynamic parameters in dilute solid solutions of the Ag-Au system

    NASA Astrophysics Data System (ADS)

    Bogdanov, V. I.; Bol'shov, L. A.; Korneichuk, E. A.; Popov, V. A.; Korneichuk, S. K.; Badanin, D. A.

    2015-07-01

    The thermodynamic parameters of interaction and the enthalpy parameters are of fundamental importance in the theory of solutions, i.e., the coefficients of the expansion of partial excess thermodynamic functions into series in terms of the concentrations of the dissolved components. In the approximation of pairwise interactions between the impurity atoms in the solution, the above parameters can be computed using the methods of the density-functional theory in the electron theory of alloys. As an example, the substitutional solid solutions of Au in Ag have been chosen, which are formed by atoms of the components with close chemical properties, in which the deformation interactions should be small, and in which there is no need to take into account the complex magnetic contributions to the pair potentials. The total energy of the dilute solution of Au in Ag and the contributions from the chemical and strain-induced interactions to the potentials of pairwise interactions are calculated up to the seventh coordination shell. Quite satisfactory agreement with the thermodynamic parameters obtained from the experimental data has been obtained.

  20. Reference values for volumetric capnography-derived non-invasive parameters in healthy individuals.

    PubMed

    Tusman, Gerardo; Gogniat, Emiliano; Bohm, Stephan H; Scandurra, Adriana; Suarez-Sipmann, Fernando; Torroba, Agustin; Casella, Federico; Giannasi, Sergio; Roman, Eduardo San

    2013-06-01

    The aim of this study was to determine typical values for non-invasive volumetric capnography (VCap) parameters for healthy volunteers and anesthetized individuals. VCap was obtained by a capnograph connected to the airway opening. We prospectively studied 33 healthy volunteers 32 ± 6 years of age weighing 70 ± 13 kg at a height of 171 ± 11 cm in the supine position. Data from these volunteers were compared with a cohort of similar healthy anesthetized patients ventilated with the following settings: tidal volume (VT) of 6-8 mL/kg, respiratory rate 10-15 bpm, PEEP of 5-6 cmH₂O and FiO₂ of 0.5. Volunteers showed better clearance of CO₂ compared to anesthetized patients as indicated by (median and interquartile range): (1) an increased elimination of CO₂ per mL of VT of 0.028 (0.005) in volunteers versus 0.023 (0.003) in anesthetized patients, p < 0.05; (2) a lower normalized slope of phase III of 0.26 (0.17) in volunteers versus 0.39 (0.38) in anesthetized patients, p < 0.05; and (3) a lower Bohr dead space ratio of 0.23 (0.05) in volunteers versus 0.28 (0.05) in anesthetized patients, p < 0.05. This study presents reference values for non-invasive volumetric capnography-derived parameters in healthy individuals. Mechanical ventilation and anesthesia altered these values significantly. PMID:23389294

  1. The Atlas of Vesta Spectral Parameters derived from the mapping spectrometer VIR onboard NASA/Dawn

    NASA Astrophysics Data System (ADS)

    Frigeri, A.; De Sanctis, M.; Ammannito, E.; Tosi, F.; Capria, M.; Capaccioni, F.; Zambon, F.; Palomba, E.; Magni, G.; Jaumann, R.; Raymond, C. A.; Russell, C. T.

    2013-12-01

    From 2011 to 2012 the Visible and Infrared Mapping Spectrometer (VIR) onboard NASA/Dawn spacecraft has mapped the surface of Vesta from three different orbital heights, acquiring infrared and visible spectra from 0.2 to 5 microns, sampled in 864 channels with a spatial resolution up to about 150 m/pixel. From the large amount of spectra retrieved we have derived spectral parameters which can be combined to identify specific physical and compositional states. To start with, we have computed the band center and depth for band I and band II of pyroxenes. Pyroxene's band center I and II are commonly associated with a compositional variation. For example, orthopyroxene bands shift towards longer wavelengths with increasing amounts of iron, while clinopyroxene bands shift towards longer wavelengths with increasing calcium content. Band depths are related to scattering effects, associated to the abundance and the grain size of the absorber. Mapping these parameters on the surface allow to detect terrain units compositions and physical-state in their stratigraphic context. We have produced an atlas of digital maps, projected following the 15-quadrangle scheme commonly adopted for small sized planetary bodies. The digital maps have geospatial metadata and are available in GIS and other scientific programming language formats. A special imagery product has been produced, where the geomorphologic context from the Framing Camera, and the IAU nomenclature have been added to the mineralogic maps. This way we have both quantitative digital maps and print-ready maps. Digital maps are useful in statistical and geo-processing studies, while print-ready maps represent an easy to be consulted high-level data products. As with the atlas we are combining data acquired at very different observing geometries and in different phases of the mission, filtering has been necessary and an iterative process to project data produces results that are incrementally more consistent as we detect and

  2. The derivation of constraints on the msugra parameter space from the entropy of dark matter halos

    SciTech Connect

    Cabral-Rosetti, L. G.; Mondragon, M.; Nellen, L.; Nunez, D.; Sussmann, R.; Zavala, J.

    2009-04-20

    We derive an expression for the entropy of a present dark matter halo described by a Navarro-Frenk-White modified model with a central core. We obtain an expression for the relic abundance of neutralinos by comparing this entropy of the halo with the value it had during the freeze-out era. Using WMAP observations, we constrain the parameter space for mSUGRA models. Combining our results with the usual abundance criteria, we are able to discriminate clearly among different validity regions for tan {beta} values. For this, we require both criteria to be consistent within a 2{sigma} bound of the WMAP observations for the relic density: 0.112<{omega}h{sup 2}<0.122. We find that for sgn {mu} = +1, small values of tan {beta} are not favored; only for tan {beta}{approx}50 are both criteria significantly consistent. Both criteria allow us to put a lower bound on the neutralino mass, m{sub {chi}}{>=}141 GeV.

  3. CONNECTION BETWEEN DYNAMICALLY DERIVED INITIAL MASS FUNCTION NORMALIZATION AND STELLAR POPULATION PARAMETERS

    SciTech Connect

    McDermid, Richard M.; Cappellari, Michele; Bayet, Estelle; Bureau, Martin; Davies, Roger L.; Alatalo, Katherine; Blitz, Leo; Bois, Maxime; Bournaud, Frédéric; Duc, Pierre-Alain; Davis, Timothy A.; De Zeeuw, P. T.; Emsellem, Eric; Kuntschner, Harald; Khochfar, Sadegh; Krajnović, Davor; Morganti, Raffaella; Oosterloo, Tom; Naab, Thorsten; and others

    2014-09-10

    We report on empirical trends between the dynamically determined stellar initial mass function (IMF) and stellar population properties for a complete, volume-limited sample of 260 early-type galaxies from the ATLAS{sup 3D} project. We study trends between our dynamically derived IMF normalization α{sub dyn} ≡ (M/L){sub stars}/(M/L){sub Salp} and absorption line strengths, and interpret these via single stellar population-equivalent ages, abundance ratios (measured as [α/Fe]), and total metallicity, [Z/H]. We find that old and alpha-enhanced galaxies tend to have on average heavier (Salpeter-like) mass normalization of the IMF, but stellar population does not appear to be a good predictor of the IMF, with a large range of α{sub dyn} at a given population parameter. As a result, we find weak α{sub dyn}-[α/Fe] and α{sub dyn} –Age correlations and no significant α{sub dyn} –[Z/H] correlation. The observed trends appear significantly weaker than those reported in studies that measure the IMF normalization via the low-mass star demographics inferred through stellar spectral analysis.

  4. High-resolution polar climate parameters derived from 1-km AVHRR data

    SciTech Connect

    Hutchinson, T.A.; Scambos, T.A.

    1997-11-01

    This paper describes the development of a time-series of composites of albedo, surface temperature, and sea ice motion. The composites will be generated from high-resolution (Local Area Coverage and High Resolution Picture Transmission) Advanced Very High Resolution Radiometer (AVHRR). Composites of albedo and surface (skin) temperature will be derived from AVHRR data within three hours of two selected local times (0400 and 1400 for the northern hemisphere, and 0200 and 1600 for the southern hemisphere) for each day. These products will be gridded at 1.25 km cell size in an equal-area projection compatible with recent gridded products from Special Sensor Microwave/Imager data and planned products from the TIROS Operational Verticle Sounder and other AVHRR data sets. Sea ice motion will be calculated once per day by comparing clear-sky image data of sea ice over a three-day period, and reported on a 1.25 km grid. A brief discussion of a reconnaissance survey of the output geophysical parameters for the Northern Hemisphere between August and October 1993 is also presented. 9 refs., 5 figs., 2 tabs.

  5. Effect of including torsional parameters for histidine-metal interactions in classical force fields for metalloproteins.

    PubMed

    Mera-Adasme, Raúl; Sadeghian, Keyarash; Sundholm, Dage; Ochsenfeld, Christian

    2014-11-20

    Classical force-field parameters of the metal site of metalloproteins usually comprise only the partial charges of the involved atoms, as well as the bond-stretching and bending parameters of the metal-ligand interactions. Although for certain metal ligands such as histidine residues, the torsional motions at the metal site play an important role for the dynamics of the protein, no such terms have been considered to be crucial in the parametrization of the force fields, and they have therefore been omitted in the parametrization. In this work, we have optimized AMBER-compatible force-field parameters for the reduced state of the metal site of copper, zinc superoxide dismutase (SOD1) and assessed the effect of including torsional parameters for the histidine-metal interactions in molecular dynamics simulations. On the basis of the obtained results, we recommend that torsion parameters of the metal site are included when processes at the metal site are investigated or when free-energy calculations are performed. As the torsion parameters mainly affect the structure of the metal site, other kinds of structural studies can be performed without considering the torsional parameters of the metal site.

  6. Effect of including torsional parameters for histidine-metal interactions in classical force fields for metalloproteins.

    PubMed

    Mera-Adasme, Raúl; Sadeghian, Keyarash; Sundholm, Dage; Ochsenfeld, Christian

    2014-11-20

    Classical force-field parameters of the metal site of metalloproteins usually comprise only the partial charges of the involved atoms, as well as the bond-stretching and bending parameters of the metal-ligand interactions. Although for certain metal ligands such as histidine residues, the torsional motions at the metal site play an important role for the dynamics of the protein, no such terms have been considered to be crucial in the parametrization of the force fields, and they have therefore been omitted in the parametrization. In this work, we have optimized AMBER-compatible force-field parameters for the reduced state of the metal site of copper, zinc superoxide dismutase (SOD1) and assessed the effect of including torsional parameters for the histidine-metal interactions in molecular dynamics simulations. On the basis of the obtained results, we recommend that torsion parameters of the metal site are included when processes at the metal site are investigated or when free-energy calculations are performed. As the torsion parameters mainly affect the structure of the metal site, other kinds of structural studies can be performed without considering the torsional parameters of the metal site. PMID:25410708

  7. Deriving structural parameters of semi-resolved star clusters. FitClust: a program for crowded fields

    NASA Astrophysics Data System (ADS)

    Narbutis, D.; Semionov, D.; Stonkutė, R.; de Meulenaer, P.; Mineikis, T.; Bridžius, A.; Vansevičius, V.

    2014-09-01

    Context. An automatic tool to derive structural parameters of semi-resolved star clusters located in crowded stellar fields in nearby galaxies is needed for homogeneous processing of archival frames. Aims: We have developed a program that automatically derives the structural parameters of star clusters and estimates errors by accounting for individual stars and variable sky background. Methods: Models of observed frames consist of the cluster's surface brightness distribution, convolved with a point spread function; the stars, represented by the same point spread function; and a smoothly variable sky background. The cluster's model is fitted within a large radius by using the Levenberg-Marquardt and Markov chain Monte Carlo algorithms to derive structural parameters, the flux of the cluster, and individual fluxes of all well-resolved stars. Results: FitClust, a program to derive structural parameters of semi-resolved clusters in crowded stellar fields, was developed and is available for free use. The program was tested on simulated cluster frames, and was used to measure clusters of the M31 galaxy in Subaru Suprime-Cam frames. Conclusions: Accounting for bright resolved stars and variable sky background significantly improves the accuracy of derived structural parameters of star clusters. However, their uncertainty remains dominated by the stochastic noise of unresolved stars.

  8. Erosion relevant topographical parameters derived from different height models - a comparative study from the Indian Lesser Himalayas

    NASA Astrophysics Data System (ADS)

    Datta, Pawanjeet; Schack-Kirchner, Helmer; Maier, Martin

    2010-05-01

    Topography is a crucial surface characteristic in soil erosion modelling studies. Soil erosion models use a digital elevation model (DEM) to derive the topographical characteristics. In a majority of cases, it is incorporated as a given parameter and is not tested extensively in contrast to soil, land use and climate related parameters. However, the data accuracy in case of topographical parameters depends largely on the derivation method and the resolution of the DEM. This study compares erosion relevant parameters - elevation, slope, aspect and topographical LS-factor computed from three DEMs at original resolutions and a 20m interpolated resolution for a 13 km2 watershed located in the Indian Lesser Himalayas. The DEMs used were a digitized DEM generated from contour lines on a 1:50,000 topographical map, a SRTM DEM at 90m resolution and an ASTER DEM at 15m resolution. The DEM derived topographical parameters were compared with 152 field measurements from the catchment. Significant differences across the DEMs were observed for all the parameters. The high resolution ASTER DEM was observed to fail for the mountainous watershed. TOPO DEM which is, theoretically, more detailed showed similar behavior to the coarser SRTM DEM in its variability from the field measurements. Field control as well as mixed regression modeling show SRTM DEM to be the DEM of choice for the study area and it was found to be reliable at catchment scale but not at sub-watershed or hillslope scales. Keywords: soil erosion modelling, DEM, topographical parameters, Lesser Himalaya

  9. Crystallization processes derived from the interaction of urine and dolostone

    NASA Astrophysics Data System (ADS)

    Cámara, Beatriz; Alvarez de Buergo, Monica; Fort, Rafael

    2015-04-01

    The increase in the number of pets (mostly dogs), homeless people and the more recent open-air drinking sessions organized by young people in historical centers of European cities, derive on the augmentation of urinations on stone façades of the built cultural heritage. Up to now this process has been considered only under an undesirable aesthetical point of view and the insalubrious conditions it creates, together with the cleaning costs that the local governments have to assume. This study aims to confirm urine as a real source of soluble salts that can trigger the decay of building materials, especially of those of built cultural heritage of the historical centers of the cities, which are suffering the new social scenario described above. For this purpose, an experimental setup was designed and performed in the laboratory to simulate this process. 5 cm side cubic specimens of dolostone were subjected to 100 testing cycles of urine absorption by capillarity. The necessary amount of urine was collected by donors and stored following clinical protocol conditions. Each cycle consisted of imbibitions of the specimens in 3 mm high urine sheet for 3 hours, drying at 40°C in an oven for 20 hours and 1 hour cooling in a dessicator. At the end of the 100 cycles, small pieces of the specimens were cut, observed and analyzed with the aid of an environmental scanning electron microscope, which presents the advantage of no sample preparation. The sampled pieces were selected considering there were different sections in height in the specimens: a) a bottom section that corresponds to the section that has been immersed in the urine solution (3 mm); b) an interface section, immediately above the immersed area, which is the area most affected by the urine capillarity process, characterized by a strong yellowish color; c) the section that we have named as section of influence, which is subjected to the capillary absorption, although not so strongly than the interface section

  10. Intermolecular interactions between imidazole derivatives intercalated in layered solids. Substituent group effect

    SciTech Connect

    González, M.; Lemus-Santana, A.A.; Rodríguez-Hernández, J.; Aguirre-Velez, C.I.; Knobel, M.; Reguera, E.

    2013-08-15

    This study sheds light on the intermolecular interactions between imidazole derive molecules (2-methyl-imidazole, 2-ethyl-imidazole and benzimidazole) intercalated in T[Ni(CN){sub 4}] layers to form a solid of formula unit T(ImD){sub 2}[Ni(CN){sub 4}]. These hybrid inorganic–organic solids were prepared by soft chemical routes and their crystal structures solved and refined from X-ray powder diffraction data. The involved imidazole derivative molecules were found coordinated through the pyridinic N atom to the axial positions for the metal T in the T[Ni(CN){sub 4}] layer. In the interlayers region ligand molecules from neighboring layers remain stacked in a face-to-face configuration through dipole–dipole and quadrupole–quadrupole interactions. These intermolecular interactions show a pronounced dependence on the substituent group and are responsible for an ImD-pillaring concatenation of adjacent layers. This is supported by the structural information and the recorded magnetic data in the 2–300 K temperature range. The samples containing Co and Ni are characterized by presence of spin–orbit coupling and pronounced temperature dependence for the effective magnetic moment except for 2-ethyl-imidazole related to the local distortion for the metal coordination environment. For this last one ligand a weak ferromagnetic ordering ascribed to a super-exchange interaction between T metals from neighboring layers through the ligands π–π interaction was detected. - Graphical abstract: In the interlayers region imidazole derivative molecules are oriented according to their dipolar and quadrupolar interactions and minimizing the steric impediment. Highlights: • Imidazole derivatives intercalation compounds. • Intermolecular interaction between intercalated imidazole derivatives. • Hybrid inorganic–organic solids. • Pi–pi interactions and ferromagnetic coupling. • Dipolar and quadrupolar interactions between intercalated imidazole derivatives.

  11. The Thirring interaction in the two-dimensional axial-current-pseudoscalar derivative coupling model

    SciTech Connect

    Belvedere, L.V. . E-mail: armflavio@if.uff.br

    2006-12-15

    We reexamine the two-dimensional model of massive fermions interacting with a massless pseudoscalar field via axial-current derivative coupling. The hidden Thirring interaction in the axial-derivative coupling model is exhibited compactly by performing a canonical field transformation on the Bose field algebra and the model is mapped into the Thirring model with an additional vector-current-scalar derivative interaction (Schroer-Thirring model). The Fermi field operator is rewritten in terms of the Mandelstam soliton operator coupled to a free massless scalar field. The charge sectors of the axial-derivative model are mapped into the charge sectors of the massive Thirring model. The complete bosonized version of the model is presented. The bosonized composite operators of the quantum Hamiltonian are obtained as the leading operators in the Wilson short distance expansions.

  12. Estimating crop net primary production using national inventory data and MODIS-derived parameters

    NASA Astrophysics Data System (ADS)

    Bandaru, Varaprasad; West, Tristram O.; Ricciuto, Daniel M.; César Izaurralde, R.

    2013-06-01

    National estimates of spatially-resolved cropland net primary production (NPP) are needed for diagnostic and prognostic modeling of carbon sources, sinks, and net carbon flux between land and atmosphere. Cropland NPP estimates that correspond with existing cropland cover maps are needed to drive biogeochemical models at the local scale as well as national and continental scales. Existing satellite-based NPP products tend to underestimate NPP on croplands. An Agricultural Inventory-based Light Use Efficiency (AgI-LUE) framework was developed to estimate individual crop biophysical parameters for use in estimating crop-specific NPP over large multi-state regions. The method is documented here and evaluated for corn (Zea mays L.) and soybean (Glycine max L. Merr.) in Iowa and Illinois in 2006 and 2007. The method includes a crop-specific Enhanced Vegetation Index (EVI), shortwave radiation data estimated using the Mountain Climate Simulator (MTCLIM) algorithm, and crop-specific LUE per county. The combined aforementioned variables were used to generate spatially-resolved, crop-specific NPP that corresponds to the Cropland Data Layer (CDL) land cover product. Results from the modeling framework captured the spatial NPP gradient across croplands of Iowa and Illinois, and also represented the difference in NPP between years 2006 and 2007. Average corn and soybean NPP from AgI-LUE was 917 g C m-2 yr-1 and 409 g C m-2 yr-1, respectively. This was 2.4 and 1.1 times higher, respectively, for corn and soybean compared to the MOD17A3 NPP product. Site comparisons with flux tower data show AgI-LUE NPP in close agreement with tower-derived NPP, lower than inventory-based NPP, and higher than MOD17A3 NPP. The combination of new inputs and improved datasets enabled the development of spatially explicit and reliable NPP estimates for individual crops over large regional extents.

  13. Estimating crop net primary production using inventory data and MODIS-derived parameters

    SciTech Connect

    Bandaru, Varaprasad; West, Tristram O.; Ricciuto, Daniel M.; Izaurralde, Roberto C.

    2013-06-03

    National estimates of spatially-resolved cropland net primary production (NPP) are needed for diagnostic and prognostic modeling of carbon sources, sinks, and net carbon flux. Cropland NPP estimates that correspond with existing cropland cover maps are needed to drive biogeochemical models at the local scale and over national and continental extents. Existing satellite-based NPP products tend to underestimate NPP on croplands. A new Agricultural Inventory-based Light Use Efficiency (AgI-LUE) framework was developed to estimate individual crop biophysical parameters for use in estimating crop-specific NPP. The method is documented here and evaluated for corn and soybean crops in Iowa and Illinois in years 2006 and 2007. The method includes a crop-specific enhanced vegetation index (EVI) from the Moderate Resolution Imaging Spectroradiometer (MODIS), shortwave radiation data estimated using Mountain Climate Simulator (MTCLIM) algorithm and crop-specific LUE per county. The combined aforementioned variables were used to generate spatially-resolved, crop-specific NPP that correspond to the Cropland Data Layer (CDL) land cover product. The modeling framework represented well the gradient of NPP across Iowa and Illinois, and also well represented the difference in NPP between years 2006 and 2007. Average corn and soybean NPP from AgI-LUE was 980 g C m-2 yr-1 and 420 g C m-2 yr-1, respectively. This was 2.4 and 1.1 times higher, respectively, for corn and soybean compared to the MOD17A3 NPP product. Estimated gross primary productivity (GPP) derived from AgI-LUE were in close agreement with eddy flux tower estimates. The combination of new inputs and improved datasets enabled the development of spatially explicit and reliable NPP estimates for individual crops over large regional extents.

  14. Thermodynamic Interactions between Polystyrene and Long-Chain Poly(n-Alkyl Acrylates) Derived from Plant Oils.

    PubMed

    Wang, Shu; Robertson, Megan L

    2015-06-10

    Vegetable oils and their fatty acids are promising sources for the derivation of polymers. Long-chain poly(n-alkyl acrylates) and poly(n-alkyl methacrylates) are readily derived from fatty acids through conversion of the carboxylic acid end-group to an acrylate or methacrylate group. The resulting polymers contain long alkyl side-chains with around 10-22 carbon atoms. Regardless of the monomer source, the presence of alkyl side-chains in poly(n-alkyl acrylates) and poly(n-alkyl methacrylates) provides a convenient mechanism for tuning their physical properties. The development of structured multicomponent materials, including block copolymers and blends, containing poly(n-alkyl acrylates) and poly(n-alkyl methacrylates) requires knowledge of the thermodynamic interactions governing their self-assembly, typically described by the Flory-Huggins interaction parameter χ. We have investigated the χ parameter between polystyrene and long-chain poly(n-alkyl acrylate) homopolymers and copolymers: specifically we have included poly(stearyl acrylate), poly(lauryl acrylate), and their random copolymers. Lauryl and stearyl acrylate were chosen as model alkyl acrylates derived from vegetable oils and have alkyl side-chain lengths of 12 and 18 carbon atoms, respectively. Polystyrene is included in this study as a model petroleum-sourced polymer, which has wide applicability in commercially relevant multicomponent polymeric materials. Two independent methods were employed to measure the χ parameter: cloud point measurements on binary blends and characterization of the order-disorder transition of triblock copolymers, which were in relatively good agreement with one another. The χ parameter was found to be independent of the alkyl side-chain length (n) for large values of n (i.e., n > 10). This behavior is in stark contrast to the n-dependence of the χ parameter predicted from solubility parameter theory. Our study complements prior work investigating the interactions between

  15. Interactive effects among several stimulus parameters on the responses of striate cortical complex cells.

    PubMed

    Gawne, T J; Richmond, B J; Optican, L M

    1991-08-01

    1. Although neurons within the visual system are often described in terms of their responses to particular patterns such as bars and edges, they are actually sensitive to many different stimulus features, such as the luminances making up the patterns and the duration of presentation. Many different combinations of stimulus parameters can result in the same neuronal response, raising the problem of how the nervous system can extract information about visual stimuli from such inherently ambiguous responses. It has been shown that complex cells transmit significant amounts of information in the temporal modulation of their responses, raising the possibility that different stimulus parameters are encoded in different aspects of the response. To find out how much information is actually available about individual stimulus parameters, we examined the interactions among three stimulus parameters in the temporally modulated responses of striate cortical complex cells. 2. Sixteen black and white patterns were presented to two awake monkeys at each of four luminance-combinations and five durations, giving a total of 320 unique stimuli. Complex cells were recorded in layers 2 and 3 of striate cortex, with the stimuli centered on the receptive fields as determined by mapping with black and white bars. 3. An analysis of variance (ANOVA) was applied to these data with the three stimulus parameters of pattern, the luminance-combinations, and duration as the independent variables. The ANOVA was repeated with the magnitude and three different aspects of the temporal modulation of the response as the dependent variables. For the 19 neurons studied, many of the interactions between the different stimulus parameters were statistically significant. For some response measures the interactions accounted for more than one-half of the total response variance. 4. We also analyzed the stimulus-response relationships with the use of information theoretical techniques. We defined input codes

  16. Seven-year Wilkinson Microwave Anisotropy Probe (WMAP) Observations: Power Spectra and WMAP-derived Parameters

    NASA Astrophysics Data System (ADS)

    Larson, D.; Dunkley, J.; Hinshaw, G.; Komatsu, E.; Nolta, M. R.; Bennett, C. L.; Gold, B.; Halpern, M.; Hill, R. S.; Jarosik, N.; Kogut, A.; Limon, M.; Meyer, S. S.; Odegard, N.; Page, L.; Smith, K. M.; Spergel, D. N.; Tucker, G. S.; Weiland, J. L.; Wollack, E.; Wright, E. L.

    2011-02-01

    The WMAP mission has produced sky maps from seven years of observations at L2. We present the angular power spectra derived from the seven-year maps and discuss the cosmological conclusions that can be inferred from WMAP data alone. With the seven-year data, the temperature (TT) spectrum measurement has a signal-to-noise ratio per multipole that exceeds unity for l < 919; and in band powers of width Δl = 10, the signal-to-noise ratio exceeds unity up to l = 1060. The third acoustic peak in the TT spectrum is now well measured by WMAP. In the context of a flat ΛCDM model, this improvement allows us to place tighter constraints on the matter density from WMAP data alone, Ω m h 2 = 0.1334+0.0056 -0.0055, and on the epoch of matter-radiation equality, z eq = 3196+134 -133. The temperature-polarization (TE) spectrum is detected in the seven-year data with a significance of 20σ, compared to 13σ with the five-year data. We now detect the second dip in the TE spectrum near l ~ 450 with high confidence. The TB and EB spectra remain consistent with zero, thus demonstrating low systematic errors and foreground residuals in the data. The low-l EE spectrum, a measure of the optical depth due to reionization, is detected at 5.5σ significance when averaged over l = 2-7: l(l + 1)C EE l /(2π) = 0.074+0.034 -0.025 μK2 (68% CL). We now detect the high-l, 24 <= l <= 800, EE spectrum at over 8σ. The BB spectrum, an important probe of gravitational waves from inflation, remains consistent with zero; when averaged over l = 2-7, l(l + 1)C BB l /(2π) < 0.055 μK2 (95% CL). The upper limit on tensor modes from polarization data alone is a factor of two lower with the seven-year data than it was using the five-year data. The data remain consistent with the simple ΛCDM model: the best-fit TT spectrum has an effective χ2 of 1227 for 1170 degrees of freedom, with a probability to exceed of 9.6%. The allowable volume in the six-dimensional space of ΛCDM parameters has been reduced

  17. Analysis and validation of severe storm parameters derived from TITAN in Southeast Brazil

    NASA Astrophysics Data System (ADS)

    Gomes, Ana Maria; Held, Gerhard; Vernini, Rafael; Demetrio Souza, Caio

    2014-05-01

    The implementation of TITAN (Thundestorm Identification, Tracking and Nowcasting) System at IPMet in December 2005 has provided real-time access to the storm severity parameters derived from radar reflectivity, which are being used to identify and alert of potentially severe storms within the 240 km quantitative ranges of the Bauru and Presidente Prudente S-band radars. The potential of these tools available with the TITAN system is being evaluated by using the hail reports received from voluntary hail observers to cross-check the occurrence of hail within the radar range against the TITAN predictions. Part of the ongoing research at IPMet aims to determine "signatures" in severe events and therefore, as from 2008, an online standard form was introduced, allowing for greater detail on the occurrence of a severe event within the 240 km ranges of both radars. The model for the hail report was based on the one initially deployed by the Alberta Hail Program, in Canada, and also by the Hail Observer Network established by the CSIR (Council for Scientific and Industrial Research), in Pretoria, South Africa, where it was used for more than 25 years. The TITAN system was deployed to obtain the tracking properties of storms for this analysis. A cell was defined by the thresholds of 40 dBZ for the reflectivity and 16 km3 for the volume, observed at least in two consecutive volume scans (15 minutes). Besides tracking and Nowcasting the movement of storm cells, TITAN comprises algorithms that allow the identification of potentially severe storm "signatures", such as the hail metrics, to indicate the probability of hail (POH), based on a combination of radar data and the knowledge of the vertical temperature distribution of the atmosphere. Another two parameters, also related to hail producing storms, called FOKR (Foote-Krauss) index and HMA (Hail Mass Aloft) index is also included. The period from 2008 to 2013 was used to process all available information about storm

  18. A Novel Approach for Deriving Force Field Torsion Angle Parameters Accounting for Conformation-Dependent Solvation Effects.

    PubMed

    Zgarbová, Marie; Luque, F Javier; Šponer, Jiří; Otyepka, Michal; Jurečka, Petr

    2012-09-11

    A procedure for deriving force field torsion parameters including certain previously neglected solvation effects is suggested. In contrast to the conventional in vacuo approaches, the dihedral parameters are obtained from the difference between the quantum-mechanical self-consistent reaction field and Poisson-Boltzmann continuum solvation models. An analysis of the solvation contributions shows that two major effects neglected when torsion parameters are derived in vacuo are (i) conformation-dependent solute polarization and (ii) solvation of conformation-dependent charge distribution. Using the glycosidic torsion as an example, we demonstrate that the corresponding correction for the torsion potential is substantial and important. Our approach avoids double counting of solvation effects and provides parameters that may be used in combination with any of the widely used nonpolarizable discrete solvent models, such as TIPnP or SPC/E, or with continuum solvent models. Differences between our model and the previously suggested solvation models are discussed. Improvements were demonstrated for the latest AMBER RNA χOL3 parameters derived with inclusion of solvent effects in a previous publication (Zgarbova et al. J. Chem. Theory Comput.2011, 7, 2886). The described procedure may help to provide consistently better force field parameters than the currently used parametrization approaches.

  19. Size-density scaling in protists and the links between consumer-resource interaction parameters.

    PubMed

    Delong, John P; Vasseur, David A; Meiri, Shai

    2012-11-01

    Recent work indicates that the interaction between body-size-dependent demographic processes can generate macroecological patterns such as the scaling of population density with body size. In this study, we evaluate this possibility for grazing protists and also test whether demographic parameters in these models are correlated after controlling for body size. We compiled data on the body-size dependence of consumer-resource interactions and population density for heterotrophic protists grazing algae in laboratory studies. We then used nested dynamic models to predict both the height and slope of the scaling relationship between population density and body size for these protists. We also controlled for consumer size and assessed links between model parameters. Finally, we used the models and the parameter estimates to assess the individual- and population-level dependence of resource use on body-size and prey-size selection. The predicted size-density scaling for all models matched closely to the observed scaling, and the simplest model was sufficient to predict the pattern. Variation around the mean size-density scaling relationship may be generated by variation in prey productivity and area of capture, but residuals are relatively insensitive to variation in prey size selection. After controlling for body size, many consumer-resource interaction parameters were correlated, and a positive correlation between residual prey size selection and conversion efficiency neutralizes the apparent fitness advantage of taking large prey. Our results indicate that widespread community-level patterns can be explained with simple population models that apply consistently across a range of sizes. They also indicate that the parameter space governing the dynamics and the steady states in these systems is structured such that some parts of the parameter space are unlikely to represent real systems. Finally, predator-prey size ratios represent a kind of conundrum, because they are

  20. Variation of photon interaction parameters with energy for some Cu-Pb alloys

    SciTech Connect

    Singh, Tejbir Kaur, Sarpreet; Kaur, Parminder; Kaur, Harvinder; Singh, Parjit S.

    2015-08-28

    Various photon interaction parameters (mass attenuation coefficients, effective atomic numbers and effective electron numbers) have been computed for different compositions of Cu-Pb alloys in the wide energy regime of 1 keV to 100 GeV. The mass attenuation coefficients have been computed using mixture rule with the help of WinXCom (mass attenuation coefficient database for elements). The variation of mass attenuation coefficients, effective atomic numbers and electron density has been analysed and discussed in terms of dominance of different photon interaction processes viz. Compton scattering, photoelectric effect and pair production.

  1. Variation of photon interaction parameters with energy for some Cu-Pb alloys

    NASA Astrophysics Data System (ADS)

    Singh, Tejbir; Kaur, Sarpreet; Kaur, Parminder; Kaur, Harvinder; Singh, Parjit S.

    2015-08-01

    Various photon interaction parameters (mass attenuation coefficients, effective atomic numbers and effective electron numbers) have been computed for different compositions of Cu-Pb alloys in the wide energy regime of 1 keV to 100 GeV. The mass attenuation coefficients have been computed using mixture rule with the help of WinXCom (mass attenuation coefficient database for elements). The variation of mass attenuation coefficients, effective atomic numbers and electron density has been analysed and discussed in terms of dominance of different photon interaction processes viz. Compton scattering, photoelectric effect and pair production.

  2. Estimating cropland NPP using national crop inventory and MODIS derived crop specific parameters

    NASA Astrophysics Data System (ADS)

    Bandaru, V.; West, T. O.; Ricciuto, D. M.

    2011-12-01

    Estimates of cropland net primary production (NPP) are needed as input for estimates of carbon flux and carbon stock changes. Cropland NPP is currently estimated using terrestrial ecosystem models, satellite remote sensing, or inventory data. All three of these methods have benefits and problems. Terrestrial ecosystem models are often better suited for prognostic estimates rather than diagnostic estimates. Satellite-based NPP estimates often underestimate productivity on intensely managed croplands and are also limited to a few broad crop categories. Inventory-based estimates are consistent with nationally collected data on crop yields, but they lack sub-county spatial resolution. Integrating these methods will allow for spatial resolution consistent with current land cover and land use, while also maintaining total biomass quantities recorded in national inventory data. The main objective of this study was to improve cropland NPP estimates by using a modification of the CASA NPP model with individual crop biophysical parameters partly derived from inventory data and MODIS 8day 250m EVI product. The study was conducted for corn and soybean crops in Iowa and Illinois for years 2006 and 2007. We used EVI as a linear function for fPAR, and used crop land cover data (56m spatial resolution) to extract individual crop EVI pixels. First, we separated mixed pixels of both corn and soybean that occur when MODIS 250m pixel contains more than one crop. Second, we substituted mixed EVI pixels with nearest pure pixel values of the same crop within 1km radius. To get more accurate photosynthetic active radiation (PAR), we applied the Mountain Climate Simulator (MTCLIM) algorithm with the use of temperature and precipitation data from the North American Land Data Assimilation System (NLDAS-2) to generate shortwave radiation data. Finally, county specific light use efficiency (LUE) values of each crop for years 2006 to 2007 were determined by application of mean county inventory

  3. Estimation of the solubility parameters of model plant surfaces and agrochemicals: a valuable tool for understanding plant surface interactions

    PubMed Central

    2012-01-01

    Background Most aerial plant parts are covered with a hydrophobic lipid-rich cuticle, which is the interface between the plant organs and the surrounding environment. Plant surfaces may have a high degree of hydrophobicity because of the combined effects of surface chemistry and roughness. The physical and chemical complexity of the plant cuticle limits the development of models that explain its internal structure and interactions with surface-applied agrochemicals. In this article we introduce a thermodynamic method for estimating the solubilities of model plant surface constituents and relating them to the effects of agrochemicals. Results Following the van Krevelen and Hoftyzer method, we calculated the solubility parameters of three model plant species and eight compounds that differ in hydrophobicity and polarity. In addition, intact tissues were examined by scanning electron microscopy and the surface free energy, polarity, solubility parameter and work of adhesion of each were calculated from contact angle measurements of three liquids with different polarities. By comparing the affinities between plant surface constituents and agrochemicals derived from (a) theoretical calculations and (b) contact angle measurements we were able to distinguish the physical effect of surface roughness from the effect of the chemical nature of the epicuticular waxes. A solubility parameter model for plant surfaces is proposed on the basis of an increasing gradient from the cuticular surface towards the underlying cell wall. Conclusions The procedure enabled us to predict the interactions among agrochemicals, plant surfaces, and cuticular and cell wall components, and promises to be a useful tool for improving our understanding of biological surface interactions. PMID:23151272

  4. Derivation of site-specific relationships between hydraulic parameters and p-wave velocities based on hydraulic and seismic tomography

    SciTech Connect

    Brauchler, R.; Doetsch, J.; Dietrich, P.; Sauter, M.

    2012-01-10

    In this study, hydraulic and seismic tomographic measurements were used to derive a site-specific relationship between the geophysical parameter p-wave velocity and the hydraulic parameters, diffusivity and specific storage. Our field study includes diffusivity tomograms derived from hydraulic travel time tomography, specific storage tomograms, derived from hydraulic attenuation tomography, and p-wave velocity tomograms, derived from seismic tomography. The tomographic inversion was performed in all three cases with the SIRT (Simultaneous Iterative Reconstruction Technique) algorithm, using a ray tracing technique with curved trajectories. The experimental set-up was designed such that the p-wave velocity tomogram overlaps the hydraulic tomograms by half. The experiments were performed at a wellcharacterized sand and gravel aquifer, located in the Leine River valley near Göttingen, Germany. Access to the shallow subsurface was provided by direct-push technology. The high spatial resolution of hydraulic and seismic tomography was exploited to derive representative site-specific relationships between the hydraulic and geophysical parameters, based on the area where geophysical and hydraulic tests were performed. The transformation of the p-wave velocities into hydraulic properties was undertaken using a k-means cluster analysis. Results demonstrate that the combination of hydraulic and geophysical tomographic data is a promising approach to improve hydrogeophysical site characterization.

  5. Simple model for deriving [ital sdg] interacting boson model Hamiltonians: [sup 150]Nd example

    SciTech Connect

    Devi, Y.D.; Kota, V.K.B. )

    1993-07-01

    A simple and yet useful model for deriving [ital sdg] interacting boson model (IBM) Hamiltonians is to assume that single-boson energies derive from identical particle ([ital pp] and [ital nn]) interactions and proton, neutron single-particle energies, and that the two-body matrix elements for bosons derive from [ital pn] interaction, with an IBM-2 to IBM-1 projection of the resulting [ital p]-[ital n] [ital sdg] IBM Hamiltonian. The applicability of this model in generating [ital sdg] IBM Hamiltonians is demonstrated, using a single-[ital j]-shell Otsuka-Arima-Iachello mapping of the quadrupole and hexadecupole operators in proton and neutron spaces separately and constructing a quadrupole-quadrupole plus hexadecupole-hexadecupole Hamiltonian in the analysis of the spectra, [ital B]([ital E]2)'s, and [ital E]4 strength distribution in the example of [sup 150]Nd.

  6. Interactions between specific parameters of MDMA use and cognitive and psychopathological measures.

    PubMed

    Wagner, Daniel; Adolph, Sophia; Koester, Philip; Becker, Benjamin; Gouzoulis-Mayfrank, Euphrosyne; Daumann, Joerg

    2015-04-01

    The aim of the present study was to investigate the relevance of different parameters of 3,4-methylenedioxymethamphetamine (MDMA) use, including age of first use, cumulative lifetime dose and highest daily dose for predicting cognitive performance and self-reported psychopathology. Moreover, interactions between those parameters were examined. Ninety-six new MDMA users were interviewed to assess their drug use, and they completed a battery of cognitive tests concerning attention and information processing speed, episodic memory and executive functioning and self-reported psychopathology. Subjects participated again after 1year to provide follow-up data. Significant associations between age of first use and cumulative lifetime dose have been found for attention and information processing speed. Furthermore, the results showed a significant effect of age of first use on the recognition performance of the episodic memory. The findings of the current study provide a first estimation of the interactions between different MDMA use parameters. Future research should focus upon additional parameters of drug use and concentrate on consequent follow-up effects.

  7. Bottom-up modeling approach for the quantitative estimation of parameters in pathogen-host interactions

    PubMed Central

    Lehnert, Teresa; Timme, Sandra; Pollmächer, Johannes; Hünniger, Kerstin; Kurzai, Oliver; Figge, Marc Thilo

    2015-01-01

    Opportunistic fungal pathogens can cause bloodstream infection and severe sepsis upon entering the blood stream of the host. The early immune response in human blood comprises the elimination of pathogens by antimicrobial peptides and innate immune cells, such as neutrophils or monocytes. Mathematical modeling is a predictive method to examine these complex processes and to quantify the dynamics of pathogen-host interactions. Since model parameters are often not directly accessible from experiment, their estimation is required by calibrating model predictions with experimental data. Depending on the complexity of the mathematical model, parameter estimation can be associated with excessively high computational costs in terms of run time and memory. We apply a strategy for reliable parameter estimation where different modeling approaches with increasing complexity are used that build on one another. This bottom-up modeling approach is applied to an experimental human whole-blood infection assay for Candida albicans. Aiming for the quantification of the relative impact of different routes of the immune response against this human-pathogenic fungus, we start from a non-spatial state-based model (SBM), because this level of model complexity allows estimating a priori unknown transition rates between various system states by the global optimization method simulated annealing. Building on the non-spatial SBM, an agent-based model (ABM) is implemented that incorporates the migration of interacting cells in three-dimensional space. The ABM takes advantage of estimated parameters from the non-spatial SBM, leading to a decreased dimensionality of the parameter space. This space can be scanned using a local optimization approach, i.e., least-squares error estimation based on an adaptive regular grid search, to predict cell migration parameters that are not accessible in experiment. In the future, spatio-temporal simulations of whole-blood samples may enable timely

  8. Enthalpic parameters of interaction between diglycylglycine and polyatomic alcohols in aqueous solutions

    NASA Astrophysics Data System (ADS)

    Mezhevoi, I. N.; Badelin, V. G.

    2015-12-01

    Integral enthalpies of solution Δsol H m of diglycylglycine in aqueous solutions of glycerol, ethylene glycol, and 1,2-propylene glycol are measured via solution calorimetry. The experimental data are used to calculate the standard enthalpies of solution (Δsol H°) and transfer (Δtr H°) of the tripeptide from water to aqueous solutions of polyatomic alcohols. The enthalpic pairwise coefficients h xy of interactions between the tripeptide and polyatomic alcohol molecules are calculated using the McMillan-Mayer solution theory and are found to have positive values. The findings are discussed using the theory of estimating various types of interactions in ternary systems and the effect the structural features of interacting biomolecules have on the thermochemical parameters of diglycylglycine dissolution.

  9. Strong Ligand-Protein Interactions Derived from Diffuse Ligand Interactions with Loose Binding Sites.

    PubMed

    Marsh, Lorraine

    2015-01-01

    Many systems in biology rely on binding of ligands to target proteins in a single high-affinity conformation with a favorable ΔG. Alternatively, interactions of ligands with protein regions that allow diffuse binding, distributed over multiple sites and conformations, can exhibit favorable ΔG because of their higher entropy. Diffuse binding may be biologically important for multidrug transporters and carrier proteins. A fine-grained computational method for numerical integration of total binding ΔG arising from diffuse regional interaction of a ligand in multiple conformations using a Markov Chain Monte Carlo (MCMC) approach is presented. This method yields a metric that quantifies the influence on overall ligand affinity of ligand binding to multiple, distinct sites within a protein binding region. This metric is essentially a measure of dispersion in equilibrium ligand binding and depends on both the number of potential sites of interaction and the distribution of their individual predicted affinities. Analysis of test cases indicates that, for some ligand/protein pairs involving transporters and carrier proteins, diffuse binding contributes greatly to total affinity, whereas in other cases the influence is modest. This approach may be useful for studying situations where "nonspecific" interactions contribute to biological function. PMID:26064949

  10. Strong Ligand-Protein Interactions Derived from Diffuse Ligand Interactions with Loose Binding Sites

    PubMed Central

    2015-01-01

    Many systems in biology rely on binding of ligands to target proteins in a single high-affinity conformation with a favorable ΔG. Alternatively, interactions of ligands with protein regions that allow diffuse binding, distributed over multiple sites and conformations, can exhibit favorable ΔG because of their higher entropy. Diffuse binding may be biologically important for multidrug transporters and carrier proteins. A fine-grained computational method for numerical integration of total binding ΔG arising from diffuse regional interaction of a ligand in multiple conformations using a Markov Chain Monte Carlo (MCMC) approach is presented. This method yields a metric that quantifies the influence on overall ligand affinity of ligand binding to multiple, distinct sites within a protein binding region. This metric is essentially a measure of dispersion in equilibrium ligand binding and depends on both the number of potential sites of interaction and the distribution of their individual predicted affinities. Analysis of test cases indicates that, for some ligand/protein pairs involving transporters and carrier proteins, diffuse binding contributes greatly to total affinity, whereas in other cases the influence is modest. This approach may be useful for studying situations where “nonspecific” interactions contribute to biological function. PMID:26064949

  11. Study of interaction between human serum albumin and three phenanthridine derivatives: fluorescence spectroscopy and computational approach.

    PubMed

    Liu, Jianming; Yue, Yuanyuan; Wang, Jing; Yan, Xuyang; Liu, Ren; Sun, Yangyang; Li, Xiaoge

    2015-06-15

    Over the past decades, phenanthridine derivatives have captured the imagination of many chemists due to their wide applications. In the present work, the interaction between phenanthridine derivatives benzo [4,5]imidazo[1,2-a]thieno[2,3-c]quinoline (BTQ), benzo[4,5]imidazo[1,2-a]furo[2,3-c]quinoline (BFQ), 5,6-dimethylbenzo[4,5]imidazo[1,2-a]furo[2,3-c]quinoline (DFQ) and human serum albumin (HSA) were investigated by molecular modeling techniques and spectroscopic methods. The results of molecular modeling simulations revealed that the phenanthridine derivatives could bind on both site I in HSA. Fluorescence data revealed that the fluorescence quenching of HSA by phenanthridine derivatives were the result of the formation of phenanthridine derivatives-HSA complex, and the binding intensity between three phenanthridine derivatives and HSA was BTQ>BFQ>DFQ. Thermodynamics confirmed that the interaction were entropy driven with predominantly hydrophobic forces. The effects of some biological metal ions and toxic ions on the binding affinity between phenanthridine derivatives and HSA were further examined.

  12. Study of interaction between human serum albumin and three phenanthridine derivatives: Fluorescence spectroscopy and computational approach

    NASA Astrophysics Data System (ADS)

    Liu, Jianming; Yue, Yuanyuan; Wang, Jing; Yan, Xuyang; Liu, Ren; Sun, Yangyang; Li, Xiaoge

    2015-06-01

    Over the past decades, phenanthridine derivatives have captured the imagination of many chemists due to their wide applications. In the present work, the interaction between phenanthridine derivatives benzo [4,5]imidazo[1,2-a]thieno[2,3-c]quinoline (BTQ), benzo[4,5]imidazo[1,2-a]furo[2,3-c]quinoline (BFQ), 5,6-dimethylbenzo[4,5]imidazo[1,2-a]furo[2,3-c]quinoline (DFQ) and human serum albumin (HSA) were investigated by molecular modeling techniques and spectroscopic methods. The results of molecular modeling simulations revealed that the phenanthridine derivatives could bind on both site I in HSA. Fluorescence data revealed that the fluorescence quenching of HSA by phenanthridine derivatives were the result of the formation of phenanthridine derivatives-HSA complex, and the binding intensity between three phenanthridine derivatives and HSA was BTQ > BFQ > DFQ. Thermodynamics confirmed that the interaction were entropy driven with predominantly hydrophobic forces. The effects of some biological metal ions and toxic ions on the binding affinity between phenanthridine derivatives and HSA were further examined.

  13. Weak Interactions Govern the Viscosity of Concentrated Antibody Solutions: High-Throughput Analysis Using the Diffusion Interaction Parameter

    PubMed Central

    Connolly, Brian D.; Petry, Chris; Yadav, Sandeep; Demeule, Barthélemy; Ciaccio, Natalie; Moore, Jamie M.R.; Shire, Steven J.; Gokarn, Yatin R.

    2012-01-01

    Weak protein-protein interactions are thought to modulate the viscoelastic properties of concentrated antibody solutions. Predicting the viscoelastic behavior of concentrated antibodies from their dilute solution behavior is of significant interest and remains a challenge. Here, we show that the diffusion interaction parameter (kD), a component of the osmotic second virial coefficient (B2) that is amenable to high-throughput measurement in dilute solutions, correlates well with the viscosity of concentrated monoclonal antibody (mAb) solutions. We measured the kD of 29 different mAbs (IgG1 and IgG4) in four different solvent conditions (low and high ion normality) and found a linear dependence between kD and the exponential coefficient that describes the viscosity concentration profiles (|R| ≥ 0.9). Through experimentally measured effective charge measurements, under low ion normality where the electroviscous effect can dominate, we show that the mAb solution viscosity is poorly correlated with the mAb net charge (|R| ≤ 0.6). With this large data set, our results provide compelling evidence in support of weak intermolecular interactions, in contrast to the notion that the electroviscous effect is important in governing the viscoelastic behavior of concentrated mAb solutions. Our approach is particularly applicable as a screening tool for selecting mAbs with desirable viscosity properties early during lead candidate selection. PMID:22828333

  14. Evaluating the Spatio-Temporal Factors that Structure Network Parameters of Plant-Herbivore Interactions

    PubMed Central

    López-Carretero, Antonio; Díaz-Castelazo, Cecilia; Boege, Karina; Rico-Gray, Víctor

    2014-01-01

    Despite the dynamic nature of ecological interactions, most studies on species networks offer static representations of their structure, constraining our understanding of the ecological mechanisms involved in their spatio-temporal stability. This is the first study to evaluate plant-herbivore interaction networks on a small spatio-temporal scale. Specifically, we simultaneously assessed the effect of host plant availability, habitat complexity and seasonality on the structure of plant-herbivore networks in a coastal tropical ecosystem. Our results revealed that changes in the host plant community resulting from seasonality and habitat structure are reflected not only in the herbivore community, but also in the emergent properties (network parameters) of the plant-herbivore interaction network such as connectance, selectiveness and modularity. Habitat conditions and periods that are most stressful favored the presence of less selective and susceptible herbivore species, resulting in increased connectance within networks. In contrast, the high degree of selectivennes (i.e. interaction specialization) and modularity of the networks under less stressful conditions was promoted by the diversification in resource use by herbivores. By analyzing networks at a small spatio-temporal scale we identified the ecological factors structuring this network such as habitat complexity and seasonality. Our research offers new evidence on the role of abiotic and biotic factors in the variation of the properties of species interaction networks. PMID:25340790

  15. Reconstructed historical land cover and biophysical parameters for studies of land-atmosphere interactions within the eastern United States

    USGS Publications Warehouse

    Steyaert, L.T.; Knox, R.G.

    2008-01-01

    Over the past 350 years, the eastern half of the United States experienced extensive land cover changes. These began with land clearing in the 1600s, continued with widespread deforestation, wetland drainage, and intensive land use by 1920, and then evolved to the present-day landscape of forest regrowth, intensive agriculture, urban expansion, and landscape fragmentation. Such changes alter biophysical properties that are key determinants of land-atmosphere interactions (water, energy, and carbon exchanges). To understand the potential implications of these land use transformations, we developed and analyzed 20-km land cover and biophysical parameter data sets for the eastern United States at 1650, 1850, 1920, and 1992 time slices. Our approach combined potential vegetation, county-level census data, soils data, resource statistics, a Landsat-derived land cover classification, and published historical information on land cover and land use. We reconstructed land use intensity maps for each time slice and characterized the land cover condition. We combined these land use data with a mutually consistent set of biophysical parameter classes, to characterize the historical diversity and distribution of land surface properties. Time series maps of land surface albedo, leaf area index, a deciduousness index, canopy height, surface roughness, and potential saturated soils in 1650, 1850, 1920, and 1992 illustrate the profound effects of land use change on biophysical properties of the land surface. Although much of the eastern forest has returned, the average biophysical parameters for recent landscapes remain markedly different from those of earlier periods. Understanding the consequences of these historical changes will require land-atmosphere interactions modeling experiments.

  16. Electronic polarizability, optical basicity, and interaction parameter of La2O3 and related glasses

    NASA Astrophysics Data System (ADS)

    Honma, T.; Benino, Y.; Fujiwara, T.; Komatsu, T.; Sato, R.; Dimitrov, V.

    2002-03-01

    The electronic polarizability and optical basicity of La2O3 and related glasses have been determined from ultraviolet absorption spectra and calculations based on the Lorentz-Lorenz equation. The optical basicity for La2O3 oxide is found to be 1.07, being much larger compared with typical glass-forming oxides such as B2O3 (0.42) and SiO2 (0.48) but being similar to heavy element oxides such as TeO2 (0.93). The Yamashita and Kurosawa's interaction parameter of La2O3 is 0.03 Å-3, indicating that La2O3 is classified as a normal ionic (basic) oxide, i.e., an ionic bonding character in the La3+-O bond is proposed. Close correlations are confirmed among optical basicity, interaction parameter, and oxygen 1s binding energy in x-ray photoelectron (XPS) spectra for La2O3-P2O5 and other La2O3-containing glasses. It is found from XPS and Raman spectra that La3+ ions in La2O3-P2O5 glasses act as network modifiers, supporting an ionic bonding character in the La3+-O bond. The parameters related to electronic polarizability in La2O3 determined in the present study would be useful for the design of rare-earth containing optical functional glasses.

  17. Prediction of drug-target interaction by label propagation with mutual interaction information derived from heterogeneous network.

    PubMed

    Yan, Xiao-Ying; Zhang, Shao-Wu; Zhang, Song-Yao

    2016-02-01

    The identification of potential drug-target interaction pairs is very important, which is useful not only for providing greater understanding of protein function, but also for enhancing drug research, especially for drug function repositioning. Recently, numerous machine learning-based algorithms (e.g. kernel-based, matrix factorization-based and network-based inference methods) have been developed for predicting drug-target interactions. All these methods implicitly utilize the assumption that similar drugs tend to target similar proteins and yield better results for predicting interactions between drugs and target proteins. To further improve the accuracy of prediction, a new method of network-based label propagation with mutual interaction information derived from heterogeneous networks, namely LPMIHN, is proposed to infer the potential drug-target interactions. LPMIHN separately performs label propagation on drug and target similarity networks, but the initial label information of the target (or drug) network comes from the drug (or target) label network and the known drug-target interaction bipartite network. The independent label propagation on each similarity network explores the cluster structure in its network, and the label information from the other network is used to capture mutual interactions (bicluster structures) between the nodes in each pair of the similarity networks. As compared to other recent state-of-the-art methods on the four popular benchmark datasets of binary drug-target interactions and two quantitative kinase bioactivity datasets, LPMIHN achieves the best results in terms of AUC and AUPR. In addition, many of the promising drug-target pairs predicted from LPMIHN are also confirmed on the latest publicly available drug-target databases such as ChEMBL, KEGG, SuperTarget and Drugbank. These results demonstrate the effectiveness of our LPMIHN method, indicating that LPMIHN has a great potential for predicting drug-target interactions. PMID

  18. An investigation of ab initio shell-model interactions derived by no-core shell model

    NASA Astrophysics Data System (ADS)

    Wang, XiaoBao; Dong, GuoXiang; Li, QingFeng; Shen, CaiWan; Yu, ShaoYing

    2016-09-01

    The microscopic shell-model effective interactions are mainly based on the many-body perturbation theory (MBPT), the first work of which can be traced to Brown and Kuo's first attempt in 1966, derived from the Hamada-Johnston nucleon-nucleon potential. However, the convergence of the MBPT is still unclear. On the other hand, ab initio theories, such as Green's function Monte Carlo (GFMC), no-core shell model (NCSM), and coupled-cluster theory with single and double excitations (CCSD), have made many progress in recent years. However, due to the increasing demanding of computing resources, these ab initio applications are usually limited to nuclei with mass up to A = 16. Recently, people have realized the ab initio construction of valence-space effective interactions, which is obtained through a second-time renormalization, or to be more exactly, projecting the full-manybody Hamiltonian into core, one-body, and two-body cluster parts. In this paper, we present the investigation of such ab initio shell-model interactions, by the recent derived sd-shell effective interactions based on effective J-matrix Inverse Scattering Potential (JISP) and chiral effective-field theory (EFT) through NCSM. In this work, we have seen the similarity between the ab initio shellmodel interactions and the interactions obtained by MBPT or by empirical fitting. Without the inclusion of three-body (3-bd) force, the ab initio shell-model interactions still share similar defects with the microscopic interactions by MBPT, i.e., T = 1 channel is more attractive while T = 0 channel is more repulsive than empirical interactions. The progress to include more many-body correlations and 3-bd force is still badly needed, to see whether such efforts of ab initio shell-model interactions can reach similar precision as the interactions fitted to experimental data.

  19. Physicochemical study on interactions between T-2 and HT-2 toxin derivatives and cyclodextrins

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Physicochemical interactions occurring between fluorescent anthracene derivatives of T-2 and HT-2 toxins and different cyclodextrins (CDs) were investigated in aqueous solutions by means of UV-Vis absorption, fluorescence emission, and Dynamic Light Scattering. Binding constant values and physicoche...

  20. Automation of SimSphere Land Surface Model Use as a Standalone Application and Integration With EO Data for Deriving Key Land Surface Parameters

    NASA Astrophysics Data System (ADS)

    Petropoulos, George P.; Konstas, Ioannis; Carlson, Toby N.

    2013-04-01

    Use of simulation process models has played a key role in extending our abilities to study Earth system processes and enhancing our understanding on how different components of it interplay. Use of such models combined with Earth Observation (EO) data provides a promising direction towards deriving accurately spatiotemporal estimates of key parameters characterising land surface interactions, by combining the horizontal coverage and spectral resolution of remote sensing data with the vertical coverage and fine temporal continuity of those models. SimSphere is such a software toolkit written in Java for simulating the interactions of soil, vegetation and atmosphere layers of the Earth's land surface. Its use is at present continually expanding worldwide both as an educational and as a research tool for scientific investigations. It is being used either as a stand-alone application or synergistically with EO data. Herein we present recent advancements introduced to SimSphere in different aspects of the model aiming to make its use more robust when used both as a standalone application and synergistically with EO data. We have extensively tested and updated the model code, as well as enhanced it with new functionalities. These included for example taking into account the thermal inertia variation in soil moisture, simulating additional parameters characterising land surface interactions, automating the model use when integrating it with EO data via the "triangle" method and developing batch processing operations. Use of these recently introduced to the model functionalities are illustrated herein using a variety of examples. Our work is significant to the users' community of the model and very timely, given the potential use of SimSphere in an EO-based method being under development for deriving operationally regional estimates of energy fluxes and soil moisture from EO data provided by non-commercial vendors. KEYWORDS: land surface interactions, land surface process

  1. Signal Intensities Derived from Different NMR Probes and Parameters Contribute to Variations in Quantification of Metabolites

    PubMed Central

    Finkel, Michael; Karnovsky, Alla; Woehler, Scott; Lewis, Michael J.; Chang, David; Stringer, Kathleen A.

    2014-01-01

    We discovered that serious issues could arise that may complicate interpretation of metabolomic data when identical samples are analyzed at more than one NMR facility, or using slightly different NMR parameters on the same instrument. This is important because cross-center validation metabolomics studies are essential for the reliable application of metabolomics to clinical biomarker discovery. To test the reproducibility of quantified metabolite data at multiple sites, technical replicates of urine samples were assayed by 1D-1H-NMR at the University of Alberta and the University of Michigan. Urine samples were obtained from healthy controls under a standard operating procedure for collection and processing. Subsequent analysis using standard statistical techniques revealed that quantitative data across sites can be achieved, but also that previously unrecognized NMR parameter differences can dramatically and widely perturb results. We present here a confirmed validation of NMR analysis at two sites, and report the range and magnitude that common NMR parameters involved in solvent suppression can have on quantitated metabolomics data. Specifically, saturation power levels greatly influenced peak height intensities in a frequency-dependent manner for a number of metabolites, which markedly impacted the quantification of metabolites. We also investigated other NMR parameters to determine their effects on further quantitative accuracy and precision. Collectively, these findings highlight the importance of and need for consistent use of NMR parameter settings within and across centers in order to generate reliable, reproducible quantified NMR metabolomics data. PMID:24465670

  2. On the Origin of Differences in Helicity Parameters Derived from Data of Two Solar Magnetographs

    NASA Astrophysics Data System (ADS)

    Xu, Haiqing; Zhang, Hongqi; Kuzanyan, K.; Sakurai, T.

    2016-09-01

    We analyzed how sensitivity and accuracy in solar magnetic field measurements may affect the values of mean current helicity density hc and twist parameter α_{av} by comparing these values obtained from two magnetographs (SMFT at Beijing and SFT at Mitaka, Tokyo). When we computed the helicity parameters from the SFT data, we replaced the values of the longitudinal field component, transverse field strength, and transverse field azimuth angle with those from the SMFT data and examined the differences. The results show that the correlation coefficient and the fraction of the data that agree in signs of hc or α_{av} increase when an SFT parameter is substituted by the corresponding SMFT parameter because one source of discrepancy is removed. The increase in correlation coefficient is largest when the azimuthal angles and transverse field strengths are set identical in the two instruments; the correlation coefficient of hc ( α_{av}) increases from 0.74 (0.56) to 0.86 (0.78), respectively, indicating that the differences in the transverse field strength and its azimuthal angle are the largest source of discrepancy in the values of hc or α_{av}. We found a nonlinear relationship in the components of the magnetic field between the two instruments for some data samples; we conclude that this is due to the discrepancy in the calibration procedure between the two instruments. This nonlinearity can be another source of difference in determining helical parameters between the two instruments.

  3. On the Origin of Differences in Helicity Parameters Derived from Data of Two Solar Magnetographs

    NASA Astrophysics Data System (ADS)

    Xu, Haiqing; Zhang, Hongqi; Kuzanyan, K.; Sakurai, T.

    2016-10-01

    We analyzed how sensitivity and accuracy in solar magnetic field measurements may affect the values of mean current helicity density hc and twist parameter α_{av} by comparing these values obtained from two magnetographs (SMFT at Beijing and SFT at Mitaka, Tokyo). When we computed the helicity parameters from the SFT data, we replaced the values of the longitudinal field component, transverse field strength, and transverse field azimuth angle with those from the SMFT data and examined the differences. The results show that the correlation coefficient and the fraction of the data that agree in signs of hc or α_{av} increase when an SFT parameter is substituted by the corresponding SMFT parameter because one source of discrepancy is removed. The increase in correlation coefficient is largest when the azimuthal angles and transverse field strengths are set identical in the two instruments; the correlation coefficient of hc (α_{av}) increases from 0.74 (0.56) to 0.86 (0.78), respectively, indicating that the differences in the transverse field strength and its azimuthal angle are the largest source of discrepancy in the values of hc or α_{av}. We found a nonlinear relationship in the components of the magnetic field between the two instruments for some data samples; we conclude that this is due to the discrepancy in the calibration procedure between the two instruments. This nonlinearity can be another source of difference in determining helical parameters between the two instruments.

  4. Interaction of uncharged bile salt derivatives with the ileal bile salt transport system.

    PubMed

    Bundy, R; Mauskopf, J; Walker, J T; Lack, L

    1977-05-01

    Two series of uncharged conjugated bile salt derivatives, N-conjugates of ethanolamine and 3-amino-1,2-propanediol were studied for interaction with the ileal bile salt transport system. Evidence for interaction is threefold. 1) In everted gut sac experiments more material was removed from the mucosal compartment when ileal sacs were used. 2) These derivatives inhibited the in vitro transport of taurocholate. 3) In vivo intestinal perfusion demonstrated greater absorption from ileum than from jejunum. Number three demonstrates that such interactions are followed by transmucosal movement. Their uphill transport was less than taurocholate transport. The Na(+) requirement for cholyl-3-amino-1,2-propanediol interaction with the system was greater than for taurocholate. This observation is similar to that previously observed with taurodehydrocholate, which had a greater Na(+) requirement for transport than taurocholate. Therefore removal of the anionic charge, as well as distortion of steroid shape, increases the Na(+) requirement for substrate interaction with the transport system. These observations support our hypothesis that this interaction involves two recognition components; one includes the steroid moiety, the other a coulombic interaction between the anionic bile salt and a cationic membrane site. Additionally the membrane would have an anionic group to accomodate the Na(+). Both factors (steroidal and coulombic) operate for optimal substrate attachment. Simultaneously the system's affinity for Na(+) increases and active transport then proceeds.

  5. Low-energy parameters of neutron-neutron interaction in the effective-range approximation

    SciTech Connect

    Babenko, V. A.; Petrov, N. M.

    2013-06-15

    The effect of the mass difference between the charged and neutral pions on the low-energy parameters of nucleon-nucleon interaction in the {sup 1}S{sub 0} state is studied in the effective-range approximation. On the basis of experimental values of the singlet parameters of neutron-proton scattering and the experimental value of the virtual-state energy for the neutron-neutron systemin the {sup 1}S{sub 0} state, the following values were obtained for the neutron-neutron scattering length and effective range: a{sub nn} = -16.59(117) fm and r{sub nn} = 2.83(11) fm. The calculated values agree well with present-day experimental results.

  6. Temperature evaluation of traveling-wave ultrasonic motor considering interaction between temperature rise and motor parameters.

    PubMed

    Li, Shiyang; Ou, Wenchu; Yang, Ming; Guo, Chao; Lu, Cunyue; Hu, Junhui

    2015-03-01

    In this paper, a novel model for evaluating the temperature of traveling-wave ultrasonic motor (TWUSM) is developed. The proposed model, where the interaction between the temperature rise and motor parameters is considered, differs from the previous reported models with constant parameters. In this model, losses and temperature rises of the motor were evaluated based on the temperature-related varying parameters: the feedback voltage Vaux of the stator, dielectric permittivity ɛ and dielectric loss factor tanδ. At each new temperature, Vaux, ɛ and tanδ were updated. The feasibility and effectiveness of this proposed model was verified by comparing the predicted temperatures with the measured one. The effects of driving voltage, driving frequency and ambient temperature on the predicted temperature were also analyzed. The results show that the proposed model has more accurate predicted temperature than that with constant parameters. This will be very useful for the optimal design, reducing the heat loss, improvement of control and reliability life of TWUSM.

  7. Effect of the structure of gallic acid and its derivatives on their interaction with plant ferritin.

    PubMed

    Wang, Qunqun; Zhou, Kai; Ning, Yong; Zhao, Guanghua

    2016-12-15

    Gallic acid and its derivatives co-exist with protein components in foodstuffs, but there is few report on their interaction with proteins. On the other hand, plant ferritin represents not only a novel class of iron supplement, but also a new nanocarrier for encapsulation of bioactive nutrients. However, plant ferritin is easy to be degraded by pepsin in the stomach, thereby limiting its application. Herein, we investigated the interaction of gallic acid and its derivatives with recombinant soybean seed H-2 ferritin (rH-2). We found that these phenolic acids interacted with rH-2 in a structure-dependent manner; namely, gallic acid (GA), methyl gallate (MEGA) and propyl gallate (PG) having three HO groups can bind to rH-2, while their analogues with two HO groups cannot. Consequently, such binding largely inhibited ferritin degradation by pepsin. These findings advance our understanding of the relationship between the structure and function of phenolic acids.

  8. Using isothermal titration calorimetry to determine thermodynamic parameters of protein-glycosaminoglycan interactions.

    PubMed

    Dutta, Amit K; Rösgen, Jörg; Rajarathnam, Krishna

    2015-01-01

    It has now become increasingly clear that a complete atomic description of how biomacromolecules recognize each other requires knowledge not only of the structures of the complexes but also of how kinetics and thermodynamics drive the binding process. In particular, such knowledge is lacking for protein-glycosaminoglycan (GAG) complexes. Isothermal titration calorimetry (ITC) is the only technique that can provide various thermodynamic parameters-enthalpy, entropy, free energy (binding constant), and stoichiometry-from a single experiment. Here we describe different factors that must be taken into consideration in carrying out ITC titrations to obtain meaningful thermodynamic data of protein-GAG interactions.

  9. Effect of thermal history on Mossbauer signature and hyperfine interaction parameters of copper ferrite

    SciTech Connect

    Modi, K. B. Raval, P. Y.; Dulera, S. V.; Kathad, C. R.; Shah, S. J.; Trivedi, U. N.; Chandra, Usha

    2015-06-24

    Two specimens of copper ferrite, CuFe{sub 2}O{sub 4}, have been synthesized by double sintering ceramic technique with different thermal history i.e. slow cooled and quenched. X-ray diffractometry has confirmed single phase fcc spinel structure for slow cooled sample while tetragonal distortion is present in quenched sample. Mossbauer spectral analysis for slow-cooled copper ferrite reveals super position of two Zeeman split sextets along with paramagnetic singlet in the centre position corresponds to delafossite (CuFeO{sub 2}) phase that is completely absent in quenched sample. The hyperfine interaction parameters are highly influenced by heat treatment employed.

  10. Microscopic calculation of interacting boson model parameters by potential-energy surface mapping

    SciTech Connect

    Bentley, I.; Frauendorf, S.

    2011-06-15

    A coherent state technique is used to generate an interacting boson model (IBM) Hamiltonian energy surface which is adjusted to match a mean-field energy surface. This technique allows the calculation of IBM Hamiltonian parameters, prediction of properties of low-lying collective states, as well as the generation of probability distributions of various shapes in the ground state of transitional nuclei, the last two of which are of astrophysical interest. The results for krypton, molybdenum, palladium, cadmium, gadolinium, dysprosium, and erbium nuclei are compared with experiment.

  11. Effect of thermal history on Mossbauer signature and hyperfine interaction parameters of copper ferrite

    NASA Astrophysics Data System (ADS)

    Modi, K. B.; Raval, P. Y.; Dulera, S. V.; Kathad, C. R.; Shah, S. J.; Trivedi, U. N.; Chandra, Usha

    2015-06-01

    Two specimens of copper ferrite, CuFe2O4, have been synthesized by double sintering ceramic technique with different thermal history i.e. slow cooled and quenched. X-ray diffractometry has confirmed single phase fcc spinel structure for slow cooled sample while tetragonal distortion is present in quenched sample. Mossbauer spectral analysis for slow-cooled copper ferrite reveals super position of two Zeeman split sextets along with paramagnetic singlet in the centre position corresponds to delafossite (CuFeO2) phase that is completely absent in quenched sample. The hyperfine interaction parameters are highly influenced by heat treatment employed.

  12. Impulse source versus dodecahedral loudspeaker for measuring parameters derived from the impulse response in room acoustics.

    PubMed

    San Martín, Ricardo; Arana, Miguel; Machín, Jorge; Arregui, Abel

    2013-07-01

    This study investigates the performance of dodecahedral and impulse sources when measuring acoustic parameters in enclosures according to ISO 3382-1 [Acoustics-Measurement of room acoustic parameters. Part 1: Performance spaces (International Organization for Standardization, Geneva, Switzerland, 2009)]. In general, methods using speakers as a sound source are limited by their frequency response and directivity. On the other hand, getting impulse responses from impulse sources typically involves a lack of repeatability, and it is usually necessary to average several measurements for each position. Through experiments in different auditoriums that recreate typical situations in which the measurement standard is applied, it is found that using impulse sources leads to greater variation in the results, especially at low frequencies. However, this prevents subsequent dispersions due to variables that this technique does not require, such as the orientation of the emitting source. These dispersions may be relevant at high frequencies exceeding the established tolerance criteria for certain parameters. Finally, a new descriptor for dodecahedral sources reflecting the influence their lack of omnidirectionality produces on measuring acoustic parameters is proposed.

  13. Implicit Solvation Parameters Derived from Explicit Water Forces in Large-Scale Molecular Dynamics Simulations

    PubMed Central

    2012-01-01

    Implicit solvation is a mean force approach to model solvent forces acting on a solute molecule. It is frequently used in molecular simulations to reduce the computational cost of solvent treatment. In the first instance, the free energy of solvation and the associated solvent–solute forces can be approximated by a function of the solvent-accessible surface area (SASA) of the solute and differentiated by an atom–specific solvation parameter σiSASA. A procedure for the determination of values for the σiSASA parameters through matching of explicit and implicit solvation forces is proposed. Using the results of Molecular Dynamics simulations of 188 topologically diverse protein structures in water and in implicit solvent, values for the σiSASA parameters for atom types i of the standard amino acids in the GROMOS force field have been determined. A simplified representation based on groups of atom types σgSASA was obtained via partitioning of the atom–type σiSASA distributions by dynamic programming. Three groups of atom types with well separated parameter ranges were obtained, and their performance in implicit versus explicit simulations was assessed. The solvent forces are available at http://mathbio.nimr.mrc.ac.uk/wiki/Solvent_Forces. PMID:23180979

  14. Deriving parameters of a fundamental detachment model for cohesive soils from flume and jet erosion tests

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The erosion rate of cohesive soils is commonly quantified using the excess shear stress equation, dependent on two major soil parameters: the critical shear stress and the erodibility coefficient. A submerged jet test (JET – Jet Erosion Test) is one method that has been developed for measuring thes...

  15. Altitudinal spread of area and area changes: a case study for deriving new parameters for monitoring Alpine glaciers

    NASA Astrophysics Data System (ADS)

    Fischer, Andrea

    2015-04-01

    A time series of four glacier inventories for the Austrian Alps between the little ice age maximum and today reveals shifts in the altitudinal range of the maximum glacier-covered area and in the altitudes where the greatest changes in size of the area took place. These shifts are the result of the specific mass balance, the ice thickness distribution, but also of changes in ice dynamics and have already been subject to studies within the last two centuries. The time series of inventories now allows i) a derivation of these parameters for all glaciers in the Austrian Alps and ii) a comparison of these topographic parameters with records of directly measured ELAs and ice flow velocities. For the Austrian Alps, the altitudinal zone with the maximum ice cover shifted from 2950 m in 1969 to 2925 m in 1998 and 3025 m in 2006. The maximum area changes took place at elevations of 2675 m (2006 to 1998) and 2850 m (1998 to 1969). Thorough empirical investigation and theoretical foundation are needed to show if these area shifts can be related to shifts of the ELA and responses of the ice flow velocity or not. As a first step, the suggested potential parameters are investigated for the glaciers and periods where direct mass balance data are available. The mean ELAs for the above named periods for the seven mass balance glaciers shifted by 112 m from 2945 m (1971-1980) to 3057 m (1981-2000), and by 23 m to 3079 m (2001-2010). From the comparison of geodetic and direct mass balance, the elevation of zero altitudinal change can be derived and compared to the ELA. Like the ELA, all topographically derived parameters are governed not only by climate, but also by the individual topographic properties of specific glaciers. Thus further investigations of a larger sample of mass balance glaciers are needed to find out if these parameters are suitable for automatic glacier monitoring.

  16. Photometric parameter maps of the Moon derived from LROC WAC images

    NASA Astrophysics Data System (ADS)

    Sato, H.; Robinson, M. S.; Hapke, B. W.; Denevi, B. W.; Boyd, A. K.

    2013-12-01

    Spatially resolved photometric parameter maps were computed from 21 months of Lunar Reconnaissance Orbiter Camera (LROC) Wide Angle Camera (WAC) images. Due to a 60° field-of-view (FOV), the WAC achieves nearly global coverage of the Moon each month with more than 50% overlap from orbit-to-orbit. From the repeat observations at various viewing and illumination geometries, we calculated Hapke bidirectional reflectance model parameters [1] for 1°x1° "tiles" from 70°N to 70°S and 0°E to 360°E. About 66,000 WAC images acquired from February 2010 to October 2011 were converted from DN to radiance factor (I/F) though radiometric calibration, partitioned into gridded tiles, and stacked in a time series (tile-by-tile method [2]). Lighting geometries (phase, incidence, emission) were computed using the WAC digital terrain model (100 m/pixel) [3]. The Hapke parameters were obtained by model fitting against I/F within each tile. Among the 9 parameters of the Hapke model, we calculated 3 free parameters (w, b, and hs) by setting constant values for 4 parameters (Bco=0, hc=1, θ, φ=0) and interpolating 2 parameters (c, Bso). In this simplification, we ignored the Coherent Backscatter Opposition Effect (CBOE) to avoid competing CBOE and Shadow Hiding Opposition Effect (SHOE). We also assumed that surface regolith porosity is uniform across the Moon. The roughness parameter (θ) was set to an averaged value from the equator (× 3°N). The Henyey-Greenstein double lobe function (H-G2) parameter (c) was given by the 'hockey stick' relation [4] (negative correlation) between b and c based on laboratory measurements. The amplitude of SHOE (Bso) was given by the correlation between w and Bso at the equator (× 3°N). Single scattering albedo (w) is strongly correlated to the photometrically normalized I/F, as expected. The c shows an inverse trend relative to b due to the 'hockey stick' relation. The parameter c is typically low for the maria (0.08×0.06) relative to the

  17. Correlation between the carbonization temperature and the physical parameters of porous carbons derived from Yucca flaccida

    NASA Astrophysics Data System (ADS)

    Krzesinska, M.; Zachariasz, J.

    2007-08-01

    The purpose of the study was to develop monolithic ecological carbon materials of high porosity from the woody stems of yucca (Yucca flaccida). Monolithic blocks cut from the stem were carbonized in a nitrogen atmosphere, at the temperature range from 300°C to 950°C with the constant heating rate. The resultant carbon materials were characterized by dimensional changes, yield of char, elemental analysis, and various physical parameters: the true density, the bulk porosity, the longitudinal ultrasonic wave velocity and elastic anisotropy. The thermal decomposition study (TGA) was also performed. The microstructure of longitudinal and transverse sections of stems of raw and carbonized yucca were analysed by SEM. All parameters studied and the microscopic observations were discussed in relation to the pyrolysis temperature.

  18. Comparison of CME three-dimensional parameters derived from single and multi-spacecraft

    NASA Astrophysics Data System (ADS)

    LEE, Harim; Moon, Yong-Jae; Na, Hyeonock; Jang, Soojeong

    2014-06-01

    Several geometrical models (e.g., cone and flux rope models) have been suggested to infer three-dimensional parameters of CMEs using multi-view observations (STEREO/SECCHI) and single-view observations (SOHO/LASCO). To prepare for when only single view observations are available, we have made a test whether the cone model parameters from single-view observations are consistent with those from multi-view ones. For this test, we select 35 CMEs which are identified as CMEs, whose angular widths are larger than 180 degrees, by one spacecraft and as limb CMEs by the other ones. For this we use SOHO/LASCO and STEREO/SECCHI data during the period from 2010 December to 2011 July when two spacecraft were separated by 90±10 degrees. In this study, we compare the 3-D parameters of these CMEs from three different methods: (1) a triangulation method using STEREO/SECCHI and SOHO/LASCO data, (2) a Graduated Cylindrical Shell (GCS) flux rope model using STEREO/SECCHI data, and (3) an ice cream cone model using SOHO/LASCO data. The parameters used for comparison are radial velocities, angular widths and source location (angle γ between the propagation direction and the plan of the sky). We find that the radial velocities and the γ-values from three methods are well correlated with one another (CC > 0.8). However, angular widths from the three methods are somewhat different with the correlation coefficients of CC > 0.4. We also find that the correlation coefficients between the locations from the three methods and the active region locations are larger than 0.9, implying that most of the CMEs are radially ejected.

  19. Novel interactions of fluorinated nucleotide derivatives targeting orotidine-5′-monophosphate decarboxylase

    PubMed Central

    Lewis, Melissa; Avina, Maria Elena Meza; Wei, Lianhu; Crandall, Ian E.; Bello, Angelica Mara; Poduch, Ewa; Liu, Yan; Paige, Christopher J.; Kain, Kevin C.; Pai, Emil F.; Kotra, Lakshmi P.

    2011-01-01

    Fluorinated nucleosides and nucleotides are of considerable interest to medicinal chemists due to their antiviral, anticancer, and other biological activities. However, their direct interactions at target binding sites are not well understood. A new class of 2′-deoxy-2′-fluoro-C6-substituted uridine and UMP derivatives were synthesized and evaluated as inhibitors of orotidine-5′-monophosphate decarboxylase (ODCase). These compounds were synthesized from the key intermediate, fully-protected 2′-deoxy-2′-fluorouridine. Among the synthesized compounds, 2′-deoxy-2′-fluoro-6-iodo-UMP covalently inhibited human ODCase with a second-order rate constant of 0.62 ± 0.02 M−1sec−1. Interestingly, the 6-cyano-2′-fluoro derivative covalently interacted with ODCase defying the conventional thinking, where its ribosyl derivative undergoes transformation into BMP by ODCase. This confirms that the 2′-fluoro moiety influences the chemistry at the C6 position of the nucleotides, thus interactions in the active site of ODCase. Molecular interactions of the 2′-fluorinated nucleotides are compared to those with the 3′-fluorinated nucleotides bound to the corresponding target enzyme, and the carbohydrate moieties were shown to bind in different conformations. PMID:21417464

  20. Interactive Visual Analytics Approch for Exploration of Geochemical Model Simulations with Different Parameter Sets

    NASA Astrophysics Data System (ADS)

    Jatnieks, Janis; De Lucia, Marco; Sips, Mike; Dransch, Doris

    2015-04-01

    Many geoscience applications can benefit from testing many combinations of input parameters for geochemical simulation models. It is, however, a challenge to screen the input and output data from the model to identify the significant relationships between input parameters and output variables. For addressing this problem we propose a Visual Analytics approach that has been developed in an ongoing collaboration between computer science and geoscience researchers. Our Visual Analytics approach uses visualization methods of hierarchical horizontal axis, multi-factor stacked bar charts and interactive semi-automated filtering for input and output data together with automatic sensitivity analysis. This guides the users towards significant relationships. We implement our approach as an interactive data exploration tool. It is designed with flexibility in mind, so that a diverse set of tasks such as inverse modeling, sensitivity analysis and model parameter refinement can be supported. Here we demonstrate the capabilities of our approach by two examples for gas storage applications. For the first example our Visual Analytics approach enabled the analyst to observe how the element concentrations change around previously established baselines in response to thousands of different combinations of mineral phases. This supported combinatorial inverse modeling for interpreting observations about the chemical composition of the formation fluids at the Ketzin pilot site for CO2 storage. The results indicate that, within the experimental error range, the formation fluid cannot be considered at local thermodynamical equilibrium with the mineral assemblage of the reservoir rock. This is a valuable insight from the predictive geochemical modeling for the Ketzin site. For the second example our approach supports sensitivity analysis for a reaction involving the reductive dissolution of pyrite with formation of pyrrothite in presence of gaseous hydrogen. We determine that this reaction

  1. Mitochondrial DNA Fragmentation to Monitor Processing Parameters in High Acid, Plant-Derived Foods.

    PubMed

    Caldwell, Jane M; Pérez-Díaz, Ilenys M; Harris, Keith; Hassan, Hosni M; Simunovic, Josip; Sandeep, K P

    2015-12-01

    Mitochondrial DNA (mtDNA) fragmentation was assessed in acidified foods. Using quantitative polymerase chain reaction, Ct values measured from fresh, fermented, pasteurized, and stored cucumber mtDNA were determined to be significantly different (P > 0.05) based on processing and shelf-life. This indicated that the combination of lower temperature thermal processes (hot-fill at 75 °C for 15 min) and acidified conditions (pH = 3.8) was sufficient to cause mtDNA fragmentation. In studies modeling high acid juices, pasteurization (96 °C, 0 to 24 min) of tomato serum produced Ct values which had high correlation to time-temperature treatment. Primers producing longer amplicons (approximately 1 kb) targeting the same mitochondrial gene gave greater sensitivity in correlating time-temperature treatments to Ct values. Lab-scale pasteurization studies using Ct values derived from the longer amplicon differentiated between heat treatments of tomato serum (95 °C for <2 min). MtDNA fragmentation was shown to be a potential new tool to characterize low temperature (<100 °C) high acid processes (pH < 4.6), nonthermal processes such as vegetable fermentation and holding times of acidified, plant-derived products. PMID:26556214

  2. Mitochondrial DNA Fragmentation to Monitor Processing Parameters in High Acid, Plant-Derived Foods.

    PubMed

    Caldwell, Jane M; Pérez-Díaz, Ilenys M; Harris, Keith; Hassan, Hosni M; Simunovic, Josip; Sandeep, K P

    2015-12-01

    Mitochondrial DNA (mtDNA) fragmentation was assessed in acidified foods. Using quantitative polymerase chain reaction, Ct values measured from fresh, fermented, pasteurized, and stored cucumber mtDNA were determined to be significantly different (P > 0.05) based on processing and shelf-life. This indicated that the combination of lower temperature thermal processes (hot-fill at 75 °C for 15 min) and acidified conditions (pH = 3.8) was sufficient to cause mtDNA fragmentation. In studies modeling high acid juices, pasteurization (96 °C, 0 to 24 min) of tomato serum produced Ct values which had high correlation to time-temperature treatment. Primers producing longer amplicons (approximately 1 kb) targeting the same mitochondrial gene gave greater sensitivity in correlating time-temperature treatments to Ct values. Lab-scale pasteurization studies using Ct values derived from the longer amplicon differentiated between heat treatments of tomato serum (95 °C for <2 min). MtDNA fragmentation was shown to be a potential new tool to characterize low temperature (<100 °C) high acid processes (pH < 4.6), nonthermal processes such as vegetable fermentation and holding times of acidified, plant-derived products.

  3. Thermal analysis to derive energetic quality parameters of soil organic matter?

    NASA Astrophysics Data System (ADS)

    Peikert, Benjamin; Schaumann, Gabriele Ellen

    2014-05-01

    Many studies have dealt with thermal analysis for characterisation of soil and soil organic matter. It is a versatile tool assessing various physicochemical properties of the sample during heating and/or cooling. Especially the combination of different detection methods is highly promising. In this contribution, we will discuss the combination of thermogravimetry (TGA) with differential scanning calorimetry (DSC) in one single thermal analysis device. TGA alone helps distinguishment of soil and soil organic matter fractions with respect to their resistance towards combustion and allows a quantitative assignment of thermolabile and recalcitrant OM fractions. Combination with DSC in the same device, allows determination of energy transformation during the combustion process. Therefore, it becomes possible to determine not only the calorific value of the organic matter, but also of its fractions. We will show the potential of using the calorific values of OM fractions as quality parameter - exemplified for the analysis of soils polluted with organic matter from the olive oil production. The pollution history of these samples is largely unknown. As expected, TGA indicated a relative enrichment of the labile carbon fraction in contaminated samples with respect to the controls. The calorific values of the thermolabile and the recalcitrant fractions differ from each other, and those of the recalcitrant fractions of the polluted samples were higher than of those of the unpolluted controls. Further analyses showed correlation of the calorific value of this fraction with soil water repellency and the carbon isotopic ratio. The synthesis of our current data suggests that the content of thermolabile fraction, the isotopic ratio and calorific value of the recalcitrant fraction are useful indicators for characterizing the degree of decomposition of OMW organic matter. In this contribution, we will further discuss the potential of using the energetic parameters a quality

  4. Novel peptide-mediated interactions derived from high-resolution 3-dimensional structures.

    PubMed

    Stein, Amelie; Aloy, Patrick

    2010-05-01

    Many biological responses to intra- and extracellular stimuli are regulated through complex networks of transient protein interactions where a globular domain in one protein recognizes a linear peptide from another, creating a relatively small contact interface. These peptide stretches are often found in unstructured regions of proteins, and contain a consensus motif complementary to the interaction surface displayed by their binding partners. While most current methods for the de novo discovery of such motifs exploit their tendency to occur in disordered regions, our work here focuses on another observation: upon binding to their partner domain, motifs adopt a well-defined structure. Indeed, through the analysis of all peptide-mediated interactions of known high-resolution three-dimensional (3D) structure, we found that the structure of the peptide may be as characteristic as the consensus motif, and help identify target peptides even though they do not match the established patterns. Our analyses of the structural features of known motifs reveal that they tend to have a particular stretched and elongated structure, unlike most other peptides of the same length. Accordingly, we have implemented a strategy based on a Support Vector Machine that uses this features, along with other structure-encoded information about binding interfaces, to search the set of protein interactions of known 3D structure and to identify unnoticed peptide-mediated interactions among them. We have also derived consensus patterns for these interactions, whenever enough information was available, and compared our results with established linear motif patterns and their binding domains. Finally, to cross-validate our identification strategy, we scanned interactome networks from four model organisms with our newly derived patterns to see if any of them occurred more often than expected. Indeed, we found significant over-representations for 64 domain-motif interactions, 46 of which had not been

  5. Derivation of the physical parameters for strong and weak flares from the Hα line

    NASA Astrophysics Data System (ADS)

    Semeida, M. A.; Rashed, M. G.

    2016-06-01

    The two flares of 19 and 30 July 1999 were observed in the Hα line using the multichannel flare spectrograph (MFS) at the Astronomical Institute in Ondřejov, Czech Republic. We use a modified cloud method to fit the Hα line profiles which avoids using the background profile. We obtain the four parameters of the two flares: the source function, the optical thickness at line center, the line-of-sight velocity and the Doppler width. The observed asymmetry profiles have been reproduced by the theoretical ones based on our model. A discussion is made about the results of strong and weak flares using the present method.

  6. Spatial representation in the social interaction potential metric: an analysis of scale and parameter sensitivity

    NASA Astrophysics Data System (ADS)

    Li, Xiao; Farber, Steven

    2016-10-01

    The social interaction potential (SIP) metric measures urban structural constraints on social interaction opportunities of a metropolitan region based on the time geographic concept of joint accessibility. Previous implementations of the metric used an interaction surface based on census tracts and the locations of their centroids. This has been shown to be a shortcoming, as the metric strongly depends on the scale of the zoning system in the region, making it difficult to compare the SIP metric between metropolitan regions. This research explores the role of spatial representation in the SIP metric and identifies a suitable grid-based representation that allows for comparison between regions while retaining cost-effectiveness with respect to computational burden. We also report on findings from an extensive sensitivity analysis investigating the SIP metric's input parameters such as a travel flow congestion factor and the length of the allowable time budget for social activities. The results provide new insights on the role of the modifiable areal unit problem in the computation of time geographic measures of accessibility.

  7. Plant-Derived Polyphenols Interact with Staphylococcal Enterotoxin A and Inhibit Toxin Activity

    PubMed Central

    Shimamura, Yuko; Aoki, Natsumi; Sugiyama, Yuka; Tanaka, Takashi; Murata, Masatsune; Masuda, Shuichi

    2016-01-01

    This study was performed to investigate the inhibitory effects of 16 different plant-derived polyphenols on the toxicity of staphylococcal enterotoxin A (SEA). Plant-derived polyphenols were incubated with the cultured Staphylococcus aureus C-29 to investigate the effects of these samples on SEA produced from C-29 using Western blot analysis. Twelve polyphenols (0.1–0.5 mg/mL) inhibited the interaction between the anti-SEA antibody and SEA. We examined whether the polyphenols could directly interact with SEA after incubation of these test samples with SEA. As a result, 8 polyphenols (0.25 mg/mL) significantly decreased SEA protein levels. In addition, the polyphenols that interacted with SEA inactivated the toxin activity of splenocyte proliferation induced by SEA. Polyphenols that exerted inhibitory effects on SEA toxic activity had a tendency to interact with SEA. In particular, polyphenol compounds with 1 or 2 hexahydroxydiphenoyl groups and/or a galloyl group, such as eugeniin, castalagin, punicalagin, pedunculagin, corilagin and geraniin, strongly interacted with SEA and inhibited toxin activity at a low concentration. These polyphenols may be used to prevent S. aureus infection and staphylococcal food poisoning. PMID:27272505

  8. Plant-Derived Polyphenols Interact with Staphylococcal Enterotoxin A and Inhibit Toxin Activity.

    PubMed

    Shimamura, Yuko; Aoki, Natsumi; Sugiyama, Yuka; Tanaka, Takashi; Murata, Masatsune; Masuda, Shuichi

    2016-01-01

    This study was performed to investigate the inhibitory effects of 16 different plant-derived polyphenols on the toxicity of staphylococcal enterotoxin A (SEA). Plant-derived polyphenols were incubated with the cultured Staphylococcus aureus C-29 to investigate the effects of these samples on SEA produced from C-29 using Western blot analysis. Twelve polyphenols (0.1-0.5 mg/mL) inhibited the interaction between the anti-SEA antibody and SEA. We examined whether the polyphenols could directly interact with SEA after incubation of these test samples with SEA. As a result, 8 polyphenols (0.25 mg/mL) significantly decreased SEA protein levels. In addition, the polyphenols that interacted with SEA inactivated the toxin activity of splenocyte proliferation induced by SEA. Polyphenols that exerted inhibitory effects on SEA toxic activity had a tendency to interact with SEA. In particular, polyphenol compounds with 1 or 2 hexahydroxydiphenoyl groups and/or a galloyl group, such as eugeniin, castalagin, punicalagin, pedunculagin, corilagin and geraniin, strongly interacted with SEA and inhibited toxin activity at a low concentration. These polyphenols may be used to prevent S. aureus infection and staphylococcal food poisoning. PMID:27272505

  9. Prognostic value of parameters derived from white blood cell and differential counts in patients receiving palliative radiotherapy

    PubMed Central

    Saito, Tetsuo; Toya, Ryo; Matsuyama, Tomohiko; Semba, Akiko; Matsuyama, Keiya; Oya, Natsuo

    2016-01-01

    The aim of the present study was to identify white blood cell (WBC) parameters with high prognostic value for the survival of patients receiving palliative radiotherapy. The prognostic value of seven parameters derived from WBC and differential counts was retrospectively evaluated in patients who underwent palliative radiotherapy between October, 2010 and June, 2013. The analyzed parameters were the total WBC count, the absolute and relative lymphocyte count, the absolute and relative neutrophil count, and the neutrophil-to-lymphocyte and lymphocyte-to-monocyte ratios. Following univariate analysis, multivariate Cox regression analysis was performed to adjust for gender, age, disease type, previous chemotherapy, previous radiotherapy and the levels of albumin and lactate dehydrogenase. A total of 220 patients with a median survival of 4.7 months were identified. All seven parameters were found to be statistically significant predictors of survival on univariate Cox regression analysis (P<0.05). Of these parameters, the low relative lymphocyte and high relative neutrophil counts were consistent predictors of poor survival in patients who received chemotherapy within 1 month prior to blood sampling (n=68) and in patients who received steroid treatment at the time of sampling (n=49). Multivariate Cox regression analysis revealed that the relative lymphocyte and neutrophil counts were independent predictors of survival in all 220 patients (P<0.05). In conclusion, relative lymphocyte and neutrophil counts were of high prognostic value for the survival of patients receiving palliative radiotherapy, even in those receiving medications that affect WBC and differential counts. PMID:27602221

  10. Prognostic value of parameters derived from white blood cell and differential counts in patients receiving palliative radiotherapy

    PubMed Central

    Saito, Tetsuo; Toya, Ryo; Matsuyama, Tomohiko; Semba, Akiko; Matsuyama, Keiya; Oya, Natsuo

    2016-01-01

    The aim of the present study was to identify white blood cell (WBC) parameters with high prognostic value for the survival of patients receiving palliative radiotherapy. The prognostic value of seven parameters derived from WBC and differential counts was retrospectively evaluated in patients who underwent palliative radiotherapy between October, 2010 and June, 2013. The analyzed parameters were the total WBC count, the absolute and relative lymphocyte count, the absolute and relative neutrophil count, and the neutrophil-to-lymphocyte and lymphocyte-to-monocyte ratios. Following univariate analysis, multivariate Cox regression analysis was performed to adjust for gender, age, disease type, previous chemotherapy, previous radiotherapy and the levels of albumin and lactate dehydrogenase. A total of 220 patients with a median survival of 4.7 months were identified. All seven parameters were found to be statistically significant predictors of survival on univariate Cox regression analysis (P<0.05). Of these parameters, the low relative lymphocyte and high relative neutrophil counts were consistent predictors of poor survival in patients who received chemotherapy within 1 month prior to blood sampling (n=68) and in patients who received steroid treatment at the time of sampling (n=49). Multivariate Cox regression analysis revealed that the relative lymphocyte and neutrophil counts were independent predictors of survival in all 220 patients (P<0.05). In conclusion, relative lymphocyte and neutrophil counts were of high prognostic value for the survival of patients receiving palliative radiotherapy, even in those receiving medications that affect WBC and differential counts.

  11. Derivation of the cosmological density parameter Omega0 from large-scale flows.

    PubMed Central

    Rowan-Robinson, M

    1993-01-01

    Methods for determining the cosmological density parameter 0 from large-scale flows are reviewed. Very consistent results using infrared astronomical satellite (IRAS) data have been obtained by different groups with completely independent methods. The two main methods involve either using maps of the galaxy distribution to predict the peculiar velocity of the Local Group or directly comparing the density field inferred from the IRAS galaxy distribution with the peculiar velocities inferred from optical distance methods. All methods based on IRAS data are consistent with Omega0 = 0.7 +/- 0.1, or if Omega0 = 1, with a bias parameter b = 1.2 +/- 0.1. Various problems associated with the method are discussed, including the issue of which waveband is optimum for such studies, bias, the universality of the luminosity function, and the convergence of the dipole. The lower values of 0 obtained in optical studies may indicate a higher degree of bias toward regions of high total matter-density for elliptical galaxies. A new study using the whole IRAS point source catalog to 0.6 jansky is described, which gives results consistent with other IRAS studies. PMID:11607394

  12. Geostatistical analysis of tritium, groundwater age and other noble gas derived parameters in California.

    PubMed

    Visser, A; Moran, J E; Hillegonds, Darren; Singleton, M J; Kulongoski, Justin T; Belitz, Kenneth; Esser, B K

    2016-03-15

    Key characteristics of California groundwater systems related to aquifer vulnerability, sustainability, recharge locations and mechanisms, and anthropogenic impact on recharge are revealed in a spatial geostatistical analysis of a unique data set of tritium, noble gases and other isotopic analyses unprecedented in size at nearly 4000 samples. The correlation length of key groundwater residence time parameters varies between tens of kilometers ((3)H; age) to the order of a hundred kilometers ((4)Heter; (14)C; (3)Hetrit). The correlation length of parameters related to climate, topography and atmospheric processes is on the order of several hundred kilometers (recharge temperature; δ(18)O). Young groundwater ages that highlight regional recharge areas are located in the eastern San Joaquin Valley, in the southern Santa Clara Valley Basin, in the upper LA basin and along unlined canals carrying Colorado River water, showing that much of the recent recharge in central and southern California is dominated by river recharge and managed aquifer recharge. Modern groundwater is found in wells with the top open intervals below 60 m depth in the southeastern San Joaquin Valley, Santa Clara Valley and Los Angeles basin, as the result of intensive pumping and/or managed aquifer recharge operations.

  13. CPT Profiling and Laboratory Data Correlations for Deriving of Selected Geotechnical Parameter

    NASA Astrophysics Data System (ADS)

    Bulko, Roman; Drusa, Marián; Vlček, Jozef; Mečár, Martin

    2015-12-01

    Currently, can be seen a new trend in engineering geological survey, where laboratory analysis are replaced by in situ testing methods, which are more efficient and cost effective, and time saving too. A regular engineering geological survey cannot be provided by simple core drillings, macroscopic description (sometimes very subjective), and then geotechnical parameters are established based on indicative standardized values or archive values from previous geotechnical standards. The engineering geological survey is trustworthy if is composed of laboratory and in-situ testing supplemented by indirect methods of testing, [1]. The prevalence of rotary core drilling for obtaining laboratory soil samples from various depths (every 1 to 3 m), cannot be a more enhanced as continues evaluation of strata and properties e.g. by CPT Piezocone (every 1 cm). Core drillings survey generally uses small amounts of soil samples, but this is resulting to a lower representation of the subsoil and underestimation of parameters. Higher amounts of soil samples make laboratory testing time-consuming and results from this testing can be influenced by the storage and processing of the soil samples. Preference for geotechnical surveys with in situ testing is therefore a more suitable option. In situ testing using static and dynamic penetration tests can be used as a supplement or as a replacement for the (traditional) methods of surveying.

  14. Geostatistical analysis of tritium, groundwater age and other noble gas derived parameters in California.

    PubMed

    Visser, A; Moran, J E; Hillegonds, Darren; Singleton, M J; Kulongoski, Justin T; Belitz, Kenneth; Esser, B K

    2016-03-15

    Key characteristics of California groundwater systems related to aquifer vulnerability, sustainability, recharge locations and mechanisms, and anthropogenic impact on recharge are revealed in a spatial geostatistical analysis of a unique data set of tritium, noble gases and other isotopic analyses unprecedented in size at nearly 4000 samples. The correlation length of key groundwater residence time parameters varies between tens of kilometers ((3)H; age) to the order of a hundred kilometers ((4)Heter; (14)C; (3)Hetrit). The correlation length of parameters related to climate, topography and atmospheric processes is on the order of several hundred kilometers (recharge temperature; δ(18)O). Young groundwater ages that highlight regional recharge areas are located in the eastern San Joaquin Valley, in the southern Santa Clara Valley Basin, in the upper LA basin and along unlined canals carrying Colorado River water, showing that much of the recent recharge in central and southern California is dominated by river recharge and managed aquifer recharge. Modern groundwater is found in wells with the top open intervals below 60 m depth in the southeastern San Joaquin Valley, Santa Clara Valley and Los Angeles basin, as the result of intensive pumping and/or managed aquifer recharge operations. PMID:26803267

  15. Effects of the Stellar Component on Derived Physical Parameters of Galactic H II Regions

    NASA Astrophysics Data System (ADS)

    Robledo-Rella, V.

    2000-05-01

    We present results of long-slit spatially integrated (~ 7 arcmin2) spectroscopy (3600 - 10200 Å in the central regions of Carina, M8 and M20. We obtained two types of spectra: neb \\ (pure nebular) and all \\ (nebular plus stellar). The stellar effect increases along the Balmer series, with neb/all \\ ~ 1.20 at Hdelta, but could be much stronger (~ 1.7) for weaker lines beyond H8. The resulting neb \\ dereddened spectra give slightly higher electron temperatures which yield (O/H) smaller (~ 0.10-0.30 dex), (N/H) higher (~ 0.05-0.10 dex), (Ne/H) smaller (~ 0.25-0.40 dex), and (Ar/H) smaller (~ 0.15-0.30 dex), with respect to the all \\ case. Although these differences are roughly within the uncertainties, they could be important in deriving accurate chemical compositions in extragalactic nebula where the stars are not resolved.

  16. Fast spinning strange stars: possible ways to constrain interacting quark matter parameters

    NASA Astrophysics Data System (ADS)

    Bhattacharyya, Sudip; Bombaci, Ignazio; Logoteta, Domenico; Thampan, Arun V.

    2016-04-01

    For a set of equation of state (EoS) models involving interacting strange quark matter, characterized by an effective bag constant (Beff) and a perturbative quantum chromodynamics corrections term (a4), we construct fully general relativistic equilibrium sequences of rapidly spinning strange stars for the first time. Computation of such sequences is important to study millisecond pulsars and other fast spinning compact stars. Our EoS models can support a gravitational mass (MG) and a spin frequency (ν) at least up to ≈3.0 M⊙ and ≈1250 Hz, respectively, and hence are fully consistent with measured MG and ν values. This paper reports the effects of Beff and a4 on measurable compact star properties, which could be useful to find possible ways to constrain these fundamental quark matter parameters, within the ambit of our EoS models. We confirm that a lower Beff allows a higher mass. Besides, for known MG and ν, measurable parameters, such as stellar radius, radius-to-mass ratio and moment of inertia, increase with the decrease of Beff. Our calculations also show that a4 significantly affects the stellar rest mass and the total stellar binding energy. As a result, a4 can have signatures in evolutions of both accreting and non-accreting compact stars, and the observed distribution of stellar mass and spin and other source parameters. Finally, we compute the parameter values of two important pulsars, PSR J1614-2230 and PSR J1748-2446ad, which may have implications to probe their evolutionary histories, and for constraining EoS models.

  17. Fermi orbital derivatives in self-interaction corrected density functional theory: Applications to closed shell atoms

    SciTech Connect

    Pederson, Mark R.

    2015-02-14

    A recent modification of the Perdew-Zunger self-interaction-correction to the density-functional formalism has provided a framework for explicitly restoring unitary invariance to the expression for the total energy. The formalism depends upon construction of Löwdin orthonormalized Fermi-orbitals which parametrically depend on variational quasi-classical electronic positions. Derivatives of these quasi-classical electronic positions, required for efficient minimization of the self-interaction corrected energy, are derived and tested, here, on atoms. Total energies and ionization energies in closed-shell singlet atoms, where correlation is less important, using the Perdew-Wang 1992 Local Density Approximation (PW92) functional, are in good agreement with experiment and non-relativistic quantum-Monte-Carlo results albeit slightly too low.

  18. A quantitative analysis of weak intermolecular interactions & quantum chemical calculations (DFT) of novel chalcone derivatives

    NASA Astrophysics Data System (ADS)

    Chavda, Bhavin R.; Gandhi, Sahaj A.; Dubey, Rahul P.; Patel, Urmila H.; Barot, Vijay M.

    2016-05-01

    The novel chalcone derivatives have widespread applications in material science and medicinal industries. The density functional theory (DFT) is used to optimized the molecular structure of the three chalcone derivatives (M-I, II, III). The observed discrepancies between the theoretical and experimental (X-ray data) results attributed to different environments of the molecules, the experimental values are of the molecule in solid state there by subjected to the intermolecular forces, like non-bonded hydrogen bond interactions, where as isolated state in gas phase for theoretical studies. The lattice energy of all the molecules have been calculated using PIXELC module in Coulomb -London -Pauli (CLP) package and is partitioned into corresponding coulombic, polarization, dispersion and repulsion contributions. Lattice energy data confirm and strengthen the finding of the X-ray results that the weak but significant intermolecular interactions like C-H…O, Π- Π and C-H… Π plays an important role in the stabilization of crystal packing.

  19. Secondary microseism generation mechanisms and microseism derived ocean wave parameters, NE Atlantic, West of Ireland.

    NASA Astrophysics Data System (ADS)

    Donne, S. E.; Bean, C. J.; Lokmer, I.; Nicolau, M.; O'Neill, M.

    2014-12-01

    Ocean waves, driven by atmospheric processes, generate faint continuous Earth vibrations known as microseisms (Bromirski, 1999). Under certain conditions, ocean waves travelling in opposite directions may interact with one another producing a partial or full standing wave. This wave-wave interaction produces a pressure profile, unattenuated with depth, which exerts a pressure change at the seafloor, resulting in secondary microseisms in the 0.1-0.33 Hz band. There are clear correlations between microseism amplitude and storm and ocean wave intensity. We aim to determine ocean wave heights in the Northeast Atlantic offshore Ireland at individual buoy locations, using terrestrially recorded microseism signals. Two evolutionary approaches are used: Artificial Neural Networks (ANN) and Grammatical Evolution (GE). These systems learn to interpret particular input patterns and corresponding outputs and expose the often complex underlying relationship between them. They learn by example and are therefore entirely data driven so data selection is extremely important for the success of the methods. An analysis and comparison of the performance of these methods for a five month period in 2013 will be presented showing that ocean wave characteristics may be reconstructed using microseism amplitudes, adopting a purely data driven approach. There are periods during the year when the estimations made from both the GE and ANN are delayed in time by 10 to 20 hours when compared to the target buoy measurements. These delays hold important information about the totality of the conditions needed for microseism generation, an analysis of which will be presented.

  20. Effective interactions containing {partial_derivative}{center_dot}W{sup {plus_minus}} and {partial_derivative}{center_dot}Z factors

    SciTech Connect

    Einhorn, M.B.; Wudka, J.

    1997-03-01

    The effects of effective interactions containing the factors {partial_derivative}{center_dot}W{sup {plus_minus}} and {partial_derivative}{center_dot}Z is studied within a consistent effective Lagrangian formalism. It is shown that such terms are redundant. {copyright} {ital 1997} {ital The American Physical Society}

  1. Cooperative water-SOM interactions derived from the organic compound effect on SOM hydration

    NASA Astrophysics Data System (ADS)

    Borisover, Mikhail

    2014-05-01

    Interactions of water molecules with soil organic matter (SOM) may affect the ability of SOM to participate in multiple physical, chemical and biological processes. Specifically, water-SOM interactions may have a profound effect on interactions of organic compounds with SOM which is often considered as a major natural sorbent controlling the environmental fate of organic pollutants in the soil environment. Quantification of water - SOM interactions may be carried out by using water vapor sorption isotherms. However, water sorption isotherms providing macroscopic thermodynamic data do not allow examining water-SOM interactions on a microenvironment scale. The examination of water-SOM interactions in a local SOM environment may be carried out by determining the response of the SOM hydration to sorption of probe organic compounds. Recently, the model-free approach was proposed which allows quantifying effects of sorbing organic molecules on water - SOM interactions, by using relatively more available data on the effect of water activity on organic compound - SOM interactions. Therefore, this thermodynamic approach was applied to the experimental data describing sorption of organic compounds by SOM, both from the vapor and liquid phases, at various water activities. Hence, the response of water interactions with the model SOM materials such as a humic acid and an organic matter-rich peat soil to the presence of various organic sorbates was evaluated. Depending on a molecular structure of organic sorbates probing various molecular environments in SOM, the SOM-bound water may be driven in or out of the SOM sorbents. Organic compounds containing the atoms of oxygen, nitrogen or sulfur and preferring a relatively "polar" SOM microenvironment demonstrate the distinct enhancing effect on water-SOM interactions. In contrast, the "low-polarity" organic compounds, e.g., hydrocarbons or their halogen-substituted derivatives, produce a weakening effect on water-SOM interactions

  2. Comparison of cloud microphysical parameters derived from surface and satellite measurements during FIRE phase 2

    NASA Technical Reports Server (NTRS)

    Young, David F.; Minnis, Patrick; Snider, Jack; Uttal, Taneil; Intrieri, Janet M.; Matrosov, Sergey

    1993-01-01

    Cloud microphysical properties are an important component in climate model parameterizations of water transport, cloud radiative exchange, and latent heat processes. Estimation of effective cloud particle size, liquid or ice water content, and optical depth from satellite-based instrumentation is needed to develop a climatology of cloud microphysical properties and to better understand and model cloud processes in atmospheric circulation. These parameters are estimated from two different surface data sets taken at Coffeyville, Kansas, during the First ISCCP Regional Experiment (FIRE) Phase-2 Intensive Field Observation (IFO) period (November 13 - December 7, 1991). Satellite data can also provide information about optical depth and effective particle size. This paper explores the combination of the FIRE-2 surface and satellite data to determine each of the cloud microphysical properties.

  3. Lunar tidal acceleration obtained from satellite-derived ocean tide parameters

    NASA Technical Reports Server (NTRS)

    Goad, C. C.; Douglas, B. C.

    1978-01-01

    One hundred sets of mean elements of GEOS-3 computed at 2-day intervals yielded observation equations for the M sub 2 ocean tide from the long periodic variations of the inclination and node of the orbit. The 2nd degree Love number was given the value k sub 2 = 0.30 and the solid tide phase angle was taken to be zero. Combining obtained equations with results for the satellite 1967-92A gives the M sub 2 ocean tide parameter values. Under the same assumption of zero solid tide phase lag, the lunar tidal acceleration was found mostly due to the C sub 22 term in the expansion of the M sub 2 tide with additional small contributions from the 0 sub 1 and N sub 2 tides. Using Lambeck's (1975) estimates for the latter, the obtained acceleration in lunar longitudal in excellent agreement with the most recent determinations from ancient and modern astronomical data.

  4. Gravity wave parameters derived from traveling ionospheric disturbances observations in the auroral zone

    SciTech Connect

    Natorf, L.; Schlegel, K.; Wernik, A.W. Space Research Centre, Warsaw )

    1992-12-01

    Large-scale wavelike fluctuations of ion velocity, as measured by the European incoherent scatter radar along the geomagnetic field line, have been attributed to gravity wave effects. The height-dependent parameters of the causative gravity waves are calculated, taking into account the neutral horizontal wind and the electric field. The results are compared with the solutions of a dissipative dispersion relation. Much better agreement is achieved for the imaginary part of the vertical wave vector than for its real part. The calculated wave damping is greater than that given by theory. The possible reasons for this are discussed. It is suggested that E x B drift of the ions and vertical neutral winds, which are characteristic features of the auroral zone ionosphere, may contribute to the observed discrepancies. 40 refs.

  5. Lunar tidal acceleration obtained from satellite-derived ocean tide parameters

    NASA Technical Reports Server (NTRS)

    Goad, C. C.; Douglas, B. C.

    1978-01-01

    Observation equations for the M2 ocean tide are computed from Geos 3 data for the long periodic variations of the inclination and node of the orbit. M2 ocean tide parameter values C22+ = 3.23 + or - 0.25 cm, epsilon 22+ = 331 + or - 6 deg, and epsilon 42+ = 113 + or - 6 deg are determined. With the assumption of zero solid tide phase lag, the lunar tidal acceleration is mostly (85%) due to the C22+ term in the expansion of the M2 tide with additional small contributions from the O1 and N2 tides. The calculated value for the tidal acceleration in lunar longitude is -27.4 + or - 3 arc sec/sq (100 yr) which is similar to values determined from astronomical data. The mean elements of Geos 3 are presented in tabular form.

  6. Accuracy of Geophysical Parameters Derived from AIRS/AMSU as a Function of Fractional Cloud Cover

    NASA Technical Reports Server (NTRS)

    Susskind, Joel; Barnet, Chris; Blaisdell, John; Iredell, Lena; Keita, Fricky; Kouvaris, Lou; Molnar, Gyula; Chahine, Moustafa

    2006-01-01

    AIRS was launched on EOS Aqua on May 4,2002, together with AMSU A and HSB, to form a next generation polar orbiting infrared and microwave atmospheric sounding system. The primary products of AIRS/AMSU are twice daily global fields of atmospheric temperature-humidity profiles, ozone profiles, sea/land surface skin temperature, and cloud related parameters including OLR. The sounding goals of AIRS are to produce 1 km tropospheric layer mean temperatures with an rms error of lK, and layer precipitable water with an rms error of 20 percent, in cases with up to 80 percent effective cloud cover. The basic theory used to analyze Atmospheric InfraRed Sounder/Advanced Microwave Sounding Unit/Humidity Sounder Brazil (AIRS/AMSU/HSB) data in the presence of clouds, called the at-launch algorithm, was described previously. Pre-launch simulation studies using this algorithm indicated that these results should be achievable. Some modifications have been made to the at-launch retrieval algorithm as described in this paper. Sample fields of parameters retrieved from AIRS/AMSU/HSB data are presented and validated as a function of retrieved fractional cloud cover. As in simulation, the degradation of retrieval accuracy with increasing cloud cover is small and the RMS accuracy of lower tropospheric temperature retrieved with 80 percent cloud cover is about 0.5 K poorer than for clear cases. HSB failed in February 2003, and consequently HSB channel radiances are not used in the results shown in this paper. The AIRS/AMSU retrieval algorithm described in this paper, called Version 4, become operational at the Goddard DAAC (Distributed Active Archive Center) in April 2003 and is being used to analyze near-real time AIRS/AMSU data. Historical AIRS/AMSU data, going backwards from March 2005 through September 2002, is also being analyzed by the DAAC using the Version 4 algorithm.

  7. Coupling parameters of many-body interactions for the Al(100) surface state: A high-resolution angle-resolved photoemission spectroscopy study

    NASA Astrophysics Data System (ADS)

    Jiang, J.; Shimada, K.; Hayashi, H.; Iwasawa, H.; Aiura, Y.; Namatame, H.; Taniguchi, M.

    2011-10-01

    We examined the dimensionless coupling parameters of many-body interactions for a free-electron-like surface-derived state in Al(100) by means of high-resolution angle-resolved photoemission spectroscopy. A kink structure was found to exist in the energy-band dispersion near the Fermi level (EF), which was attributed to the electron-phonon interaction. At 50 K, the coupling parameters of the electron-phonon and electron-electron interactions were estimated as λep=0.67±0.05 and λee˜0.003, respectively, indicating that the effective mass enhancement was mainly derived from the electron-phonon interaction. The temperature dependence of the kink structure, as measured by λep(T), was consistent with a theoretical calculation based on the Eliashberg function. A quasiparticle peak with a width of 15-20 meV was found near EF, which was explained well by the simulated spectral function incorporating the self-energy evaluated in this study. We found that the electrons at the surface were strongly scattered by the defects at the surface and that the linewidth was significantly broadened (Γ0=0.238±0.006 eV).

  8. Quantifying Parameter Sensitivity, Interaction and Transferability in Hydrologically Enhanced Versions of Noah-LSM over Transition Zones

    NASA Technical Reports Server (NTRS)

    Rosero, Enrique; Yang, Zong-Liang; Wagener, Thorsten; Gulden, Lindsey E.; Yatheendradas, Soni; Niu, Guo-Yue

    2009-01-01

    We use sensitivity analysis to identify the parameters that are most responsible for shaping land surface model (LSM) simulations and to understand the complex interactions in three versions of the Noah LSM: the standard version (STD), a version enhanced with a simple groundwater module (GW), and version augmented by a dynamic phenology module (DV). We use warm season, high-frequency, near-surface states and turbulent fluxes collected over nine sites in the US Southern Great Plains. We quantify changes in the pattern of sensitive parameters, the amount and nature of the interaction between parameters, and the covariance structure of the distribution of behavioral parameter sets. Using Sobol s total and first-order sensitivity indexes, we show that very few parameters directly control the variance of the model output. Significant parameter interaction occurs so that not only the optimal parameter values differ between models, but the relationships between parameters change. GW decreases parameter interaction and appears to improve model realism, especially at wetter sites. DV increases parameter interaction and decreases identifiability, implying it is overparameterized and/or underconstrained. A case study at a wet site shows GW has two functional modes: one that mimics STD and a second in which GW improves model function by decoupling direct evaporation and baseflow. Unsupervised classification of the posterior distributions of behavioral parameter sets cannot group similar sites based solely on soil or vegetation type, helping to explain why transferability between sites and models is not straightforward. This evidence suggests a priori assignment of parameters should also consider climatic differences.

  9. Mathematical models for prediction of rheological parameters in vinasses derived from sugar cane

    NASA Astrophysics Data System (ADS)

    Chacua, Leidy M.; Ayala, Germán; Rojas, Hernán; Agudelo, Ana C.

    2016-04-01

    The rheological behaviour of vinasses derived from sugar cane was studied as a function of time (0 and 600 s), soluble solids content (44 and 60 °Brix), temperature (10 and 50°C), and shear rate (0.33 and 1.0 s-1). The results indicated that vinasses were time-independent at 25°C, where shear stress values ranged between 0.01 and 0.08 Pa. Flow curves showed a shear-thinning rheological behaviour in vinasses with a flow behaviour index between 0.69 and 0.89, for temperature between 10 and 20°C. With increasing temperature, the flow behaviour index was modified, reaching values close to 1.0. The Arrhenius model described well the thermal activation of shear stress and the consistency coefficient as a function of temperature. Activation energy from the Arrhenius model ranged between 31 and 45 kJ mol-1. Finally, the consistency coefficient as a function of the soluble solids content and temperature was well fitted using an exponential model (R2 = 0.951), showing that the soluble solids content and temperature have an opposite effect on consistency coefficient values.

  10. Convex Lens-induced Confinement to Visualize Biopolymers and Interaction Parameters

    NASA Astrophysics Data System (ADS)

    Stabile, Frank; Berard, Daniel; Henkin, Gil; Shayegan, Marjan; Michaud, François; Leslie, Sabrina

    In this poster, we present a versatile CLiC (Convex Lens-induced Confinement) microscopy system to access a broad range of biopolymer visualization and interaction parameters. In the CLiC technique, the curved surface of a convex lens is used to deform a flexible coverslip above a glass substrate, creating a nanoscale gap that can be tuned during an experiment to load and confine molecules into nanoscale features, both linear and circular, embedded in the bottom substrate. We demonstrate and characterize massively parallel DNA nanochannel-based stretching, building on prior work. Further, we demonstrate controlled insertion of reagent molecules within the CLiC imaging chamber. We visualize real-time reaction dynamics of nanoconfined species, including dye/DNA intercalation and DNA/DNA ligation reactions, demonstrating the versatility of this nanoscale microscopy platform.

  11. Polymerase/DNA interactions and enzymatic activity: multi-parameter analysis with electro-switchable biosurfaces

    NASA Astrophysics Data System (ADS)

    Langer, Andreas; Schräml, Michael; Strasser, Ralf; Daub, Herwin; Myers, Thomas; Heindl, Dieter; Rant, Ulrich

    2015-07-01

    The engineering of high-performance enzymes for future sequencing and PCR technologies as well as the development of many anticancer drugs requires a detailed analysis of DNA/RNA synthesis processes. However, due to the complex molecular interplay involved, real-time methodologies have not been available to obtain comprehensive information on both binding parameters and enzymatic activities. Here we introduce a chip-based method to investigate polymerases and their interactions with nucleic acids, which employs an electrical actuation of DNA templates on microelectrodes. Two measurement modes track both the dynamics of the induced switching process and the DNA extension simultaneously to quantitate binding kinetics, dissociation constants and thermodynamic energies. The high sensitivity of the method reveals previously unidentified tight binding states for Taq and Pol I (KF) DNA polymerases. Furthermore, the incorporation of label-free nucleotides can be followed in real-time and changes in the DNA polymerase conformation (finger closing) during enzymatic activity are observable.

  12. Kinetics of surface segregation in metallic alloys with first-principles interaction parameters

    SciTech Connect

    Wille, L.T. |; Ouannasser, S.; Dreysse, H.

    1996-12-31

    The authors report the results of Monte Carlo simulations of the kinetics of surface segregation at the (001) face of CuNi and MoW alloys. These two systems were selected because they are based on different lattice structures and show contrasting segregation behavior: CuNi exhibits a monotonic profile, while that of MoW is oscillatory. To describe the energetics they have determined a set of effective cluster interactions (ECI) which govern the ordering or clustering tendencies of these alloys. The ECI were obtained by means of tight-binding electronic structure calculations in which no adjustable or experimentally determined parameters were used. Equilibrium segregation profiles are calculated and a series of quenches are performed. The layer concentrations are studied as a function of time and the existence of metastable phases in the surface region is investigated.

  13. Parameters of Nocilla gas/surface interaction model from measured accomodation coefficients

    NASA Technical Reports Server (NTRS)

    Collins, Frank G.; Knox, E. C.

    1994-01-01

    Free-molecule aerodynamic coefficients are computed for a flat plate surface element at various angles of attack using the normal and tangential accomodation coefficients and the Nocilla model of the gas/surface interaction. The Nocilla model assumes that the molecules reflect from a surface in the form of a drifting Maxwellian with a mean velocity at a specific temperature. The computations use curve fits of the angular variation of the existing measurements of the accomodation coefficients and of the parameters in the Nocilla model. The two methods indicate that a surface element has considerably more lift than predicted by an assumption of diffuse scattering. In other respects the predictions by the two methods do not agree.

  14. Polymerase/DNA interactions and enzymatic activity: multi-parameter analysis with electro-switchable biosurfaces

    PubMed Central

    Langer, Andreas; Schräml, Michael; Strasser, Ralf; Daub, Herwin; Myers, Thomas; Heindl, Dieter; Rant, Ulrich

    2015-01-01

    The engineering of high-performance enzymes for future sequencing and PCR technologies as well as the development of many anticancer drugs requires a detailed analysis of DNA/RNA synthesis processes. However, due to the complex molecular interplay involved, real-time methodologies have not been available to obtain comprehensive information on both binding parameters and enzymatic activities. Here we introduce a chip-based method to investigate polymerases and their interactions with nucleic acids, which employs an electrical actuation of DNA templates on microelectrodes. Two measurement modes track both the dynamics of the induced switching process and the DNA extension simultaneously to quantitate binding kinetics, dissociation constants and thermodynamic energies. The high sensitivity of the method reveals previously unidentified tight binding states for Taq and Pol I (KF) DNA polymerases. Furthermore, the incorporation of label-free nucleotides can be followed in real-time and changes in the DNA polymerase conformation (finger closing) during enzymatic activity are observable. PMID:26174478

  15. Optical performance monitoring of QPSK data channels by use of neural networks trained with parameters derived from asynchronous constellation diagrams.

    PubMed

    Jargon, Jeffrey A; Wu, Xiaoxia; Choi, Hyeon Yeong; Chung, Yun C; Willner, Alan E

    2010-03-01

    We demonstrate a technique for performance monitoring of quadrature phase-shift keying data channels by simultaneously identifying optical signal-to-noise ratio (OSNR), chromatic dispersion (CD), and polarization-mode dispersion (PMD) using neural networks trained with parameters derived from asynchronous constellation diagrams. A correlation coefficient of 0.987 is reported for a set of testing data from a 40 Gbps return-to-zero, quadrature phase-shift keying (RZ-QPSK) system. The root-mean-square (RMS) errors are 0.77 dB for OSNR, 18.71 ps/nm for CD, and 1.17 ps for DGD.

  16. Composite genome map and recombination parameters derived from three archetypal lineages of Toxoplasma gondii

    PubMed Central

    Khan, Asis; Taylor, Sonya; Su, Chunlei; Mackey, Aaron J.; Boyle, Jon; Cole, Robert; Glover, Darius; Tang, Keliang; Paulsen, Ian T.; Berriman, Matt; Boothroyd, John C.; Pfefferkorn, Elmer R.; Dubey, J. P.; Ajioka, James W.; Roos, David S.; Wootton, John C.; Sibley, L. David

    2005-01-01

    Toxoplasma gondii is a highly successful protozoan parasite in the phylum Apicomplexa, which contains numerous animal and human pathogens. T.gondii is amenable to cellular, biochemical, molecular and genetic studies, making it a model for the biology of this important group of parasites. To facilitate forward genetic analysis, we have developed a high-resolution genetic linkage map for T.gondii. The genetic map was used to assemble the scaffolds from a 10X shotgun whole genome sequence, thus defining 14 chromosomes with markers spaced at ∼300 kb intervals across the genome. Fourteen chromosomes were identified comprising a total genetic size of ∼592 cM and an average map unit of ∼104 kb/cM. Analysis of the genetic parameters in T.gondii revealed a high frequency of closely adjacent, apparent double crossover events that may represent gene conversions. In addition, we detected large regions of genetic homogeneity among the archetypal clonal lineages, reflecting the relatively few genetic outbreeding events that have occurred since their recent origin. Despite these unusual features, linkage analysis proved to be effective in mapping the loci determining several drug resistances. The resulting genome map provides a framework for analysis of complex traits such as virulence and transmission, and for comparative population genetic studies. PMID:15911631

  17. Probing NMR parameters, structure and dynamics of 5-nitroimidazole derivatives. Density functional study of prototypical radiosensitizers.

    PubMed

    Ramalho, Teodorico C; Bühl, Michael

    2005-02-01

    The 15N chemical shifts of metronidazole (1), secnidazole (2), nimorazole (3) and tinidazole (4), radiosensitizers based on the 5-nitroimidazole motif, are reported. A detailed computational study of 1 is presented, calling special attention to the performance of various theoretical methods in reproducing the 13C and 15N data observed in solution. The most sophisticated approach involves density functional-based Car-Parrinello molecular dynamics simulations (CPMD) of 1 in aqueous solution (BP86 level) and averaging chemical shifts over snapshots from the trajectory. In the NMR calculations for these snapshots (performed at the B3LYP level), a small number of discrete water molecules are retained, and the remaining bulk solution effects are included via a polarizable continuum model (PCM). A similarly good accord with experiment is obtained from much less involved, static geometry optimization and NMR computation of pristine 1 employing a PCM approach. Solvent effects on delta(15N), which are of the order of up to 20 ppm, are not due to changes in geometric parameters upon solvation, but arise from the direct response of the electronic wavefunction to the presence of the solvent, which can be represented by discrete molecules and/or the dielectric bulk. PMID:15558660

  18. [Fluorescent derivatives of diphtheria toxin subunit B and their interaction with Vero cells].

    PubMed

    Kaberniuk, A A; Labyntsev, A Iu; Kolybo, D V; Oliĭnyk, O S; Redchuk, T A; Korotkevych, N V; Horchev, V F; Karakhim, S O; Komisarenko, S V

    2009-01-01

    Diphtheria toxin's B subunit provides toxin interaction with its receptor on the cell surface and translocation of toxin's A subunit from endosome to cytozole of sensitive cells. Functional analogues of B subunit with fluorescent label are considered as perspective tools for studying the above mentioned processes. The aim of the work was to obtain fluorescent B subunit analogues and to detect the specificity of their interaction with Vero line cells. B subunit fluorescent analogues were obtained in two different ways. The first one was B subunit chemical conjugation with fluorescein isothiocyanate and the second one was genetic fusion of recombinant B subunit chain with enhanced green fluorescent protein chain. Specific interaction of B subunit fluorescent derivatives with Vero cells was studied by flow cytometry and confocal microscopy. Using competitive analysis it was shown that B subunit fluorescent analogues possessed different affinity for cells. The affinity of EGFP-SbB was higher than FITC-SbB. Our results indicate the possibility to use the fluorescent derivatives of B subunit as tools for identification of diphtheria toxin's receptor (HB-EGF) expression on the cell surface as well as for studying the interaction and penetration of diphtheria toxin to the cell.

  19. Retrieving high-resolution surface solar radiation with cloud parameters derived by combining MODIS and MTSAT data

    NASA Astrophysics Data System (ADS)

    Tang, Wenjun; Qin, Jun; Yang, Kun; Liu, Shaomin; Lu, Ning; Niu, Xiaolei

    2016-03-01

    Cloud parameters (cloud mask, effective particle radius, and liquid/ice water path) are the important inputs in estimating surface solar radiation (SSR). These parameters can be derived from MODIS with high accuracy, but their temporal resolution is too low to obtain high-temporal-resolution SSR retrievals. In order to obtain hourly cloud parameters, an artificial neural network (ANN) is applied in this study to directly construct a functional relationship between MODIS cloud products and Multifunctional Transport Satellite (MTSAT) geostationary satellite signals. In addition, an efficient parameterization model for SSR retrieval is introduced and, when driven with MODIS atmospheric and land products, its root mean square error (RMSE) is about 100 W m-2 for 44 Baseline Surface Radiation Network (BSRN) stations. Once the estimated cloud parameters and other information (such as aerosol, precipitable water, ozone) are input to the model, we can derive SSR at high spatiotemporal resolution. The retrieved SSR is first evaluated against hourly radiation data at three experimental stations in the Haihe River basin of China. The mean bias error (MBE) and RMSE in hourly SSR estimate are 12.0 W m-2 (or 3.5 %) and 98.5 W m-2 (or 28.9 %), respectively. The retrieved SSR is also evaluated against daily radiation data at 90 China Meteorological Administration (CMA) stations. The MBEs are 9.8 W m-2 (or 5.4 %); the RMSEs in daily and monthly mean SSR estimates are 34.2 W m-2 (or 19.1 %) and 22.1 W m-2 (or 12.3 %), respectively. The accuracy is comparable to or even higher than two other radiation products (GLASS and ISCCP-FD), and the present method is more computationally efficient and can produce hourly SSR data at a spatial resolution of 5 km.

  20. Retrieving high-resolution surface solar radiation with cloud parameters derived by combining MODIS and MTSAT data

    NASA Astrophysics Data System (ADS)

    Tang, W.; Qin, J.; Yang, K.; Liu, S.; Lu, N.; Niu, X.

    2015-12-01

    Cloud parameters (cloud mask, effective particle radius and liquid/ice water path) are the important inputs in determining surface solar radiation (SSR). These parameters can be derived from MODIS with high accuracy but their temporal resolution is too low to obtain high temporal resolution SSR retrievals. In order to obtain hourly cloud parameters, the Artificial Neural Network (ANN) is applied in this study to directly construct a functional relationship between MODIS cloud products and Multi-functional Transport Satellite (MTSAT) geostationary satellite signals. Meanwhile, an efficient parameterization model for SSR retrieval is introduced and, when driven with MODIS atmospheric and land products, its root mean square error (RMSE) is about 100 W m-2 for 44 Baseline Surface Radiation Network (BSRN) stations. Once the estimated cloud parameters and other information (such as aerosol, precipitable water, ozone and so on) are input to the model, we can derive SSR at high spatio-temporal resolution. The retrieved SSR is first evaluated against hourly radiation data at three experimental stations in the Haihe River Basin of China. The mean bias error (MBE) and RMSE in hourly SSR estimate are 12.0 W m-2 (or 3.5 %) and 98.5 W m-2 (or 28.9 %), respectively. The retrieved SSR is also evaluated against daily radiation data at 90 China Meteorological Administration (CMA) stations. The MBEs are 9.8 W m-2 (5.4 %); the RMSEs in daily and monthly-mean SSR estimates are 34.2 W m-2 (19.1 %) and 22.1 W m-2 (12.3 %), respectively. The accuracy is comparable or even higher than other two radiation products (GLASS and ISCCP-FD), and the present method is more computationally efficient and can produce hourly SSR data at a spatial resolution of 5 km.

  1. On the ability of molecular dynamics force fields to recapitulate NMR derived protein side chain order parameters.

    PubMed

    O'Brien, Evan S; Wand, A Joshua; Sharp, Kim A

    2016-06-01

    Molecular dynamics (MD) simulations have become a central tool for investigating various biophysical questions with atomistic detail. While many different proxies are used to qualify MD force fields, most are based on largely structural parameters such as the root mean square deviation from experimental coordinates or nuclear magnetic resonance (NMR) chemical shifts and residual dipolar couplings. NMR derived Lipari-Szabo squared generalized order parameter (O(2) ) values of amide NH bond vectors of the polypeptide chain were also often employed for refinement and validation. However, with a few exceptions, side chain methyl symmetry axis order parameters have not been incorporated into experimental reference sets. Using a test set of five diverse proteins, the performance of several force fields implemented in the NAMDD simulation package was examined. It was found that simulations employing explicit water implemented using the TIP3 model generally performed significantly better than those using implicit water in reproducing experimental methyl symmetry axis O(2) values. Overall the CHARMM27 force field performs nominally better than two implementations of the Amber force field. It appeared that recent quantum mechanics modifications to side chain torsional angles of leucine and isoleucine in the Amber force field have significantly hindered proper motional modeling for these residues. There remained significant room for improvement as even the best correlations of experimental and simulated methyl group Lipari-Szabo generalized order parameters fall below an R(2) of 0.8.

  2. Five organic salts assembled from carboxylic acids and bis-imidazole derivatives through collective noncovalent interactions

    NASA Astrophysics Data System (ADS)

    Jin, Shouwen; Guo, Jianzhong; Liu, Li; Wang, Daqi

    2011-10-01

    Five multicomponent crystals of bis(imidazole) derivatives have been prepared with 5-nitrosalicylic acid, 5-sulfosalicylic acid, and phthalic acid. The five crystalline forms reported are organic salts of which the crystal structures have all been determined by X-ray diffraction. The results presented herein indicate that the strength and directionality of the N sbnd H⋯O, O sbnd H⋯O, and N sbnd H⋯N hydrogen bonds (ionic or neutral) between carboxylic acids and ditopic imidazoles are sufficient to bring about the formation of binary organic salts. All supramolecular architectures of the organic salts 1- 5 involve extensive O sbnd H⋯O, and N sbnd H⋯O hydrogen bonds as well as other noncovalent interactions. The role of weak and strong noncovalent interactions in the crystal packing is ascertained. These noncovalent interactions combined, all the complexes displayed 3D framework structure.

  3. Interaction of Salmonella enterica Serovar Typhimurium with Intestinal Organoids Derived from Human Induced Pluripotent Stem Cells.

    PubMed

    Forbester, Jessica L; Goulding, David; Vallier, Ludovic; Hannan, Nicholas; Hale, Christine; Pickard, Derek; Mukhopadhyay, Subhankar; Dougan, Gordon

    2015-07-01

    The intestinal mucosa forms the first line of defense against infections mediated by enteric pathogens such as salmonellae. Here we exploited intestinal "organoids" (iHOs) generated from human induced pluripotent stem cells (hIPSCs) to explore the interaction of Salmonella enterica serovar Typhimurium with iHOs. Imaging and RNA sequencing were used to analyze these interactions, and clear changes in transcriptional signatures were detected, including altered patterns of cytokine expression after the exposure of iHOs to bacteria. S. Typhimurium microinjected into the lumen of iHOs was able to invade the epithelial barrier, with many bacteria residing within Salmonella-containing vacuoles. An S. Typhimurium invA mutant defective in the Salmonella pathogenicity island 1 invasion apparatus was less capable of invading the iHO epithelium. Hence, we provide evidence that hIPSC-derived organoids are a promising model of the intestinal epithelium for assessing interactions with enteric pathogens.

  4. DERIVING THE PHYSICAL PARAMETERS OF A SOLAR EJECTION WITH AN ISOTROPIC MAGNETOHYDRODYNAMIC EVOLUTIONARY MODEL

    SciTech Connect

    Berdichevsky, Daniel B.; Stenborg, Guillermo; Vourlidas, Angelos

    2011-11-01

    The time-space evolution of a {approx}50 Degree-Sign wide coronal mass ejection (CME) on 2007 May 21 is followed remotely with the Solar Terrestrial Relations Observatory heliospheric imager HI-1, and measured in situ near Venus by the MESSENGER and Venus-Express spacecraft. The paper compares the observations of the CME structure with a simple, analytical magnetohydrodynamic force-free solution. It corresponds to a self-similar evolution, which gives a consistent picture of the main spatial-temporal features for both remote and in situ observations. Our main findings are (1) the self-similar evolution allows us to map the CME bright front into about 1/3 of the whole interplanetary counterpart of the coronal mass ejection (ICME, i.e., corresponding to the in situ observed passage of the plasma and magnetic field structure), in good quantitative agreement with the imaging measurements, (2) the cavity following the CME front maps into the rest of the ICME structure, 80% or more of which is consistent with a force free, cylindrically shaped flux rope, and (3) time and space conditions constrain the translational speed of the FR center to 301 km s{sup -1}, and the expansion speed of the FR core to 26 km s{sup -1}. A careful determination of the ICME cross-section and volume allows us to calculate the mass of the CME bright region (4.3 {+-} 1.1 10{sup 14} g) from the in situ measurements of the proton number density, which we assume to be uniform inside the bright region, of excellent agreement with the value estimated from the SECCHI HI-1 observations for the same structure. We provide model estimates for several global parameters including FR helicity ({approx}2 Multiplication-Sign 10{sup 26} Weber{sup 2}).

  5. Interactions among thermal parameters determine offspring sex under temperature-dependent sex determination.

    PubMed

    Warner, Daniel A; Shine, Richard

    2011-01-22

    In many animals, temperatures experienced by developing embryos determine offspring sex (e.g. temperature-dependent sex determination, TSD), but most studies focus strictly on the effects of mean temperature, with little emphasis on the importance of thermal fluctuations. In the jacky dragon (Amphibolurus muricatus), an Australian lizard with TSD, data from nests in the field demonstrate that offspring sex ratios are predictable from thermal fluctuations but not from mean nest temperatures. To clarify this paradox, we incubated eggs in a factorial experiment with two levels of mean temperature and three levels of diel fluctuation. We show that offspring sex is determined by an interaction between these critical thermal parameters. Intriguingly, because these two thermal descriptors shift in opposing directions throughout the incubation season, this interactive effect inhibits seasonal shifts in sex ratio. Hence, our results suggest that TSD can yield offspring sex ratios that resemble those produced under genotypic sex-determining systems. These findings raise important considerations for understanding the diversity of TSD reaction norms, for designing experiments that evaluate the evolutionary significance of TSD, and for predicting sex ratios under past and future climate change scenarios.

  6. Interactions among thermal parameters determine offspring sex under temperature-dependent sex determination

    PubMed Central

    Warner, Daniel A.; Shine, Richard

    2011-01-01

    In many animals, temperatures experienced by developing embryos determine offspring sex (e.g. temperature-dependent sex determination, TSD), but most studies focus strictly on the effects of mean temperature, with little emphasis on the importance of thermal fluctuations. In the jacky dragon (Amphibolurus muricatus), an Australian lizard with TSD, data from nests in the field demonstrate that offspring sex ratios are predictable from thermal fluctuations but not from mean nest temperatures. To clarify this paradox, we incubated eggs in a factorial experiment with two levels of mean temperature and three levels of diel fluctuation. We show that offspring sex is determined by an interaction between these critical thermal parameters. Intriguingly, because these two thermal descriptors shift in opposing directions throughout the incubation season, this interactive effect inhibits seasonal shifts in sex ratio. Hence, our results suggest that TSD can yield offspring sex ratios that resemble those produced under genotypic sex-determining systems. These findings raise important considerations for understanding the diversity of TSD reaction norms, for designing experiments that evaluate the evolutionary significance of TSD, and for predicting sex ratios under past and future climate change scenarios. PMID:20685704

  7. Coulomb interaction parameters in bcc iron: an LDA+DMFT study.

    PubMed

    Belozerov, A S; Anisimov, V I

    2014-09-17

    We study the influence of Coulomb interaction parameters on electronic structure and magnetic properties of paramagnetic bcc Fe by means of the local density approximation plus dynamical mean-field theory approach. We consider the local Coulomb interaction in the density-density form as well as in the form with spin rotational invariance approximated by averaging over all directions of the quantization axis. Our results indicate that the magnetic properties of bcc Fe are mainly affected by the Hund's rule coupling J rather than by the Hubbard U. By employing the constrained density functional theory approach in the basis of Wannier functions of spd character, we obtain U = 4 eV and J = 0.9 eV. In spite of the widespread belief that U = 4 eV is too large for bcc Fe, our calculations with the obtained values of U and J result in a satisfactory agreement with the experiment. The correlation effects caused by U are found to be weak even for large U = 6 eV. The agreement between the calculated and experimental Curie temperatures is further improved if J is reduced to 0.8 eV. However, with the decrease of J, the effective local magnetic moment moves further away from the experimental value.

  8. Coulomb interaction parameters in bcc iron: an LDA+DMFT study

    NASA Astrophysics Data System (ADS)

    Belozerov, A. S.; Anisimov, V. I.

    2014-09-01

    We study the influence of Coulomb interaction parameters on electronic structure and magnetic properties of paramagnetic bcc Fe by means of the local density approximation plus dynamical mean-field theory approach. We consider the local Coulomb interaction in the density-density form as well as in the form with spin rotational invariance approximated by averaging over all directions of the quantization axis. Our results indicate that the magnetic properties of bcc Fe are mainly affected by the Hund's rule coupling J rather than by the Hubbard U. By employing the constrained density functional theory approach in the basis of Wannier functions of spd character, we obtain U = 4 eV and J = 0.9 eV. In spite of the widespread belief that U = 4 eV is too large for bcc Fe, our calculations with the obtained values of U and J result in a satisfactory agreement with the experiment. The correlation effects caused by U are found to be weak even for large U = 6 eV. The agreement between the calculated and experimental Curie temperatures is further improved if J is reduced to 0.8 eV. However, with the decrease of J, the effective local magnetic moment moves further away from the experimental value.

  9. Structural evolution in Pt isotopes with the interacting boson model Hamiltonian derived from the Gogny energy density functional

    SciTech Connect

    Nomura, K.; Otsuka, T.; Rodriguez-Guzman, R.; Sarriguren, P.; Robledo, L. M.

    2011-01-15

    Spectroscopic calculations are carried out for the description of the shape/phase transition in Pt nuclei in terms of the interacting boson model (IBM) Hamiltonian derived from (constrained) Hartree-Fock-Bogoliubov (HFB) calculations with the finite range and density-dependent Gogny-D1S energy density functional. Assuming that the many-nucleon driven dynamics of nuclear surface deformation can be simulated by effective bosonic degrees of freedom, the Gogny-D1S potential energy surface (PES) with quadrupole degrees of freedom is mapped onto the corresponding PES of the IBM. By using this mapping procedure, the parameters of the IBM Hamiltonian, relevant to the low-lying quadrupole collective states, are derived as functions of the number of valence nucleons. Merits of both Gogny-HFB and IBM approaches are utilized so that the spectra and the wave functions in the laboratory system are calculated precisely. The experimental low-lying spectra of both ground-state and sideband levels are well reproduced. From the systematics of the calculated spectra and the reduced E2 transition probabilities B(E2), the prolate-to-oblate shape/phase transition is shown to take place quite smoothly as a function of neutron number N in the considered Pt isotopic chain, for which the {gamma} softness plays an essential role. All of these spectroscopic observables behave consistently with the relevant PES and the derived parameters of the IBM Hamiltonian as functions of N. Spectroscopic predictions are also made for those nuclei that do not have enough experimental E2 data.

  10. Spatial Prediction of Soil Classes by Using Soil Weathering Parameters Derived from vis-NIR Spectroscopy

    NASA Astrophysics Data System (ADS)

    Ramirez-Lopez, Leonardo; Alexandre Dematte, Jose

    2010-05-01

    There is consensus in the scientific community about the great need of spatial soil information. Conventional mapping methods are time consuming and involve high costs. Digital soil mapping has emerged as an area in which the soil mapping is optimized by the application of mathematical and statistical approaches, as well as the application of expert knowledge in pedology. In this sense, the objective of the study was to develop a methodology for the spatial prediction of soil classes by using soil spectroscopy methodologies related with fieldwork, spectral data from satellite image and terrain attributes in simultaneous. The studied area is located in São Paulo State, and comprised an area of 473 ha, which was covered by a regular grid (100 x 100 m). In each grid node was collected soil samples at two depths (layers A and B). There were extracted 206 samples from transect sections and submitted to soil analysis (clay, Al2O3, Fe2O3, SiO2 TiO2, and weathering index). The first analog soil class map (ASC-N) contains only soil information regarding from orders to subgroups of the USDA Soil Taxonomy System. The second (ASC-H) map contains some additional information related to some soil attributes like color, ferric levels and base sum. For the elaboration of the digital soil maps the data was divided into three groups: i) Predicted soil attributes of the layer B (related to the soil weathering) which were obtained by using a local soil spectral library; ii) Spectral bands data extracted from a Landsat image; and iii) Terrain parameters. This information was summarized by a principal component analysis (PCA) in each group. Digital soil maps were generated by supervised classification using a maximum likelihood method. The trainee information for this classification was extracted from five toposequences based on the analog soil class maps. The spectral models of weathering soil attributes shown a high predictive performance with low error (R2 0.71 to 0.90). The spatial

  11. Fibronectin on the Surface of Myeloma Cell-derived Exosomes Mediates Exosome-Cell Interactions.

    PubMed

    Purushothaman, Anurag; Bandari, Shyam Kumar; Liu, Jian; Mobley, James A; Brown, Elizabeth E; Sanderson, Ralph D

    2016-01-22

    Exosomes regulate cell behavior by binding to and delivering their cargo to target cells; however, the mechanisms mediating exosome-cell interactions are poorly understood. Heparan sulfates on target cell surfaces can act as receptors for exosome uptake, but the ligand for heparan sulfate on exosomes has not been identified. Using exosomes isolated from myeloma cell lines and from myeloma patients, we identify exosomal fibronectin as a key heparan sulfate-binding ligand and mediator of exosome-cell interactions. We discovered that heparan sulfate plays a dual role in exosome-cell interaction; heparan sulfate on exosomes captures fibronectin, and on target cells it acts as a receptor for fibronectin. Removal of heparan sulfate from the exosome surface releases fibronectin and dramatically inhibits exosome-target cell interaction. Antibody specific for the Hep-II heparin-binding domain of fibronectin blocks exosome interaction with tumor cells or with marrow stromal cells. Regarding exosome function, fibronectin-mediated binding of exosomes to myeloma cells activated p38 and pERK signaling and expression of downstream target genes DKK1 and MMP-9, two molecules that promote myeloma progression. Antibody against fibronectin inhibited the ability of myeloma-derived exosomes to stimulate endothelial cell invasion. Heparin or heparin mimetics including Roneparstat, a modified heparin in phase I trials in myeloma patients, significantly inhibited exosome-cell interactions. These studies provide the first evidence that fibronectin binding to heparan sulfate mediates exosome-cell interactions, revealing a fundamental mechanism important for exosome-mediated cross-talk within tumor microenvironments. Moreover, these results imply that therapeutic disruption of fibronectin-heparan sulfate interactions will negatively impact myeloma tumor growth and progression. PMID:26601950

  12. Fibronectin on the Surface of Myeloma Cell-derived Exosomes Mediates Exosome-Cell Interactions.

    PubMed

    Purushothaman, Anurag; Bandari, Shyam Kumar; Liu, Jian; Mobley, James A; Brown, Elizabeth E; Sanderson, Ralph D

    2016-01-22

    Exosomes regulate cell behavior by binding to and delivering their cargo to target cells; however, the mechanisms mediating exosome-cell interactions are poorly understood. Heparan sulfates on target cell surfaces can act as receptors for exosome uptake, but the ligand for heparan sulfate on exosomes has not been identified. Using exosomes isolated from myeloma cell lines and from myeloma patients, we identify exosomal fibronectin as a key heparan sulfate-binding ligand and mediator of exosome-cell interactions. We discovered that heparan sulfate plays a dual role in exosome-cell interaction; heparan sulfate on exosomes captures fibronectin, and on target cells it acts as a receptor for fibronectin. Removal of heparan sulfate from the exosome surface releases fibronectin and dramatically inhibits exosome-target cell interaction. Antibody specific for the Hep-II heparin-binding domain of fibronectin blocks exosome interaction with tumor cells or with marrow stromal cells. Regarding exosome function, fibronectin-mediated binding of exosomes to myeloma cells activated p38 and pERK signaling and expression of downstream target genes DKK1 and MMP-9, two molecules that promote myeloma progression. Antibody against fibronectin inhibited the ability of myeloma-derived exosomes to stimulate endothelial cell invasion. Heparin or heparin mimetics including Roneparstat, a modified heparin in phase I trials in myeloma patients, significantly inhibited exosome-cell interactions. These studies provide the first evidence that fibronectin binding to heparan sulfate mediates exosome-cell interactions, revealing a fundamental mechanism important for exosome-mediated cross-talk within tumor microenvironments. Moreover, these results imply that therapeutic disruption of fibronectin-heparan sulfate interactions will negatively impact myeloma tumor growth and progression.

  13. Assessment of Speckle-Tracking Echocardiography-Derived Global Deformation Parameters During Supine Exercise in Children.

    PubMed

    Liu, Michael Y; Tacy, Theresa; Chin, Clifford; Obayashi, Derek Y; Punn, Rajesh

    2016-03-01

    Exercise echocardiography is an underutilized tool in pediatrics with current applications including detecting segmental wall abnormalities, assessing the utility of global ventricular function, and measuring pulmonary hemodynamics. No prior study has applied speckle-tracking echocardiography (STE) during exercise echocardiography in children. The aim of this study was to determine the feasibility of measuring speckle-tracking-derived peak systolic velocities, global longitudinal and circumferential strain, and global strain rates at various phases of exercise. Ninety-seven healthy children underwent cardiopulmonary exercise testing using supine cycle ergometry. The exercise stress test consisted of baseline pulmonary function testing, monitoring of blood pressure and heart rate responses, electrocardiographic recordings, and oxygen saturations while subjects pedaled against a ramp protocol based on body weight. Echocardiographic measurements and specifically speckle-tracking analysis were performed during exercise at baseline, at a heart rate of 160 beats per minute and at 10 min after exercise. Peak systolic velocity, peak systolic strain, and peak systolic strain rate at these three phases were compared in the subjects in which all measurements were accurately obtained. We were able to complete peak velocity, strain, and strain rate measurements in all three exercise phases for 36 out of the 97 subjects tested. There was no significant difference between the feasibility of measuring circumferential versus longitudinal strain (p = 0.25, B-corrected = 0.75). In the 36 subjects studied, the magnitude of circumferential strain values decreased from -18.3 ± 4.8 to -13.7 ± 4.0 % from baseline to HR 160 (p < 0.0001, B-corrected < 0.0001), before returning to -19.6 ± 4.4 % at recovery (p = 0.19 when compared to baseline). Longitudinal strain did not vary significantly from baseline to HR 160 (from -17.7 ± 4.4 to -16.6 ± 4.4 %, p = 0.16); likewise the average

  14. Analysis of Toxic Amyloid Fibril Interactions at Natively Derived Membranes by Ellipsometry

    PubMed Central

    Smith, Rachel A. S.; Nabok, Aleksey; Blakeman, Ben J. F.; Xue, Wei-Feng; Abell, Benjamin; Smith, David P.

    2015-01-01

    There is an ongoing debate regarding the culprits of cytotoxicity associated with amyloid disorders. Although small pre-fibrillar amyloid oligomers have been implicated as the primary toxic species, the fibrillar amyloid material itself can also induce cytotoxicity. To investigate membrane disruption and cytotoxic effects associated with intact and fragmented fibrils, the novel in situ spectroscopic technique of Total Internal Reflection Ellipsometry (TIRE) was used. Fibril lipid interactions were monitored using natively derived whole cell membranes as a model of the in vivo environment. We show that fragmented fibrils have an increased ability to disrupt these natively derived membranes by causing a loss of material from the deposited surface when compared with unfragmented fibrils. This effect was corroborated by observations of membrane disruption in live cells, and by dye release assay using synthetic liposomes. Through these studies we demonstrate the use of TIRE for the analysis of protein-lipid interactions on natively derived lipid surfaces, and provide an explanation on how amyloid fibrils can cause a toxic gain of function, while entangled amyloid plaques exert minimal biological activity. PMID:26172440

  15. Computational study of enantioselective interaction between C60 fullerene and its derivatives with L-histidine.

    PubMed

    Lal, Bhajan

    2007-04-01

    The mechanism of the enantioselective binding of L-histidine with C(60) fullerene and its derivatives, (1,2-methanofullerene C(60))-61-carboxylic acid, diethyl (1,2-methanofullerene C(60))-61-61-dicarboxylate and tert-butyl (1,2-methanofullerene C(60))-61-carboxylate based chiral selectors was studied by quantum chemical calculations. All the molecules were fully optimized at RHF/6-31G* basis set. Relative energies between the different complexes were subsequently estimated with single-point electronic energies computed using Møller-Plesset perturbation theory (MP2). Stability and feasibility of all the generated structures were supported by their respective energy minima and fundamental frequencies. It was observed that interaction of fullerene derivatives with L-histidine is due to the existence of hydrogen bonding forces during the complex formation. The intermolecular forces, flow of atomic charges, binding energy, hardness, dipole moment and localization of electrostatic potential are in agreement with enantioselective interaction of L-histidine with C(60) fullerene and its derivatives. It is found that theoretical evaluation to be consistent with the experimental data.

  16. Tuning the adsorption interactions of imidazole derivatives with specific metal cations.

    PubMed

    Liu, Haining; Bara, Jason E; Turner, C Heath

    2014-06-01

    In this work, we report a computational study of the interactions between metal cations and imidazole derivatives in the gas phase. We first performed a systematic assessment of various density functionals and basis sets for predicting the binding energies between metal cations and the imidazoles. We find that the M11L functional in combination with the 6-311++G(d,p) basis set provides the best compromise between accuracy and computational cost with our metal···imidazole complexes. We then evaluated the binding of a series of metal cations, including Li(+), Na(+), K(+), Co(2+), Ni(2+), Cu(2+), Zn(2+), Cd(2+), Ba(2+), Hg(2+), and Pb(2+), with several substituted imidazole derivatives. We find that electron-donating groups increase the metal-binding energy, whereas electron-withdrawing groups decrease the metal-binding energy. Furthermore, the binding energy trends can be rationalized by the hardness of the metal cations and imidazole derivatives, providing a quick way to estimate the metal···imidazole binding strength. This insight can enable efficient screening protocols for identifying effective imidazole-based solvents and membranes for metal adsorption and provide a framework for understanding metal···imidazole interactions in biological systems.

  17. Analysis of Toxic Amyloid Fibril Interactions at Natively Derived Membranes by Ellipsometry.

    PubMed

    Smith, Rachel A S; Nabok, Aleksey; Blakeman, Ben J F; Xue, Wei-Feng; Abell, Benjamin; Smith, David P

    2015-01-01

    There is an ongoing debate regarding the culprits of cytotoxicity associated with amyloid disorders. Although small pre-fibrillar amyloid oligomers have been implicated as the primary toxic species, the fibrillar amyloid material itself can also induce cytotoxicity. To investigate membrane disruption and cytotoxic effects associated with intact and fragmented fibrils, the novel in situ spectroscopic technique of Total Internal Reflection Ellipsometry (TIRE) was used. Fibril lipid interactions were monitored using natively derived whole cell membranes as a model of the in vivo environment. We show that fragmented fibrils have an increased ability to disrupt these natively derived membranes by causing a loss of material from the deposited surface when compared with unfragmented fibrils. This effect was corroborated by observations of membrane disruption in live cells, and by dye release assay using synthetic liposomes. Through these studies we demonstrate the use of TIRE for the analysis of protein-lipid interactions on natively derived lipid surfaces, and provide an explanation on how amyloid fibrils can cause a toxic gain of function, while entangled amyloid plaques exert minimal biological activity.

  18. Chemical and molecular aspects on interactions of galanthamine and its derivatives with cholinesterases.

    PubMed

    Gulcan, Hayrettin O; Orhan, Ilkay E; Sener, Bilge

    2015-01-01

    Dual action of galanthamine as potent cholinesterase inhibitor and nicotinic modulator has attracted a great attention to be used in the treatment of AD. Consequently, galanthamine, a natural alkaloid isolated from a Galanthus species (snowdrop, Amaryllidaceae), has become an attractive model compound for synthesis of its novel derivatives to discover new drug candidates. Numerous studies have been done to elucidate interactions between galanthamine and its different derivatives and the enzymes; acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) using in vitro and in silico experimental models. The in vitro studies revealed that galanthamine inhibits AChE in strong, competitive, long-acting, and reversible manner as well as BChE, although its selectivity towards AChE is much higher than BChE. The in silico studies carried out by employing molecular docking experiments as well as molecular dynamics simulations pointed out to existence of strong interactions of galanthamine with the active gorge of AChE, mostly of Torpedo californica (the Pasific electric ray) origin. In this review, we evaluate the mainstays of cholinesterase inhibitory action of galanthamine and its various derivatives from the point of view of chemical and molecular aspects. PMID:25483718

  19. Chemical and molecular aspects on interactions of galanthamine and its derivatives with cholinesterases.

    PubMed

    Gulcan, Hayrettin O; Orhan, Ilkay E; Sener, Bilge

    2015-01-01

    Dual action of galanthamine as potent cholinesterase inhibitor and nicotinic modulator has attracted a great attention to be used in the treatment of AD. Consequently, galanthamine, a natural alkaloid isolated from a Galanthus species (snowdrop, Amaryllidaceae), has become an attractive model compound for synthesis of its novel derivatives to discover new drug candidates. Numerous studies have been done to elucidate interactions between galanthamine and its different derivatives and the enzymes; acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) using in vitro and in silico experimental models. The in vitro studies revealed that galanthamine inhibits AChE in strong, competitive, long-acting, and reversible manner as well as BChE, although its selectivity towards AChE is much higher than BChE. The in silico studies carried out by employing molecular docking experiments as well as molecular dynamics simulations pointed out to existence of strong interactions of galanthamine with the active gorge of AChE, mostly of Torpedo californica (the Pasific electric ray) origin. In this review, we evaluate the mainstays of cholinesterase inhibitory action of galanthamine and its various derivatives from the point of view of chemical and molecular aspects.

  20. Synthesis and description of intermolecular interactions in new sulfonamide derivatives of tranexamic acid

    NASA Astrophysics Data System (ADS)

    Ashfaq, Muhammad; Arshad, Muhammad Nadeem; Danish, Muhammad; Asiri, Abdullah M.; Khatoon, Sadia; Mustafa, Ghulam; Zolotarev, Pavel N.; Butt, Rabia Ayub; Şahin, Onur

    2016-01-01

    Tranexamic acid (4-aminomethyl-cyclohexanecarboxylic acid) was reacted with sulfonyl chlorides to produce structurally related four sulfonamide derivatives using simple and environmental friendly method to check out their three-dimensional behavior and van der Walls interactions. The molecules were crystallized in different possibilities, as it is/after alkylation at its O and N atoms/along with a co-molecule. All molecules were crystallized in monoclinic crystal system with space group P21/n, P21/c and P21/a. X-ray studies reveal that the molecules stabilized themselves by different kinds of hydrogen bonding interactions. The molecules are getting connected through O-H⋯O hydrogen bonds to form inversion dimers which are further connected through N-H⋯O interactions. The molecules in which N and O atoms were alkylated showed non-classical interaction and generated centro-symmetric R22(24) ring motif. The co-crystallized host and guest molecules are connected to each other via O-H⋯O interactions to generate different ring motifs. By means of the ToposPro software an analysis of the topologies of underlying nets that correspond to molecular packings and hydrogen-bonded networks in structures under consideration was carried out.

  1. Reversibility of the interactions between a novel surfactant derived from lysine and biomolecules.

    PubMed

    Martín, Victoria Isabel; Sarrión, Beatriz; López-López, Manuel; López-Cornejo, Pilar; Robina, Inmaculada; Moyá, María Luisa

    2015-11-01

    In this work the novel cationic surfactant derived from lysine (S)-5-acetamido-6-(dodecylamino)-N,N,N-trimethyl-6-oxohexan-1-ammonium chloride, LYCl, was prepared and the physicochemical characterization of its aqueous solutions was carried out. The binding of LYCl to bovine serum albumin, BSA, and to double stranded calf thymus DNA, ctDNA, was investigated using several techniques. Results show that LYCl binding to BSA is followed by a decrease in the α-helix content caused by the unfolding of the protein. LYCl association to ctDNA mainly occurs through groove binding and electrostatic interactions. These interactions cause morphological changes in the polynucleotide from an elongated coil structure to a more compact globular structure, resulting in the compaction of ctDNA. Addition of β-cyclodextrin, β-CD, to the BSA-LYCl and ctDNA-LYCl complexes is followed by the refolding of BSA and the decompaction of ctDNA. This can be explained by the ability of β-CD to hinder BSA-LYCl and ctDNA-LYCl interactions due to the stronger and more specific β-CD-LYCl hydrophobic interactions. The stoichiometry of the β-CD:LYCl inclusion complex and its formation equilibrium constant were determined in this work. The reported procedure using β-CD is an efficient way to refold proteins and to decompact DNA, after the morphological changes caused in the biomolecules by their interaction with cationic surfactants.

  2. Interactions of Indole Derivatives with β-Cyclodextrin: A Quantitative Structure-Property Relationship Study

    PubMed Central

    Šoškić, Milan; Porobić, Ivana

    2016-01-01

    Retention factors for 31 indole derivatives, most of them with auxin activity, were determined by high-performance liquid chromatography, using bonded β-cyclodextrin as a stationary phase. A three-parameter QSPR (quantitative structure-property relationship) model, based on physico-chemical and structural descriptors was derived, which accounted for about 98% variations in the retention factors. The model suggests that the indole nucleus occupies the relatively apolar cavity of β-cyclodextrin while the carboxyl group of the indole -3-carboxylic acids makes hydrogen bonds with the hydroxyl groups of β-cyclodextrin. The length and flexibility of the side chain containing carboxyl group strongly affect the binding of these compounds to β-cyclodextrin. Non-acidic derivatives, unlike the indole-3-carboxylic acids, are poorly retained on the column. A reasonably well correlation was found between the retention factors of the indole-3-acetic acids and their relative binding affinities for human serum albumin, a carrier protein in the blood plasma. A less satisfactory correlation was obtained when the retention factors of the indole derivatives were compared with their affinities for auxin-binding protein 1, a plant auxin receptor. PMID:27124734

  3. New amphiphilic neamine derivatives active against resistant Pseudomonas aeruginosa and their interactions with lipopolysaccharides.

    PubMed

    Sautrey, Guillaume; Zimmermann, Louis; Deleu, Magali; Delbar, Alicia; Souza Machado, Luiza; Jeannot, Katy; Van Bambeke, Françoise; Buyck, Julien M; Decout, Jean-Luc; Mingeot-Leclercq, Marie-Paule

    2014-08-01

    The development of novel antimicrobial agents is urgently required to curb the widespread emergence of multidrug-resistant bacteria like colistin-resistant Pseudomonas aeruginosa. We previously synthesized a series of amphiphilic neamine derivatives active against bacterial membranes, among which 3',6-di-O-[(2"-naphthyl)propyl]neamine (3',6-di2NP), 3',6-di-O-[(2"-naphthyl)butyl]neamine (3',6-di2NB), and 3',6-di-O-nonylneamine (3',6-diNn) showed high levels of activity and low levels of cytotoxicity (L. Zimmermann et al., J. Med. Chem. 56:7691-7705, 2013). We have now further characterized the activity of these derivatives against colistin-resistant P. aeruginosa and studied their mode of action; specifically, we characterized their ability to interact with lipopolysaccharide (LPS) and to alter the bacterial outer membrane (OM). The three amphiphilic neamine derivatives were active against clinical colistin-resistant strains (MICs, about 2 to 8 μg/ml), The most active one (3',6-diNn) was bactericidal at its MIC and inhibited biofilm formation at 2-fold its MIC. They cooperatively bound to LPSs, increasing the outer membrane permeability. Grafting long and linear alkyl chains (nonyl) optimized binding to LPS and outer membrane permeabilization. The effects of amphiphilic neamine derivatives on LPS micelles suggest changes in the cross-bridging of lipopolysaccharides and disordering in the hydrophobic core of the micelles. The molecular shape of the 3',6-dialkyl neamine derivatives induced by the nature of the grafted hydrophobic moieties (naphthylalkyl instead of alkyl) and the flexibility of the hydrophobic moiety are critical for their fluidifying effect and their ability to displace cations bridging LPS. Results from this work could be exploited for the development of new amphiphilic neamine derivatives active against colistin-resistant P. aeruginosa.

  4. Thermodynamics and kinetic studies in the binding interaction of cyclic naphthalene diimide derivatives with double stranded DNAs.

    PubMed

    Islam, Md Monirul; Fujii, Satoshi; Sato, Shinobu; Okauchi, Tatsuo; Takenaka, Shigeori

    2015-08-01

    Previously, we reported our investigations of the interaction between a cyclic naphthalene diimide derivative (cNDI 1) and double stranded DNA (dsDNA) (Bioorg. Med. Chem.2014, 22, 2593). Here, we report the synthesis of the novel cNDI 2, which has shorter linker chains than cNDI 1. We performed comparative investigations of the interactions of both cNDI 1 and cNDI 2 with different types of dsDNA, including analysis of their thermodynamics and kinetics. Interactions between the cNDIs and calf thymus DNA (CT-DNA), poly[d(A-T)]2, or poly[d(G-C)]2 were explored by physicochemical and biochemical methods, including UV-Vis spectroscopy, circular dichroism (CD) spectroscopy, stopped-flow kinetics, and a topoisomerase I assay. Upon addition of cNDIs to CT-DNA, the existence of an induced CD signal at approximately the wavelength of the naphthalene diimide chromophore and unwinding of the DNA duplex, as detected by the topoisomerase I assay, revealed that cNDIs bound to the DNA duplex. As indicated by the steric constraint in the formation of the complex, bis-threading intercalation was the more favorable binding mode. UV-Vis spectroscopic titration of the cNDIs with DNA duplexes showed affinities on the order of 10(5)-10(6)M(-1), with a stoichiometry of one cNDI molecule per four DNA base pairs. Thermodynamic parameters (ΔG, ΔH, and ΔS) based on the van't Hoff equation indicated that exothermic and entropy-dependent hydrophobic interactions played a major role in the reaction. Stopped-flow association and dissociation analysis showed that cNDI interactions with poly[d(G-C)]2 were more stable and had a slower dissociation rate than their interactions with poly[d(A-T)]2 and CT-DNA. Measurement of ionic strength indicated that electrostatic attraction is also an important component of the interaction between cNDIs and CT-DNA. Because of its longer linker chain, cNDI 1 showed higher binding selectivity, a more entropically favorable interaction, and much slower dissociation

  5. Thermodynamics and kinetic studies in the binding interaction of cyclic naphthalene diimide derivatives with double stranded DNAs.

    PubMed

    Islam, Md Monirul; Fujii, Satoshi; Sato, Shinobu; Okauchi, Tatsuo; Takenaka, Shigeori

    2015-08-01

    Previously, we reported our investigations of the interaction between a cyclic naphthalene diimide derivative (cNDI 1) and double stranded DNA (dsDNA) (Bioorg. Med. Chem.2014, 22, 2593). Here, we report the synthesis of the novel cNDI 2, which has shorter linker chains than cNDI 1. We performed comparative investigations of the interactions of both cNDI 1 and cNDI 2 with different types of dsDNA, including analysis of their thermodynamics and kinetics. Interactions between the cNDIs and calf thymus DNA (CT-DNA), poly[d(A-T)]2, or poly[d(G-C)]2 were explored by physicochemical and biochemical methods, including UV-Vis spectroscopy, circular dichroism (CD) spectroscopy, stopped-flow kinetics, and a topoisomerase I assay. Upon addition of cNDIs to CT-DNA, the existence of an induced CD signal at approximately the wavelength of the naphthalene diimide chromophore and unwinding of the DNA duplex, as detected by the topoisomerase I assay, revealed that cNDIs bound to the DNA duplex. As indicated by the steric constraint in the formation of the complex, bis-threading intercalation was the more favorable binding mode. UV-Vis spectroscopic titration of the cNDIs with DNA duplexes showed affinities on the order of 10(5)-10(6)M(-1), with a stoichiometry of one cNDI molecule per four DNA base pairs. Thermodynamic parameters (ΔG, ΔH, and ΔS) based on the van't Hoff equation indicated that exothermic and entropy-dependent hydrophobic interactions played a major role in the reaction. Stopped-flow association and dissociation analysis showed that cNDI interactions with poly[d(G-C)]2 were more stable and had a slower dissociation rate than their interactions with poly[d(A-T)]2 and CT-DNA. Measurement of ionic strength indicated that electrostatic attraction is also an important component of the interaction between cNDIs and CT-DNA. Because of its longer linker chain, cNDI 1 showed higher binding selectivity, a more entropically favorable interaction, and much slower dissociation

  6. A compilation of rate parameters of water-mineral interaction kinetics for application to geochemical modeling

    USGS Publications Warehouse

    Palandri, James L.; Kharaka, Yousif K.

    2004-01-01

    Geochemical reaction path modeling is useful for rapidly assessing the extent of water-aqueous-gas interactions both in natural systems and in industrial processes. Modeling of some systems, such as those at low temperature with relatively high hydrologic flow rates, or those perturbed by the subsurface injection of industrial waste such as CO2 or H2S, must account for the relatively slow kinetics of mineral-gas-water interactions. We have therefore compiled parameters conforming to a general Arrhenius-type rate equation, for over 70 minerals, including phases from all the major classes of silicates, most carbonates, and many other non-silicates. The compiled dissolution rate constants range from -0.21 log moles m-2 s-1 for halite, to -17.44 log moles m-2 s-1 for kyanite, for conditions far from equilibrium, at 25 ?C, and pH near neutral. These data have been added to a computer code that simulates an infinitely well-stirred batch reactor, allowing computation of mass transfer as a function of time. Actual equilibration rates are expected to be much slower than those predicted by the selected computer code, primarily because actual geochemical processes commonly involve flow through porous or fractured media, wherein the development of concentration gradients in the aqueous phase near mineral surfaces, which results in decreased absolute chemical affinity and slower reaction rates. Further differences between observed and computed reaction rates may occur because of variables beyond the scope of most geochemical simulators, such as variation in grain size, aquifer heterogeneity, preferred fluid flow paths, primary and secondary mineral coatings, and secondary minerals that may lead to decreased porosity and clogged pore throats.

  7. Specific interactions between amyloid-β peptide and curcumin derivatives: Ab initio molecular simulations

    NASA Astrophysics Data System (ADS)

    Ishimura, Hiromi; Kadoya, Ryushi; Suzuki, Tomoya; Murakawa, Takeru; Shulga, Sergiy; Kurita, Noriyuki

    2015-07-01

    Alzheimer's disease is caused by accumulation of amyloid-β (Aβ) peptides in a brain. To suppress the production of Aβ peptides, it is effective to inhibit the cleavage of amyloid precursor protein (APP) by secretases. However, because the secretases also play important roles to produce vital proteins for human body, inhibitors for the secretases may have side effects. To propose new agents for protecting the cleavage site of APP from the attacking of the γ-secretase, we have investigated here the specific interactions between a short APP peptide and curcumin derivatives, using protein-ligand docking as well as ab initio molecular simulations.

  8. Interaction of Salmonella Typhimurium with Dendritic Cells Derived from Pluripotent Embryonic Stem Cells

    PubMed Central

    Rossi, Raffaella; Hale, Christine; Goulding, David; Andrews, Robert; Abdellah, Zarah; Fairchild, Paul J.; Dougan, Gordon

    2012-01-01

    Using an in vitro differentiation protocol we isolated cells with the properties of dendritic cells (DCs) from immunologically refractive pluripotent murine embryonic stem cells (ESCs). These ES-derived dendritic cells (ESDCs) expressed cytokines and were able to present antigen to a T cell line. Infection of ESDCs with Salmonella Typhimurium stimulated the expression of immune cell markers and thousands of murine genes, many associated with the immune response. Consequently, this system provides a novel in vitro model, amenable to genetic modification, for monitoring host/pathogen interactions. PMID:23284947

  9. Rational Design, Synthesis and Evaluation of Coumarin Derivatives as Protein-protein Interaction Inhibitors.

    PubMed

    De Luca, Laura; Agharbaoui, Fatima E; Gitto, Rosaria; Buemi, Maria Rosa; Christ, Frauke; Debyser, Zeger; Ferro, Stefania

    2016-09-01

    Herein we describe the design and synthesis of a new series of coumarin derivatives searching for novel HIV-1 integrase (IN) allosteric inhibitors. All new obtained compounds were tested in order to evaluate their ability to inhibit the interaction between the HIV-1 IN enzyme and the nuclear protein lens epithelium growth factor LEDGF/p75. A combined approach of docking and molecular dynamic simulations has been applied to clarify the activity of the new compounds. Specifically, the binding free energies by using the method of molecular mechanics-generalized Born surface area (MM-GBSA) was calculated, whereas hydrogen bond occupancies were monitored throughout simulations methods.

  10. Rational Design, Synthesis and Evaluation of Coumarin Derivatives as Protein-protein Interaction Inhibitors.

    PubMed

    De Luca, Laura; Agharbaoui, Fatima E; Gitto, Rosaria; Buemi, Maria Rosa; Christ, Frauke; Debyser, Zeger; Ferro, Stefania

    2016-09-01

    Herein we describe the design and synthesis of a new series of coumarin derivatives searching for novel HIV-1 integrase (IN) allosteric inhibitors. All new obtained compounds were tested in order to evaluate their ability to inhibit the interaction between the HIV-1 IN enzyme and the nuclear protein lens epithelium growth factor LEDGF/p75. A combined approach of docking and molecular dynamic simulations has been applied to clarify the activity of the new compounds. Specifically, the binding free energies by using the method of molecular mechanics-generalized Born surface area (MM-GBSA) was calculated, whereas hydrogen bond occupancies were monitored throughout simulations methods. PMID:27546050

  11. Weak inter-actions in the crystal structures of two indole derivatives.

    PubMed

    Kerr, Jamie R; Trembleau, Laurent; Storey, John M D; Wardell, James L; Harrison, William T A

    2016-07-01

    We describe the syntheses and crystal structures of two indole derivatives, namely a second monoclinic polymorph of ethyl 5-chloro-1H-indole-2-carboxyl-ate C11H10ClNO2, (I), and ethyl 5-chloro-3-iodo-1H-indole-2-carboxyl-ate, C11H9ClINO2, (II). In their crystal structures, both compounds form inversion dimers linked by pairs of N-H⋯O hydrogen bonds, which generate R 2 (2)(10) loops. The dimers are linked into double chains in (I) and sheets in (II) by a variety of weak inter-actions, including π-π stacking, C-I⋯π, C-Cl-π inter-actions and I⋯Cl halogen bonds. PMID:27555941

  12. Herb–drug interaction prediction based on the high specific inhibition of andrographolide derivatives towards UDP-glucuronosyltransferase (UGT) 2B7

    SciTech Connect

    Ma, Hai-Ying; Sun, Dong-Xue; Cao, Yun-Feng; Ai, Chun-Zhi; Qu, Yan-Qing; Hu, Cui-Min; Jiang, Changtao; Dong, Pei-Pei; Sun, Xiao-Yu; Hong, Mo; Tanaka, Naoki; Gonzalez, Frank J.; and others

    2014-05-15

    Herb–drug interaction strongly limits the clinical application of herbs and drugs, and the inhibition of herbal components towards important drug-metabolizing enzymes (DMEs) has been regarded as one of the most important reasons. The present study aims to investigate the inhibition potential of andrographolide derivatives towards one of the most important phase II DMEs UDP-glucuronosyltransferases (UGTs). Recombinant UGT isoforms (except UGT1A4)-catalyzed 4-methylumbelliferone (4-MU) glucuronidation reaction and UGT1A4-catalyzed trifluoperazine (TFP) glucuronidation were employed to firstly screen the andrographolide derivatives' inhibition potential. High specific inhibition of andrographolide derivatives towards UGT2B7 was observed. The inhibition type and parameters (K{sub i}) were determined for the compounds exhibiting strong inhibition capability towards UGT2B7, and human liver microsome (HLMs)-catalyzed zidovudine (AZT) glucuronidation probe reaction was used to furtherly confirm the inhibition behavior. In combination of inhibition parameters (K{sub i}) and in vivo concentration of andrographolide and dehydroandrographolide, the potential in vivo inhibition magnitude was predicted. Additionally, both the in vitro inhibition data and computational modeling results provide important information for the modification of andrographolide derivatives as selective inhibitors of UGT2B7. Taken together, data obtained from the present study indicated the potential herb–drug interaction between Andrographis paniculata and the drugs mainly undergoing UGT2B7-catalyzed metabolic elimination, and the andrographolide derivatives as potential candidates for the selective inhibitors of UGT2B7. - Highlights: • Specific inhibition of andrographolide derivatives towards UGT2B7. • Herb-drug interaction related withAndrographis paniculata. • Guidance for design of UGT2B7 specific inhibitors.

  13. Interactions of a Tetrazine Derivative with Biomembrane Constituents: A Langmuir Monolayer Study.

    PubMed

    Nakahara, Hiromichi; Hagimori, Masayori; Mukai, Takahiro; Shibata, Osamu

    2016-07-01

    Tetrazine (Tz) is expected to be used for bioimaging and as an analytical reagent. It is known to react very fast with trans-cyclooctene under water in organic chemistry. Here, to understand the interaction between Tz and biomembrane constituents, we first investigated the interfacial behavior of a newly synthesized Tz derivative comprising a C18-saturated hydrocarbon chain (rTz-C18) using a Langmuir monolayer spread at the air-water interface. Surface pressure (π)-molecular area (A) and surface potential (ΔV)-A isotherms were measured for monolayers of rTz-C18 and biomembrane constituents such as dipalmitoylphosphatidylcholine (DPPC), dipalmitoylphosphatidylglycerol (DPPG), dipalmitoyl phosphatidylethanolamine (DPPE), palmitoyl sphingomyelin (PSM), and cholesterol (Ch). The lateral interaction between rTz-C18 and the lipids was thermodynamically elucidated from the excess Gibbs free energy of mixing and two-dimensional phase diagram. The binary monolayers except for the Ch system indicated high miscibility or affinity. In particular, rTz-C18 was found to interact more strongly with DPPE, which is a major constituent of the inner surface of cell membranes. The phase behavior and morphology upon monolayer compression were investigated by using Brewster angle microscopy (BAM), fluorescence microscopy (FM), and atomic force microscopy (AFM). The BAM and FM images of the DPPC/rTz-C18, DPPG/rTz-C18, and PSM/rTz-C18 systems exhibited a coexistence state of two different liquid-condensed domains derived mainly from monolayers of phospholipids and phospholipids-rTz-C18. From these morphological observations, it is worthy to note that rTz-C18 is possible to interact with a limited amount of the lipids except for DPPE.

  14. Interaction between tachyplesin I, an antimicrobial peptide derived from horseshoe crab, and lipopolysaccharide.

    PubMed

    Kushibiki, Takahiro; Kamiya, Masakatsu; Aizawa, Tomoyasu; Kumaki, Yasuhiro; Kikukawa, Takashi; Mizuguchi, Mineyuki; Demura, Makoto; Kawabata, Shun-ichiro; Kawano, Keiichi

    2014-03-01

    Lipopolysaccharide (LPS) is a major constituent of the outer membrane of Gram-negative bacteria and is the very first site of interactions with antimicrobial peptides (AMPs). In order to gain better insight into the interaction between LPS and AMPs, we determined the structure of tachyplesin I (TP I), an antimicrobial peptide derived from horseshoe crab, in its bound state with LPS and proposed the complex structure of TP I and LPS using a docking program. CD and NMR measurements revealed that binding to LPS slightly extends the two β-strands of TP I and stabilizes the whole structure of TP I. The fluorescence wavelength of an intrinsic tryptophan of TP I and fluorescence quenching in the presence or absence of LPS indicated that a tryptophan residue is incorporated into the hydrophobic environment of LPS. Finally, we succeeded in proposing a structural model for the complex of TP I and LPS by using a docking program. The calculated model structure suggested that the cationic residues of TP I interact with phosphate groups and saccharides of LPS, whereas hydrophobic residues interact with the acyl chains of LPS. PMID:24389234

  15. Interaction between tachyplesin I, an antimicrobial peptide derived from horseshoe crab, and lipopolysaccharide.

    PubMed

    Kushibiki, Takahiro; Kamiya, Masakatsu; Aizawa, Tomoyasu; Kumaki, Yasuhiro; Kikukawa, Takashi; Mizuguchi, Mineyuki; Demura, Makoto; Kawabata, Shun-ichiro; Kawano, Keiichi

    2014-03-01

    Lipopolysaccharide (LPS) is a major constituent of the outer membrane of Gram-negative bacteria and is the very first site of interactions with antimicrobial peptides (AMPs). In order to gain better insight into the interaction between LPS and AMPs, we determined the structure of tachyplesin I (TP I), an antimicrobial peptide derived from horseshoe crab, in its bound state with LPS and proposed the complex structure of TP I and LPS using a docking program. CD and NMR measurements revealed that binding to LPS slightly extends the two β-strands of TP I and stabilizes the whole structure of TP I. The fluorescence wavelength of an intrinsic tryptophan of TP I and fluorescence quenching in the presence or absence of LPS indicated that a tryptophan residue is incorporated into the hydrophobic environment of LPS. Finally, we succeeded in proposing a structural model for the complex of TP I and LPS by using a docking program. The calculated model structure suggested that the cationic residues of TP I interact with phosphate groups and saccharides of LPS, whereas hydrophobic residues interact with the acyl chains of LPS.

  16. Comparative study of halogen- and hydrogen-bond interactions between benzene derivatives and dimethyl sulfoxide.

    PubMed

    Zheng, Yan-Zhen; Deng, Geng; Zhou, Yu; Sun, Hai-Yuan; Yu, Zhi-Wu

    2015-08-24

    The halogen bond, similar to the hydrogen bond, is an important noncovalent interaction and plays important roles in diverse chemistry-related fields. Herein, bromine- and iodine-based halogen-bonding interactions between two benzene derivatives (C6 F5 Br and C6 F5 I) and dimethyl sulfoxide (DMSO) are investigated by using IR and NMR spectroscopy and ab initio calculations. The results are compared with those of interactions between C6 F5 Cl/C6 F5 H and DMSO. First, the interaction energy of the hydrogen bond is stronger than those of bromine- and chlorine-based halogen bonds, but weaker than iodine-based halogen bond. Second, attractive energies depend on 1/r(n) , in which n is between three and four for both hydrogen and halogen bonds, whereas all repulsive energies are found to depend on 1/r(8.5) . Third, the directionality of halogen bonds is greater than that of the hydrogen bond. The bromine- and iodine-based halogen bonds are strict in this regard and the chlorine-based halogen bond only slightly deviates from 180°. The directional order is iodine-based halogen bond>bromine-based halogen bond>chlorine-based halogen bond>hydrogen bond. Fourth, upon the formation of hydrogen and halogen bonds, charge transfers from DMSO to the hydrogen- and halogen-bond donors. The CH3 group contributes positively to stabilization of the complexes.

  17. Interaction of antimicrobial preservatives with blow-fill-seal packs: correlating sorption with solubility parameters.

    PubMed

    Amin, Aeshna; Dare, Manish; Sangamwar, Abhay; Bansal, Arvind Kumar

    2012-01-01

    The aim of this work was to study the interaction of four commonly used ophthalmic antimicrobial preservatives [benzyl alcohol (BA), chlorbutol (CBL), benzalkonium chloride (BKC), and chlorhexidine gluconate (CG)] with Blow-Fill-Seal (BFS) packs. Effect of packaging material [low-density polyethylene (LDPE), polypropylene (PP)], humidity (25% RH, 75% RH) and concentration (0.5, 1.0, 2.0 mM BA/CBL in LDPE) was studied. BKC and CG gave negligible loss (<4%) in BFS packs over a period of 3 months. BA and CBL, however, gave marked losses in LDPE (ca. 70-90%) and PP (ca. 7-25%) packs. Humidity did not have any effect on the sorption loss of any preservative. Loss of BA switched from Case II to anomalous behavior with increasing initial concentration. A two-stage sorption behavior was inherent at all concentrations. Loss of CBL followed anomalous behavior with biphasic kinetics of loss. It was concluded that all the four preservatives were appropriate for use in PP BFS packs. However, only BKC and CG were amenable to be used in LDPE BFS packs. Lastly, an empirical expression consisting of the "solubility parameter distance" and "molar volume" of preservatives was developed to correlate the preservative loss in LDPE with the physicochemical properties of the preservatives.

  18. Dynamic interactions between hydrogeological and exposure parameters in daily dose prediction under uncertainty and temporal variability.

    PubMed

    Kumar, Vikas; de Barros, Felipe P J; Schuhmacher, Marta; Fernàndez-Garcia, Daniel; Sanchez-Vila, Xavier

    2013-12-15

    We study the time dependent interaction between hydrogeological and exposure parameters in daily dose predictions due to exposure of humans to groundwater contamination. Dose predictions are treated stochastically to account for an incomplete hydrogeological and geochemical field characterization, and an incomplete knowledge of the physiological response. We used a nested Monte Carlo framework to account for uncertainty and variability arising from both hydrogeological and exposure variables. Our interest is in the temporal dynamics of the total dose and their effects on parametric uncertainty reduction. We illustrate the approach to a HCH (lindane) pollution problem at the Ebro River, Spain. The temporal distribution of lindane in the river water can have a strong impact in the evaluation of risk. The total dose displays a non-linear effect on different population cohorts, indicating the need to account for population variability. We then expand the concept of Comparative Information Yield Curves developed earlier (see de Barros et al. [29]) to evaluate parametric uncertainty reduction under temporally variable exposure dose. Results show that the importance of parametric uncertainty reduction varies according to the temporal dynamics of the lindane plume. The approach could be used for any chemical to aid decision makers to better allocate resources towards reducing uncertainty.

  19. [Optical Analysis of the Interaction of Mercaptan Derivatives of Nanogold Particles with Carcinoembryonic Antigen].

    PubMed

    Zeng, Hong-juan; Zhao, Ran-lin; Wang, De-shun; Li, Cai-xia; Liu, Yi-yao

    2016-02-01

    be prepared. In this paper, novel mercaptan derivative of nanogold particles are prepared and studied using transmission electron microscopy (TEM), ultra-violet-visible absorption spectra (UV-Vis), fluorescence emission (FE) spectrum and infrared spectrum (IR) methods. The UV-Vis and FE results show the presence of new ligands mercaptan, more electrons from the orbit of ligand which can excite to the central ion related orbits and increase fluorescence of gold. Fluorescence sensitization effect was observed when mercaptan derivatives of nanogold interacted with carcinoembryonic antigen (CEA) and no fluorescence sensitization effect was found when nanogold interacted with carcinoembryonic antigen (CEA). The study of CEA hyperchromic mechanism of mercaptan derivatives nanogold and the CEA by the method of infrared spectrum, shows that the randomized OH bonds in the Au-protein interaction, showed more on the outside of the plane of bending vibration after the interaction with the mercaptan derivative nanogold, making the energy transfer from mercaptan derivatives nanogold to protein easy; leading to its fluorescence sensitization effect.

  20. [Optical Analysis of the Interaction of Mercaptan Derivatives of Nanogold Particles with Carcinoembryonic Antigen].

    PubMed

    Zeng, Hong-juan; Zhao, Ran-lin; Wang, De-shun; Li, Cai-xia; Liu, Yi-yao

    2016-02-01

    be prepared. In this paper, novel mercaptan derivative of nanogold particles are prepared and studied using transmission electron microscopy (TEM), ultra-violet-visible absorption spectra (UV-Vis), fluorescence emission (FE) spectrum and infrared spectrum (IR) methods. The UV-Vis and FE results show the presence of new ligands mercaptan, more electrons from the orbit of ligand which can excite to the central ion related orbits and increase fluorescence of gold. Fluorescence sensitization effect was observed when mercaptan derivatives of nanogold interacted with carcinoembryonic antigen (CEA) and no fluorescence sensitization effect was found when nanogold interacted with carcinoembryonic antigen (CEA). The study of CEA hyperchromic mechanism of mercaptan derivatives nanogold and the CEA by the method of infrared spectrum, shows that the randomized OH bonds in the Au-protein interaction, showed more on the outside of the plane of bending vibration after the interaction with the mercaptan derivative nanogold, making the energy transfer from mercaptan derivatives nanogold to protein easy; leading to its fluorescence sensitization effect. PMID:27209753

  1. Interaction with Serum Albumin As a Factor of the Photodynamic Efficacy of Novel Bacteriopurpurinimide Derivatives

    PubMed Central

    Akimova, Akimova; Rychkov, G. N.; Grin, M. A.; Filippova, N. A.; Golovina, G. V.; Durandin, N. A.; Vinogradov, A. M.; Kokrashvili, T. A.; Mironov, A. F.; Shtil, A. A.; Kuzmin, V. A.

    2015-01-01

    Optimization of the chemical structure of antitumor photosensitizers (PSs) is aimed at increasing their affinity to a transport protein, albumin and irreversible light-induced tumor cell damage. Bacteriopurpurinimide derivatives are promising PSs thanks to their ability to absorb light in the near infrared spectral region. Using spectrophotometry, we show that two new bacteriopurpurinimide derivatives with different substituents at the N atoms of the imide exocycle and the pyrrole ring A are capable of forming non-covalent complexes with human serum albumin (HSA). The association constant (calculated with the Benesi-Hildebrand equation) for N-ethoxybacteriopurpurinimide ethyloxime (compound 1) is higher than that for the methyl ether of methoxybacteriopurpurinimide (compound 2) (1.18×105 M-1 vs. 1.26×104 M-1, respectively). Molecular modeling provides details of the atomic interactions between 1 and 2 and amino acid residues in the FA1 binding site of HSA. The ethoxy group stabilizes the position of 1 within this site due to hydrophobic interaction with the protein. The higher affinity of 1 for HSA makes this compound more potent than 2 in photodynamic therapy for cultured human colon carcinoma cells. Photoactivation of 1 and 2 in cells induces rapid (within a few minutes of irradiation) necrosis. This mechanism of cell death may be efficient for eliminating tumors resistant to other therapies. PMID:25927008

  2. An Excel tool for deriving key photosynthetic parameters from combined gas exchange and chlorophyll fluorescence: theory and practice.

    PubMed

    Bellasio, Chandra; Beerling, David J; Griffiths, Howard

    2016-06-01

    Combined photosynthetic gas exchange and modulated fluorometres are widely used to evaluate physiological characteristics associated with phenotypic and genotypic variation, whether in response to genetic manipulation or resource limitation in natural vegetation or crops. After describing relatively simple experimental procedures, we present the theoretical background to the derivation of photosynthetic parameters, and provide a freely available Excel-based fitting tool (EFT) that will be of use to specialists and non-specialists alike. We use data acquired in concurrent variable fluorescence-gas exchange experiments, where A/Ci and light-response curves have been measured under ambient and low oxygen. From these data, the EFT derives light respiration, initial PSII (photosystem II) photochemical yield, initial quantum yield for CO2 fixation, fraction of incident light harvested by PSII, initial quantum yield for electron transport, electron transport rate, rate of photorespiration, stomatal limitation, Rubisco (ribulose 1·5-bisphosphate carboxylase/oxygenase) rate of carboxylation and oxygenation, Rubisco specificity factor, mesophyll conductance to CO2 diffusion, light and CO2 compensation point, Rubisco apparent Michaelis-Menten constant, and Rubisco CO2 -saturated carboxylation rate. As an example, a complete analysis of gas exchange data on tobacco plants is provided. We also discuss potential measurement problems and pitfalls, and suggest how such empirical data could subsequently be used to parameterize predictive photosynthetic models.

  3. Automated procedure to derive fundamental parameters of B and A stars: Application to the young cluster NGC 3293

    NASA Astrophysics Data System (ADS)

    Aydi, E.; Gebran, M.; Monier, R.; Royer, F.; Lobel, A.; Blomme, R.

    2014-12-01

    This work describes a procedure to derive several fundamental parameters such as the effective temperature, surface gravity, equatorial rotational velocity and microturbulent velocity. In this work, we have written a numerical procedure in Python which finds the best fit between a grid of synthetic spectra and the observed spectra by minimizing a standard chi-square. LTE model atmospheres were calculated using the ATLAS9 code and were used as inputs to the spectrum synthesis code SYNSPEC48 in order to compute a large grid of synthetic Balmer line profiles. This new procedure has been applied to a large number of new observations (GIRAFFE spectra) of B and A stars members of the young open cluster NGC3293. These observations are part of the GAIA ESO Survey. Takeda's procedure was also used to derive rotational velocities and microturbulent velocities. The results have been compared to previous determinations by other authors and are found to agree with them. As a first result, we concluded that using this procedure, an accuracy of ± 200 K could be achieved in effective temperature and ± 0.2 dex in surface gravities.

  4. Comparison of dual-echo DSC-MRI- and DCE-MRI-derived contrast agent kinetic parameters.

    PubMed

    Quarles, C Chad; Gore, John C; Xu, Lei; Yankeelov, Thomas E

    2012-09-01

    The application of dynamic susceptibility contrast (DSC) MRI methods to assess brain tumors is often confounded by the extravasation of contrast agent (CA). Disruption of the blood-brain barrier allows CA to leak out of the vasculature leading to additional T(1), T(2) and T(2) relaxation effects in the extravascular space, thereby affecting the signal intensity time course in a complex manner. The goal of this study was to validate a dual-echo DSC-MRI approach that separates and quantifies the T(1) and T(2) contributions to the acquired signal and enables the estimation of the volume transfer constant, K(trans), and the volume fraction of the extravascular extracellular space, v(e). To test the validity of this approach, DSC-MRI- and dynamic contrast enhanced (DCE) MRI-derived K(trans) and v(e) estimates were spatially compared in both 9L and C6 rat brain tumor models. A high degree of correlation (concordance correlation coefficients >0.83, Pearson's r>0.84) and agreement was found between the DSC-MRI- and DCE-MRI-derived measurements. These results indicate that dual-echo DSC-MRI can be used to simultaneously extract reliable DCE-MRI kinetic parameters in brain tumors in addition to conventional blood volume and blood flow metrics.

  5. Using Electronic Properties of Adamantane Derivatives to Analyze their Ion Channel Interactions: Implications for Alzheimer's Disease

    NASA Astrophysics Data System (ADS)

    Bonacum, Jason

    2013-03-01

    The derivatives of adamantane, which is a cage-like diamondoid structure, can be used as pharmaceuticals for the treatment of various diseases and disorders such as Alzheimer's disease. These drugs interact with ion channels, and they act by electronically and physically hindering the ion transport. The electronic properties of each compound influence the location and level of ion channel hindrance, and the specific use of each compound depends on the functional groups that are attached to the adamantane base chain. Computational analysis and molecular simulations of these different derivatives and the ion channels can provide useful insight into the effect that the functional groups have on the properties of the compounds. Using this information, conclusions can be made about the pharmaceutical mechanisms, as well as how to improve them or create new beneficial compounds. Focusing on the electronic properties, such as the dipole moments of the derivatives and amino acids in the ion channels, can provide more efficient predictions of how these drugs work and how they can be enhanced. Department of Energy Grant DE-FG02-06ER46304

  6. Comparison of biokinetics and biliary imaging parameters of four /sup 99m/Tc iminodiacetic acid derivatives in normal subjects

    SciTech Connect

    Bobba, V.V.; Krishnamurthy, G.T.; Kingston, E.; Brown, P.H.; Eklem, M.; Turner, F.E.

    1983-02-01

    The biokinetics (blood clearance, urinary excretion, hepatic peak time, uptake, and excretion t-1/2) and the imaging parameters (the time of appearance of the common bile duct, gallbladder, and duodenum) were determined in 34 normal subjects using /sup 99m/Tc diethyl (EIDA), /sup 99m/Tc dimethyl (HIDA), /sup 99m/Tc paraisopropyl (PIPIDA), and /sup 99m/Tc parabutyl (PBIDA) iminodiacetic acid derivatives. The blood and hepatic clearance of the four agents were significantly different (P less than 0.05) from each other. The 24-hour urinary excretion of PBIDA was significantly lower (P less than 0.05) than the urinary excretion of the other three agents. There was no difference among the four agents in the time of appearance of the gallbladder and duodenum. The time of appearance of the common bile duct was significantly delayed with PBIDA. The maximum intensity of the common bile duct usually occurred between 20 to 40 minutes with all four agents. However, gallbladder intensity continued to increase up to 3 hours. It is concluded that in the presence of normal liver function, all four /sup 99m/Tc IDA agents show definite differences in biokinetics but these differences do not have a major effect on biliary imaging parameters. If imaging alone is the primary goal, the selection of any one of the four agents will meet the clinican's need satisfactorily.

  7. An optimized wild bootstrap method for evaluation of measurement uncertainties of DTI-derived parameters in human brain.

    PubMed

    Zhu, Tong; Liu, Xiaoxu; Connelly, Patrick R; Zhong, Jianhui

    2008-04-15

    Evaluation of measurement uncertainties (or errors) in diffusion tensor-derived parameters is essential to quantify the sensitivity and specificity of these quantities as potential surrogate biomarkers for pathophysiological processes with diffusion tensor imaging (DTI). Computational methods such as the Monte Carlo simulation have provided insights into characterization of the measurement uncertainty in DTI. However, due to the complexity of real brain data as well as different sources of variations during the image acquisition, a robust estimator for DTI measurement uncertainty in human brain is required. Recent studies have shown that wild bootstrap, a novel nonparametric statistical method, can potentially provide effective estimations of DTI measurement uncertainties in human brain DTI data. In this study, we further optimized the DTI application of the wild bootstrap method for typical clinical applications. We evaluated the validity of wild bootstrap utilizing numerical simulations with different combinations of DTI protocol parameters and wild bootstrap experimental designs, and quantitatively compared estimates of uncertainties from wild bootstrapping with those from Monte Carlo simulations. Our results demonstrate that a wild bootstrap implementation using at least 1000 wild bootstrap iterations with a type II or type III heteroskedasticity consistent covariance matrix estimator provides robust evaluations of most DTI protocols.

  8. Variability of DTM-derived, morphometric parameters versus cell size. An example of application in Calabria (Southern Italy)

    NASA Astrophysics Data System (ADS)

    Rago, Valeria; Caloiero, Paola; Pellegrino, Annamaria Daniela; Iovine, Giulio G. R.; Terranova, Oreste G.; Pascale, Stefania

    2016-04-01

    Applications of DTM-derived morphometry are nowadays common in many fields of land-use planning, including the protection from natural hazards (cf. e.g. Iovine et al. 2013; 2014). For example, the mathematical modelling of physical processes that occur at slope or basin scales makes extensive use of quantitative parameters that describe the shape of Earth surface. Unfortunately, the values of these parameters depend on the detail with which the territory is represented. Therefore, different relationships must be adopted to describe the same physical processes at different scales. In this study, as part of a wide-ranging research aimed at modelling of geo-hydrological processes, a systematic and rigorous assessment of variability of the morphometric parameters against cell sizes is addressed. The study area under consideration is the whole Calabrian territory, extended about 15075 square kilometres. The region has recently been zoned into eleven homogeneous geomorphological sectors (Antronico et al., 2010). For each geomorphological sector, DTMs have been derived from topographic maps at 1:5000 scale, with cell sizes of 5, 10, 20 and 40 m. The following morphometric parameters - among those most frequently used in land management - have then been evaluated for the above DTMs: altitude, steepness of slope, aspect, plan and profile curvatures, slope length, topographical wetness index, stream power index, topographic position index, terrain ruggedness index, slope length factor. The first results show a marked dependence on cell size for some of the considered parameters. In other cases, such dependence seems not significant. Mathematical relationships are proposed between cell size and considered parameters, also taking into account the geomorphological contexts examined. Based on the above relationships, the most suitable scale to be used for modelling physical processes in a given area of interest can be selected. References Antronico L., L. Borselli, R. Coscarelli

  9. Quantum mechanically derived AMBER-compatible heme parameters for various states of the cytochrome P450 catalytic cycle

    PubMed Central

    Shahrokh, Kumars; Orendt, Anita; Yost, Garold; Cheatham, Tom

    2011-01-01

    Molecular mechanics (MM) methods are computationally affordable tools for screening chemical libraries of novel compounds for sites of P450 metabolism. One challenge for MM methods has been the absence of a consistent and transferable set of parameters for the heme within the P450 active-site. Experimental data indicates that mammalian P450 enzymes vary greatly in the size, architecture, and plasticity of their active sites. Thus, obtaining x-ray based geometries for the development of accurate MM parameters for the major classes of hepatic P450 remains a daunting task. Our previous work with preliminary gas-phase quantum mechanics (QM) derived atomic partial charges, greatly improved the accuracy of docking studies of raloxifene to CYP3A4. We have therefore developed and tested a consistent set of transferable MM parameters based on gas-phase QM calculations of two model systems of the heme—a truncated (T-HM) and a full (F-HM) for four states of the P450 catalytic cycle. Our results indicate that the use of the atomic partial charges from the F-HM model further improves the accuracy of docked predictions for raloxifene to CYP3A4. Different patterns for substrate docking are also observed depending on the choice of heme model and state. Newly parameterized heme models are tested in implicit and explicitly solvated MD simulations in the absence and presence of enzyme structures, for CYP3A4, and appear to be stable on the nanosecond simulation timescale. The new force field for the various heme states may aid the community for simulations of P450 enzymes and other heme containing enzymes. PMID:21997754

  10. Interaction mechanism exploration of HEA derivatives as BACE1 inhibitors by in silico analysis.

    PubMed

    Wu, Qian; Li, Xianguo; Gao, Qingping; Wang, Jinghui; Li, Yan; Yang, Ling

    2016-04-01

    The β-site amyloid precursor protein cleaving enzyme 1 (BACE1) initiates the generation of β-amyloid (Aβ) peptides which play a critical early role in the pathogenesis of Alzheimer's disease (AD), and thus it is a prime target for lowering the Aβ levels to treat AD. In the present work, a dataset of 128 promising hydroxyethylamine (HEA) derivatives as newly synthesized BACE1 inhibitors was selected to perform simulations by using 3D-QSAR, molecular docking and molecular dynamics (MD) approaches, to explore the binding mode and structural determinants required for high inhibitory potency. The resultant optimal comparative molecular similarity indices analysis (CoMSIA) model displays strong predictability (Q(2) = 0.503, Rncv(2) = 0.854, Rpre(2) = 0.905). Docking and MD simulations demonstrate that these HEAs bind to BACE1 in a site which occupies the S1, S1' and S2' pockets, with a "mantodea" conformation that is mainly stabilized by the H-bond interactions. Moreover, the structural determinants of these HEA analogues are as follows: (1) the P2' region is sensitive to the steric bulk; (2) the atom at the 2-position of the five-membered heterocyclic group (ring A) as an H-bond acceptor is conducive to the hydrogen bonding interaction, while the atom at the 6-position is detrimental; (3) introduction of the H-bond acceptor and/or donor groups into the P1' region is crucial to the inhibitory potency improvement. These models and the derived information may help provide a better understanding of both the binding mode and specific interactions of HEA-based BACE1 inhibitors, and facilitate corresponding lead optimization and novel inhibitor design.

  11. Nitric oxide regulates cell behavior on an interactive cell-derived extracellular matrix scaffold.

    PubMed

    Xing, Qi; Zhang, Lijun; Redman, Travis; Qi, Shaohai; Zhao, Feng

    2015-12-01

    During tissue injury and wound healing process, there are dynamic reciprocal interactions among cells, extracellular matrix (ECM), and mediating molecules which are crucial for functional tissue repair. Nitric oxide (NO) is one of the key mediating molecules that can positively regulate various biological activities involved in wound healing. Various ECM components serve as binding sites for cells and mediating molecules, and the interactions further stimulate cellular activities. Human mesenchymal stem cells (hMSCs) can migrate to the wound site and contribute to tissue regeneration through differentiation and paracrine signaling. The objective of this work was to investigate the regulatory effect of NO on hMSCs in an interactive ECM-rich microenvironment. In order to mimic the in vivo stromal environment in wound site, a cell-derived ECM scaffold that was able to release NO within the range of in vivo wound fluid NO level was fabricated. Results showed that the micro-molar level of NO released from the ECM scaffold had an inhibitory effect on cellular activities of hMSCs. The NO impaired cell growth, altered cell morphology, disrupted the F-actin organization, also decreased the expression of focal adhesion related molecules integrin α5 and paxillin. These results may contribute to the elucidation of how NO acts on hMSCs in wound healing process.

  12. Different N-H⋯π inter-actions in two indole derivatives.

    PubMed

    Kerr, Jamie R; Trembleau, Laurent; Storey, John M D; Wardell, James L; Harrison, William T A

    2016-05-01

    We describe the syntheses and crystal structures of two indole derivatives, namely 6-isopropyl-3-(2-nitro-1-phenyl-eth-yl)-1H-indole, C19H20N2O2, (I), and 2-(4-meth-oxy-phen-yl)-3-(2-nitro-1-phenyl-eth-yl)-1H-indole, C23H20N2O3, (II); the latter crystallizes with two mol-ecules (A and B) with similar conformations (r.m.s. overlay fit = 0.139 Å) in the asymmetric unit. Despite the presence of O atoms as potential acceptors for classical hydrogen bonds, the dominant inter-molecular inter-action in each crystal is an N-H⋯π bond, which generates chains in (I) and A+A and B+B inversion dimers in (II). A different aromatic ring acts as the acceptor in each case. The packing is consolidated by C-H⋯π inter-actions in each case but aromatic π-π stacking inter-actions are absent. PMID:27308022

  13. Engineering interaction between bone marrow derived endothelial cells and electrospun surfaces for artificial vascular graft applications.

    PubMed

    Ahmed, Furqan; Dutta, Naba K; Zannettino, Andrew; Vandyke, Kate; Choudhury, Namita Roy

    2014-04-14

    The aim of this investigation was to understand and engineer the interactions between endothelial cells and the electrospun (ES) polyvinylidene fluoride-co-hexafluoropropylene (PVDF-HFP) nanofiber surfaces and evaluate their potential for endothelialization. Elastomeric PVDF-HFP samples were electrospun to evaluate their potential use as small diameter artificial vascular graft scaffold (SDAVG) and compared with solvent cast (SC) PVDF-HFP films. We examined the consequences of fibrinogen adsorption onto the ES and SC samples for endothelialisation. Bone marrow derived endothelial cells (BMEC) of human origin were incubated with the test and control samples and their attachment, proliferation, and viability were examined. The nature of interaction of fibrinogen with SC and ES samples was investigated in detail using ELISA, XPS, and FTIR techniques. The pristine SC and ES PVDF-HFP samples displayed hydrophobic and ultrahydrophobic behavior and accordingly, exhibited minimal BMEC growth. Fibrinogen adsorbed SC samples did not significantly enhance endothelial cell binding or proliferation. In contrast, the fibrinogen adsorbed electrospun surfaces showed a clear ability to modulate endothelial cell behavior. This system also represents an ideal model system that enables us to understand the natural interaction between cells and their extracellular environment. The research reported shows potential of ES surfaces for artificial vascular graft applications. PMID:24564790

  14. Functional analysis of Mycoplasma arthritidis-derived mitogen interactions with class II molecules.

    PubMed Central

    Bernatchez, C; Al-Daccak, R; Mayer, P E; Mehindate, K; Rink, L; Mecheri, S; Mourad, W

    1997-01-01

    The ability of superantigens (SAGs) to trigger various cellular events via major histocompatibility complex (MHC) class II molecules is largely mediated by their mode of interaction. Having two MHC class II binding sites, staphylococcal enterotoxin A (SEA) is able to dimerize MHC class II molecules on the cell surface and consequently induces cytokine gene expression in human monocytes. In contrast, cross-linking with specific monoclonal antibodies or T-cell receptor is required for staphylococcal enterotoxin B (SEB) and toxic shock syndrome toxin 1 (TSST-1) to induce similar responses. In the present study, we report how Mycoplasma arthritidis-derived mitogen (MAM) may interact with MHC class II molecules to induce cytokine gene expression in human monocytes. The data presented indicate that MAM-induced cytokine gene expression in human monocytes is Zn2+ dependent. The MAM-induced response is completely abolished by pretreatment with SEA mutants that have lost their capacity to bind either the MHC class II alpha or beta chain, with wild-type SEB, or with wild-type TSST-1, suggesting that MAM induces cytokine gene expression most probably by inducing dimerization of class II molecules. In addition, it seems that SEA and MAM interact with the same or overlapping binding sites on the MHC class II beta chain and, on the other hand, that they bind to the alpha chain most probably through the regions that are involved in SEB and TSST-1 binding. PMID:9169724

  15. Nitric oxide regulates cell behavior on an interactive cell-derived extracellular matrix scaffold.

    PubMed

    Xing, Qi; Zhang, Lijun; Redman, Travis; Qi, Shaohai; Zhao, Feng

    2015-12-01

    During tissue injury and wound healing process, there are dynamic reciprocal interactions among cells, extracellular matrix (ECM), and mediating molecules which are crucial for functional tissue repair. Nitric oxide (NO) is one of the key mediating molecules that can positively regulate various biological activities involved in wound healing. Various ECM components serve as binding sites for cells and mediating molecules, and the interactions further stimulate cellular activities. Human mesenchymal stem cells (hMSCs) can migrate to the wound site and contribute to tissue regeneration through differentiation and paracrine signaling. The objective of this work was to investigate the regulatory effect of NO on hMSCs in an interactive ECM-rich microenvironment. In order to mimic the in vivo stromal environment in wound site, a cell-derived ECM scaffold that was able to release NO within the range of in vivo wound fluid NO level was fabricated. Results showed that the micro-molar level of NO released from the ECM scaffold had an inhibitory effect on cellular activities of hMSCs. The NO impaired cell growth, altered cell morphology, disrupted the F-actin organization, also decreased the expression of focal adhesion related molecules integrin α5 and paxillin. These results may contribute to the elucidation of how NO acts on hMSCs in wound healing process. PMID:26074441

  16. Interaction between chitosan and uranyl ions. Role of physical and physicochemical parameters on the kinetics of sorption

    SciTech Connect

    Piron, E. |; Accominotti, M.; Domard, A.

    1997-03-19

    This work corresponds to the first part of our studies on the interactions between chitosan particles dispersed in water and uranyl ions. The measurements were obtained by ICP, and we considered the role of various physical and physicochemical parameters related to chitosan. We showed that the crystallinity, the particle dimensions, and the swelling in water of chitosan are parameters which are connected together and govern the kinetic laws of metal diffusion and sorption. The molecular mobility of the polymer chains is then essential parameter. 31 refs., 5 figs., 3 tabs.

  17. Interaction of human immunodeficiency virus type 1 Tat-derived peptides with TAR RNA.

    PubMed

    Long, K S; Crothers, D M

    1995-07-11

    Basic peptides from the carboxy terminus of the human immunodeficiency virus type 1 (HIV-1) Tat protein bind to the stem-loop region of TAR RNA, spanning a trinucleotide bulge, with high affinity and moderate specificity. Previous studies have demonstrated that TAR RNA contains a specific arginine binding pocket. A series of 24 amino acid Tat-derived peptides with one or two arginines has been evaluated as possible structural models of the wild-type peptide in its interaction with TAR RNA, using gel electrophoretic methods and circular dichroism (CD) spectroscopy. Dissociation rate measurements indicate that these peptides form complexes with TAR RNA that are significantly less stable kinetically than the wild-type complex. Through a combination of dissociation and association rate measurements, we estimate that wild-type Tat peptide and TAR RNA interact with a Kd of about 16 pM. Together with competition experiments, these results confirm that band shift gel titration methods significantly underestimate absolute peptide-RNA binding affinities in the subnanomolar range. Through competition experiments with bulge mutants of TAR RNA, we demonstrate that peptides that form longer lived complexes with wild-type TAR RNA also show greater discrimination over TAR RNA bulge mutants. Difference CD spectra show that the Tat-derived peptides do not induce the same changes in TAR RNA as the wild-type peptide. The difference CD spectrum of argininamide bound to TAR RNA is most similar to that of the wild-type peptide-TAR RNA complex, implying that the differences in CD spectra upon complex formation are mostly due to changes in TAR RNA conformation.

  18. Probing deep into the interaction of a fluorescent chalcone derivative and bovine serum albumin (BSA): an experimental and computational study.

    PubMed

    Alvim, Haline G O; Fagg, Emma L; de Oliveira, Aline L; de Oliveira, Heibbe C B; Freitas, Sonia M; Xavier, Mary-Ann E; Soares, Thereza A; Gomes, Alexandre F; Gozzo, Fabio C; Silva, Wender A; Neto, Brenno A D

    2013-08-01

    In the present manuscript, a novel fluorescent chalcone derivative is synthesized and its photophysical properties are fully characterized. The designed fluorophore is applied as a probe to study protein-dye interactions with bovine serum albumin. Circular dichroism gave interesting results on the thermodynamics of the interaction. NMR spectroscopy, especially relaxation measurements, revealed the atoms in the chalcone derivative that interacts with the protein upon binding. Molecular docking calculations indicate that the most favourable binding sites are near the two tryptophan residues. Furthermore, ab initio and DFT calculations offer insights into the reactivity and physicochemical properties of this novel fluorophore. PMID:23680860

  19. A methodology for determining interactions in probabilistic safety assessment models by varying one parameter at a time.

    PubMed

    Borgonovo, Emanuele

    2010-03-01

    In risk analysis problems, the decision-making process is supported by the utilization of quantitative models. Assessing the relevance of interactions is an essential information in the interpretation of model results. By such knowledge, analysts and decisionmakers are able to understand whether risk is apportioned by individual factor contributions or by their joint action. However, models are oftentimes large, requiring a high number of input parameters, and complex, with individual model runs being time consuming. Computational complexity leads analysts to utilize one-parameter-at-a-time sensitivity methods, which prevent one from assessing interactions. In this work, we illustrate a methodology to quantify interactions in probabilistic safety assessment (PSA) models by varying one parameter at a time. The method is based on a property of the functional ANOVA decomposition of a finite change that allows to exactly determine the relevance of factors when considered individually or together with their interactions with all other factors. A set of test cases illustrates the technique. We apply the methodology to the analysis of the core damage frequency of the large loss of coolant accident of a nuclear reactor. Numerical results reveal the nonadditive model structure, allow to quantify the relevance of interactions, and to identify the direction of change (increase or decrease in risk) implied by individual factor variations and by their cooperation.

  20. Determination of the Polymer-Solvent Interaction Parameter for PEG Hydrogels in Water: Application of a Self Learning Algorithm

    PubMed Central

    Akalp, Umut; Chu, Stanley; Skaalure, Stacey C.; Bryant, Stephanie J.; Doostan, Alireza; Vernerey, Franck J.

    2015-01-01

    Concentrating on the case of poly(ethylene glycol) hydrogels, this paper introduces a methodology that enables a natural integration between the development of a so-called mechanistic model and experimental data relating material’s processing to response. In a nutshell, we develop a data-driven modeling component that is able to learn and indirectly infer its own parameters and structure by observing experimental data. Using this method, we investigate the relationship between processing conditions, microstructure and chemistry (cross-link density and polymer-solvent interactions) and response (swelling and elasticity) of non-degradable and degradable PEG hydrogels. We show that the method not only enables the determination of the polymer-solvent interaction parameter, but also it predicts that this parameter, among others, varies with processing conditions and degradation. The proposed methodology therefore offers a new approach that accounts for subtle changes in the hydrogel processing. PMID:25999615

  1. Glionitrin A, an antibiotic-antitumor metabolite derived from competitive interaction between abandoned mine microbes

    SciTech Connect

    Park, H.B.; Kown, H.C.; Lee, C.H.; Yang, H.O.

    2009-02-15

    The nutrient conditions present in abandoned coal mine drainages create an extreme environment where defensive and offensive microbial interactions could be critical for survival and fitness. Coculture of a mine drainage-derived Sphingomonas bacterial strain, KMK-001, and a mine drainage-derived Aspergillus fumigatus fungal strain, KMC-901, resulted in isolation of a new diketopiperazine disulfide, glionitrin A (1). Compound 1 was not detected in monoculture broths of KMK-001 or KMC-901. The structure of 1, a (3S,10aS) diketopiperazine disulfide containing a nitro aromatic ring, was based on analysis of MS, NMR, and circular dichroism spectra and confirmed by X-ray crystal data. Glionitrin A displayed significant antibiotic activity against a series of microbes including methicillin-resistant Staphylococcus aureus. An in vitro MTT cytotoxicity assay revealed that 1 had potent submicromolar cytotoxic activity against four human cancer cell lines: HCT-116, A549, AGS, and DU145. The results provide further evidence that microbial coculture can produce novel biologically relevant molecules.

  2. Insights into the interactions between maleimide derivates and GSK3β combining molecular docking and QSAR.

    PubMed

    Quesada-Romero, Luisa; Mena-Ulecia, Karel; Tiznado, William; Caballero, Julio

    2014-01-01

    Many protein kinase (PK) inhibitors have been reported in recent years, but only a few have been approved for clinical use. The understanding of the available molecular information using computational tools is an alternative to contribute to this process. With this in mind, we studied the binding modes of 77 maleimide derivates inside the PK glycogen synthase kinase 3 beta (GSK3β) using docking experiments. We found that the orientations that these compounds adopt inside GSK3β binding site prioritize the formation of hydrogen bond (HB) interactions between the maleimide group and the residues at the hinge region (residues Val135 and Asp133), and adopt propeller-like conformations (where the maleimide is the propeller axis and the heterocyclic substituents are two slanted blades). In addition, quantitative structure-activity relationship (QSAR) models using CoMSIA methodology were constructed to explain the trend of the GSK3β inhibitory activities for the studied compounds. We found a model to explain the structure-activity relationship of non-cyclic maleimide (NCM) derivatives (54 compounds). The best CoMSIA model (training set included 44 compounds) included steric, hydrophobic, and HB donor fields and had a good Q(2) value of 0.539. It also predicted adequately the most active compounds contained in the test set. Furthermore, the analysis of the plots of the steric CoMSIA field describes the elements involved in the differential potency of the inhibitors that can be considered for the selection of suitable inhibitors. PMID:25010341

  3. Insights into the Interactions between Maleimide Derivates and GSK3β Combining Molecular Docking and QSAR

    PubMed Central

    Quesada-Romero, Luisa; Mena-Ulecia, Karel; Tiznado, William; Caballero, Julio

    2014-01-01

    Many protein kinase (PK) inhibitors have been reported in recent years, but only a few have been approved for clinical use. The understanding of the available molecular information using computational tools is an alternative to contribute to this process. With this in mind, we studied the binding modes of 77 maleimide derivates inside the PK glycogen synthase kinase 3 beta (GSK3β) using docking experiments. We found that the orientations that these compounds adopt inside GSK3β binding site prioritize the formation of hydrogen bond (HB) interactions between the maleimide group and the residues at the hinge region (residues Val135 and Asp133), and adopt propeller-like conformations (where the maleimide is the propeller axis and the heterocyclic substituents are two slanted blades). In addition, quantitative structure–activity relationship (QSAR) models using CoMSIA methodology were constructed to explain the trend of the GSK3β inhibitory activities for the studied compounds. We found a model to explain the structure–activity relationship of non-cyclic maleimide (NCM) derivatives (54 compounds). The best CoMSIA model (training set included 44 compounds) included steric, hydrophobic, and HB donor fields and had a good Q2 value of 0.539. It also predicted adequately the most active compounds contained in the test set. Furthermore, the analysis of the plots of the steric CoMSIA field describes the elements involved in the differential potency of the inhibitors that can be considered for the selection of suitable inhibitors. PMID:25010341

  4. Graphical method for deriving an effective interaction with a new vertex function

    SciTech Connect

    Suzuki, K.; Okamoto, R.; Kumagai, H.; Fujii, S.

    2011-02-15

    Introducing a new vertex function, Z(E), of an energy variable E, we derive a new equation for the effective interaction. The equation is obtained by replacing the Q box in the Krenciglowa-Kuo (KK) method with Z(E). This new approach can be viewed as an extension of the KK method. We show that this equation can be solved both in iterative and noniterative ways. We observe that the iteration procedure with Z(E) brings about fast convergence compared to the usual KK method. It is shown that, as in the KK approach, the procedure of calculating the effective interaction can be reduced to determining the true eigenvalues of the original Hamiltonian H and they can be obtained as the positions of intersections of graphs generated from Z(E). We find that this graphical method yields always precise results and reproduces any of the true eigenvalues of H. The calculation in the present approach can be made regardless of overlaps with the model space and energy differences between unperturbed energies and the eigenvalues of H. We find also that Z(E) is a well-behaved function of E and has no singularity. These characteristics of the present approach ensure stability in actual calculations and would be helpful to resolve some difficulties due to the presence of poles in the Q box. Performing test calculations, we verify numerically theoretical predictions made in the present approach.

  5. Derivation and assessment of phase-shifted, disordered vector field models for frustrated solvent interactions

    PubMed Central

    Weber, Jeffrey K.; Pande, Vijay S.

    2013-01-01

    The structure and properties of water at biological interfaces differ drastically from bulk due to effects including confinement and the presence of complicated charge distributions. This non-bulk-like behavior generally arises from water frustration, wherein all favorable interactions among water molecules cannot be simultaneously satisfied. While the frustration of interfacial water is ubiquitous in the cell, the role this frustration plays in mediating biophysical processes like protein folding is not well understood. To investigate the impact of frustration at interfaces, we here derive a general field theoretic model for the interaction of bulk and disordered vector fields at an embedded surface. We calculate thermodynamic and correlation functions for the model in two and three dimensions, and we compare our results to Monte Carlo simulations of lattice system analogs. In our analysis, we see that field-field cross correlations near the interface in the model give rise to a loss in entropy like that seen in glassy systems. We conclude by assessing our theory's utility as a coarse-grained model for water at polar biological interfaces. PMID:23464179

  6. Hyperconjugative and Electrostatic Interactions as Anomeric Triggers in Archetypical 1,4-Dioxane Derivatives.

    PubMed

    Ortega, Pilar Gema Rodríguez; Montejo, Manuel; López González, Juan Jesús

    2016-02-16

    The anomeric effect accounts for the greater thermodynamic stability of axially arranged six-membered heterocycles holding an electronegative substituent at the C1 position. Within a frame of no general consensus, two different theories are typically claimed to justify this effect mostly based on either hyperconjugative or electrostatic factors. Here we report a theoretical-experimental study of the role of both as anomeric triggers in two archetypical 1,4-dioxane derivatives, using a suitable combination of spectroscopic (IR and vibrational circular dichroism) and computational techniques for the analysis of the solvation environment effect in their anomeric choices. VCD and IR spectroscopies are used as conformer-discriminating tools: a detailed analysis of the evolution of the spectral profiles allows assessing the theoretically predicted changes in the experimental α/β ratios when changing the polar solvent, which are fully explained on the basis of an extensive NBO energy partition scheme that provides a detailed view of the role of hyperconjugative and electrostatic interactions as anomeric regulators. Our results suggest that the anomeric equilibrium cannot be described by a single stereoelectronic effect but by the combined contribution of hyperconjugation and electrostatic repulsions, so that the β-anomeric choice in polar solvents is markedly driven by the strong attenuation of electrostatic repulsive interactions that occurs in solution. PMID:26663638

  7. Interactions of a biocompatible water-soluble anthracenyl polymer derivative with double-stranded DNA.

    PubMed

    Deiana, Marco; Mettra, Bastien; Matczyszyn, Katarzyna; Piela, Katarzyna; Pitrat, Delphine; Olesiak-Banska, Joanna; Monnereau, Cyrille; Andraud, Chantal; Samoc, Marek

    2015-11-11

    We have studied the interaction of a polymeric water soluble anthracenyl derivative () with salmon testes DNA. The results from UV-Vis, fluorescence, Fourier transform infrared (FT-IR) and circular dichroism spectroscopies indicate that the groove binding process regulates the interaction between and DNA. The binding constants, calculated by absorption spectroscopy at 298, 304 and 310 K, were equal to 3.2 × 10(5) M(-1), 4.7 × 10(5) M(-1), and 6.6 × 10(5) M(-1) respectively, proving a relatively high affinity of for salmon testes DNA. Results of Hoechst 33258 displacement assays strongly support the groove binding mode of to DNA. The association stoichiometry of the :DNA adduct was found to be 1 for every 5 base pairs. FT-IR spectra, recorded at different /DNA molar ratios, indicate the involvement of the phosphate groups and adenine and thymine DNA bases in the association process. Thermodynamic results suggest that hydrophobic forces regulate the binding of with DNA without excluding some extent of involvement of van der Waals forces and hydrogen bonding arising due to surface binding between the hydrophilic polymeric arms of the ligand and the functional groups positioned on the edge of the groove. The resulting composite biomaterial could constitute a valuable candidate for future biological and/or photonic applications.

  8. Effect of the electronic structure of quinoline and its derivatives on the capacity for intermolecular interactions

    SciTech Connect

    Privalova, N.Yu.; Sokolova, I.V.

    1985-05-01

    Calculations of the ground and excited states of quinoline and its 20H-, 70H-, 7NH2-, 7N(CH3)2-, and 7N(C2H5)2- substituted derivatives were undertaken by the INDO method, and the effect of intramolecular proton transfer (IPT) on their electronic structure was studied. The proton-accepting capacity of the compounds for intermolecular interactions was estimated by the molecular electrostatic potential method. It was shown that the proton-accepting capacity with respect to intermolecular interactions increases during the tautomeric transformation of the enolic form of 2-OH-quinoline to its keto form. The change in the basicity of the two forms of the molecules is affected by the orbital nature, and the multiplicity of the state is also important for the keto form. Substitution by electron-donating groups leads to increase in the proton-accepting capacity of both forms of the compounds in the S0, S/sub */, and T/sub */ states.

  9. Deriving C4 photosynthetic parameters from combined gas exchange and chlorophyll fluorescence using an Excel tool: theory and practice.

    PubMed

    Bellasio, Chandra; Beerling, David J; Griffiths, Howard

    2016-06-01

    The higher photosynthetic potential of C4 plants has led to extensive research over the past 50 years, including C4 -dominated natural biomes, crops such as maize, or for evaluating the transfer of C4 traits into C3 lineages. Photosynthetic gas exchange can be measured in air or in a 2% Oxygen mixture using readily available commercial gas exchange and modulated PSII fluorescence systems. Interpretation of these data, however, requires an understanding (or the development) of various modelling approaches, which limit the use by non-specialists. In this paper we present an accessible summary of the theory behind the analysis and derivation of C4 photosynthetic parameters, and provide a freely available Excel Fitting Tool (EFT), making rigorous C4 data analysis accessible to a broader audience. Outputs include those defining C4 photochemical and biochemical efficiency, the rate of photorespiration, bundle sheath conductance to CO2 diffusion and the in vivo biochemical constants for PEP carboxylase. The EFT compares several methodological variants proposed by different investigators, allowing users to choose the level of complexity required to interpret data. We provide a complete analysis of gas exchange data on maize (as a model C4 organism and key global crop) to illustrate the approaches, their analysis and interpretation. © 2015 John Wiley & Sons Ltd. PMID:26286697

  10. Deriving C4 photosynthetic parameters from combined gas exchange and chlorophyll fluorescence using an Excel tool: theory and practice.

    PubMed

    Bellasio, Chandra; Beerling, David J; Griffiths, Howard

    2016-06-01

    The higher photosynthetic potential of C4 plants has led to extensive research over the past 50 years, including C4 -dominated natural biomes, crops such as maize, or for evaluating the transfer of C4 traits into C3 lineages. Photosynthetic gas exchange can be measured in air or in a 2% Oxygen mixture using readily available commercial gas exchange and modulated PSII fluorescence systems. Interpretation of these data, however, requires an understanding (or the development) of various modelling approaches, which limit the use by non-specialists. In this paper we present an accessible summary of the theory behind the analysis and derivation of C4 photosynthetic parameters, and provide a freely available Excel Fitting Tool (EFT), making rigorous C4 data analysis accessible to a broader audience. Outputs include those defining C4 photochemical and biochemical efficiency, the rate of photorespiration, bundle sheath conductance to CO2 diffusion and the in vivo biochemical constants for PEP carboxylase. The EFT compares several methodological variants proposed by different investigators, allowing users to choose the level of complexity required to interpret data. We provide a complete analysis of gas exchange data on maize (as a model C4 organism and key global crop) to illustrate the approaches, their analysis and interpretation. © 2015 John Wiley & Sons Ltd.

  11. Getting a feel for parameters: using interactive parallel plots as a tool for parameter identification in the new rainfall-runoff model WALRUS

    NASA Astrophysics Data System (ADS)

    Brauer, Claudia; Torfs, Paul; Teuling, Ryan; Uijlenhoet, Remko

    2015-04-01

    Recently, we developed the Wageningen Lowland Runoff Simulator (WALRUS) to fill the gap between complex, spatially distributed models often used in lowland catchments and simple, parametric models which have mostly been developed for mountainous catchments (Brauer et al., 2014ab). This parametric rainfall-runoff model can be used all over the world in both freely draining lowland catchments and polders with controlled water levels. The open source model code is implemented in R and can be downloaded from www.github.com/ClaudiaBrauer/WALRUS. The structure and code of WALRUS are simple, which facilitates detailed investigation of the effect of parameters on all model variables. WALRUS contains only four parameters requiring calibration; they are intended to have a strong, qualitative relation with catchment characteristics. Parameter estimation remains a challenge, however. The model structure contains three main feedbacks: (1) between groundwater and surface water; (2) between saturated and unsaturated zone; (3) between catchment wetness and (quick/slow) flowroute division. These feedbacks represent essential rainfall-runoff processes in lowland catchments, but increase the risk of parameter dependence and equifinality. Therefore, model performance should not only be judged based on a comparison between modelled and observed discharges, but also based on the plausibility of the internal modelled variables. Here, we present a method to analyse the effect of parameter values on internal model states and fluxes in a qualitative and intuitive way using interactive parallel plotting. We applied WALRUS to ten Dutch catchments with different sizes, slopes and soil types and both freely draining and polder areas. The model was run with a large number of parameter sets, which were created using Latin Hypercube Sampling. The model output was characterised in terms of several signatures, both measures of goodness of fit and statistics of internal model variables (such as the

  12. Highly loaded interactive mixtures for dry powder inhalers: prediction of the adhesion capacity using surface energy and solubility parameters.

    PubMed

    Wagner, K G; Dowe, U; Zadnik, J

    2005-05-01

    In order to correlate drug adhesion properties of a highly loaded interactive mixture for the use in dry powder inhalers with the surface energy and to establish a link to the solubility parameter, surface free energy was detected for micronized substances (salbutamol sulfate, salbutamol base, theophylline and alpha-lactose monohydrate) using inverse gas chromatography (IGC). Interactive mixtures with coarse crystalline alpha-lactose monohydrate as a carrier were prepared at loading levels from 7.5 to 20% (w/w) and analyzed with respect to their adhesion capacity (CA) using the air jet sieving method. Solubility parameters were taken from literature or calculated. As a result the CA was independent of the drug load and correlated linearly with volume specific surface energy interaction (SEIv) values of the adherents (R2 = 0.98498). A link between SEIv and the size normalized solubility parameter (delta(tot)/d50) was found. Consequently, plotting delta(tot)/d50 versus CA resulted also in a strong linear relationship (R2 = 0.99140). Overall a powerful tool was established to judge and quantify adhesion properties of highly loaded interactive mixtures even for estimates in early preformulation at a time where just the molecular structure of the active ingredient is known.

  13. Using Multistate Reweighting to Rapidly and Efficiently Explore Molecular Simulation Parameters Space for Nonbonded Interactions.

    PubMed

    Paliwal, Himanshu; Shirts, Michael R

    2013-11-12

    Multistate reweighting methods such as the multistate Bennett acceptance ratio (MBAR) can predict free energies and expectation values of thermodynamic observables at poorly sampled or unsampled thermodynamic states using simulations performed at only a few sampled states combined with single point energy reevaluations of these samples at the unsampled states. In this study, we demonstrate the power of this general reweighting formalism by exploring the effect of simulation parameters controlling Coulomb and Lennard-Jones cutoffs on free energy calculations and other observables. Using multistate reweighting, we can quickly identify, with very high sensitivity, the computationally least expensive nonbonded parameters required to obtain a specified accuracy in observables compared to the answer obtained using an expensive "gold standard" set of parameters. We specifically examine free energy estimates of three molecular transformations in a benchmark molecular set as well as the enthalpy of vaporization of TIP3P. The results demonstrates the power of this multistate reweighting approach for measuring changes in free energy differences or other estimators with respect to simulation or model parameters with very high precision and/or very low computational effort. The results also help to identify which simulation parameters affect free energy calculations and provide guidance to determine which simulation parameters are both appropriate and computationally efficient in general.

  14. Chaotic processes using the two-parameter derivative with non-singular and non-local kernel: Basic theory and applications

    NASA Astrophysics Data System (ADS)

    Doungmo Goufo, Emile Franc

    2016-08-01

    After having the issues of singularity and locality addressed recently in mathematical modelling, another question regarding the description of natural phenomena was raised: How influent is the second parameter β of the two-parameter Mittag-Leffler function E α , β ( z ) , z ∈ ℂ ? To answer this question, we generalize the newly introduced one-parameter derivative with non-singular and non-local kernel [A. Atangana and I. Koca, Chaos, Solitons Fractals 89, 447 (2016); A. Atangana and D. Bealeanu (e-print)] by developing a similar two-parameter derivative with non-singular and non-local kernel based on Eα,β(z). We exploit the Agarwal/Erdelyi higher transcendental functions together with their Laplace transforms to explicitly establish the Laplace transform's expressions of the two-parameter derivatives, necessary for solving related fractional differential equations. Explicit expression of the associated two-parameter fractional integral is also established. Concrete applications are done on atmospheric convection process by using Lorenz non-linear simple system. Existence result for the model is provided and a numerical scheme established. As expected, solutions exhibit chaotic behaviors for α less than 0.55, and this chaos is not interrupted by the impact of β. Rather, this second parameter seems to indirectly squeeze and rotate the solutions, giving an impression of twisting. The whole graphics seem to have completely changed its orientation to a particular direction. This is a great observation that clearly shows the substantial impact of the second parameter of Eα,β(z), certainly opening new doors to modeling with two-parameter derivatives.

  15. Chaotic processes using the two-parameter derivative with non-singular and non-local kernel: Basic theory and applications.

    PubMed

    Doungmo Goufo, Emile Franc

    2016-08-01

    After having the issues of singularity and locality addressed recently in mathematical modelling, another question regarding the description of natural phenomena was raised: How influent is the second parameter β of the two-parameter Mittag-Leffler function Eα,β(z), z∈ℂ? To answer this question, we generalize the newly introduced one-parameter derivative with non-singular and non-local kernel [A. Atangana and I. Koca, Chaos, Solitons Fractals 89, 447 (2016); A. Atangana and D. Bealeanu (e-print)] by developing a similar two-parameter derivative with non-singular and non-local kernel based on Eα , β(z). We exploit the Agarwal/Erdelyi higher transcendental functions together with their Laplace transforms to explicitly establish the Laplace transform's expressions of the two-parameter derivatives, necessary for solving related fractional differential equations. Explicit expression of the associated two-parameter fractional integral is also established. Concrete applications are done on atmospheric convection process by using Lorenz non-linear simple system. Existence result for the model is provided and a numerical scheme established. As expected, solutions exhibit chaotic behaviors for α less than 0.55, and this chaos is not interrupted by the impact of β. Rather, this second parameter seems to indirectly squeeze and rotate the solutions, giving an impression of twisting. The whole graphics seem to have completely changed its orientation to a particular direction. This is a great observation that clearly shows the substantial impact of the second parameter of Eα , β(z), certainly opening new doors to modeling with two-parameter derivatives. PMID:27586622

  16. Chaotic processes using the two-parameter derivative with non-singular and non-local kernel: Basic theory and applications.

    PubMed

    Doungmo Goufo, Emile Franc

    2016-08-01

    After having the issues of singularity and locality addressed recently in mathematical modelling, another question regarding the description of natural phenomena was raised: How influent is the second parameter β of the two-parameter Mittag-Leffler function Eα,β(z), z∈ℂ? To answer this question, we generalize the newly introduced one-parameter derivative with non-singular and non-local kernel [A. Atangana and I. Koca, Chaos, Solitons Fractals 89, 447 (2016); A. Atangana and D. Bealeanu (e-print)] by developing a similar two-parameter derivative with non-singular and non-local kernel based on Eα , β(z). We exploit the Agarwal/Erdelyi higher transcendental functions together with their Laplace transforms to explicitly establish the Laplace transform's expressions of the two-parameter derivatives, necessary for solving related fractional differential equations. Explicit expression of the associated two-parameter fractional integral is also established. Concrete applications are done on atmospheric convection process by using Lorenz non-linear simple system. Existence result for the model is provided and a numerical scheme established. As expected, solutions exhibit chaotic behaviors for α less than 0.55, and this chaos is not interrupted by the impact of β. Rather, this second parameter seems to indirectly squeeze and rotate the solutions, giving an impression of twisting. The whole graphics seem to have completely changed its orientation to a particular direction. This is a great observation that clearly shows the substantial impact of the second parameter of Eα , β(z), certainly opening new doors to modeling with two-parameter derivatives.

  17. Electronic polarizability and interaction parameter of gadolinium tungsten borate glasses with high WO{sub 3} content

    SciTech Connect

    Taki, Yukina; Shinozaki, Kenji; Honma, Tsuyoshi; Dimitrov, Vesselin; Komatsu, Takayuki

    2014-12-15

    Glasses with the compositions of 25Gd{sub 2}O{sub 3}–xWO{sub 3}–(75−x)B{sub 2}O{sub 3} with x=25–65 were prepared by using a conventional melt quenching method, and their electronic polarizabilities, optical basicities Λ(n{sub o}), and interaction parameters A(n{sub o}) were estimated from density and refractive index measurements in order to clarify the feature of electronic polarizability and bonding states in the glasses with high WO{sub 3} contents. The optical basicity of the glasses increases monotonously with the substitution of WO{sub 3} for B{sub 2}O{sub 3}, and contrary the interaction parameter decreases monotonously with increasing WO{sub 3} content. A good linear correlation was observed between Λ(n{sub o}) and A(n{sub o}) and between the glass transition temperature and A(n{sub o}). It was proposed that Gd{sub 2}O{sub 3} oxide belongs to the category of basic oxide with a value of A(n{sub o})=0.044 Å{sup −3} as similar to WO{sub 3}. The relationship between the glass formation and electronic polarizability in the glasses was discussed, and it was proposed that the glasses with high WO{sub 3} and Gd{sub 2}O{sub 3} contents would be a floppy network system consisting of mainly basic oxides. - Graphical abstract: This figure shows the correlation between the optical basicity and interaction parameter in borate-based glasses. The data obtained in the present study for Gd{sub 2}O{sub 3}–WO{sub 3}–B{sub 2}O{sub 3} glasses are locating in the correlation line for other borate glasses. These results shown in Fig. 8 clearly demonstrate that Gd{sub 2}O{sub 3}–WO{sub 3}–B{sub 2}O{sub 3} glasses having a wide range of optical basicity and interaction parameter are regarded as glasses consisting of acidic and basic oxides. - Highlights: • Gd{sub 2}O{sub 3}–WO{sub 3}–B{sub 2}O{sub 3} glasses with high WO{sub 3} contents were prepared. • Electronic polarizability and interaction parameter were estimated. • Optical basicity increases

  18. Computed Tomography-Derived Parameters of Myocardial Morphology and Function in Black and White Patients With Acute Chest Pain.

    PubMed

    Takx, Richard A P; Vliegenthart, Rozemarijn; Schoepf, U Joseph; Abro, Joseph A; Nance, John W; Ebersberger, Ullrich; Bamberg, Fabian; Carr, Christine M; Apfaltrer, Paul

    2016-02-01

    Blacks have higher mortality and hospitalization rates because of congestive heart failure compared with white counterparts. Differences in cardiac structure and function may contribute to the racial disparity in cardiovascular outcomes. Our aim was to compare computed tomography (CT)-derived cardiac measurements between black patients with acute chest pain and age- and gender-matched white patients. We performed a retrospective analysis under an institutional review board waiver and in Health Insurance Portability and Accountability Act compliance. We investigated patients who underwent cardiac dual-source CT for acute chest pain. Myocardial mass, left ventricular (LV) ejection fraction, LV end-systolic volume, and LV end-diastolic volume were quantified using an automated analysis algorithm. Septal wall thickness and cardiac chamber diameters were manually measured. Measurements were compared by independent t test and linear regression. The study population consisted of 300 patients (150 black-mean age 54 ± 12 years; 46% men; 150 white-mean age 55 ± 11 years; 46% men). Myocardial mass was larger for blacks compared with white (176.1 ± 58.4 vs 155.9 ± 51.7 g, p = 0.002), which remained significant after adjusting for age, gender, body mass index, and hypertension. Septal wall thickness was slightly greater (11.9 ± 2.7 vs 11.2 ± 3.1 mm, p = 0.036). The LV inner diameter was moderately larger in black patients in systole (32.3 ± 9.0 vs 30.1 ± 5.4 ml, p = 0.010) and in diastole (50.1 ± 7.8 vs 48.9 ± 5.2 ml, p = 0.137), as well as LV end-diastolic volume (134.5 ± 42.7 vs 128.2 ± 30.6 ml, p = 0.143). Ejection fraction was nonsignificantly lower in blacks (67.1 ± 13.5% vs 69.0 ± 9.6%, p = 0.169). In conclusion, CT-derived myocardial mass was larger in blacks compared with whites, whereas LV functional parameters were generally not statistically different, suggesting that LV mass might be a possible contributing factor to the higher rate of cardiac events

  19. Investigating earthquake self-similarity using a 20 year catalog of source parameters derived from InSAR data

    NASA Astrophysics Data System (ADS)

    Funning, G.; Ferreira, A. M.; Weston, J. M.; Bloomfield, H.

    2013-12-01

    The question of how moment release in earthquakes scales to other earthquake source parameters, such as fault length and average slip, is a long-standing controversy (e.g. Scholz, 1982, 1994; Romanowicz, 1992). It is a problem that speaks to issues of earthquake source mechanics, specifically the self-similarity of earthquakes - is stress drop constant across all magnitudes? Theoretically, two end-member scaling models have been proposed - the so-called ';W-model', whereby seismic moment scales linearly with fault length, and the alternative ';L-model', where moment scales with the square of fault length. Existing data on earthquake rupture dimensions, typically from field observations or aftershock locations, do not conclusively favor one over the other. A W-model implies a constant stress drop for all earthquakes in the same tectonic setting, and therefore that earthquakes are self-similar. The L-model does not imply self-similarity, but is consistent with the idea that ';large earthquakes' (i.e. earthquakes that rupture the full thickness of the brittle upper crust) grow by increasing their rupture length, with average slip being proportional to fault length. To address this problem, we use a compilation of source parameter information from over 130 published studies of 101 individual earthquakes (Mw 4.7-9.0) studied using InSAR. There are several reasons to suggest that this information will be highly suitable for the study of earthquake scaling. The high spatial resolution and centimetric precision of InSAR data provide strong constraints on estimates of fault length and slip. In addition, in a previous study, we found good agreement between moment estimates from InSAR studies and the Global CMT catalog, derived from long-period seismic data (Weston et al., 2011). Considering events of all mechanisms together, we find a scaling relationship between moment (M0) and fault length (L), such that M0 ∝ L1.8. We find differences in this power law exponent with

  20. S-wave velocity structure and site effect parameters derived from microtremor arrays in the Western Plain of Taiwan

    NASA Astrophysics Data System (ADS)

    Kuo, Chun-Hsiang; Chen, Chun-Te; Lin, Che-Min; Wen, Kuo-Liang; Huang, Jyun-Yan; Chang, Shun-Chiang

    2016-10-01

    In this study, microtremor array measurements were conducted at 45 sites in the Western Plain of Taiwan. The arrays were approximately 30 m or 60 m in radius, depending on the site. The maximum-likelihood frequency-wavenumber method was adopted to obtain the phase velocities of Rayleigh waves, and then a genetic algorithm technique based on an inversion scheme of the fundamental mode of the Rayleigh waves' dispersion curves was applied to calculate a preliminary S-wave velocity (Vs) profile at each site. Because a layer of thick sediment covers the bedrock in the Western Plain of Taiwan, microtremor arrays in this size range cannot estimate the structure of the entire sediment. Therefore, this study implemented further inversion of the horizontal-to-vertical spectral ratios of the microtremors to estimate the deeper structures up to the bedrock of Vs greater than 1000 m/s. Previously logged velocity profiles for different depths at or near our study sites were collected and compared with the Vs profiles derived from our microtremor array measurements; the results were found to be highly comparable. Therefore, we could delineate the depth distributions for the layer depths for Vs = 600 m/s and 1000 m/s in this region. The depth for Vs = 600 m/s is approximately 50 m in the piedmont area and approximately 300 m at the coastline; moreover, the depths for Vs = 1000 m/s increase from 200 m in the piedmont area to approximately 1000 m at the coastline. The depths for Vs = 1.0 km/s (Z1.0), which is an important parameter that accounts for the basin effect in recent ground motion prediction equations, are consequently available at the study sites. The distribution of Z1.0 as a function of Vs30 indicates higher similarity to that in Japan than in the San Francisco Bay area.

  1. Parameter Estimation of Computationally Expensive Watershed Models Through Efficient Multi-objective Optimization and Interactive Decision Analytics

    NASA Astrophysics Data System (ADS)

    Akhtar, Taimoor; Shoemaker, Christine

    2016-04-01

    Watershed model calibration is inherently a multi-criteria problem. Conflicting trade-offs exist between different quantifiable calibration criterions indicating the non-existence of a single optimal parameterization. Hence, many experts prefer a manual approach to calibration where the inherent multi-objective nature of the calibration problem is addressed through an interactive, subjective, time-intensive and complex decision making process. Multi-objective optimization can be used to efficiently identify multiple plausible calibration alternatives and assist calibration experts during the parameter estimation process. However, there are key challenges to the use of multi objective optimization in the parameter estimation process which include: 1) multi-objective optimization usually requires many model simulations, which is difficult for complex simulation models that are computationally expensive; and 2) selection of one from numerous calibration alternatives provided by multi-objective optimization is non-trivial. This study proposes a "Hybrid Automatic Manual Strategy" (HAMS) for watershed model calibration to specifically address the above-mentioned challenges. HAMS employs a 3-stage framework for parameter estimation. Stage 1 incorporates the use of an efficient surrogate multi-objective algorithm, GOMORS, for identification of numerous calibration alternatives within a limited simulation evaluation budget. The novelty of HAMS is embedded in Stages 2 and 3 where an interactive visual and metric based analytics framework is available as a decision support tool to choose a single calibration from the numerous alternatives identified in Stage 1. Stage 2 of HAMS provides a goodness-of-fit measure / metric based interactive framework for identification of a small subset (typically less than 10) of meaningful and diverse set of calibration alternatives from the numerous alternatives obtained in Stage 1. Stage 3 incorporates the use of an interactive visual

  2. Biophysical analysis of the interaction of granulysin-derived peptides with enterobacterial endotoxins.

    PubMed

    Chen, Xi; Howe, Jörg; Andrä, Jörg; Rössle, Manfred; Richter, Walter; da Silva, Ana Paula Galvão; Krensky, Alan M; Clayberger, Carol; Brandenburg, Klaus

    2007-10-01

    To combat infections by Gram-negative bacteria, it is not only necessary to kill the bacteria but also to neutralize pathogenicity factors such as endotoxin (lipopolysaccharide, LPS). The development of antimicrobial peptides based on mammalian endotoxin-binding proteins is a promising tool in the fight against bacterial infections, and septic shock syndrome. Here, synthetic peptides derived from granulysin (Gra-pep) were investigated in microbiological and biophysical assays to understand their interaction with LPS. We analyzed the influence of the binding of Gra-pep on (1) the acyl chain melting of the hydrophobic moiety of LPS, lipid A, by Fourier-transform spectroscopy, (2) the aggregate structure of LPS by small-angle X-ray scattering and cryo-transmission electron microscopy, and 3) the enthalpy change by isothermal titration calorimetry. In addition, the influence of Gra-pep on the incorporation of LPS and LPS-LBP (lipopolysaccharide-binding protein) complexes into negatively charged liposomes was monitored. Our findings demonstrate a characteristic change in the aggregate structure of LPS into multilamellar stacks in the presence of Gra-pep, but little or no change of acyl chain fluidity. Neutralization of LPS by Gra-pep is not due to a scavenging effect in solution, but rather proceeds after incorporation into target membranes, suggesting a requisite membrane-bound step.

  3. Interaction of cinnamic acid derivatives with β-cyclodextrin in water: experimental and molecular modeling studies.

    PubMed

    Liu, Benguo; Zeng, Jie; Chen, Chen; Liu, Yonglan; Ma, Hanjun; Mo, Haizhen; Liang, Guizhao

    2016-03-01

    Cyclodextrins (CDs) can be used to improve the solubility and stability of cinnamic acid derivatives (CAs). However, there was no detailed report about understanding the effects of the substituent groups in the benzene ring on the inclusion behavior between CAs and CDs in aqueous solution. Here, the interaction of β-CD with CAs, including caffeic acid, ferulic acid, and p-coumaric acid, in water was investigated by phase-solubility method, UV, fluorescence, and (1)H NMR spectroscopy, together with ONIOM (our Own N-layer Integrated Orbital molecular Mechanics)-based QM/MM (Quantum Mechanics/Molecular Mechanics) calculations. Experimental results demonstrated that CAs could form 1:1 stoichiometric inclusion complex with β-CD by non-covalent bonds, and that the maximum apparent stability constants were found in caffeic acid (176M(-1)) followed by p-coumaric acid (160M(-1)) and ferulic acid (133M(-1)). Moreover, our calculations reasonably illustrated the binding orientations of β-CD with CAs determined by experimental observations.

  4. Non-covalent interactions involving halogenated derivatives of capecitabine and thymidylate synthase: a computational approach.

    PubMed

    Rahman, Adhip; Hoque, Mohammad Mazharol; Khan, Mohammad A K; Sarwar, Mohammed G; Halim, Mohammad A

    2016-01-01

    Capecitabine, a fluoropyrimidine prodrug, has been a frequently chosen ligand for the last one and half decades to inhibit thymidylate synthase (TYMS) for treatment of colorectal cancer. TYMS is a key enzyme for de novo synthesis of deoxythymidine monophosphate and subsequent synthesis of DNA. Recent years have also seen the trait of modifying ligands using halogens and trifluoromethyl (-CF3) group to ensure enhanced drug performance. In this study, in silico modification of capecitabine with Cl, Br, I atoms and -CF3 group has been performed. Density functional theory has been employed to optimize the drug molecules and elucidate their thermodynamic and electrical properties such as Gibbs free energy, enthalpy, electronic energy, dipole moment and frontier orbital features (HOMO-LUMO gap, hardness and softness). Flexible and rigid molecular docking have been implemented between drugs and the receptor TYMS. Both inter- and intra-molecular non-covalent interactions involving the amino acid residues of TYMS and the drug molecules are explored in details. The drugs were superimposed on the resolved crystal structure (at 1.9 Å) of ZD1694/dUMP/TYMS system to shed light on similarity of the binding of capecitabine, and its modifiers, to that of ZD1694. Together, these results may provide more insights prior to synthesizing halogen-directed derivatives of capecitabine for anticancer treatment. PMID:27026843

  5. Purification of scatter factor, a fibroblast-derived basic protein that modulates epithelial interactions and movement.

    PubMed Central

    Gherardi, E; Gray, J; Stoker, M; Perryman, M; Furlong, R

    1989-01-01

    Scatter factor is a fibroblast-derived protein that causes separation of contiguous epithelial cells and increased local mobility of unanchored cells. Highly purified scatter factor has been obtained by a combination of ion-exchange and reverse-phase chromatography from serum-free medium conditioned by a ras-transformed clone (D4) of mouse NIH 3T3 fibroblasts. Under nonreducing conditions scatter factor has a pI of approximately 9.5 and migrates in SDS/polyacrylamide gels as a single band at approximately 62 kDa from which epithelial scatter activity can be recovered. Treatment with reducing agents destroys biological activity and is associated with the appearance of two major bands at approximately 57 and approximately 30 kDa. Whether both the 57-kDa and 30-kDa polypeptides are required for biological activity remains to be established. All the activities observed in crude medium conditioned by cells producing scatter factor are retained by highly purified preparations of scatter factor. These include (i) increased local movement, modulation of morphology, and inhibition of junction formation by single epithelial cells and (ii) disruption of epithelial interactions and cell scattering from preformed epithelial sheets. These changes occur with picomolar concentrations of purified scatter factor and without an effect on cell growth. Images PMID:2527367

  6. INTERSTELLAR GAS FLOW PARAMETERS DERIVED FROM INTERSTELLAR BOUNDARY EXPLORER-Lo OBSERVATIONS IN 2009 AND 2010: ANALYTICAL ANALYSIS

    SciTech Connect

    Moebius, E.; Bochsler, P.; Heirtzler, D.; Kucharek, H.; Lee, M. A.; Leonard, T.; Schwadron, N. A.; Wu, X.; Petersen, L.; Valovcin, D.; Wurz, P.; Bzowski, M.; Kubiak, M. A.; Fuselier, S. A.; Crew, G.; Vanderspek, R.; McComas, D. J.; Saul, L.

    2012-02-01

    Neutral atom imaging of the interstellar gas flow in the inner heliosphere provides the most detailed information on physical conditions of the surrounding interstellar medium (ISM) and its interaction with the heliosphere. The Interstellar Boundary Explorer (IBEX) measured neutral H, He, O, and Ne for three years. We compare the He and combined O+Ne flow distributions for two interstellar flow passages in 2009 and 2010 with an analytical calculation, which is simplified because the IBEX orientation provides observations at almost exactly the perihelion of the gas trajectories. This method allows separate determination of the key ISM parameters: inflow speed, longitude, and latitude, as well as temperature. A combined optimization, as in complementary approaches, is thus not necessary. Based on the observed peak position and width in longitude and latitude, inflow speed, latitude, and temperature are found as a function of inflow longitude. The latter is then constrained by the variation of the observed flow latitude as a function of observer longitude and by the ratio of the widths of the distribution in longitude and latitude. Identical results are found for 2009 and 2010: an He flow vector somewhat outside previous determinations ({lambda}{sub ISM{infinity}} = 79.{sup 0}0+3.{sup 0}0(-3.{sup 0}5), {beta}{sub ISM{infinity}} = -4.{sup 0}9 {+-} 0.{sup 0}2, V{sub ISM{infinity}} 23.5 + 3.0(-2.0) km s{sup -1}, T{sub He} = 5000-8200 K), suggesting a larger inflow longitude and lower speed. The O+Ne temperature range, T{sub O+Ne} = 5300-9000 K, is found to be close to the upper range for He and consistent with an isothermal medium for all species within current uncertainties.

  7. Estimation of kinetic parameters related to biochemical interactions between hydrogen peroxide and signal transduction proteins

    PubMed Central

    Brito, Paula M.; Antunes, Fernando

    2014-01-01

    The lack of kinetic data concerning the biological effects of reactive oxygen species is slowing down the development of the field of redox signaling. Herein, we deduced and applied equations to estimate kinetic parameters from typical redox signaling experiments. H2O2-sensing mediated by the oxidation of a protein target and the switch-off of this sensor, by being converted back to its reduced form, are the two processes for which kinetic parameters are determined. The experimental data required to apply the equations deduced is the fraction of the H2O2 sensor protein in the reduced or in the oxidized state measured in intact cells or living tissues after exposure to either endogenous or added H2O2. Either non-linear fittings that do not need transformation of the experimental data or linearized plots in which deviations from the equations are easily observed can be used. The equations were shown to be valid by fitting to them virtual time courses simulated with a kinetic model. The good agreement between the kinetic parameters estimated in these fittings and those used to simulate the virtual time courses supported the accuracy of the kinetic equations deduced. Finally, equations were successfully tested with real data taken from published experiments that describe redox signaling mediated by the oxidation of two protein tyrosine phosphatases, PTP1B and SHP-2, which are two of the few H2O2-sensing proteins with known kinetic parameters. Whereas for PTP1B estimated kinetic parameters fitted in general the present knowledge, for SHP-2 results obtained suggest that reactivity toward H2O2 as well as the rate of SHP-2 regeneration back to its reduced form are higher than previously thought. In conclusion, valuable quantitative kinetic data can be estimated from typical redox signaling experiments, thus improving our understanding about the complex processes that underlie the interplay between oxidative stress and redox signaling responses. PMID:25325054

  8. Estimation of kinetic parameters related to biochemical interactions between hydrogen peroxide and signal transduction proteins

    NASA Astrophysics Data System (ADS)

    Brito, Paula; Antunes, Fernando

    2014-10-01

    The lack of kinetic data concerning the biological effects of reactive oxygen species is slowing down the development of the field of redox signaling. Herein, we deduced and applied equations to estimate kinetic parameters from typical redox signaling experiments. H2O2-sensing mediated by the oxidation of a protein target and the switch-off of this sensor, by being converted back to its reduced form, are the two processes for which kinetic parameters are determined. The experimental data required to apply the equations deduced is the fraction of the H2O2 sensor protein in the reduced or in the oxidized state measured in intact cells or living tissues after exposure to either endogenous or added H2O2. Either non-linear fittings that do not need transformation of the experimental data or linearized plots in which deviations from the equations are easily observed can be used. The equations were shown to be valid by fitting to them virtual time courses simulated with a kinetic model. The good agreement between the kinetic parameters estimated in these fittings and those used to simulate the virtual time courses supported the accuracy of the kinetic equations deduced. Finally, equations were successfully tested with real data taken from published experiments that describe redox signaling mediated by the oxidation of two protein tyrosine phosphatases, PTP1B and SHP-2, which are two of the few H2O2-sensing proteins with known kinetic parameters. Whereas for PTP1B estimated kinetic parameters fitted in general the present knowledge, for SHP-2 results obtained suggest that reactivity towards H2O2 as well as the rate of SHP-2 regeneration back to its reduced form are higher than previously thought. In conclusion, valuable quantitative kinetic data can be estimated from typical redox signaling experiments, thus improving our understanding about the complex processes that underline the interplay between oxidative stress and redox signaling responses.

  9. Estimation of kinetic parameters related to biochemical interactions between hydrogen peroxide and signal transduction proteins.

    PubMed

    Brito, Paula M; Antunes, Fernando

    2014-01-01

    The lack of kinetic data concerning the biological effects of reactive oxygen species is slowing down the development of the field of redox signaling. Herein, we deduced and applied equations to estimate kinetic parameters from typical redox signaling experiments. H2O2-sensing mediated by the oxidation of a protein target and the switch-off of this sensor, by being converted back to its reduced form, are the two processes for which kinetic parameters are determined. The experimental data required to apply the equations deduced is the fraction of the H2O2 sensor protein in the reduced or in the oxidized state measured in intact cells or living tissues after exposure to either endogenous or added H2O2. Either non-linear fittings that do not need transformation of the experimental data or linearized plots in which deviations from the equations are easily observed can be used. The equations were shown to be valid by fitting to them virtual time courses simulated with a kinetic model. The good agreement between the kinetic parameters estimated in these fittings and those used to simulate the virtual time courses supported the accuracy of the kinetic equations deduced. Finally, equations were successfully tested with real data taken from published experiments that describe redox signaling mediated by the oxidation of two protein tyrosine phosphatases, PTP1B and SHP-2, which are two of the few H2O2-sensing proteins with known kinetic parameters. Whereas for PTP1B estimated kinetic parameters fitted in general the present knowledge, for SHP-2 results obtained suggest that reactivity toward H2O2 as well as the rate of SHP-2 regeneration back to its reduced form are higher than previously thought. In conclusion, valuable quantitative kinetic data can be estimated from typical redox signaling experiments, thus improving our understanding about the complex processes that underlie the interplay between oxidative stress and redox signaling responses.

  10. Lens epithelium-derived growth factor/p75 interacts with the transposase-derived DDE domain of PogZ.

    PubMed

    Bartholomeeusen, Koen; Christ, Frauke; Hendrix, Jelle; Rain, Jean-Christophe; Emiliani, Stéphane; Benarous, Richard; Debyser, Zeger; Gijsbers, Rik; De Rijck, Jan

    2009-04-24

    Lens epithelium-derived growth factor/p75 (LEDGF/p75) is a prominent cellular interaction partner of human immunodeficiency virus-1 (HIV-1) integrase, tethering the preintegration complex to the host chromosome. In light of the development of LEDGF/p75-integrase interaction inhibitors, it is essential to understand the cell biology of LEDGF/p75. We identified pogZ as new cellular interaction partner of LEDGF/p75. Analogous to lentiviral integrase, pogZ, a domesticated transposase, carries a DDE domain, the major determinant for LEDGF/p75 interaction. Using different in vitro and in vivo approaches, we corroborated the interaction between the C terminus of LEDGF/p75 and the DDE domain of pogZ, revealing an overlap in the binding of pogZ and HIV-1 integrase. Competition experiments showed that integrase is efficient in displacing pogZ from LEDGF/p75. Moreover, pogZ does not seem to play a role as a restriction factor of HIV. The finding that LEDGF/p75 is capable of interacting with a DDE domain protein that is not a lentiviral integrase points to a profound role of LEDGF/p75 in DDE domain protein function.

  11. Evolutionary model selection and parameter estimation for protein-protein interaction network based on differential evolution algorithm

    PubMed Central

    Huang, Lei; Liao, Li; Wu, Cathy H.

    2016-01-01

    Revealing the underlying evolutionary mechanism plays an important role in understanding protein interaction networks in the cell. While many evolutionary models have been proposed, the problem about applying these models to real network data, especially for differentiating which model can better describe evolutionary process for the observed network urgently remains as a challenge. The traditional way is to use a model with presumed parameters to generate a network, and then evaluate the fitness by summary statistics, which however cannot capture the complete network structures information and estimate parameter distribution. In this work we developed a novel method based on Approximate Bayesian Computation and modified Differential Evolution (ABC-DEP) that is capable of conducting model selection and parameter estimation simultaneously and detecting the underlying evolutionary mechanisms more accurately. We tested our method for its power in differentiating models and estimating parameters on the simulated data and found significant improvement in performance benchmark, as compared with a previous method. We further applied our method to real data of protein interaction networks in human and yeast. Our results show Duplication Attachment model as the predominant evolutionary mechanism for human PPI networks and Scale-Free model as the predominant mechanism for yeast PPI networks. PMID:26357273

  12. Interactive initialization of heat flux parameters for numerical models using satellite temperature measurements

    NASA Technical Reports Server (NTRS)

    Carlson, T. N. (Principal Investigator)

    1981-01-01

    Efforts were made (1) to bring the image processing and boundary layer model operation into a completely interactive mode and (2) to test a method for determining the surface energy budget and surface moisture availability and thermal inertia on a scale appreciably larger than that of the city. A region a few hundred kilometers on a side centered over southern Indiana was examined.

  13. Effect of Pressure on Polyolefin Blends Miscibility: Scaling of the Interaction Parameter with Density

    NASA Astrophysics Data System (ADS)

    Rabeony, M.; Lohse, D. J.; Garner, R. T.; Han, S. J.; Migler, K.; Graessley, W. W.

    1998-03-01

    We have performed a combination of SANS, cloud point, and PVT measurements to investigate the effect of pressure on the miscibility of polyolefin blends. Both blends with ambient upper critical solution temperature (UCST) and lower critical solution temperature (LCST) have been investigated and the pressure coefficient for the critical temperature determined. In both cases, increasing pressure raises the critical temperature, i.e., increasing pressure destabilizes the mixed state for UCST blends, while it increases the degree of miscibility for LCST blends. For UCST blends, the pressure and temperature dependence of the interaction energies collapse on a single master curve when plotted against the mean density of the blend. The simplicity of this behavior suggests a simple equation of state and can be related to the nature of the van de Waals interactions between these saturated hydrocarbons. These results also allow a straightforward prediction of the pressure effect on miscibility from the PVT data of the pure components and the temperature dependence of the interaction energy at ambient pressure. No such simple behavior was found in blends exhibiting LCST where the interaction energies depend on P and T in a complex manner.

  14. Estimating Dbh of Trees Employing Multiple Linear Regression of the best Lidar-Derived Parameter Combination Automated in Python in a Natural Broadleaf Forest in the Philippines

    NASA Astrophysics Data System (ADS)

    Ibanez, C. A. G.; Carcellar, B. G., III; Paringit, E. C.; Argamosa, R. J. L.; Faelga, R. A. G.; Posilero, M. A. V.; Zaragosa, G. P.; Dimayacyac, N. A.

    2016-06-01

    Diameter-at-Breast-Height Estimation is a prerequisite in various allometric equations estimating important forestry indices like stem volume, basal area, biomass and carbon stock. LiDAR Technology has a means of directly obtaining different forest parameters, except DBH, from the behavior and characteristics of point cloud unique in different forest classes. Extensive tree inventory was done on a two-hectare established sample plot in Mt. Makiling, Laguna for a natural growth forest. Coordinates, height, and canopy cover were measured and types of species were identified to compare to LiDAR derivatives. Multiple linear regression was used to get LiDAR-derived DBH by integrating field-derived DBH and 27 LiDAR-derived parameters at 20m, 10m, and 5m grid resolutions. To know the best combination of parameters in DBH Estimation, all possible combinations of parameters were generated and automated using python scripts and additional regression related libraries such as Numpy, Scipy, and Scikit learn were used. The combination that yields the highest r-squared or coefficient of determination and lowest AIC (Akaike's Information Criterion) and BIC (Bayesian Information Criterion) was determined to be the best equation. The equation is at its best using 11 parameters at 10mgrid size and at of 0.604 r-squared, 154.04 AIC and 175.08 BIC. Combination of parameters may differ among forest classes for further studies. Additional statistical tests can be supplemented to help determine the correlation among parameters such as Kaiser- Meyer-Olkin (KMO) Coefficient and the Barlett's Test for Spherecity (BTS).

  15. Robustness of single and interdependent scale-free interaction networks with various parameters

    NASA Astrophysics Data System (ADS)

    Wang, Shuai; Liu, Jing

    2016-10-01

    The robustness of scale-free networks has attracted increasing attentions recently. It has been shown that scale-free networks are tolerant to random failures but fragile under malicious attacks. However, most existing studies focus on scale-free networks with fixed exponent (around 3) and assortativity (around 0), and the relationship between robustness and these parameters has not been studied systematically. Therefore, in this paper, we study the change of robustness along with different parameters, including scaling exponent and assortativity, of scale-free networks; moreover, the robustness of interdependent networks is also studied. In the experiments, synthetic single scale-free networks with varying scaling exponents are constructed and adjusted to fix assortativity. Several measures are adopted to estimate the robustness of networks under malicious and random attacks. Then, interdependent networks with varying parameters are constructed and their robustness against malicious attacks is studied. The results show that there is a positive correlation between robustness against node attacks and the scaling exponent as well as assortativity, and the positive correlation also exists in interdependent networks.

  16. Path-integral solution for a two-dimensional model with axial-vector-current--pseudoscalar derivative interaction

    SciTech Connect

    Botelho, L.C.L.

    1985-03-15

    We study a two-dimensional quantum field model with axial-vector-current--pseudoscalar derivative interaction using path-integral methods. We construct an effective Lagrangian by performing a chiral change in the fermionic variables leading to an exact solution of the model.

  17. Interaction of coal-derived synthesis gas impurities with solid oxide fuel cell metallic components

    NASA Astrophysics Data System (ADS)

    Marina, Olga A.; Pederson, Larry R.; Coyle, Christopher A.; Edwards, Danny J.; Chou, Yeong-Shyung; Cramer, Carolyn N.

    Oxidation-resistant alloys find use as interconnect materials, heat exchangers, and gas supply tubing in solid oxide fuel cell (SOFC) systems, especially when operated at temperatures below ∼800 °C. If fueled with synthesis gas derived from coal or biomass, such metallic components could be exposed to impurities contained in those fuel sources. In this study, coupons of ferritic stainless steels Crofer 22 APU and SS 441, austenitic nickel-chromium superalloy Inconel 600, and an alumina-forming high nickel alloy alumel were exposed to synthesis gas containing ≤2 ppm phosphorus, arsenic and antimony, and reaction products were tested. Crofer 22 APU coupons coated with a (Mn,Co) 3O 4 protective layer were also evaluated. Phosphorus was found to be the most reactive. On Crofer 22 APU, the (Mn,Cr) 3O 4 passivation layer reacted to form an Mn-P-O product, predicted to be manganese phosphate from thermochemical calculations, and Cr 2O 3. On SS 441, reaction of phosphorus with (Mn,Cr) 3O 4 led to the formation of manganese phosphate as well as an Fe-P product, predicted from thermochemical calculations to be Fe 3P. Minimal interactions with antimony or arsenic in synthesis gas were limited to Fe-Sb and Fe-As solid solution formation. Though not intended for use on the anode side, a (Mn,Co) 3O 4 spinel coating on Crofer 22 APU reacted with phosphorus in synthesis gas to produce products consistent with Mn 3(PO 4) 2 and Co 2P. A thin Cr 2O 3 passivation layer on Inconel 600 did not prevent the formation of nickel phosphides and arsenides and of iron phosphides and arsenides, though no reaction with Cr 2O 3 was apparent. On alumel, an Al 2O 3 passivation layer rich in Ni did not prevent the formation of nickel phosphides, arsenides, and antimonides, though no reaction with Al 2O 3 occurred. This work shows that unprotected metallic components of an SOFC stack and system can provide a sink for P, As and Sb impurities that may be present in fuel gases, and thus complicate

  18. Herb drug interaction: effect of Manix® on pharmacokinetic parameters of pefloxacin in rat model

    PubMed Central

    Odunke, Nduka Sunday; Eleje, Okonta; Christiana, Abba Chika; Peter, Ihekwereme Chibueze; Uchenna, Ekwedigwe; Matthew, Okonta

    2014-01-01

    Objective To evaluate the effect of Manix®, the commonly used polyherbal formulation on pefloxacin pharmacokinetic parameters. Methods Microbiological assay was employed using clinical isolate of Escherichia coli samples from hospitalized patients. Results Manix® altered the bioavailability parameters of pefloxacin as thus, maximal concentration (Cmax) of pefloxacin (0.91±0.31) µg/mL occurred at time to reach maximal concentration (tmax) 4.0 h while in the group that received Manix® alongside pefloxacin Cmax was (0.22±0.08) µg/mL at tmax 1.0 h respectively. The area under curve of pefloxacin alone was (7.83±5.14) µg/h/mL while with Manix® was (2.60±0.08) µg/h/mL. There was a significant difference between Cmax, tmax and area under curve between pefloxacin alone and pefloxacin after Manix® pre-treatment (P<0.05). Conclusions The concurrent use of Manix® and pefloxacin has been found to compromise the therapeutic effectiveness of pefloxacin which could lead to poor clinical outcomes in patients. PMID:25183119

  19. Characterization of Membrane Protein Interactions in Plasma Membrane Derived Vesicles with Quantitative Imaging FRET

    PubMed Central

    Sarabipour, Sarvenaz; Del Piccolo, Nuala; Hristova, Kalina

    2016-01-01

    CONSPECTUS Here we describe an experimental tool, termed Quantitative Imaging Förster Resonance Energy Transfer (QI-FRET), which enables the quantitative characterization of membrane protein interactions. The QI-FRET methodology allows us to acquire binding curves and calculate association constants for complex membrane proteins in the native plasma membrane environment. The method utilizes FRET detection, and thus requires that the proteins of interest are labeled with florescent proteins, either FRET donors or FRET acceptors. Since plasma membranes of cells have complex topologies precluding the acquisition of two-dimensional binding curves, the FRET measurements are performed in plasma membrane derived vesicles which bud off cells as a result of chemical or osmotic stress. The results overviewed here are acquired in vesicles produced with an osmotic vesiculation buffer developed in our laboratory, which does not utilize harsh chemicals. The concentrations of the donor-labeled and the acceptor-labeled proteins are determined, along with the FRET efficiencies, in each vesicle. The experiments utilize transient transfection, such that a wide variety of concentrations is sampled. Then, data from hundreds of vesicles are combined to yield dimerization curves. Here we discuss recent findings about the dimerization of receptor tyrosine kinases (RTKs), membrane proteins that control cell growth and differentiation via lateral dimerization in the plasma membrane. We focus on the dimerization of fibroblast growth factor receptor 3 (FGFR3), an RTK that plays a critically important role in skeletal development. We study the role of different FGFR3 domains in FGFR3 dimerization in the absence of ligand, and we show that FGFR3 extracellular domains inhibit unliganded dimerization, while contacts between the juxtamembrane domains, which connect the transmembrane domains to the kinase domains, stabilize the unliganded FGFR3 dimers. Since FGFR3 has been documented to harbor

  20. Insecticide resistance and nutrition interactively shape life-history parameters in German cockroaches.

    PubMed

    Jensen, Kim; Ko, Alexander E; Schal, Coby; Silverman, Jules

    2016-06-27

    Fitness-related costs of evolving insecticide resistance have been reported in a number of insect species, but the interplay between evolutionary adaptation to insecticide pressure and variable environmental conditions has received little attention. We provisioned nymphs from three German cockroach (Blattella germanica L.) populations, which differed in insecticide resistance, with either nutritionally rich or poor (diluted) diet throughout their development. One population was an insecticide-susceptible laboratory strain; the other two populations originated from a field-collected indoxacarb-resistant population, which upon collection was maintained either with or without further selection with indoxacarb. We then measured development time, survival to the adult stage, adult body size, and results of a challenge with indoxacarb. Our results show that indoxacarb resistance and poor nutritional condition increased development time and lowered adult body size, with reinforcing interactions. We also found lower survival to the adult stage in the indoxacarb-selected population, which was exacerbated by poor nutrition. In addition, nutrition imparted a highly significant effect on indoxacarb susceptibility. This study exemplifies how poor nutritional condition can aggravate the life-history costs of resistance and elevate the detrimental effects of insecticide exposure, demonstrating how environmental conditions and resistance may interactively impact individual fitness and insecticide efficacy.

  1. Insecticide resistance and nutrition interactively shape life-history parameters in German cockroaches

    PubMed Central

    Jensen, Kim; Ko, Alexander E.; Schal, Coby; Silverman, Jules

    2016-01-01

    Fitness-related costs of evolving insecticide resistance have been reported in a number of insect species, but the interplay between evolutionary adaptation to insecticide pressure and variable environmental conditions has received little attention. We provisioned nymphs from three German cockroach (Blattella germanica L.) populations, which differed in insecticide resistance, with either nutritionally rich or poor (diluted) diet throughout their development. One population was an insecticide-susceptible laboratory strain; the other two populations originated from a field-collected indoxacarb-resistant population, which upon collection was maintained either with or without further selection with indoxacarb. We then measured development time, survival to the adult stage, adult body size, and results of a challenge with indoxacarb. Our results show that indoxacarb resistance and poor nutritional condition increased development time and lowered adult body size, with reinforcing interactions. We also found lower survival to the adult stage in the indoxacarb-selected population, which was exacerbated by poor nutrition. In addition, nutrition imparted a highly significant effect on indoxacarb susceptibility. This study exemplifies how poor nutritional condition can aggravate the life-history costs of resistance and elevate the detrimental effects of insecticide exposure, demonstrating how environmental conditions and resistance may interactively impact individual fitness and insecticide efficacy. PMID:27345220

  2. The application of parameter estimation to flight measurements to obtain lateral-directional stability derivatives of an augmented jet-flap STOL airplane

    NASA Technical Reports Server (NTRS)

    Stephenson, J. D.

    1983-01-01

    Flight experiments with an augmented jet flap STOL aircraft provided data from which the lateral directional stability and control derivatives were calculated by applying a linear regression parameter estimation procedure. The tests, which were conducted with the jet flaps set at a 65 deg deflection, covered a large range of angles of attack and engine power settings. The effect of changing the angle of the jet thrust vector was also investigated. Test results are compared with stability derivatives that had been predicted. The roll damping derived from the tests was significantly larger than had been predicted, whereas the other derivatives were generally in agreement with the predictions. Results obtained using a maximum likelihood estimation procedure are compared with those from the linear regression solutions.

  3. Parameter Estimation of Binary Neutron Stars using an Effective One Body Model including Tidal Interaction

    NASA Astrophysics Data System (ADS)

    Rizzo, Monica; O'Shaughnessy, Richard; Bernuzzi, Sebastiano; Lackey, Benjamin

    2016-03-01

    Ground gravitational wave detectors, built to detect perturbations in spacetime, can pick up signals produced by inspiraling binary neutron stars, the remnants of the core collapse of massive stars. A new EOB model (Bernuzzi et al. 2015) simulates the inspiral and merger of binary neutron star systems, including how they are deformed due to tides. We used a Bayesian parameter estimation algorithm to infer how well a plausible gravitational wave detection would allow us to constrain this tidal deformability. We then compared our results to prior investigations (Wade et al. 2014) which employed a post-Newtonian-based approximation for the inspiral. I would like to thank the RIT Department of Physics and Astronomy, and the RIT Center for Computational Relativity and Gravitation.

  4. A flexible, interactive software tool for fitting the parameters of neuronal models

    PubMed Central

    Friedrich, Péter; Vella, Michael; Gulyás, Attila I.; Freund, Tamás F.; Káli, Szabolcs

    2014-01-01

    The construction of biologically relevant neuronal models as well as model-based analysis of experimental data often requires the simultaneous fitting of multiple model parameters, so that the behavior of the model in a certain paradigm matches (as closely as possible) the corresponding output of a real neuron according to some predefined criterion. Although the task of model optimization is often computationally hard, and the quality of the results depends heavily on technical issues such as the appropriate choice (and implementation) of cost functions and optimization algorithms, no existing program provides access to the best available methods while also guiding the user through the process effectively. Our software, called Optimizer, implements a modular and extensible framework for the optimization of neuronal models, and also features a graphical interface which makes it easy for even non-expert users to handle many commonly occurring scenarios. Meanwhile, educated users can extend the capabilities of the program and customize it according to their needs with relatively little effort. Optimizer has been developed in Python, takes advantage of open-source Python modules for nonlinear optimization, and interfaces directly with the NEURON simulator to run the models. Other simulators are supported through an external interface. We have tested the program on several different types of problems of varying complexity, using different model classes. As targets, we used simulated traces from the same or a more complex model class, as well as experimental data. We successfully used Optimizer to determine passive parameters and conductance densities in compartmental models, and to fit simple (adaptive exponential integrate-and-fire) neuronal models to complex biological data. Our detailed comparisons show that Optimizer can handle a wider range of problems, and delivers equally good or better performance than any other existing neuronal model fitting tool. PMID

  5. A flexible, interactive software tool for fitting the parameters of neuronal models.

    PubMed

    Friedrich, Péter; Vella, Michael; Gulyás, Attila I; Freund, Tamás F; Káli, Szabolcs

    2014-01-01

    The construction of biologically relevant neuronal models as well as model-based analysis of experimental data often requires the simultaneous fitting of multiple model parameters, so that the behavior of the model in a certain paradigm matches (as closely as possible) the corresponding output of a real neuron according to some predefined criterion. Although the task of model optimization is often computationally hard, and the quality of the results depends heavily on technical issues such as the appropriate choice (and implementation) of cost functions and optimization algorithms, no existing program provides access to the best available methods while also guiding the user through the process effectively. Our software, called Optimizer, implements a modular and extensible framework for the optimization of neuronal models, and also features a graphical interface which makes it easy for even non-expert users to handle many commonly occurring scenarios. Meanwhile, educated users can extend the capabilities of the program and customize it according to their needs with relatively little effort. Optimizer has been developed in Python, takes advantage of open-source Python modules for nonlinear optimization, and interfaces directly with the NEURON simulator to run the models. Other simulators are supported through an external interface. We have tested the program on several different types of problems of varying complexity, using different model classes. As targets, we used simulated traces from the same or a more complex model class, as well as experimental data. We successfully used Optimizer to determine passive parameters and conductance densities in compartmental models, and to fit simple (adaptive exponential integrate-and-fire) neuronal models to complex biological data. Our detailed comparisons show that Optimizer can handle a wider range of problems, and delivers equally good or better performance than any other existing neuronal model fitting tool. PMID

  6. Rifampin affects polymorphonuclear leukocyte interactions with bacterial and synthetic chemotaxins but not interactions with serum-derived chemotaxins.

    PubMed Central

    Gray, G D; Smith, C W; Hollers, J C; Chenoweth, D E; Fiegel, V D; Nelson, R D

    1983-01-01

    Three independent experimental approaches support the hypothesis that rifampin competes for receptors on polymorphonuclear leukocytes (PMLs) with small peptide chemoattractants, e.g., N-formylmethionylleucylphenylalanine (FMLP), but not with serum-derived chemoattractants (C5a). First, rifampin inhibited chemotaxis induced with FMLP but reversed the immobilization of PMLs that occurred at high FMLP concentrations. Second, rifampin competed with radiolabeled FMLP for binding sites on PMLs and displaced already-bound radiolabeled FMLP. Third, rifampin blocked and reversed the bipolar shape changes induced in PMLs by FMLP. These effects occurred at concentrations attained during rifampin therapy and were not due to rifampin toxicity. In contrast, no effect of rifampin was observed on serum-derived chemoattractants (C5a) in any of the three systems. The evidence suggests, therefore, that rifampin is a ligand for FMLP-type receptors on PMLs. PMID:6318656

  7. Disentangling fluxes of energy and matter in plasma-surface interactions: Effect of process parameters

    SciTech Connect

    Wolter, M.; Levchenko, I.; Ostrikov, K.; Kersten, H.; Kumar, S.

    2010-09-15

    The possibility to discriminate between the relative importance of the fluxes of energy and matter in plasma-surface interaction is demonstrated by the energy flux measurements in low-temperature plasmas ignited by the radio frequency discharge (power and pressure ranges 50-250 W and 8-11.5 Pa) in Ar, Ar+H{sub 2}, and Ar+H{sub 2}+CH{sub 4} gas mixtures typically used in nanoscale synthesis and processing of silicon- and carbon-based nanostructures. It is shown that by varying the gas composition and pressure, the discharge power, and the surface bias one can effectively control the surface temperature and the matter supply rates. The experimental findings are explained in terms of the plasma-specific reactions in the plasma bulk and on the surface.

  8. Kinetic model framework for aerosol and cloud surface chemistry and gas-particle interactions: Part 1 - general equations, parameters, and terminology

    NASA Astrophysics Data System (ADS)

    Pöschl, U.; Rudich, Y.; Ammann, M.

    2005-04-01

    formulations. Exemplary practical applications and model calculations illustrating the relevance of the above aspects will be presented in a companion paper (Ammann and Pöschl, 2005). We expect that the presented model framework will serve as a useful tool and basis for experimental and theoretical studies investigating and describing atmospheric aerosol and cloud surface chemistry and gas-particle interactions. In particular, it is meant to support the planning and design of laboratory experiments for the elucidation and determination of kinetic parameters; the establishment, evaluation, and quality assurance of comprehensive and self-consistent collections of rate parameters; and the development of detailed master mechanisms for process models and the derivation of simplified but yet realistic parameterizations for atmospheric and climate models.

  9. Interactions between glycine derivatives and mineral surfaces: Implications for the origins of life on planetary surfaces

    NASA Astrophysics Data System (ADS)

    Marshall-Bowman, K. J.; Cleaves, H. J.; Sverjensky, D. A.; Hazen, R. M.

    2009-12-01

    Various mechanisms could have delivered amino acids to the prebiotic Earth (Miller and Orgel 1974). The polymerization of amino acids may have been important for the origin of life, as peptides may have been components for the first self-replicating systems (Kauffman 1971; Yao et al 1998). Though amino acid concentrations in the primitive oceans were likely too dilute for significant oligomerization to occur (Cleaves et al 2009), mineral surface adsorption may have concentrated these biomolecules (Bernal 1951; Lambert 2008). Few studies have examined the catalytic effects of mineral surfaces on aqueous peptide oligomerization or degradation. As unactivated amino acid polymerization is thermodynamically unfavorable and kinetically slow in aqueous solution, we studied the reverse reaction of polymer degradation to measure potential mineral catalysis. Glycine (G) derivatives glycylglycine (GG), diketopiperazine (DKP), and glycylglycylglycine (GGG) were reacted with different minerals (calcite, hematite, montmorillonite, rutile, amorphous silica, and pyrite) in the presence of 0.05 M pH 8.1 KHCO3 buffer and 0.1 M NaCl as background electrolyte. Experiments were performed by reacting the aqueous amino acid derivative-mineral mixtures in a thermostatted oven (modified to accommodate a mechanical rotator) at 25°, 50° or 70°C. Samples were removed after 30, 60, 90, and 140 hours. Samples were then analyzed using high performance liquid chromatography to quantify the products. Besides mineral catalysis, it was determined that degradation of GGG proceeds principally via a GGG → DKP + G mechanism, rather than via GGG → GG + G. Below 70°C kinetics were generally too sluggish to detect catalytic activity over reasonable laboratory time-scales at this pH. At 70°C, pyrite was the only mineral with detectible catalytic effects on the degradation of GGG. GGG degraded ~ 1.5 - 4 x faster in the presence of pyrite than in control reactions, depending on the ratio of solution

  10. Identifying the Cognitive Needs of Visitors and Content Selection Parameters for Designing the Interactive Kiosk Software for Museums

    NASA Astrophysics Data System (ADS)

    Katre, Dinesh; Sarnaik, Mandar

    This research presents the findings of contextual interviews, visitor survey and behavioural study that were carried out in Indian museums. It originates from the hypothesis that the museum exhibits are unable to express their relevance, historical significance and related knowledge to satisfy the curiosity of visitors. Our objective is to identify the cognitive needs of museum visitors and the content selection parameters for designing the interactive kiosk software, which is expected to be set up in every thematic gallery of the museum. The kiosk software is intended to offer higher level of engaging and learnable experience to the museum visitors. The research involved participation of 100+ visitors in Indian museums. The access restrictions and constraints of museums cause cognitive deprivation of visitors and compromise the quality of experience. Therefore, the interactivity, animations and multimedia capabilities of kiosk software must be focused on overcoming these limitations.

  11. [Effect of ligand concentration on the precision of determining the parameters of ligand-receptor interaction by serial dilution methods].

    PubMed

    Bobrovnik, S A

    2004-01-01

    Earlier we suggested the method of serial dilution, which allows one to determine the parameters of ligand-receptor interaction even if the reactants are in a mixture and their concentrations are unknown. The method is especially useful if the liability of studied receptor does not allow its separation from corresponding ligand. The important prerequisite of the method's precision is that the concentration of the ligand should be sufficiently high comparing to the concentration of the receptor. In the present paper it was demonstrated that the method allows one to obtain sufficiently good precision even in the case when the concentration of the ligand is only one tenth of the receptor concentration.

  12. Dynamic calibration of higher eigenmode parameters of a cantilever in atomic force microscopy by using tip–surface interactions

    DOE PAGES

    Borysov, Stanislav S.; Forchheimer, Daniel; Haviland, David B.

    2014-10-29

    Here we present a theoretical framework for the dynamic calibration of the higher eigenmode parameters (stiffness and optical lever inverse responsivity) of a cantilever. The method is based on the tip–surface force reconstruction technique and does not require any prior knowledge of the eigenmode shape or the particular form of the tip–surface interaction. The calibration method proposed requires a single-point force measurement by using a multimodal drive and its accuracy is independent of the unknown physical amplitude of a higher eigenmode.

  13. Plasma parameters and electromagnetic forces induced by the magneto hydro dynamic interaction in a hypersonic argon flow experiment

    NASA Astrophysics Data System (ADS)

    Cristofolini, Andrea; Neretti, Gabriele; Borghi, Carlo A.

    2012-08-01

    This work proposes an experimental analysis on the magneto hydro dynamic (MHD) interaction induced by a magnetic test body immersed into a hypersonic argon flow. The characteristic plasma parameters are measured. They are related to the voltages arising in the Hall direction and to the variation of the fluid dynamic properties induced by the interaction. The tests have been performed in a hypersonic wind tunnel at Mach 6 and Mach 15. The plasma parameters are measured in the stagnation region in front of the nozzle of the wind tunnel and in the free stream region at the nozzle exit. The test body has a conical shape with the cone axis in the gas flow direction and the cone vertex against the flow. It is placed at the nozzle exit and is equipped with three permanent magnets. In the configuration adopted, the Faraday current flows in a closed loop completely immersed into the plasma of the shock layer. The electric field and the pressure variation due to MHD interaction have been measured on the test body walls. Microwave adsorption measurements have been used for the determination of the electron number density and the electron collision frequency. Continuum recombination radiation and line radiation emissions have been detected. The electron temperature has been determined by means of the spectroscopic data by using different methods. The electron number density has been also determined by means of the Stark broadening of Hα and the Hβ lines. Optical imaging has been utilized to visualize the pattern of the electric current distribution in the shock layer around the test body. The experiments show a considerable effect of the electromagnetic forces produced by the MHD interaction acting on the plasma flow around the test body. A comparison of the experimental data with simulation results shows a good agreement.

  14. Plasma parameters and electromagnetic forces induced by the magneto hydro dynamic interaction in a hypersonic argon flow experiment

    SciTech Connect

    Cristofolini, Andrea; Neretti, Gabriele; Borghi, Carlo A.

    2012-08-01

    This work proposes an experimental analysis on the magneto hydro dynamic (MHD) interaction induced by a magnetic test body immersed into a hypersonic argon flow. The characteristic plasma parameters are measured. They are related to the voltages arising in the Hall direction and to the variation of the fluid dynamic properties induced by the interaction. The tests have been performed in a hypersonic wind tunnel at Mach 6 and Mach 15. The plasma parameters are measured in the stagnation region in front of the nozzle of the wind tunnel and in the free stream region at the nozzle exit. The test body has a conical shape with the cone axis in the gas flow direction and the cone vertex against the flow. It is placed at the nozzle exit and is equipped with three permanent magnets. In the configuration adopted, the Faraday current flows in a closed loop completely immersed into the plasma of the shock layer. The electric field and the pressure variation due to MHD interaction have been measured on the test body walls. Microwave adsorption measurements have been used for the determination of the electron number density and the electron collision frequency. Continuum recombination radiation and line radiation emissions have been detected. The electron temperature has been determined by means of the spectroscopic data by using different methods. The electron number density has been also determined by means of the Stark broadening of H{sub {alpha}} and the H{sub {beta}} lines. Optical imaging has been utilized to visualize the pattern of the electric current distribution in the shock layer around the test body. The experiments show a considerable effect of the electromagnetic forces produced by the MHD interaction acting on the plasma flow around the test body. A comparison of the experimental data with simulation results shows a good agreement.

  15. Interactions between Flow Oscillations and Biochemical Parameters in the Cerebrospinal Fluid.

    PubMed

    Puy, Vincent; Zmudka-Attier, Jadwiga; Capel, Cyrille; Bouzerar, Roger; Serot, Jean-Marie; Bourgeois, Anne-Marie; Ausseil, Jérome; Balédent, Olivier

    2016-01-01

    The equilibrium between the ventricular and lumbar cerebrospinal fluid (CSF) compartments may be disturbed (in terms of flow and biochemistry) in patients with chronic hydrocephalus (CH). Using flow magnetic resonance imaging (MRI) and CSF assays, we sought to determine whether changes in CSF were associated with biochemical alterations. Nine elderly patients with CH underwent phase-contrast MRI. An index of CSF dynamics (Idyn) was defined as the product of the lumbar and ventricular CSF flows. During surgery, samples of CSF were collected from the lumbar and ventricular compartments and assayed for chloride, glucose and total protein. The lumbar/ventricular (L/V) ratio was calculated for each analyte. The ratio between measured and expected levels (Ibioch) was calculated for each analyte and compared with Idyn. Idyn varied from 0 to 100.10(3)μl(2).s(2). In contrast to the L/V ratios for chloride and glucose, the L/V ratio for total protein varied markedly from one patient to another (mean ± standard deviation (SD): 2.63 ± 1.24). The Ibioch for total protein was strongly correlated with the corresponding Idyn (Spearman's R: 0.98; p < 5 × 10(-5)).We observed correlated alterations in CSF flow and biochemical parameters in patients with CH. Our findings also highlight the value of dynamic flow analysis in the interpretation of data on CSF biochemistry. PMID:27445797

  16. Kinetic and spectral parameters of interaction of Citrobacter freundii methionine γ-lyase with amino acids.

    PubMed

    Morozova, E A; Bazhulina, N P; Anufrieva, N V; Mamaeva, D V; Tkachev, Y V; Streltsov, S A; Timofeev, V P; Faleev, N G; Demidkina, T V

    2010-10-01

    Kinetic parameters of Citrobacter freundii methionine γ-lyase were determined with substrates in γ-elimination reactions as well as the inhibition of the enzyme in the γ-elimination of L-methionine by amino acids with different structure. The data indicate an important contribution of the sulfur atom and methylene groups to the efficiency of binding of substrates and inhibitors. The rate constants of the enzyme-catalyzed exchange of C-α- and C-β-protons with deuterium were determined, as well as the kinetic isotope effect of the deuterium label in the C-α-position of inhibitors on the rate of exchange of their β-protons. Neither stereoselectivity in the β-proton exchange nor noticeable α-isotope effect on the exchange rates of β-protons was found. The ionic and tautomeric composition of the external Schiff base of methionine γ-lyase was determined. Spectral characteristics (absorption and circular dichroism spectra) of complexes with substrates and inhibitors were determined. The spectral and kinetic data indicate that deamination of aminocrotonate should be the rate-determining stage of the enzymatic reaction.

  17. Interactions between Flow Oscillations and Biochemical Parameters in the Cerebrospinal Fluid

    PubMed Central

    Puy, Vincent; Zmudka-Attier, Jadwiga; Capel, Cyrille; Bouzerar, Roger; Serot, Jean-Marie; Bourgeois, Anne-Marie; Ausseil, Jérome; Balédent, Olivier

    2016-01-01

    The equilibrium between the ventricular and lumbar cerebrospinal fluid (CSF) compartments may be disturbed (in terms of flow and biochemistry) in patients with chronic hydrocephalus (CH). Using flow magnetic resonance imaging (MRI) and CSF assays, we sought to determine whether changes in CSF were associated with biochemical alterations. Nine elderly patients with CH underwent phase-contrast MRI. An index of CSF dynamics (Idyn) was defined as the product of the lumbar and ventricular CSF flows. During surgery, samples of CSF were collected from the lumbar and ventricular compartments and assayed for chloride, glucose and total protein. The lumbar/ventricular (L/V) ratio was calculated for each analyte. The ratio between measured and expected levels (Ibioch) was calculated for each analyte and compared with Idyn. Idyn varied from 0 to 100.103μl2.s2. In contrast to the L/V ratios for chloride and glucose, the L/V ratio for total protein varied markedly from one patient to another (mean ± standard deviation (SD): 2.63 ± 1.24). The Ibioch for total protein was strongly correlated with the corresponding Idyn (Spearman’s R: 0.98; p < 5 × 10−5).We observed correlated alterations in CSF flow and biochemical parameters in patients with CH. Our findings also highlight the value of dynamic flow analysis in the interpretation of data on CSF biochemistry. PMID:27445797

  18. Human amniotic membrane-derived stromal cells (hAMSC) interact depending on breast cancer cell type through secreted molecules.

    PubMed

    Kim, Sun-Hee; Bang, So Hee; Kang, So Yeong; Park, Ki Dae; Eom, Jun Ho; Oh, Il Ung; Yoo, Si Hyung; Kim, Chan-Wha; Baek, Sun Young

    2015-02-01

    Human amniotic membrane-derived stromal cells (hAMSC) are candidates for cell-based therapies. We examined the characteristics of hAMSC including the interaction between hAMSC and breast cancer cells, MCF-7, and MDA-MB-231. Human amniotic membrane-derived stromal cells showed typical MSC properties, including fibroblast-like morphology, surface antigen expression, and mesodermal differentiation. To investigate cell-cell interaction via secreted molecules, we cultured breast cancer cells in hAMSC-conditioned medium (hAMSC-CM) and analyzed their proliferation, migration, and secretome profiles. MCF-7 and MDA-MB-231 cells exposed to hAMSC-CM showed increased proliferation and migration. However, in hAMSC-CM, MCF-7 cells proliferated significantly faster than MDA-MB-231 cells. When cultured in hAMSC-CM, MCF-7 cells migrated faster than MDA-MB-231 cells. Two cell types showed different profiles of secreted factors. MCF-7 cells expressed much amounts of IL-8, GRO, and MCP-1 in hAMSC-CM. Human amniotic membrane-derived stromal cells interact with breast cancer cells through secreted molecules. Factors secreted by hAMSCs promote the proliferation and migration of MCF-7 breast cancer cells. For much safe cell-based therapies using hAMSC, it is necessary to study carefully about interaction between hAMSC and cancer cells.

  19. Quantification of interaction and topological parameters of polyisoprene star polymers under good solvent conditions

    NASA Astrophysics Data System (ADS)

    Rai, Durgesh K.; Beaucage, Gregory; Ratkanthwar, Kedar; Beaucage, Peter; Ramachandran, Ramnath; Hadjichristidis, Nikos

    2016-05-01

    Mass fractal scaling, reflected in the mass fractal dimension df, is independently impacted by topology, reflected in the connectivity dimension c , and by tortuosity, reflected in the minimum dimension dmin. The mass fractal dimension is related to these other dimensions by df=c dmin . Branched fractal structures have a higher mass fractal dimension compared to linear structures due to a higher c , and extended structures have a lower dimension compared to convoluted self-avoiding and Gaussian walks due to a lower dmin. It is found, in this work, that macromolecules in thermodynamic equilibrium display a fixed mass fractal dimension df under good solvent conditions, regardless of chain topology. These equilibrium structures accommodate changes in chain topology such as branching c by a decrease in chain tortuosity dmin. Symmetric star polymers are used to understand the structure of complex macromolecular topologies. A recently published hybrid Unified scattering function accounts for interarm correlations in symmetric star polymers along with polymer-solvent interaction for chains of arbitrary scaling dimension. Dilute solutions of linear, three-arm and six-arm polyisoprene stars are studied under good solvent conditions in deuterated p -xylene. Reduced chain tortuosity can be viewed as steric straightening of the arms. Steric effects for star topologies are quantified, and it is found that steric straightening of arms is more significant for lower-molecular-weight arms. The observation of constant df is explained through a modification of Flory-Krigbaum theory for branched polymers.

  20. Specimen specific parameter identification of ovine lumbar intervertebral discs: On the influence of fibre-matrix and fibre-fibre shear interactions.

    PubMed

    Reutlinger, Christoph; Bürki, Alexander; Brandejsky, Vaclav; Ebert, Lars; Büchler, Philippe

    2014-02-01

    Numerical models of the intervertebral disc, which address mechanical questions commonly make use of the difference in water content between annulus and nucleus, and thus fluid and solid parts are separated. Despite this simplification, models remain complex due to the anisotropy and nonlinearity of the annulus and regional variations of the collagen fibre density. Additionally, it has been shown that cross-links make a large contribution to the stiffness of the annulus. Because of this complex composite structure, it is difficult to reproduce several sets of experimental data with one single set of material parameters. This study addresses the question to which extent the ultrastructure of the intervertebral disc should be modelled so that its moment-angle behaviour can be adequately described. Therefore, a hyperelastic constitutive law, based on continuum mechanical principles was derived, which does not only consider the anisotropy from the collagen fibres, but also interactions among the fibres and between the fibres and the ground substance. Eight ovine lumbar intervertebral discs were tested on a custom made spinal loading simulator in flexion/extension, lateral bending and axial rotation. Specimen-specific geometrical models were generated using CT images and T2 maps to distinguish between annulus fibrosus and nucleus pulposus. For the identification of the material parameters the annulus fibrosus was described with two scenarios: with and without fibre-matrix and fibre-fibre interactions. Both scenarios showed a similar behaviour on a load displacement level. Comparing model predictions to the experimental data, the mean RMS of all specimens and all load cases was 0.54±0.15° without the interaction and 0.54±0.19° when the fibre-matrix and fibre-fibre interactions were included. However, due to the increased stiffness when cross-links effects were included, this scenario showed more physiological stress-strain relations in uniaxial and biaxial stress

  1. Specimen specific parameter identification of ovine lumbar intervertebral discs: On the influence of fibre-matrix and fibre-fibre shear interactions.

    PubMed

    Reutlinger, Christoph; Bürki, Alexander; Brandejsky, Vaclav; Ebert, Lars; Büchler, Philippe

    2014-02-01

    Numerical models of the intervertebral disc, which address mechanical questions commonly make use of the difference in water content between annulus and nucleus, and thus fluid and solid parts are separated. Despite this simplification, models remain complex due to the anisotropy and nonlinearity of the annulus and regional variations of the collagen fibre density. Additionally, it has been shown that cross-links make a large contribution to the stiffness of the annulus. Because of this complex composite structure, it is difficult to reproduce several sets of experimental data with one single set of material parameters. This study addresses the question to which extent the ultrastructure of the intervertebral disc should be modelled so that its moment-angle behaviour can be adequately described. Therefore, a hyperelastic constitutive law, based on continuum mechanical principles was derived, which does not only consider the anisotropy from the collagen fibres, but also interactions among the fibres and between the fibres and the ground substance. Eight ovine lumbar intervertebral discs were tested on a custom made spinal loading simulator in flexion/extension, lateral bending and axial rotation. Specimen-specific geometrical models were generated using CT images and T2 maps to distinguish between annulus fibrosus and nucleus pulposus. For the identification of the material parameters the annulus fibrosus was described with two scenarios: with and without fibre-matrix and fibre-fibre interactions. Both scenarios showed a similar behaviour on a load displacement level. Comparing model predictions to the experimental data, the mean RMS of all specimens and all load cases was 0.54±0.15° without the interaction and 0.54±0.19° when the fibre-matrix and fibre-fibre interactions were included. However, due to the increased stiffness when cross-links effects were included, this scenario showed more physiological stress-strain relations in uniaxial and biaxial stress

  2. Characterization of extracellular vesicles in whole blood: Influence of pre-analytical parameters and visualization of vesicle-cell interactions using imaging flow cytometry.

    PubMed

    Fendl, Birgit; Weiss, René; Fischer, Michael B; Spittler, Andreas; Weber, Viktoria

    2016-09-01

    Extracellular vesicles are central players in intercellular communication and are released from the plasma membrane under tightly regulated conditions, depending on the physiological and pathophysiological state of the producing cell. Their heterogeneity requires a spectrum of methods for isolation and characterization, where pre-analytical parameters have profound impact on vesicle analysis, particularly in blood, since sampling, addition of anticoagulants, as well as post-sampling vesicle generation may influence the outcome. Here, we characterized microvesicles directly in whole blood using a combination of flow cytometry and imaging flow cytometry. We assessed the influence of sample agitation, anticoagulation, and temperature on post-sampling vesicle generation, and show that vesicle counts remained stable over time in samples stored without agitation. Storage with gentle rolling mimicking agitation, in contrast, resulted in strong release of platelet-derived vesicles in blood anticoagulated with citrate or heparin, whereas vesicle counts remained stable upon anticoagulation with EDTA. Using imaging flow cytometry, we could visualize microvesicles adhering to blood cells and revealed an anticoagulant-dependent increase in vesicle-cell aggregates over time. We demonstrate that vesicles adhere preferentially to monocytes and granulocytes in whole blood, while no microvesicles could be visualized on lymphocytes. Our data underscore the relevance of pre-analytical parameters in vesicle analysis and demonstrate that imaging flow cytometry is a suitable tool to study the interaction of extracellular vesicles with their target cells. PMID:27444383

  3. Interaction of hematoporphyrin derivative, light, and ionizing radiation in a rat glioma model

    SciTech Connect

    Kostron, H.; Swartz, M.R.; Miller, D.C.; Martuza, R.L.

    1986-03-01

    The effects of hematoporphyrin derivative, light, and cobalt 60 (/sup 60/Co) irradiation were studied in a rat glioma model using an in vivo and an in vitro clonogenic assay. There was no effect on tumor growth by visible light or by a single dose of /sup 60/Co irradiation at 4 Gy or 8 Gy, whereas 16 Gy inhibited tumor growth to 40% versus the control. Hematoporphyrin derivative alone slightly stimulated growth (P less than 0.1). Light in the presence of 10 mg hematoporphyrin derivative/kg inhibited tumor growth to 32%. /sup 60/Co irradiation in the presence of hematoporphyrin derivative produced a significant tumor growth inhibition (P less than 0.02). This growth inhibition was directly related to the concentration of hematoporphyrin derivative. The addition of /sup 60/Co to light in the presence of hematoporphyrin derivative produced a greater growth inhibition than light or /sup 60/Co irradiation alone. This effect was most pronounced when light was applied 30 minutes before /sup 60/Co irradiation. Our experiments in a subcutaneous rat glioma model suggest a radiosensitizing effect of hematoporphyrin derivative. Furthermore, the photodynamic inactivation is enhanced by the addition of /sup 60/Co irradiation. These findings may be of importance in planning new treatment modalities in malignant brain tumors.

  4. Quantification of interaction and topological parameters of polyisoprene star polymers under good solvent conditions.

    PubMed

    Rai, Durgesh K; Beaucage, Gregory; Ratkanthwar, Kedar; Beaucage, Peter; Ramachandran, Ramnath; Hadjichristidis, Nikos

    2016-05-01

    Mass fractal scaling, reflected in the mass fractal dimension d_{f}, is independently impacted by topology, reflected in the connectivity dimension c, and by tortuosity, reflected in the minimum dimension d_{min}. The mass fractal dimension is related to these other dimensions by d_{f}=cd_{min}. Branched fractal structures have a higher mass fractal dimension compared to linear structures due to a higher c, and extended structures have a lower dimension compared to convoluted self-avoiding and Gaussian walks due to a lower d_{min}. It is found, in this work, that macromolecules in thermodynamic equilibrium display a fixed mass fractal dimension d_{f} under good solvent conditions, regardless of chain topology.  These equilibrium structures accommodate changes in chain topology such as branching c by a decrease in chain tortuosity d_{min}. Symmetric star polymers are used to understand the structure of complex macromolecular topologies. A recently published hybrid Unified scattering function accounts for interarm correlations in symmetric star polymers along with polymer-solvent interaction for chains of arbitrary scaling dimension. Dilute solutions of linear, three-arm and six-arm polyisoprene stars are studied under good solvent conditions in deuterated p-xylene. Reduced chain tortuosity can be viewed as steric straightening of the arms. Steric effects for star topologies are quantified, and it is found that steric straightening of arms is more significant for lower-molecular-weight arms. The observation of constant d_{f} is explained through a modification of Flory-Krigbaum theory for branched polymers. PMID:27300939

  5. Thermodynamics calculation of protein-ligand interactions by QM/MM polarizable charge parameters.

    PubMed

    Wang, Jinan; Shao, Qiang; Cossins, Benjamin P; Shi, Jiye; Chen, Kaixian; Zhu, Weiliang

    2016-01-01

    The calculation of protein-ligand binding free energy (ΔG) is of great importance for virtual screening and drug design. Molecular dynamics (MD) simulation has been an attractive tool to investigate this scientific problem. However, the reliability of such approach is affected by many factors including electrostatic interaction calculation. Here, we present a practical protocol using quantum mechanics/molecular mechanics (QM/MM) calculations to generate polarizable QM protein charge (QMPC). The calculated QMPC of some atoms in binding pockets was obviously different from that calculated by AMBER ff03, which might significantly affect the calculated ΔG. To evaluate the effect, the MD simulations and MM/GBSA calculation with QMPC for 10 protein-ligand complexes, and the simulation results were then compared to those with the AMBER ff03 force field and experimental results. The correlation coefficient between the calculated ΔΔG using MM/GBSA under QMPC and the experimental data is .92, while that with AMBER ff03 force field is .47 for the complexes formed by streptavidin or its mutants and biotin. Moreover, the calculated ΔΔG with QMPC for the complexes formed by ERβ and five ligands is positively related to experimental result with correlation coefficient of .61, while that with AMBER ff03 charge is negatively related to experimental data with correlation coefficient of .42. The detailed analysis shows that the electrostatic polarization introduced by QMPC affects the electrostatic contribution to the binding affinity and thus, leads to better correlation with experimental data. Therefore, this approach should be useful to virtual screening and drug design.

  6. Renormalization group theory for fermions and order parameter fluctuations in interacting Fermi systems

    NASA Astrophysics Data System (ADS)

    Smirnov, Dimitry

    The dominant mode of coupled ocean-atmosphere variability in the Tropical Atlantic, the Atlantic Meridional Mode (AMM), responds strongly to seasonally dependent remote forcing. Previous studies have focused on AMM during boreal spring, when it is readily excited by ENSO and NAO forcing. However, relatively little is known about AMM variability during boreal fall, when it strongly regulates Atlantic hurricane activity and thus commands important societal impacts. A recent finding using a linear inverse model (LIM) of near-global SST anomalies suggests that the boreal fall AMM is forced by extratropical Atlantic SST anomalies and shows remarkable predictability with lead times approaching one year. To investigate the validity and mechanism of the LIM, a set of ensemble simulations are designed using an AGCM coupled to a slab-ocean. By initializing the GCM with LIM-derived SST anomalies, the main result of this research is the confirmation of the LIM result using an alternate physical framework. Excitation of the AMM is found to involve at least two processes: one is the thermodynamic, wind-evaporation-SST (WES) feedback, and the other is a low-cloud/SST feedback. The WES feedback is found to amplify the AMM-like response by a factor of three compared to when it is absent. However, SST anomalies are still found in the tropics when the WES feedback is suppressed. Meanwhile, the low-cloud-SST feedback is found to be locally important in the north tropical Atlantic stratocumulus region during boreal summer, but is unlikely to affect the large-scale AMM-like response. Additionally, we find that the GCM response depends strongly on the season of forcing (consistent with the LIM and some past studies), and also exhibits modest non-linearity initially, but progresses towards a more linear response later in the simulation. Another notable conclusion is that oceanic dynamics are not needed to explain the LIM result, as can be partly expected from the relatively short time

  7. Ecophysiological parameters for a coupled photosynthesis and stomatal conductance model derived from eddy covariance measurements in Asia

    NASA Astrophysics Data System (ADS)

    Ueyama, M.; Ichii, K.; Kobayashi, H.; Alberto, M. C. R.; Bret-Harte, M. S.; Edgar, C.; Euskirchen, E. S.; Harazono, Y.; Hirano, T.; Hirata, R.; Ide, R.; Kosugi, Y.; Machimura, T.; Mizoguchi, Y.; Ohta, T.; Ono, K.; Saigusa, N.; Saitoh, T. M.; Takagi, K.; Takanashi, S.; Zhang, Y.

    2015-12-01

    For better understanding carbon and water vapor fluxes in Asia, ecophysiological parameters of a coupled photosynthesis and stomatal conductance big-leaf model (Farquhar et al., 1980; Ball and Berry, 1987) were inversely estimated using micrometeorological data at 48 sites in Asia. The data covered various ecosystems of arctic tundra, boreal, temperate, and tropical forests, grasslands, and croplands. We applied a global optimization method; shuffled complex evolution (SCE-UA) method (Duan et al., 1993). First stomatal conductance parameters (m and b in the Ball-Berry model) were optimized for evapotranspiration, and then photosynthetic parameters (maximum carboxylation rate at 25oC; Vcmax25) were optimized for gross primarily productivity (GPP). The canopy-scale parameters were then downscaled into the leaf-scale using a two-leaf radiative transfer models and leaf area index (LAI) by MODIS. In the presentation, we will show the spatial variability of the ecophysiological parameters in terms of environmental gradients, and ecosystem types. Implications and limitations of the synthesis will be discussed. References Ball and Berry, 1987: Progress in Photosynthesis Research, pp 221-224. Duan et al., 1993: J. Optimization Theory and Applications, 76, 501-521. Farquhar et al., 1980: Planta, 149, 78-90.

  8. Redox and complexation interactions of neptunium(V) with quinonoid-enriched humic derivatives

    SciTech Connect

    Shcherbina, Natalia S.; Perminova, Irina V.; Kalmykov, Stephan N.; Kovalenko, Anton N.; Novikov, Alexander P.; Haire, Richard {Dick} G

    2007-01-01

    Actinides in their higher valence states (e.g., MO{sub 2}{sup +} and MO{sub 2}{sup 2+}, where M can be Np, Pu, etc) possess a higher potential for migration and in turn pose a substantial environmental threat. To minimize this potential for migration, reducing them to lower oxidation states (e.g., their tetravalent state) can be an attractive and efficient remedial process. These lower oxidation states are often much less soluble in natural aqueous media and are, therefore, less mobile in the environment. The research presented here focuses on assessing the performance of quinonoid-enriched humic derivatives with regards to complexing and/or reducing Np(V) present in solution. These 'designer' humics are essentially derived reducing agents that can serve as reactive components of a novel humic-based remediation technology. The derivatives are obtained by incorporating different quinonoid-moieties into leonardite humic acids. Five quinonoid-derivatives are tested in this work and all five prove more effective as reducing agents for selected actinides than the parent leonardite humic acid, and the hydroquinone derivatives are better than the catechol derivatives. The reduction kinetics and the Np(V) species formed with the different derivatives are studied via a batch mode using near-infrared (NIR)-spectroscopy. Np(V) reduction by the humic derivatives under anoxic conditions at 293 K and at pH 4.7 obeys first-order kinetics. Rate constants range from 1.70 x 10{sup -6} (parent humic acid) to 1.06 x 10{sup -5} sec{sup -1} (derivative with maximum hydroquinone content). Stability constants for Np(V)-humic complexes calculated from spectroscopic data produce corresponding Log{beta} values of 2.3 for parent humic acid and values ranging from 2.5 to 3.2 at pH 4.7 and from 3.3 to 3.7 at pH 7.4 for humic derivatives. Maximum constants are observed for hydroquinone-enriched derivatives. It is concluded that among the humic derivatives tested, the hydroquinone-enriched ones

  9. Interactions of cyclic and non-cyclic naphthalene diimide derivatives with different nucleic acids.

    PubMed

    Czerwinska, Izabella; Sato, Shinobu; Juskowiak, Bernard; Takenaka, Shigeori

    2014-05-01

    Recently, strategy based on stabilization of G-quadruplex telomeric DNA by small organic molecule has been realized by naphthalene diimide derivatives (NDIs). At the same time NDIs bind to DNA duplex as threading intercalators. Here we present cyclic derivative of naphthalene diimide (ligand 1) as DNA-binding ligand with ability to recognition of different structures of telomeric G-quadruplexes and ability to bis-intercalate to double-stranded helixes. The results have been compared to non-cyclic derivative (ligand 2) and revealed that preferential binding of ligands to nucleic acids strongly depends on their topology and structural features of ligands. PMID:24726302

  10. Application of Hansen Solubility Parameters to predict drug-nail interactions, which can assist the design of nail medicines.

    PubMed

    Hossin, B; Rizi, K; Murdan, S

    2016-05-01

    We hypothesised that Hansen Solubility Parameters (HSPs) can be used to predict drug-nail affinities. Our aims were to: (i) determine the HSPs (δD, δP, δH) of the nail plate, the hoof membrane (a model for the nail plate), and of the drugs terbinafine HCl, amorolfine HCl, ciclopirox olamine and efinaconazole, by measuring their swelling/solubility in organic liquids, (ii) predict nail-drug interactions by comparing drug and nail HSPs, and (iii) evaluate the accuracy of these predictions using literature reports of experimentally-determined affinities of these drugs for keratin, the main constituent of the nail plate and hoof. Many solvents caused no change in the mass of nail plates, a few solvents deswelled the nail, while others swelled the nail to varying extents. Fingernail and toenail HSPs were almost the same, while hoof HSPs were similar, except for a slightly lower δP. High nail-terbinafine HCl, nail-amorolfine HCl and nail-ciclopirox olamine affinities, and low nail-efinaconazole affinities were then predicted, and found to accurately match experimental reports of these drugs' affinities to keratin. We therefore propose that drug and nail Hansen Solubility Parameters may be used to predict drug-nail interactions, and that these results can assist in the design of drugs for the treatment of nail diseases, such as onychomycosis and psoriasis. To our knowledge, this is the first report of the application of HSPs in ungual research.

  11. Rational Design of Coumarin Derivatives as CK2 Inhibitors by Improving the Interaction with the Hinge Region.

    PubMed

    Zhang, Na; Chen, Wen-Juan; Zhou, Yue; Zhao, Hongtao; Zhong, Ru-Gang

    2016-01-01

    Design of novel coumarin derivatives as CK2 inhibitors were attempted by targeting the interaction with the hinge region. A set of substituents capable of forming a hydrogen bond or halogen bond with the hinge region were screened in silico, and trifluoromethyl emerges as a promising motif by forming favorable electrostatic interaction and a presumable halogen bond with the hinge region. As proof of concept, three trifluoromethyl derivatives of coumarin were synthesized and tested in vitro. The results indicated that replacement of methyl by trifluoromethyl leads to a modest 5-fold improvement in potency, with the most active compound being 0.4 µM. The newly designed compounds were further screened on one lung cancer cell line A549, showing low micromolar anti-proliferative activity.

  12. Development of an inexact-variance hydrological modeling system for analyzing interactive effects of multiple uncertain parameters

    NASA Astrophysics Data System (ADS)

    Wang, C. X.; Li, Y. P.; Zhang, J. L.; Huang, G. H.

    2015-09-01

    Uncertainty assessment of hydrological model parameters has become one of the main topics due to their significant effects on prediction in arid and semi-arid river basins. Incorporation of uncertainty assessment within hydrological models can facilitate the calibration process and improve the degree of credibility to the subsequent prediction. In this study, an inexact-variance hydrological modeling system (IVHMS) is developed for assessing parameter uncertainty on modeling outputs in the Kaidu River Basin, China. Through incorporating the techniques of type-2 fuzzy analysis (T2FA) and analysis of variance (ANOVA) within the semi-distributed land use based runoff processes (SLURP) model, IVHMS can quantitatively evaluate the individual and interactive effects of multiple uncertain parameters expressed as type-2 fuzzy sets in the hydrological modeling system. The modeling outputs indicate a good performance of SLURP model in describing the daily streamflow at the Dashankou hydrological station. Uncertainty analysis is conducted through sampling from fuzzy membership functions under different α-cut levels. The results show that, under a lower degree of plausibility (i.e. a lower α-cut level), intervals for peak and average flows are both wider; while intervals of peak and average flows become narrower under a higher degree of plausibility. Results based on ANOVA reveal that (i) precipitation factor (PF), one of main factors dominating the runoff processes, should be paid more attention in order to enhance the model performance; (ii) retention constant for fast store (RS) controls the amount and timing of the outflow from saturated zone and has a highly nonlinear effect on the average flow; (iii) the interaction between retention constant for fast store (RF) and maximum capacity for fast store (MF) has statistically significant (p < 0.05) effect on modeling outputs through affecting the maximum water holding capacity and the soil infiltration rate. The findings can

  13. Lipophilicity indices derived from the liquid chromatographic behavior observed under bimodal retention conditions (reversed phase/hydrophilic interaction): application to a representative set of pyridinium oximes.

    PubMed

    Voicu, Victor; Sârbu, Costel; Tache, Florentin; Micăle, Florina; Rădulescu, Ştefan Flavian; Sakurada, Koichi; Ohta, Hikoto; Medvedovici, Andrei

    2014-05-01

    The liquid chromatographic behavior observed under bimodal retention conditions (reversed phase and hydrophilic interaction) offers a new basis for the determination of some derived lipophilicity indices. The experiments were carried out on a representative group (30 compounds) of pyridinium oximes, therapeutically tested in acetylcholinesterase reactivation, covering a large range of lipophilic character. The chromatographic behavior was observed on a mixed mode acting stationary phase, resulting from covalent functionalization of high purity spherical silica with long chain alkyl groups terminated by a polar environment created through the vicinal diol substitution at the lasting carbon atoms (Acclaim Mixed Mode HILIC 1 column). Elution was achieved by combining different proportions of 5 mM ammonium formiate solutions in water and acetonitrile. The derived lipophilicity indices were compared with logP values resulting from different computational algorithms. The correlations between experimental and computed data sets are significant. To obtain a better insight on the transition from reversed phase to hydrophilic interaction retention mechanisms, the variation of the thermodynamic parameters determined through the van׳t Hoff approach was also discussed. PMID:24720980

  14. Cortical Amyloid Burden Differences Across Empirically-Derived Mild Cognitive Impairment Subtypes and Interaction with APOE ε4 Genotype

    PubMed Central

    Bangen, Katherine J.; Clark, Alexandra L.; Werhane, Madeline; Edmonds, Emily C.; Nation, Daniel A.; Evangelista, Nicole; Libon, David J.; Bondi, Mark W.; Delano-Wood, Lisa

    2016-01-01

    We examined cortical amyloid-β (Aβ) levels and interactions with apolipoprotein (APOE) ε4 genotype status across empirically-derived mild cognitive impairment (MCI) subgroups and cognitively normal older adults. Participants were 583 ADNI participants (444 MCI, 139 normal controls [NC]) with baseline florbetapir positron emission tomography (PET) amyloid imaging and neuropsychological testing. Of those with ADNI-defined MCI, a previous cluster analysis [1] classified 51% (n = 227) of the current sample as amnestic MCI, 8% (n = 37) as dysexecutive/mixed MCI, and 41% (n = 180) as cluster-derived normal (cognitively normal). Results demonstrated that the dysexecutive/mixed and amnestic MCI groups showed significantly greater levels of amyloid relative to the cluster-derived normal and NC groups who did not differ from each other. Additionally, 78% of the dysexecutive/mixed, 63% of the amnestic MCI, 42% of the cluster-derived normal, and 34% of the NC group exceeded the amyloid positivity threshold. Finally, a group by APOE genotype interaction demonstrated that APOE ε4 carriers within the amnestic MCI, cluster-derived normal, and NC groups showed significantly greater amyloid accumulation compared to non-carriers of their respective group. Such an interaction was not revealed within the dysexecutive/mixed MCI group which was characterized by both greater cognitive impairment and amyloid accumulation compared to the other participant groups. Our results from the ADNI cohort show considerable heterogeneity in Aβ across all groups studied, even within a group of robust NC participants. Findings suggest that conventional criteria for MCI may be susceptible to false positive diagnostic errors, and that onset of Aβ accumulation may occur earlier in APOE ε4 carriers compared to non-carriers. PMID:27031472

  15. Cortical Amyloid Burden Differences Across Empirically-Derived Mild Cognitive Impairment Subtypes and Interaction with APOE ɛ4 Genotype.

    PubMed

    Bangen, Katherine J; Clark, Alexandra L; Werhane, Madeline; Edmonds, Emily C; Nation, Daniel A; Evangelista, Nicole; Libon, David J; Bondi, Mark W; Delano-Wood, Lisa

    2016-03-29

    We examined cortical amyloid-β (Aβ) levels and interactions with apolipoprotein (APOE) ɛ4 genotype status across empirically-derived mild cognitive impairment (MCI) subgroups and cognitively normal older adults. Participants were 583 ADNI participants (444 MCI, 139 normal controls [NC]) with baseline florbetapir positron emission tomography (PET) amyloid imaging and neuropsychological testing. Of those with ADNI-defined MCI, a previous cluster analysis [1] classified 51% (n = 227) of the current sample as amnestic MCI, 8% (n = 37) as dysexecutive/mixed MCI, and 41% (n = 180) as cluster-derived normal (cognitively normal). Results demonstrated that the dysexecutive/mixed and amnestic MCI groups showed significantly greater levels of amyloid relative to the cluster-derived normal and NC groups who did not differ from each other. Additionally, 78% of the dysexecutive/mixed, 63% of the amnestic MCI, 42% of the cluster-derived normal, and 34% of the NC group exceeded the amyloid positivity threshold. Finally, a group by APOE genotype interaction demonstrated that APOE ɛ4 carriers within the amnestic MCI, cluster-derived normal, and NC groups showed significantly greater amyloid accumulation compared to non-carriers of their respective group. Such an interaction was not revealed within the dysexecutive/mixed MCI group which was characterized by both greater cognitive impairment and amyloid accumulation compared to the other participant groups. Our results from the ADNI cohort show considerable heterogeneity in Aβ across all groups studied, even within a group of robust NC participants. Findings suggest that conventional criteria for MCI may be susceptible to false positive diagnostic errors, and that onset of Aβ accumulation may occur earlier in APOE ɛ4 carriers compared to non-carriers. PMID:27031472

  16. Potential derived point charge model study of electrostatic interaction energies in some complexes of water with uracil, thymine, and cytosine.

    PubMed

    Ray, N K; Bolis, G; Shibata, M; Rein, R

    1984-01-01

    Potential derived (PD) point charges and segmental multipole moments are calculated for water, uracil, thymine, and cytosine using STO-3G quality wave functions. The PD point charges are used to estimate the electrostatic interaction energies for a series of complexes of water with these nucleic acid bases. It is shown here that the results obtained using simple PD charge model is very similar to those obtained from more elaborate segmental multipole moment analysis.

  17. Kinetic approach and estimation of the parameters of cellular interaction between the immunity system and a tumor.

    PubMed

    Kuznetsov, V A; Zhivoglyadov, V P; Stepanova, L A

    1993-01-01

    A method is suggested to estimate multi component dynamic systems, which permits, with the help of the computer-calculated kinetic curves, to obtain information about the possible mechanisms of the system component interaction. The method is based on the structural and parametrical identification of mathematical models presented in the form of a system of nonlinear differential equations, using a multi-criterial approach. Using experimental data of studies on growth kinetics and regression of multicellular tumor EMT6 line spheroids in the mouse allogenic system and the immune system cell accumulation in spheroids a mathematical model has been developed of the cellular interaction process in a spheroid. It has been stated that the rate of macrophage and neutrophil accumulation in a spheroid depends on the amount of tumor cells and is determined by the hyperbolic law (as analogous to the Michaelis-Menthen kinetics), while the accumulation of immune lymphocytes in a tumor is determined besides that by the three-cellular cooperation of lymphocytes, macrophages and tumor cells. According to the model, the inhibition of the process of neutrophil and lymphocyte (but not of macrophages) accumulation is realized through the auto-suppression mechanism. The numerical values of the process parameters, which characterise the rates of accumulation, cellular death in a tumor and of local cellular interactions intensity are obtained. PMID:8239905

  18. The explicitly correlated same number of optimized parameters (SNOOP-F12) scheme for calculating intermolecular interaction energies

    NASA Astrophysics Data System (ADS)

    Rasmussen, Troels Hels; Wang, Yang Min; Kjærgaard, Thomas; Kristensen, Kasper

    2016-05-01

    We augment the recently introduced same number of optimized parameters (SNOOP) scheme [K. Kristensen et al., J. Chem. Phys. 142, 114116 (2015)] for calculating interaction energies of molecular dimers with an F12 correction and generalize the method to enable the determination of interaction energies of general molecular clusters. The SNOOP, uncorrected (UC), and counterpoise (CP) schemes with/without an F12 correction are compared for the S22 test set of Jurečka et al. [Phys. Chem. Chem. Phys. 8, 1985 (2006)]—which consists of 22 molecular dimers of biological importance—and for water and methane molecular clusters. The calculations have been performed using the Resolution of the Identity second-order Møller-Plesset perturbation theory method. We conclude from the results that the SNOOP scheme generally yields interaction energies closer to the complete basis set limit value than the UC and CP approaches, regardless of whether the F12 correction is applied or not. Specifically, using the SNOOP scheme with an F12 correction yields the computationally most efficient way of achieving accurate results at low basis set levels. These conclusions hold both for molecular dimers and more general molecular clusters.

  19. Neutral winds derived from IRI parameters and from the HWM87 wind model for the sundial campaign of September, 1986

    NASA Technical Reports Server (NTRS)

    Miller, K. L.; Hedin, A. E.; Wilkinson, P. J.; Torr, D. G.; Richards, P. G.

    1990-01-01

    Meridional neutral winds derived from the height of the maximum ionization of the F2 layer are compared with values from results of the HWM87 empirical neutral wind model. The time period considered is the SUNDIAL-2 campaign, 21 Sept. through 5 Oct. 1986. Winds were derived from measurements by a global network of ionosondes, as well as from similar quantities generated by the International Reference Ionosphere. Global wind patterns from the three sources are similar. Differences tend to be the result of local or transient phenomena that are either too rapid to be described by the order of harmonics of the empirical models, or are the result of temporal changes not reproduced by models based on average conditions.

  20. Self-Assembly of Pyridine-Modified Lipoic Acid Derivatives on Gold and Their Interaction with Thyroxine (T4)

    PubMed Central

    Albers, Willem M.; Milani, Roberto; Tappura, Kirsi; Munter, Tony; Resnati, Giuseppe; Metrangolo, Pierangelo

    2013-01-01

    Pyridyl derivatives of lipoic acid were prepared as ligands for the study of the interaction with thyroxine (T4). Thin self-assembled films of the ligands were prepared in 70% ethanol on gold and their interaction with T4 was studied by titration experiments in an aqueous buffer solution using Surface Plasmon Resonance (SPR). The thickness and refractive index of the ligand layers were calculated from SPR spectra recorded in two media, also allowing for surface coverage and the density of the layers to be estimated. Two ligands, a 4-pyridyl and a bis(2-hydroxyethyl) derivative of lipoic acid, were selected to investigate the feasibility for producing molecularly imprinted self-assembled layers on gold for T4. The methodology was to co-assemble T4 and the ligand onto the gold surface, elute the T4 from the layer under alkaline conditions, and study the rebinding of T4 to the layer. Multiple elution/rebinding cycles were conducted in different buffer solutions, and rebinding of T4 could be observed, with a moderate binding affinity that depended greatly on the solvent used. More optimal binding was observed in HBS buffer, and the affinity of the interaction could be slightly increased when the 4-pyridyl and bis(2-hydroxy-ethyl) derivatives of lipoic acid were combined in the imprinted layer. PMID:23389045

  1. Profiling the substitution pattern of xyloglucan derivatives by integrated enzymatic hydrolysis, hydrophilic-interaction liquid chromatography and mass spectrometry.

    PubMed

    Liu, Jun; Kisonen, Victor; Willför, Stefan; Xu, Chunlin; Vilaplana, Francisco

    2016-09-01

    Plant polysaccharides constitute arguably the most complex family of biomacromolecules in terms of the stereochemistry and regiochemistry of their intramolecular linkages. The chemical modification of such polysaccharides introduces an additional level of complexity for structural determinations. We have developed an integrated analytical procedure combining selective enzymatic hydrolysis, hydrophilic interaction liquid chromatography (HILIC), and mass spectrometry (MS) to describe the substitution pattern of xyloglucan (XyG) and its chemo-enzymatic derivatives (cationic, anionic, and benzyl aminated). Enzymatic hydrolysis of XyG derivatives by a xyloglucan-specific endoglucanase (XEG) generates oligosaccharides amenable for mass spectrometric identification with distinct structures, based on enzymatic substrate recognition and hydrolytic pattern. Matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI-ToF-MS) and electrospray ionisation mass spectrometry (ESI-MS) offer qualitative mass profiling of the chemical derivatives. Separation and identification of the complex oligosaccharide profiles released by enzymatic hydrolysis is achieved by hyphenation of hydrophilic interaction liquid chromatography with mass spectrometry (HILIC-ESI-MS). Further fragmentation by tandem mass spectrometry (ESI-MS/MS) in positive mode enables the structural sequencing of modified XyG oligosaccharides and the identification of the substituent position without further derivatisation. This integrated approach can be used to obtain semi-quantitative information of the substitution pattern of hemicellulose derivatives, with fundamental implications for their modification mechanisms and performance. PMID:27524300

  2. Peptides derived from CXCL8 based on in silico analysis inhibit CXCL8 interactions with its receptor CXCR1

    NASA Astrophysics Data System (ADS)

    Jiang, Shinn-Jong; Liou, Je-Wen; Chang, Chun-Chun; Chung, Yi; Lin, Lee-Fong; Hsu, Hao-Jen

    2015-12-01

    Chemokine CXCL8 is crucial for regulation of inflammatory and immune responses via activating its cognate receptor CXCR1. In this study, molecular docking and binding free energy calculations were combined to predict the initial binding event of CXCL8 to CXCR1 for peptide drug design. The simulations reveal that in the initial binding, the N-loop of CXCL8 interacts with the N-terminus of CXCR1, which is dominated by electrostatic interactions. The derived peptides from the binding region of CXCL8 are synthesized for further confirmation. Surface plasmon resonance analyses indicate that the CXCL8 derived peptide with 14 residues is able to bind to the receptor CXCR1 derived peptide with equilibrium KD of 252 μM while the peptide encompassing a CXCL8 K15A mutation hardly binds to CXCR1 derived peptide (KD = 1553 μM). The cell experiments show that the designed peptide inhibits CXCL8-induced and LPS-activated monocytes adhesion and transmigration. However, when the peptides were mutated on two lysine residues (K15 and K20), the inhibition effects were greatly reduced indicating these two amino acids are key residues for the initial binding of CXCL8 to CXCR1. This study demonstrates that in silico prediction based functional peptide design can be effective for developing anti-inflammation drugs.

  3. Ionic composition of seawaters and derived saline solutions determined by ion chromatography and its relation to other water quality parameters.

    PubMed

    Gros, Natasa; Camões, M F; Oliveira, Cristina; Silva, M C R

    2008-11-01

    Ion chromatography (IC) presents new possibilities for assessing information about environmental samples, namely waters of various compositions, ranging from high-purity water to highly saline ones. Constant proportion between major ions present in seawater, has been assumed in the past, from which the first practical equation relating chlorinity and salinity has been developed, being later substituted by a practical salinity scale, derived from conductivity measurements relative to a standard seawater, according to internationally accepted recommended procedures. Seawaters are characterized by salinity values around 35 while derived saline solutions may present considerable changes in ionic composition, conductivity, hence on salinity. Natural and anthropogenic phenomena may introduce new issues requiring clarification for which qualitative and quantitative information from additional sources is useful, e.g. ionic composition from IC. The different ranges of concentration of major and minor species present in seawater and derived saline solutions are a challenge for the optimization of a practical methodology for composition assessment in two single IC runs, one for anions and another one for cations, which has been attained in this work. Composition of saline solutions determined by IC was critically assessed in terms of anion-cation balance and further related to conductivity and salinity measurements aiming to evaluate the quality/completeness of ion chromatographic analyses performed at preselected conditions and to search for other meaningful relations for efficient recognition/distinction between saline solutions of different types. PMID:18829032

  4. New natural shapes of non-Gaussianity from high-derivative interactions and their optimal limits from WMAP 9-year data

    SciTech Connect

    Behbahani, Siavosh R.; Mirbabayi, Mehrdad; Senatore, Leonardo; Smith, Kendrick M. E-mail: mehrdadm@ias.edu E-mail: kmsmith@perimeterinstitute.ca

    2014-11-01

    Given the fantastic experimental effort, it is important to thoroughly explore the signature space of inflationary models. The fact that higher derivative operators do not renormalize lower derivative ones allows us to find a large class of technically natural single-clock inflationary models where, in the context of the Effective Field Theory of Inflation, the leading interactions have many derivatives. We systematically explore the 3-point function induced by these models and their overlap with the standard equilateral and orthogonal templates. We find that in order to satisfactorily cover the signature space of these models, two new additional templates need to be included. We then perform the optimal analysis of the WMAP 9-year data for the resulting four templates, finding that the overall significance of a non-zero signal is between 2–2.5σ, depending on the choice of parameter space, partially driven by the preference for nonzero f{sub NL}{sup orth} in WMAP9.

  5. Mathematical model relating uniaxial compressive behavior of manufactured sand mortar to MIP-derived pore structure parameters.

    PubMed

    Tian, Zhenghong; Bu, Jingwu

    2014-01-01

    The uniaxial compression response of manufactured sand mortars proportioned using different water-cement ratio and sand-cement ratio is examined. Pore structure parameters such as porosity, threshold diameter, mean diameter, and total amounts of macropores, as well as shape and size of micropores are quantified by using mercury intrusion porosimetry (MIP) technique. Test results indicate that strains at peak stress and compressive strength decreased with the increasing sand-cement ratio due to insufficient binders to wrap up entire sand. A compression stress-strain model of normal concrete extending to predict the stress-strain relationships of manufactured sand mortar is verified and agreed well with experimental data. Furthermore, the stress-strain model constant is found to be influenced by threshold diameter, mean diameter, shape, and size of micropores. A mathematical model relating stress-strain model constants to the relevant pore structure parameters of manufactured sand mortar is developed.

  6. Mathematical Model Relating Uniaxial Compressive Behavior of Manufactured Sand Mortar to MIP-Derived Pore Structure Parameters

    PubMed Central

    Tian, Zhenghong; Bu, Jingwu

    2014-01-01

    The uniaxial compression response of manufactured sand mortars proportioned using different water-cement ratio and sand-cement ratio is examined. Pore structure parameters such as porosity, threshold diameter, mean diameter, and total amounts of macropores, as well as shape and size of micropores are quantified by using mercury intrusion porosimetry (MIP) technique. Test results indicate that strains at peak stress and compressive strength decreased with the increasing sand-cement ratio due to insufficient binders to wrap up entire sand. A compression stress-strain model of normal concrete extending to predict the stress-strain relationships of manufactured sand mortar is verified and agreed well with experimental data. Furthermore, the stress-strain model constant is found to be influenced by threshold diameter, mean diameter, shape, and size of micropores. A mathematical model relating stress-strain model constants to the relevant pore structure parameters of manufactured sand mortar is developed. PMID:25133257

  7. Analytic derivative couplings for spin-flip configuration interaction singles and spin-flip time-dependent density functional theory

    SciTech Connect

    Zhang, Xing; Herbert, John M.

    2014-08-14

    We revisit the calculation of analytic derivative couplings for configuration interaction singles (CIS), and derive and implement these couplings for its spin-flip variant for the first time. Our algorithm is closely related to the CIS analytic energy gradient algorithm and should be straightforward to implement in any quantum chemistry code that has CIS analytic energy gradients. The additional cost of evaluating the derivative couplings is small in comparison to the cost of evaluating the gradients for the two electronic states in question. Incorporation of an exchange-correlation term provides an ad hoc extension of this formalism to time-dependent density functional theory within the Tamm-Dancoff approximation, without the need to invoke quadratic response theory or evaluate third derivatives of the exchange-correlation functional. Application to several different conical intersections in ethylene demonstrates that minimum-energy crossing points along conical seams can be located at substantially reduced cost when analytic derivative couplings are employed, as compared to use of a branching-plane updating algorithm that does not require these couplings. Application to H{sub 3} near its D{sub 3h} geometry demonstrates that correct topology is obtained in the vicinity of a conical intersection involving a degenerate ground state.

  8. Interactions of Jet Fuels with Nitrile O-Rings: Petroleum-Derived versus Synthetic Fuels

    SciTech Connect

    Gormley, Robert J.; Link, Dirk D.; Baltrus, John P.; Zandhuis, Paul H.

    2009-02-19

    A transition from petroleum-derived jet fuels to blends with Fischer-Tropsch (F-T) fuels, and ultimately fully synthetic hydro-isomerized F-T fuels has raised concern about the fate of plasticizers in nitrile-butadiene rubber o-rings that are contacted by the fuels as this transition occurs. The partitioning of plasticizers and fuel molecules between nitrile o-rings and petroleum-derived, synthetic, and additized-synthetic jet fuels has been measured. Thermal desorption of o-rings soaked in the various jet fuels followed by gas chromatographic analysis with a mass spectrometric detector showed many of the plasticizer and stabilizer compounds were removed from the o-rings regardless of the contact fuel. Fuel molecules were observed to migrate into the o-rings for the petroleum-derived fuel as did both the fuel and additive for a synthetic F-T jet fuel additized with benzyl alcohol, but less for the unadditized synthetic fuel. The specific compounds or classes of compounds involved in the partitioning were identified and a semiquantitative comparison of relative partitioning of the compounds of interest was made, The results provide another step forward in improving the confidence level of using additized, fully synthetic jet fuel in the place of petroleum-derived fuel.

  9. Interactions of Jet Fuels with Nitrile O-Rings: Petroleum-Derived versus Synthetic Fuels

    SciTech Connect

    Gormely, R J; Link, D D; Baltrus, J P; Zandhuis, P H

    2009-01-01

    A transition from petroleum~derived jet fuels to blends with Fischer-Tropsch (F~T) fuels, and ultimately fully synthetic hydro-isomerized F-T fuels has raised concern about the fate of plasticizers in nitrile-butadiene rubber a-rings that are contacted by the fuels as this transition occurs. The partitioning of plasticizers and fuel molecules between nitrile a-rings and petroleum-derived, synthetic, and additized-synthetic jet fuels has been measured. Thermal desorption of o-rings soaked in the various jet fuels followed by gas chromatographic analysis with a mass spectrometric detector showed many of the plasticizer and stabilizer compounds were removed from the o-rings regardless of the contact fuel. Fuel molecules were observed to migrate into the o-rings for the petroleum-derived fuel as did both the fuel and additive for a synthetic F-T jet fuel additized with benzyl alcohol, but less for the unadditized synthetic fuel. The specific compounds or classes of compounds involved in the partitioning were identified and a semiquantitative comparison of relative partitioning of the compounds of interest was made. The results provide another step forward in improving the confidence level of using additized, fully synthetic jet fuel in the place of petroleum-derived fuel.

  10. Interactions of Jet Fuels with Nitrile O-Rings: Petroleum-Derived versus Synthetic Fuels

    SciTech Connect

    Gormley, R.J.; Link, D.D.; Baltrus, J.P.; Zandhuis, P.H.

    2008-01-01

    A transition from petroleum-derived jet fuels to blends with Fischer-Tropsch (F-T) fuels, and ultimately fully synthetic hydro-isomerized F-T fuels has raised concern about the fate of plasticizers in nitrile-butadiene rubber o-rings that are contacted by the fuels as this transition occurs. The partitioning of plasticizers and fuel molecules between nitrile o-rings and petroleum-derived, synthetic, and additized-synthetic jet fuels has been measured. Thermal desorption of o-rings soaked in the various jet fuels followed by gas chromatographic analysis with a mass spectrometric detector showed many of the plasticizer and stabilizer compounds were removed from the o-rings regardless of the contact fuel. Fuel molecules were observed to migrate into the o-rings for the petroleum-derived fuel as did both the fuel and additive for a synthetic F-T jet fuel additized with benzyl alcohol, but less for the unadditized synthetic fuel. The specific compounds or classes of compounds involved in the partitioning were identified and a semiquantitative comparison of relative partitioning of the compounds of interest was made. The results provide another step forward in improving the confidence level of using additized, fuIly synthetic jet fuel in the place of petroleum-derived fueL

  11. Interactions of Jet Fuels with Nitrile O-Rings: Petroleum-Derived versus Synthetic Fuels

    SciTech Connect

    Gormley, Robert J.; Link, Dirk D.; Baltrus, John P.; Zandhuis, Paul H.

    2009-01-01

    A transition from petroleum-derived jet fuels to blends with Fischer-Tropsch (F-T) fuels, and ultimately fully synthetic hydro-isomerized F-T fuels has raised concern about the fate of plasticizers in nitrile-butadiene rubber a-rings that are contacted by the fuels as this transition occurs. The partitioning of plasticizers and fuel molecules between nitrile a-rings and petroleum-derived, synthetic, and additized-synthetic jet fuels has been measured. Thermal desorption of o-rings soaked in the various jet fuels followed by gas chromatographic analysis with a mass spectrometric detector showed many of the plasticizer and stabilizer compounds were removed from the o-rings regardless of the contact fuel. Fuel molecules were observed to migrate into the o-rings for the petroleum-derived fuel as did both the fuel and additive for a synthetic F-T jet fuel additized with benzyl alcohol, but less for the unadditized synthetic fuel. The specific compounds or classes of compounds involved in the partitioning were identified and a semiquantitative comparison of relative partitioning of the compounds of interest was made. The results provide another step forward in improving the confidence level of using additized, fully synthetic jet fuel in the place of petroleum-derived fuel.

  12. Virus-host interactions in persistently FMDV-infected cells derived from bovine pharynx

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Foot-and-mouth disease virus (FMDV) produces a disease in cattle characterized by vesicular lesions and a persistent infection with asymptomatic low-level production of virus. Here we describe the establishment of a persistently infected primary cell culture derived from bovine pharynx tissue (PBPT)...

  13. Double porosity in fluid-saturated elastic media: deriving effective parameters by hierarchical homogenization of static problem

    NASA Astrophysics Data System (ADS)

    Rohan, Eduard; Naili, Salah; Lemaire, Thibault

    2016-09-01

    We propose a model of complex poroelastic media with periodic or locally periodic structures observed at microscopic and mesoscopic scales. Using a two-level homogenization procedure, we derive a model coherent with the Biot continuum, describing effective properties of such a hierarchically structured poroelastic medium. The effective material coefficients can be computed using characteristic responses of the micro- and mesostructures which are solutions of local problems imposed in representative volume elements describing the poroelastic medium at the two levels of heterogeneity. In the paper, we discus various combinations of the interface between the micro- and mesoscopic porosities, influence of the fluid compressibility, or solid incompressibility. Gradient of porosity is accounted for when dealing with locally periodic structures. Derived formulae for computing the poroelastic material coefficients characterize not only the steady-state responses with static fluid, but are relevant also for quasistatic problems. The model is applicable in geology, or in tissue biomechanics, in particular for modeling canalicular-lacunar porosity of bone which can be characterized at several levels.

  14. Double porosity in fluid-saturated elastic media: deriving effective parameters by hierarchical homogenization of static problem

    NASA Astrophysics Data System (ADS)

    Rohan, Eduard; Naili, Salah; Lemaire, Thibault

    2015-09-01

    We propose a model of complex poroelastic media with periodic or locally periodic structures observed at microscopic and mesoscopic scales. Using a two-level homogenization procedure, we derive a model coherent with the Biot continuum, describing effective properties of such a hierarchically structured poroelastic medium. The effective material coefficients can be computed using characteristic responses of the micro- and mesostructures which are solutions of local problems imposed in representative volume elements describing the poroelastic medium at the two levels of heterogeneity. In the paper, we discus various combinations of the interface between the micro- and mesoscopic porosities, influence of the fluid compressibility, or solid incompressibility. Gradient of porosity is accounted for when dealing with locally periodic structures. Derived formulae for computing the poroelastic material coefficients characterize not only the steady-state responses with static fluid, but are relevant also for quasistatic problems. The model is applicable in geology, or in tissue biomechanics, in particular for modeling canalicular-lacunar porosity of bone which can be characterized at several levels.

  15. Investigation of long period oscillations in the equatorial middle atmospheric parameters derived from ground and space based platforms

    NASA Astrophysics Data System (ADS)

    Swain, Debadatta; Kishore Kumar, K.; John, Sherine Rachel; Ramkumar, Geetha

    The middle atmospheric dynamics is modulated strongly by long period waves and oscilla-tions apart from short period gravity waves, tides and planetary scale waves. Owing to the importance of these phenomena in the middle atmosphere, several studies have been carried out globally using in situ measurements and models to identify and investigate the waves and oscillations as well as their forcing mechanisms. In the present work we attempt to investigate the long period oscillations in winds, temperature and ozone simultaneously over a low lati-tude station, Trivandrum (8.5o N, 77o E) using a combination of ground and satellite based observations. The long term measurements of various atmospheric parameters like winds from radiosonde/rocket flights, atmospheric radars (under ISRO's MIDAS campaign) along with temperature and ozone from SABER on TIMED satellite has for the first time enabled the simultaneous investigation of the chemistry, dynamics and thermal structure of the middle at-mosphere over this location. The study revealed several interesting features of stratospheric and mesospheric long period oscillations bringing out the salient features of QBO and SAO in particular. It was observed that stratospheric and mesospheric QBO and SAO in temperature and winds are exactly in opposite phases. The peaking altitudes of stratospheric and meso-spheric SAO in case of the three parameters are also different. The comprehensive analysis of the long period oscillations in winds, temperature and ozone simultaneously is one of the first of its kind over this location involving the three parameters contributing to middle atmospheric dynamics.

  16. Validation of Cloud Parameters Derived from Geostationary Satellites, AVHRR, MODIS, and VIIRS Using SatCORPS Algorithms

    NASA Technical Reports Server (NTRS)

    Minnis, P.; Sun-Mack, S.; Bedka, K. M.; Yost, C. R.; Trepte, Q. Z.; Smith, W. L., Jr.; Painemal, D.; Chen, Y.; Palikonda, R.; Dong, X.; Xi, B.

    2016-01-01

    Validation is a key component of remote sensing that can take many different forms. The NASA LaRC Satellite ClOud and Radiative Property retrieval System (SatCORPS) is applied to many different imager datasets including those from the geostationary satellites, Meteosat, Himiwari-8, INSAT-3D, GOES, and MTSAT, as well as from the low-Earth orbiting satellite imagers, MODIS, AVHRR, and VIIRS. While each of these imagers have similar sets of channels with wavelengths near 0.65, 3.7, 11, and 12 micrometers, many differences among them can lead to discrepancies in the retrievals. These differences include spatial resolution, spectral response functions, viewing conditions, and calibrations, among others. Even when analyzed with nearly identical algorithms, it is necessary, because of those discrepancies, to validate the results from each imager separately in order to assess the uncertainties in the individual parameters. This paper presents comparisons of various SatCORPS-retrieved cloud parameters with independent measurements and retrievals from a variety of instruments. These include surface and space-based lidar and radar data from CALIPSO and CloudSat, respectively, to assess the cloud fraction, height, base, optical depth, and ice water path; satellite and surface microwave radiometers to evaluate cloud liquid water path; surface-based radiometers to evaluate optical depth and effective particle size; and airborne in-situ data to evaluate ice water content, effective particle size, and other parameters. The results of comparisons are compared and contrasted and the factors influencing the differences are discussed.

  17. Genetic parameters and genotype x environment interaction for feed efficiency traits in steers fed grower and finisher diets.

    PubMed

    Durunna, O N; Plastow, G; Mujibi, F D N; Grant, J; Mah, J; Basarab, J A; Okine, E K; Moore, S S; Wang, Z

    2011-11-01

    The objective of this study was to examine the genetic parameters and genetic correlations of feed efficiency traits in steers (n = 490) fed grower or finisher diets in 2 feeding periods. A bivariate model was used to estimate phenotypic and genetic parameters using steers that received the grower and finisher diets in successive feeding periods, whereas a repeated animal model was used to estimate the permanent environmental effects. Genetic correlations between the grower-fed and finisher-fed regimens were 0.50 ± 0.48 and 0.78 ± 0.43 for residual feed intake (RFI) and G:F, respectively. The moderate genetic correlation between the 2 feeding regimens may indicate the presence of a genotype × environment interaction for RFI. Permanent environmental effects (expressed in percentage of phenotypic variance) were detected in the grower-fed steers for ADG (38%), DMI (30%), RFI (18%), and G:F (40%) and also in the finisher-fed steers for ADG (28%), DMI (35%), metabolic mid-weight (23%), and RFI (10%). Heritability estimates were 0.08 ± 0.10 and 0.14 ± 0.15 for the grower-fed steers and 0.42 ± 0.16 and 0.40 ± 17 for the finisher-fed steers for RFI and G:F, respectively. The dependency of the RFI on the feeding regimen may have serious implications when selecting animals in the beef industry. Because of the higher cost of grains, feed efficiency in the feedlot might be overemphasized, whereas efficiency in the cow herd and the backgrounding segments may have less emphasis. These results may also favor the retention (for subsequent breeding) of cows whose steers were efficient in the feedlot sector. Therefore, comprehensive feeding trials may be necessary to provide more insight into the mechanisms surrounding genotype × environment interaction in steers. PMID:21622886

  18. Synthesis of fluorinated maltose derivatives for monitoring protein interaction by (19)F NMR.

    PubMed

    Braitsch, Michaela; Kählig, Hanspeter; Kontaxis, Georg; Fischer, Michael; Kawada, Toshinari; Konrat, Robert; Schmid, Walther

    2012-01-01

    A novel reporter system, which is applicable to the (19)F NMR investigation of protein interactions, is presented. This approach uses 2-F-labeled maltose as a spy ligand to indirectly probe protein-ligand or protein-protein interactions of proteins fused or tagged to the maltose-binding protein (MBP). The key feature is the simultaneous NMR observation of both (19)F NMR signals of gluco/manno-type-2-F-maltose-isomers; one isomer (α-gluco-type) binds to MBP and senses the protein interaction, and the nonbinding isomers (β-gluco- and/or α/β-manno-type) are utilized as internal references. Moreover, this reporter system was used for relative affinity studies of fluorinated and nonfluorinated carbohydrates to the maltose-binding protein, which were found to be in perfect agreement with published X-ray data. The results of the NMR competition experiments together with the established correlation between (19)F chemical shift data and molecular interaction patterns, suggest valuable applications for studies of protein-ligand interaction interfaces. PMID:22509216

  19. Novel insights into host-fungal pathogen interactions derived from live-cell imaging.

    PubMed

    Bain, Judith; Gow, Neil A R; Erwig, Lars-Peter

    2015-03-01

    The theoretical physicist and Nobel laureate Richard Feynman outlined in his 1959 lecture, "There's plenty of room at the bottom", the enormous possibility of producing and visualising things at smaller scales. The advent of advanced scanning and transmission electron microscopy and high-resolution microscopy has begun to open the door to visualise host-pathogen interactions at smaller scales, and spinning disc confocal and two-photon microscopy has improved our ability to study these events in real time in three dimensions. The aim of this review is to illustrate some of the advances in understanding host-fungal interactions that have been made in recent years in particular those relating to the interactions of live fungal pathogens with phagocytes. Dynamic imaging of host-pathogen interactions has recently revealed novel detail and unsuspected mechanistic insights, facilitating the dissection of the phagocytic process into its component parts. Here, we will highlight advances in our knowledge of host-fungal pathogen interactions, including the specific effects of fungal cell viability, cell wall composition and morphogenesis on the phagocytic process and try to define the relative contributions of neutrophils and macrophages to the clearance of fungal pathogens in vitro and the infected host. PMID:25398200

  20. Novel insights into host-fungal pathogen interactions derived from live-cell imaging.

    PubMed

    Bain, Judith; Gow, Neil A R; Erwig, Lars-Peter

    2015-03-01

    The theoretical physicist and Nobel laureate Richard Feynman outlined in his 1959 lecture, "There's plenty of room at the bottom", the enormous possibility of producing and visualising things at smaller scales. The advent of advanced scanning and transmission electron microscopy and high-resolution microscopy has begun to open the door to visualise host-pathogen interactions at smaller scales, and spinning disc confocal and two-photon microscopy has improved our ability to study these events in real time in three dimensions. The aim of this review is to illustrate some of the advances in understanding host-fungal interactions that have been made in recent years in particular those relating to the interactions of live fungal pathogens with phagocytes. Dynamic imaging of host-pathogen interactions has recently revealed novel detail and unsuspected mechanistic insights, facilitating the dissection of the phagocytic process into its component parts. Here, we will highlight advances in our knowledge of host-fungal pathogen interactions, including the specific effects of fungal cell viability, cell wall composition and morphogenesis on the phagocytic process and try to define the relative contributions of neutrophils and macrophages to the clearance of fungal pathogens in vitro and the infected host.

  1. Global variations in gravity-derived oceanic crustal thickness: Implications on oceanic crustal accretion and hotspot-lithosphere interactions

    NASA Astrophysics Data System (ADS)

    Lin, J.; Zhu, J.

    2012-12-01

    We present a new global model of oceanic crustal thickness based on inversion of global oceanic gravity anomaly with constrains from seismic crustal thickness profiles. We first removed from the observed marine free-air gravity anomaly all gravitational effects that can be estimated and removed using independent constraints, including the effects of seafloor topography, marine sediment thickness, and the age-dependent thermal structure of the oceanic lithosphere. We then calculated models of gravity-derived crustal thickness through inversion of the residual mantle Bouguer anomaly using best-fitting gravity-modeling parameters obtained from comparison with seismically determined crustal thickness profiles. Modeling results show that about 5% of the global crustal volume (or 9% of the global oceanic surface area) is associated with model crustal thickness <5.2 km (designated as "thin" crust), while 56% of the crustal volume (or 65% of the surface area) is associated with crustal thickness of 5.2-8.6 km thick (designated as "normal" crust). The remaining 39% of the crustal volume (or 26% of the surface area) is associated with crustal thickness >8.6 km and is interpreted to have been affected by excess magmatism. The percentage of oceanic crustal volume that is associated with thick crustal thickness (>8.6 km) varies greatly among tectonic plates: Pacific (33%), Africa (50%), Antarctic (33%), Australia (30%), South America (34%), Nazca (23%), North America (47%), India (74%), Eurasia (68%), Cocos (20%), Philippine (26%), Scotia (41%), Caribbean (89%), Arabian (82%), and Juan de Fuca (21%). We also found that distribution of thickened oceanic crust (>8.6 km) seems to depend on spreading rate and lithospheric age: (1) On ocean basins younger than 5 Ma, regions of thickened crust are predominantly associated with slow and ultraslow spreading ridges. The relatively strong lithospheric plate at slow and ultraslow ridges might facilitate the loading of large magmatic

  2. Interactions between minimum run time, modifier concentration, and efficiency parameters in a high performance liquid chromatography separation.

    PubMed

    Chester, T L; Stalcup, A M

    2011-01-14

    We modeled and studied the separation of uracil, nicotinamide, resorcinol, theobromine, theophylline, and caffeine on four C-18 columns of different lengths packed with the same stationary phase using water/methanol mobile phase at one temperature. Predictions of retention times and peak widths were compared with experimental results and were found to be sufficiently accurate for performing optimization calculations. With limits set on the required resolution and on maximum values for pressure and flow rate, calculations were performed for numerous virtual column lengths seeking the smallest possible analysis time for each length while allowing methanol concentration and flow rate to vary as required to minimize run time. Predictions were experimentally verified for the column lengths actually available. These calculations revealed the dependence of best-possible analysis time on column length, modifier concentration, flow rate, and pressure for the real system that was modeled, and provided insight into parameter interactions with respect to analysis times meeting the needs and limits specified. We show that when these parameters are considered in concert, rather than individually, conventional guidelines regarding setting their values may not always lead to the optimum. PMID:21130461

  3. Social anxiety, acute social stress, and reward parameters interact to predict risky decision-making among adolescents.

    PubMed

    Richards, Jessica M; Patel, Nilam; Daniele-Zegarelli, Teresa; MacPherson, Laura; Lejuez, C W; Ernst, Monique

    2015-01-01

    Risk-taking behavior increases during adolescence, leading to potentially disastrous consequences. Social anxiety emerges in adolescence and may compound risk-taking propensity, particularly during stress and when reward potential is high. However, the manner in which social anxiety, stress, and reward parameters interact to impact adolescent risk-taking is unclear. To clarify this question, a community sample of 35 adolescents (15-18yo), characterized as having high or low social anxiety, participated in a study over two separate days, during each of which they were exposed to either a social stress or a control condition, while performing a risky decision-making task. The task manipulated, orthogonally, reward magnitude and probability across trials. Three findings emerged. First, reward magnitude had a greater impact on the rate of risky decisions in high social anxiety (HSA) than low social anxiety (LSA) adolescents. Second, reaction times (RTs) were similar during the social stress and the control conditions for the HSA group, whereas the LSA group's RTs differed between conditions. Third, HSA adolescents showed the longest RTs on the most negative trials. These findings suggest that risk-taking in adolescents is modulated by context and reward parameters differentially as a function of social anxiety. PMID:25465884

  4. Interaction of jack bean (Canavalia ensiformis) urease and a derived peptide with lipid vesicles.

    PubMed

    Micheletto, Yasmine Miguel Serafini; Moro, Carlo Frederico; Lopes, Fernanda Cortez; Ligabue-Braun, Rodrigo; Martinelli, Anne Helene Souza; Marques, Carlos Manuel; Schroder, André Pierre; Carlini, Célia Regina; da Silveira, Nádya Pesce

    2016-09-01

    Ureases are metalloenzymes that catalyze the hydrolysis of urea to ammonia and carbon dioxide. Jack bean (Canavalia ensiformis) produces three isoforms of urease (Canatoxin, JBU and JBURE-II). Canatoxin and JBU display several biological properties independent of their ureolytic activity, such as neurotoxicity, exocytosis-inducing and pro-inflammatory effects, blood platelets activation, insecticidal and antifungal activities. The Canatoxin entomotoxic activity is mostly due to an internal peptide, named pepcanatox, released upon the hydrolysis of the protein by insect cathepsin-like digestive enzymes. Based on pepcanatox sequence, Jaburetox-2Ec was produced in Escherichia coli. JBU and its peptides were shown to permeabilize membranes through an ion channel-based mechanism. Here we studied the JBU and Jaburetox-2Ec interaction with platelet-like multilamellar liposomes (PML) using Dynamic Light Scattering and Small Angle X-ray Scattering techniques. We also analyzed the interaction of JBU with giant unilamellar vesicles (GUVs) using Fluorescence Microscopy. The interaction of vesicles with JBU led to a slight reduction of hydrodynamic radius, and caused an increase in the lamellar repeat distance of PML, suggesting a membrane disordering effect. In contrast, Jaburetox-2Ec decreased the lamellar repeat distance of PML membranes, while also diminishing their hydrodynamic radius. Fluorescence microscopy showed that the interaction of GUVs with JBU caused membrane perturbation with formation of tethers. In conclusion, JBU can interact with PML, probably by inserting its Jaburetox "domain" into the PML external membrane. Additionally, the interaction of Jaburetox-2Ec affects the vesicle's internal bilayers and hence causes more drastic changes in the PML membrane organization in comparison with JBU. PMID:27281243

  5. Evaluation of intensity and energy interaction parameters for the complexation of Pr(III) with selected nucleoside and nucleotide through absorption spectral studies.

    PubMed

    Bendangsenla, N; Moaienla, T; David Singh, Th; Sumitra, Ch; Rajmuhon Singh, N; Indira Devi, M

    2013-02-15

    The interactions of Pr(III) with nucleosides and nucleotides have been studied in different organic solvents employing absorption difference and comparative absorption spectrophotometry. The magnitudes of the variations in both energy and intensity interaction parameters were used to explore the degree of outer and inner sphere co-ordination, incidence of covalency and the extent of metal 4f-orbital involvement in chemical bonding. Various electronic spectral parameters like Slater-Condon (F(k)), Racah (E(k)), Lande parameter (ξ(4f)), Nephelauxatic ratio (β), bonding (b(1/2)), percentage covalency (δ) and intensity parameters like oscillator strength (P) and Judd Ofelt electronic dipole intensity parameter (T(λ), λ=2,4,6) have been evaluated. The variation of these evaluated parameters were employed to interpret the nature of binding of Pr(III) with different ligands i.e. Adenosine/ATP in presence and absence of Ca(2+).

  6. Effect of biologically active substances derived from hydrobionts of the Pacific Ocean on parameters of lipid metabolism during experimental hypercholesterolemia.

    PubMed

    Kuznetsova, T A; Kryzhanovskii, S P; Bogdanovich, L N; Besednova, N N

    2014-12-01

    We studied the effect of biologically active substances derived from hydrobionts, namely maristim (natural product from sea urchin roe) and fucolam (polysaccharides of fucoidan and calcium alginate from brown algae) on blood biochemistry in the mouse model of nutritional hypercholesterolemia. Maristim and fucolam are found to be capable to normalize the levels of the major indicators of lipid and carbohydrate metabolism and aminotransferase enzyme activity in terms of atherogenic load. Correction action of biologically active substances is more expressed in combined application. Identified experimentally normalizing effects of maristim and on lipid and carbohydrate metabolism allow us to recommend the further study in clinical trials of these biologically active substances and based on them additives. PMID:25430644

  7. OPACOS: OVRO POST-AGB CO (1-0) EMISSION SURVEY. I. DATA AND DERIVED NEBULAR PARAMETERS

    SciTech Connect

    Sanchez Contreras, C.; Sahai, R.

    2012-11-15

    We have performed interferometric observations of the {sup 12}CO (J = 1-0) emission in a sample of 27 objects spanning different evolutionary stages from the late asymptotic giant branch (late-AGB), through the post-AGB (pAGB) phase, and to the planetary nebula (PN) stage, but dominated by pAGB objects and young PNs ({>=}81%). In this paper (the first in a series) we present our maps and main nebular properties derived for the whole sample. Observations were performed with the Caltech Millimeter Array at the Owens Valley Radio Observatory. The angular resolution obtained in our survey ranges between 2.''3 and 10.''7. The {sup 13}CO and C{sup 18}O (J = 1-0) transitions as well as the 2.6 mm continuum emission have also been observed in several objects. The detection statistics in the {sup 12}CO, {sup 13}CO, C{sup 18}O transitions and 2.6 mm continuum are 89%, 83%, 0%, and 37%, respectively. We report first detections of {sup 12}CO (J = 1-0) emission in 13 targets and confirm emission from several previous marginal detections. The molecular envelope probed by {sup 12}CO (J = 1-0) emission is extended for 18 (out of 24) sources; envelope asymmetries and/or velocity gradients are found in most extended objects. Our data have been used to derive accurate target coordinates and systemic velocities and to characterize the envelope size, morphology, and kinematics. We also provide an estimate of the total molecular mass and the fraction of it contained in fast flows, lower limits to the linear momentum and to the isotopic {sup 12}C/{sup 13}C ratio, as well as the AGB mass-loss rate and timescale for sources with extended CO emission.

  8. Derivation of Structure Parameters of Temperature and Humidity in the Convective Boundary Layer from Large-Eddy Simulations and Implications for the Interpretation of Scintillometer Observations

    NASA Astrophysics Data System (ADS)

    Maronga, Björn; Moene, Arnold F.; van Dinther, Daniëlle; Raasch, Siegfried; Bosveld, Fred C.; Gioli, Beniamino

    2013-07-01

    We derive the turbulent structure parameters of temperature CT^2 and humidity C_q^2 from high-resolution large-eddy simulations (LES) of a homogeneously-heated convective boundary layer. Boundary conditions and model forcing were derived from measurements at Cabauw in The Netherlands. Three different methods to obtain the structure-parameters from LES are investigated. The shape of the vertical structure-parameter profiles from all three methods compare well with former experimental and LES results. Depending on the method, deviations in the magnitude up to a factor of two are found and traced back to the effects of discretization and numerical dissipation of the advection scheme. Furthermore, we validate the LES data with airborne and large-aperture scintillometer (LAS) measurements at Cabauw. Virtual path measurements are used to study the variability of CT^2 in the mixed layer and surface layer and its implications for airborne and LAS measurements. A high variability of CT^2 along a given horizontal path in the LES data is associated with plumes (high values) and downdrafts (low values). The path average of CT^2 varies rapidly in time due to the limited path length. The LES results suggest that measured path averages require sufficient temporal averaging and an adequate ratio of path length to height above the ground for the LAS in order to approach the domain average of CT^2.

  9. Quantitative analysis of the interaction between l-methionine derivative and oligonucleotides.

    PubMed

    Mota, Élia; Sousa, Fani; Queiroz, João A; Cruz, Carla

    2015-04-01

    This study explores the use of l-methionine derivative as a potential affinity ligand for nucleic acids purification. The l-methionine derivative is synthesized by activation of the carboxylic acid group with 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide/N-hydroxysuccinimide follow by immobilization on amine sensor surface, previously activated and treated with ethylenediamine. Their affinity towards oligonucleotides has been determined by surface plasmon resonance biosensor. The highest affinity is found for cytosine and thymine, followed by adenine, whereas the lowest affinity is found for guanine. For hetero-oligonucleotides the affinity order is CCCTTT > CCCAAA ≈ AAATTT > GGGTTT, showing that nucleotides with cytosine have the highest affinity, and the presence of guanine reduces the affinity, corroborating with the results obtained with homo-oligonucleotides.

  10. Polycationic pillar[5]arene derivatives: interaction with DNA and biological applications.

    PubMed

    Nierengarten, Iwona; Nothisen, Marc; Sigwalt, David; Biellmann, Thomas; Holler, Michel; Remy, Jean-Serge; Nierengarten, Jean-François

    2013-12-16

    Dendritic pillar[5]arene derivatives have been efficiently prepared by grafting dendrons with peripheral Boc-protected amine subunits onto a preconstructed pillar[5]arene scaffold. Upon cleavage of the Boc-protected groups, water-soluble pillar[5]arene derivatives with 20 (13) and 40 (14) peripheral ammonium groups have been obtained. The capability of these compounds to form stable nanoparticles with plasmid DNA has been demonstrated by gel electrophoresis, transmission electron microscopy (TEM), and dynamic light scattering (DLS) investigations. Transfection efficiencies of the self-assembled 13/pCMV-Luc and 14/pCMV-Luc polyplexes have been evaluated in vitro with HeLa cells. The transfection efficiencies found for both compounds are good, and pillar[5]arenes 13 and 14 show very low toxicity if any.

  11. Trace metals, melanin-based pigmentation and their interaction influence immune parameters in feral pigeons (Columba livia).

    PubMed

    Chatelain, M; Gasparini, J; Frantz, A

    2016-04-01

    Understanding the effects of trace metals emitted by anthropogenic activities on wildlife is of great concern in urban ecology; yet, information on how they affect individuals, populations, communities and ecosystems remains scarce. In particular, trace metals may impact survival by altering the immune system response to parasites. Plumage melanin is assumed to influence the effects of trace metals on immunity owing to its ability to bind metal ions in feathers and its synthesis being coded by a pleiotropic gene. We thus hypothesized that trace metal exposure would interact with plumage colouration in shaping immune response. We experimentally investigated the interactive effect between exposure to an environmentally relevant range of zinc and/or lead and melanin-based plumage colouration on components of the immune system in feral pigeons (Columba livia). We found that zinc increased anti-keyhole limpet hemocyanin (KLH) IgY primary response maintenance, buffered the negative effect of lead on anti-KLH IgY secondary response maintenance and tended to increase T-cell mediated phytohaemagglutinin (PHA) skin response. Lead decreased the peak of the anti-KLH IgY secondary response. In addition, pheomelanic pigeons exhibited a higher secondary anti-KLH IgY response than did eumelanic ones. Finally, T-cell mediated PHA skin response decreased with increasing plumage eumelanin level of birds exposed to lead. Neither treatments nor plumage colouration correlated with endoparasite intensity. Overall, our study points out the effects of trace metals on some parameters of birds' immunity, independently from other confounding urbanization factors, and underlines the need to investigate their impacts on other life history traits and their consequences in the ecology and evolution of host-parasite interactions.

  12. Interaction of fluorescently labeled triethyleneglycol and peptide derivatives with β-cyclodextrin.

    PubMed

    Alouini, Mohamed-Anis; Moustoifa, El-Farouck; Rubio-Albenque, Sandra; Berthelot, Thomas; Fery-Forgues, Suzanne; Déléris, Gérard

    2014-02-24

    A triethyleneglycol (TEG) chain, a linear peptide, and a cyclic peptide labeled with 7-methoxycoumarin-3-carboxylic acid (MC) and 7-diethylaminocoumarin-3-carboxylic acid (DAC) were used to thoroughly study Förster resonance energy transfer (FRET) in inclusion complexes. (1) H NMR evidence was given for the formation of a 1:1 inclusion complex between β-cyclodextrin (β-CD) and the fluorophore moieties of model compounds. The binding constant was 20 times higher for DAC than for MC derivatives. Molecular modeling provided additional information. The UV/Vis absorption and fluorescence properties were studied and the energy transfer process was quantified. Fluorescence quenching was particularly strong for the peptide derivatives. The presence of β-CDs reduced the FRET efficiency slightly. Dye-labeled peptide derivatives can thus be used to form inclusion complexes with β-CDs and retain most of their FRET properties. This paves the way for their subsequent use in analytical devices that are designed to measure the activity of matrix metalloproteinases.

  13. Hill Interaction Matrix (HIM): The Conceptual Framework, Derived Rating Scales, and an Updated Bibliography

    ERIC Educational Resources Information Center

    Hill, W. Fawcett

    1977-01-01

    Essentially, the HIM is a systematic set of categories developed for use in understanding and classifying interaction in small groups, especially therapy groups. It has, however, been used not only on T-groups, encounter groups, discussion groups, and such, but also on individual and dyadic counseling sessions. (Author)

  14. Training and Deriving Precalculus Relations: A Small-Group, Web-Interactive Approach

    ERIC Educational Resources Information Center

    McGinty, Jenny; Ninness, Chris; McCuller, Glen; Rumph, Robin; Goodwin, Andrea; Kelso, Ginger; Lopez, Angie; Kelly, Elizabeth

    2012-01-01

    A small-group, web-interactive approach to teaching precalculus concepts was investigated. Following an online pretest, 3 participants were given a brief (15 min) presentation on the details of reciprocal math relations and how they operate on the coordinate axes. During baseline, participants were tested regarding their ability to construct…

  15. Do osteopathic physicians differ in patient interaction from allopathic physicians? An empirically derived approach.

    PubMed

    Carey, Timothy S; Motyka, Thomas M; Garrett, Joanne M; Keller, Robert B

    2003-07-01

    Colleges of osteopathic medicine teach osteopathic principles, which provide a different approach to and interaction with patients than principles taught in allopathic medical schools. The authors examined whether osteopathic primary care physicians' interactions with patients reflect the principles of osteopathic medicine when compared with allopathic physicians' interactions. The principles of osteopathic medicine were adapted to elements that could be measured from an audio recording. This 26-item index was refined with two focus groups of practicing osteopathic physicians. Fifty-four patient visits to 11 osteopathic and 7 allopathic primary care physicians in Maine for screening physicals, headache, low back pain, and hypertension were recorded on audiotape and were dual-abstracted. When the 26-item index of osteopathic principles was summed, the osteopathic physicians had consistently higher scores (11 vs. 6.9; P = .01) than allopathic physicians, and visit length was similar (22 minutes vs. 20 minutes, respectively). Twenty-three of the 26 items were used more commonly by the osteopathic physicians. Osteopathic physicians were more likely than allopathic physicians to use patients' first names; explain etiologic factors to patients; and discuss social, family, and emotional impact of illnesses. In this study, osteopathic physicians were easily distinguishable from allopathic physicians by their verbal interactions with patients. Future studies should replicate this finding as well as determine whether it correlates with patient outcomes and satisfaction.

  16. Derivation of stellar parameters from Gaia RVS spectra with prediction uncertainty using Generative Artificial Neural Networks (GANNs)

    NASA Astrophysics Data System (ADS)

    Manteiga, Minia; Dafonte, Jose Carlos; Ulla, Ana; Alvarez, Marco Antonio; Garabato, Daniel; Fustes, Diego

    2015-08-01

    The main purpose of Gaia Radial Velocity Spectrograph (RVS) is to measure the radial velocity of stars in the near infrared CaII spectral region. However, RVS will be used also for estimating the main stellar astrophysical parameters: effective temperature (Teff), logarithm of surface gravity (logg), abundance of metal elements with respect to hydrogen ([Fe/H]) and abundance of alpha elements with respect to iron ([α/Fe]). The software package being developed by Gaia DPAC (Data Processing and Analysis Consorcium) is composed by a bunch of modules which address the problem of parameterization from different perspectives This work focuses on developments carried out in the framework of one of these modules, called ANN, that is based on the application of Artificial Neural Networks.ANNs are a great tool that offers non-linear regression capabilities to any degree of complexity. Furthermore, they can provide accurate predictions when new data is presented to them, since they can generalize their solutions. However, in principle, ANNs are not able to give a measure of uncertainty over their predictions. Giving a measure of uncertainty over predictions is desirable in application domains where posterior inferences need to assess the quality of the predictions, especially when the behaviour of the system is not completely known. This is the case of data analysis coming from complex scientific missions like Gaia. This work presents a new architecture for ANNs, Generative ANNs (GANNs), that models the forward function instead of the inverse one. The advantage of forward modelling is that it estimates the actual observation, so that the fit between the estimated observation and the actual observation can be assessed, which allows for novelty detection, model evaluation and active learning. Furthermore, GANNs can be integrated in a Bayesian framework, which allows to estimate the full posterior distribution over the parameters of interest, to perform model comparisons, etc.

  17. Deriving Parameters of Topographic Diffusion and Incision Models by Simulating Space-Time Equivalent Valley Evolution with LiDAR DTM

    NASA Astrophysics Data System (ADS)

    Yeh, C.; Chan, Y.; Lin, M.

    2010-12-01

    Generally, the changes of landscapes are caused by interactions among many surface processes in a long time. According to previous studies in decades, some of the surface processes such as sediment transport and fluvial erosion effects dominate landform shapes. Those two effects of dominant surface processes can be represented by diffusion and incision models, which have been expressed by mathematical forms. In this study, we're going to combine these two models of which interactions are considered simultaneously to simulate the valley evolution on the tableland. The LiDAR DTM, possessing advantages of higher resolution and getting real terrain, help us observe fine surface features and infer spatial geometric variations, lateral slope and channel width changes, without collecting multi-period aerial photographs. In addition, we chose the Linkou Tableland in Taiwan as our study area because it has some characteristics such as flat terrain, horizontal and simple strata, and homogeneous composition of gravel to simplify assumptions in our model. The most important task in this study, however, is how to calibrate the parameters being included the model . These parameters, including diffusion coefficient (κ), erosion coefficient (λ), and two fitted parameters (m and n, related with drainage area and local slope respectively), usually imply essential information about landform evolution. Just like decoding the secrets of evolving processes, we'll probably deduce the generation time of valleys or estimate the surface erosion rate. Finally, we will discuss three conclusions in the end of this study: 1) The influence of interactions involving diffusion and incision effects. We also discuss the sensitivity of each numerical parameter. 2) Assessing the evolution time of valleys, even at the whole tableland, from mathematical modeling. 3) Estimating the erosion rate applied to engineering in gravel stratum.

  18. Ab initio calculation of the effective on-site Coulomb interaction parameters for half-metallic magnets

    NASA Astrophysics Data System (ADS)

    Şaşıoğlu, Ersoy; Galanakis, Iosif; Friedrich, Christoph; Blügel, Stefan

    2013-10-01

    Correlation effects play an important role in the electronic structure of half-metallic (HM) magnets. In particular, they give rise to nonquasiparticle states above (or below) the Fermi energy at finite temperatures that reduce the spin polarization and, as a consequence, the efficiency of spintronics devices. Employing the constrained random-phase approximation (cRPA) within the full-potential linearized augmented-plane-wave (FLAPW) method using maximally localized Wannier functions, we calculate the strength of the effective on-site Coulomb interaction (Hubbard U and Hund exchange J) between localized electrons in different classes of HM magnets considering: (i) sp-electron ferromagnets in rock-salt structure, (ii) zinc-blende 3d binary ferromagnets, as well as (iii) ferromagnetic and ferrimagnetic semi- and full-Heusler compounds. For HM sp-electron ferromagnets, the calculated Hubbard U parameters are between 2.7 and 3.9 eV, while for transition-metal-based HM compounds, they lie between 1.7 and 3.8 eV, being smallest for MnAs (Mn-3d orbitals) and largest for Cr2CoGa (Co-3d orbitals). For the HM full-Heusler compounds, the Hubbard U parameters are comparable to the ones in elementary 3d transition metals, while for semi-Heusler compounds, they are slightly smaller. We show that the increase of the Hubbard U with structural complexity, i.e., from MnAs to Cr2CoGa, stems from the screening of the p electrons of the nonmagnetic sp atoms. The p-electron screening turns out to be more efficient for MnAs than for Cr2CoGa. The calculated Hubbard U parameters for CrAs, NiMnSb, and Co2MnSi are about two times smaller than previous estimates based on the constrained local-density approximation (cLDA) method. Furthermore, the width of the correlated d or p bands of the studied compounds is usually smaller than the calculated Hubbard U parameters. Thus these HM magnets should be classified as weakly correlated materials.

  19. Distal radius strength: a comparison of DXA-derived vs pQCT-measured parameters in adolescent females.

    PubMed

    Dowthwaite, Jodi N; Hickman, Rebecca M; Kanaley, Jill A; Ploutz-Snyder, Robert J; Spadaro, Joseph A; Scerpella, Tamara A

    2009-01-01

    Although quantitative computed tomography (QCT) is considered the gold standard for in vivo densitometry, dual-energy X-ray absorptiometry (DXA) scans assess larger bone regions and are more appropriate for pediatric longitudinal studies. Unfortunately, DXA does not yield specific bone architectural output. To address this issue in healthy, postmenarcheal girls, Sievänen's distal radius formulae [1996] were applied to derive indices of bone geometry, volumetric bone mineral density (vBMD), and strength from DXA data; results were compared to peripheral quantitative computed tomography (pQCT) output. Contemporaneous scans were performed on the left, distal radii of 35 gymnasts, ex-gymnasts, and nongymnasts (aged 13.3-20.4 yr, mean 16.6 yr). For 4% and 33% regions, pQCT measured cross-sectional areas (CSAs) and vBMD; comparable DXA indices were generated at ultradistal and 1/3 regions. Index of structural strength in axial compression was calculated from 4% pQCT and DXA output for comparison; 33% pQCT strength-strain index was compared to 1/3 DXA section modulus. Sievänen DXA indices were significantly, positively correlated with pQCT output (R=+0.61 to +0.98; p<0.0001). At the distal radius, in healthy postmenarcheal girls, Sievänen's method yielded potentially useful DXA indices of diaphyseal cortical CSA and bone strength at both the diaphysis (section modulus) and the metaphysis (index of structural strength in axial compression).

  20. The 27-28 October 1986 FIRE IFO cirrus case study: Cirrus parameter relationships derived from satellite and lidar data

    NASA Technical Reports Server (NTRS)

    Minnis, Patrick; Young, David F.; Sassen, Kenneth; Alvarez, Joseph M.; Grund, Christian J.

    1989-01-01

    Cirrus cloud radiative and physical characteristics are determined using a combination of ground-based, aircraft, and satellite measurements taken as part of the First ISCCP Regional Experiment (FIRE) Cirrus Intensive Field Observations (IFO) during October and November 1986. Lidar backscatter data are used to define cloud base, center, and top heights and the corresponding temperatures. Coincident GOES 4 km visible (0.65 microns) and 8 km infrared window (11.5 microns) radiances are analyzed to determine cloud emittances and reflectances. Infrared optical depth is computed from the emittance results. Visible optical depth is derived from reflectance using a theoretical ice crystal scattering model and an empirical bidirectional reflectance mode. No clouds with visible optical depths greater than 5 or infrared optical depths less than 0.1 were used in the analysis. Average cloud thickness ranged from 0.5 km to 8 km for the 71 scenes. An average visible scattering efficiency of 2.1 was found for this data set. The results reveal a significant dependence of scattering efficiency on cloud temperature.

  1. Assessment of oxidative stress parameters of brain-derived neurotrophic factor heterozygous mice in acute stress model

    PubMed Central

    Hacioglu, Gulay; Senturk, Ayse; Ince, Imran; Alver, Ahmet

    2016-01-01

    Objective(s): Exposing to stress may be associated with increased production of reactive oxygen species (ROS). Therefore, high level of oxidative stress may eventually give rise to accumulation of oxidative damage and development of numerous neurodegenerative diseases. It has been presented that brain-derived neurotrophic factor (BDNF) supports neurons against various neurodegenerative conditions. Lately, there has been growing evidence that changes in the cerebral neurotrophic support and especially in the BDNF expression and its engagement with ROS might be important in various disorders and neurodegenerative diseases. Hence, we aimed to investigate protective effects of BDNF against stress-induced oxidative damage. Materials and Methods: Five- to six-month-old male wild-type and BDNF knock-down mice were used in this study. Activities of catalase (CAT) and superoxide dismutase (SOD) enzymes, and the amount of malondialdehyde (MDA) were assessed in the cerebral homogenates of studied groups in response to acute restraint stress. Results: Exposing to acute physiological stress led to significant elevation in the markers of oxidative stress in the cerebral cortexes of experimental groups. Conclusion: As BDNF-deficient mice were observed to be more susceptible to stress-induced oxidative damage, it can be suggested that there is a direct interplay between oxidative stress indicators and BDNF levels in the brain. PMID:27279982

  2. Scattering parameters for cold Li-Rb and Na-Rb collisions derived from variable phase theory

    SciTech Connect

    Ouerdane, H.; Jamieson, M.J.

    2004-08-01

    We show how the scattering phase shift, the s-wave scattering length, and the p-wave scattering volume can be obtained from Riccati equations derived in variable phase theory. We find general expressions that provide upper and lower bounds for the scattering length and the scattering volume. We show how, in the framework of the variable phase method, Levinson's theorem yields the number of bound states supported by a potential. We report results from a study of the heteronuclear alkali-metal dimers NaRb and LiRb. We consider ab initio molecular potentials for the X {sup 1}{sigma}{sup +} and a {sup 3}{sigma}{sup +} states of both dimers and compare and discuss results obtained from experimentally based X {sup 1}{sigma}{sup +} and a {sup 3}{sigma}{sup +} potentials of NaRb. We explore the mass dependence of the scattering data by considering all isotopomers and we calculate the numbers of bound states supported by the molecular potentials for each isotopomer.

  3. Unification of dynamic density functional theory for colloidal fluids to include inertia and hydrodynamic interactions: derivation and numerical experiments.

    PubMed

    Goddard, B D; Nold, A; Savva, N; Yatsyshin, P; Kalliadasis, S

    2013-01-23

    Starting from the Kramers equation for the phase-space dynamics of the N-body probability distribution, we derive a dynamical density functional theory (DDFT) for colloidal fluids including the effects of inertia and hydrodynamic interactions (HI). We compare the resulting theory to extensive Langevin dynamics simulations for both hard rod systems and three-dimensional hard sphere systems with radially symmetric external potentials. As well as demonstrating the accuracy of the new DDFT, by comparing with previous DDFTs which neglect inertia, HI, or both, we also scrutinize the significance of including these effects. Close to local equilibrium we derive a continuum equation from the microscopic dynamics which is a generalized Navier-Stokes-like equation with additional non-local terms governing the effects of HI. For the overdamped limit we recover analogues of existing configuration-space DDFTs but with a novel diffusion tensor. PMID:23220969

  4. Formation of intermolecular crosslinks by the actinocin derivatives with DNA in interaction under conditions of semidilute solution

    NASA Astrophysics Data System (ADS)

    Osinnikova, D. N.; Moroshkina, E. B.

    2014-12-01

    Interaction of native calf thymus DNA (ctDNA) with the actinocin derivatives containing protonated diethylamino groups, dimethylamino groups and unsubstituted amino groups and having different length of the alkyl chain have been studied by the method of viscometry. An anomalous hydrodynamic behavior of solutions of DNA with very low amount of ligands prepared under conditions of semidilute solution was revealed. We assumed that such an anomalous behavior of solutions of DNA complexes with actinocin derivatives associated with the formation of intermolecular crosslinks while the preparation of the complex was in terms of overlapping of macromolecular coils in solution. Comparative study of the hydrodynamic behavior of the DNA complexes with various actinocin structures lead us to the conclusion of the formation of crosslinks by the compounds containing protonated diethylamino groups.

  5. nd Scattering Observables Derived from the Quark-Model Baryon-Baryon Interaction

    SciTech Connect

    Fujiwara, Y.; Fukukawa, K.

    2010-05-12

    We solve the nd scattering in the Faddeev formalism, employing the NN sector of the quark-model baryon-baryon interaction fss2. The energy-dependence of the NN interaction, inherent to the (3q)-(3q) resonating-group formulation, is eliminated by the standard off-shell transformation utilizing the 1/sq root(N) factor, where N is the normalization kernel for the (3q)-(3q) system. This procedure yields an extra nonlocality, whose effect is very important to reproduce all the scattering observables below E{sub n}<=65 MeV. The different off-shell properties from the standard meson-exchange potentials, related to the non-locality of the quark-exchange kernel, yields appreciable effects to the differential cross sections and polarization observables of the nd elastic scattering, which are usually attributed to the specific properties of three-body forces.

  6. Interface contributions to the spin-orbit interaction parameters of electrons at the (001) GaAs/AlGaAs interface

    NASA Astrophysics Data System (ADS)

    Devizorova, Zh. A.; Shchepetilnikov, A. V.; Nefyodov, Yu. A.; Volkov, V. A.; Kukushkin, I. V.

    2014-09-01

    One-body mechanisms of spin splitting of the energy spectrum of 2D electrons in a one-side doped (001) GaAs/Al x Ga1 - x As quantum well have been studied theoretically and experimentally. The interfacial spin splitting has been shown to compensate (enhance) considerably the contribution of the bulk Dresselhaus (Bychkov-Rashba) mechanism. The theoretical approach is based on the solution of the effective mass equation in a quasi-triangular well supplemented by a new boundary condition at a high and atomically sharp hetero-barrier. The model takes into account the spin-orbit interaction of electrons with both bulk and interfacial crystal potential having C 2 v symmetry, as well as the lack of inversion symmetry and nonparabolicity of the conduction band in GaAs. The effective 2D spin Hamiltonian including both bulk and interface contributions to the Dresselhaus (αBIA) and Rashba (αSIA) constants has been derived. The analytical relation between these constants and the components of the anisotropic nonlinear g-factor tensor in an oblique quantizing magnetic field has been found. The experimental approach is based, on one hand, on the detection of electron spin resonance in the microwave range and, on the other hand, on photoluminescence measurements of the nonparabolicity parameter. The interface contributions to αBIA and αSIA have been found from comparison with the theory.

  7. Novel surface-based methodologies for investigating GH11 xylanase-lignin derivative interactions.

    PubMed

    Zeder-Lutz, G; Renau-Ferrer, S; Aguié-Béghin, V; Rakotoarivonina, H; Chabbert, B; Altschuh, D; Rémond, C

    2013-11-21

    The recalcitrance of lignocellulose to bioprocessing represents the core problem and remains the limiting factor in creating an economy based on lignocellulosic ethanol production. Lignin is responsible for unproductive interactions with enzymes, and understanding how lignin impairs the susceptibility of biomass to enzymatic hydrolysis represents a significant aim in optimising the biological deconstruction of lignocellulose. The objective of this study was to develop methodologies based on surface plasmon resonance (SPR), which provide novel insights into the interactions between xylanase (Tx-xyn11) and phenolic compounds or lignin oligomers. In a first approach, Tx-xyn11 was fixed onto sensor surfaces, and phenolic molecules were applied in the liquid phase. The results demonstrated weak affinity and over-stoichiometric binding, as several phenolic molecules bound to each xylanase molecule. This approach, requiring the use of soluble molecules in the liquid phase, is not applicable to insoluble lignin oligomers, such as the dehydrogenation polymer (DHP). An alternative approach was developed in which a lignin oligomer was fixed onto a sensor surface. Due to their hydrophobic properties, the preparation of stable lignin layers on the sensor surfaces represented a considerable challenge. Among the various chemical and physico-chemical approaches assayed, two approaches (physisorption via the Langmuir-Blodgett technique onto self-assembled monolayer (SAM)-modified gold and covalent coupling to a carboxylated dextran matrix) led to stable lignin layers, which allowed the study of its interactions with Tx-xyn11 in the liquid phase. Our results indicated the presence of weak and non-specific interactions between Tx-xyn11 and DHP. PMID:24071685

  8. Host-microbial interactions in the metabolism of therapeutic and diet-derived xenobiotics

    PubMed Central

    Carmody, Rachel N.; Turnbaugh, Peter J.

    2014-01-01

    Our associated microbial communities play a critical role in human health and predisposition to disease, but the degree to which they also shape therapeutic interventions is not well understood. Here, we integrate results from classic and current studies of the direct and indirect impacts of the gut microbiome on the metabolism of therapeutic drugs and diet-derived bioactive compounds. We pay particular attention to microbial influences on host responses to xenobiotics, adding to the growing consensus that treatment outcomes reflect our intimate partnership with the microbial world, and providing an initial framework from which to consider a more comprehensive view of pharmacology and nutrition. PMID:25105361

  9. Intermolecular interactions in multi-component crystals of acridinone/thioacridinone derivatives: Structural and energetics investigations

    NASA Astrophysics Data System (ADS)

    Wera, Michał; Storoniak, Piotr; Trzybiński, Damian; Zadykowicz, Beata

    2016-12-01

    A single crystal X-ray analysis of two multi-component crystals consisting of an acridinone/thioacridinone moiety and a solvent moiety - water and ammonia (1 and 2), respectively, was carried out to determine the crystal structures of obtained crystals. A theoretical approach was undertaken - using the DFT method, lattice energies calculations and Hirshfeld surfaces (HS) - to qualitatively and quantitatively assess the intermolecular interactions within the crystal. HS analysis was showed that the H⋯H, C⋯H/H⋯C and C⋯C contacts for both structures (altogether 81.6% of total Hirshfeld surface area for 1 and 79.3% for 2) and the O⋯H/H⋯O (14.3%) for 1 and the S⋯H/H⋯S (15.2%) contacts for 2 were the characteristic intermolecular contacts in the related crystal structures. Using a computational methods were confirmed that the main contribution to the stabilization of the crystal lattice of compound 1 comes from the Coulombic interactions, whereas in compound 2 electrostatic and van der Waals appear to have similar contribution to the crystal lattice energy. Theoretical calculations of the investigated compounds have also allowed to determine the energy of a single specific intermolecular interaction.

  10. Genome-wide genetic interaction analysis of glaucoma using expert knowledge derived from human phenotype networks.

    PubMed

    Hu, Ting; Darabos, Christian; Cricco, Maria E; Kong, Emily; Moore, Jason H

    2015-01-01

    The large volume of GWAS data poses great computational challenges for analyzing genetic interactions associated with common human diseases. We propose a computational framework for characterizing epistatic interactions among large sets of genetic attributes in GWAS data. We build the human phenotype network (HPN) and focus around a disease of interest. In this study, we use the GLAUGEN glaucoma GWAS dataset and apply the HPN as a biological knowledge-based filter to prioritize genetic variants. Then, we use the statistical epistasis network (SEN) to identify a significant connected network of pairwise epistatic interactions among the prioritized SNPs. These clearly highlight the complex genetic basis of glaucoma. Furthermore, we identify key SNPs by quantifying structural network characteristics. Through functional annotation of these key SNPs using Biofilter, a software accessing multiple publicly available human genetic data sources, we find supporting biomedical evidences linking glaucoma to an array of genetic diseases, proving our concept. We conclude by suggesting hypotheses for a better understanding of the disease.

  11. Synergy between optical and microwave remote sensing to derive soil and vegetation parameters from MAC Europe 1991 Experiment

    NASA Technical Reports Server (NTRS)

    Taconet, O.; Benallegue, M.; Vidal, A.; Vidal-Madjar, D.; Prevot, L.; Normand, M.

    1993-01-01

    The ability of remote sensing for monitoring vegetation density and soil moisture for agricultural applications is extensively studied. In optical bands, vegetation indices (NDVI, WDVI) in visible and near infrared reflectances are related to biophysical quantities as the leaf area index, the biomass. In active microwave bands, the quantitative assessment of crop parameters and soil moisture over agricultural areas by radar multiconfiguration algorithms remains prospective. Furthermore the main results are mostly validated on small test sites, but have still to be demonstrated in an operational way at a regional scale. In this study, a large data set of radar backscattering has been achieved at a regional scale on a French pilot watershed, the Orgeval, along two growing seasons in 1988 and 1989 (mainly wheat and corn). The radar backscattering was provided by the airborne scatterometer ERASME, designed at CRPE, (C and X bands and HH and VV polarizations). Empirical relationships to estimate water crop and soil moisture over wheat in CHH band under actual field conditions and at a watershed scale are investigated. Therefore, the algorithms developed in CHH band are applied for mapping the surface conditions over wheat fields using the AIRSAR and TMS images collected during the MAC EUROPE 1991 experiment. The synergy between optical and microwave bands is analyzed.

  12. Determination of the parameters of binding between lipopolysaccharide and chitosan and its N-acetylated derivative using a gravimetric piezoquartz biosensor.

    PubMed

    Naberezhnykh, G A; Gorbach, V I; Kalmykova, E N; Solov'eva, T F

    2015-03-01

    The interaction of endotoxin (lipopolysaccharide - LPS) with low molecular weight chitosan (5.5 kDa), its N-acylated derivative and chitoliposomes was studied using a gravimetric piezoelectric quartz crystal microbalance biosensor. The optimal conditions for the formation of a biolayer based on immobilized LPS on the resonator surface and its regeneration were elaborated. The association and dissociation rate constants for LPS binding to chitosans were determined and the affinity constants (Kaf) were calculated based on the data on changes in the oscillation frequency of the quartz crystal resonator. The Kaf values correlated with the ones obtained using other methods. The affinity of N-acylated chitosan binding to LPS was higher than that of the parent chitosan binding to LPS. Based on the results obtained, we suggest that water-soluble N-acylated derivatives of chitosan with low degree of substitution of amino groups could be useful compounds for endotoxin binding and neutralization. PMID:25637889

  13. Thermodynamics of interaction and structure of DNA complexes with phenacylimidazo[5,1-a]isoquinoline derivatives

    NASA Astrophysics Data System (ADS)

    Osinnikova, D. N.; Moroshkina, E. B.; Glushkina, D. M.

    2015-12-01

    Interaction of native calf thymus DNA (ctDNA) with phenacylimidazo[5,1- a]isoquinoline derivatives was studied by the methods of spectrophotometry, viscometry, isothermal titration calorimetry (ITC) and dynamic birefringence. It was found that both of investigated compounds form complexes with the DNA molecule, the structure of compounds affects the mode of binding these ligands to DNA. The primary binding mode can not be described by the classical models of groove binding or intercalation. It has been suggested that the primary mode of binding is "partial intercalation".

  14. Repeated forced swimming impairs prepulse inhibition and alters brain-derived neurotrophic factor and astroglial parameters in rats.

    PubMed

    Borsoi, Milene; Antonio, Camila Boque; Müller, Liz Girardi; Viana, Alice Fialho; Hertzfeldt, Vivian; Lunardi, Paula Santana; Zanotto, Caroline; Nardin, Patrícia; Ravazzolo, Ana Paula; Rates, Stela Maris Kuze; Gonçalves, Carlos-Alberto

    2015-01-01

    Glutamate perturbations and altered neurotrophin levels have been strongly associated with the neurobiology of neuropsychiatric disorders. Environmental stress is a risk factor for mood disorders, disrupting glutamatergic activity in astrocytes in addition to cognitive behaviours. Despite the negative impact of stress-induced neuropsychiatric disorders on public health, the molecular mechanisms underlying the response of the brain to stress has yet to be fully elucidated. Exposure to repeated swimming has proven useful for evaluating the loss of cognitive function after pharmacological and behavioural interventions, but its effect on glutamate function has yet to be fully explored. In the present study, rats previously exposed to repeated forced swimming were evaluated using the novel object recognition test, object location test and prepulse inhibition (PPI) test. In addition, quantification of brain-derived neurotrophic factor (BDNF) mRNA expression and protein levels, glutamate uptake, glutathione, S100B, GluN1 subunit of N-methyl-D-aspartate receptor and calmodulin were evaluated in the frontal cortex and hippocampus after various swimming time points. We found that swimming stress selectively impaired PPI but did not affect memory recognition. Swimming stress altered the frontal cortical and hippocampal BDNF expression and the activity of hippocampal astrocytes by reducing hippocampal glutamate uptake and enhancing glutathione content in a time-dependent manner. In conclusion, these data support the assumption that astrocytes may regulate the activity of brain structures related to cognition in a manner that alters complex behaviours. Moreover, they provide new insight regarding the dynamics immediately after an aversive experience, such as after behavioural despair induction, and suggest that forced swimming can be employed to study altered glutamatergic activity and PPI disruption in rodents. PMID:25444867

  15. Repeated forced swimming impairs prepulse inhibition and alters brain-derived neurotrophic factor and astroglial parameters in rats.

    PubMed

    Borsoi, Milene; Antonio, Camila Boque; Müller, Liz Girardi; Viana, Alice Fialho; Hertzfeldt, Vivian; Lunardi, Paula Santana; Zanotto, Caroline; Nardin, Patrícia; Ravazzolo, Ana Paula; Rates, Stela Maris Kuze; Gonçalves, Carlos-Alberto

    2015-01-01

    Glutamate perturbations and altered neurotrophin levels have been strongly associated with the neurobiology of neuropsychiatric disorders. Environmental stress is a risk factor for mood disorders, disrupting glutamatergic activity in astrocytes in addition to cognitive behaviours. Despite the negative impact of stress-induced neuropsychiatric disorders on public health, the molecular mechanisms underlying the response of the brain to stress has yet to be fully elucidated. Exposure to repeated swimming has proven useful for evaluating the loss of cognitive function after pharmacological and behavioural interventions, but its effect on glutamate function has yet to be fully explored. In the present study, rats previously exposed to repeated forced swimming were evaluated using the novel object recognition test, object location test and prepulse inhibition (PPI) test. In addition, quantification of brain-derived neurotrophic factor (BDNF) mRNA expression and protein levels, glutamate uptake, glutathione, S100B, GluN1 subunit of N-methyl-D-aspartate receptor and calmodulin were evaluated in the frontal cortex and hippocampus after various swimming time points. We found that swimming stress selectively impaired PPI but did not affect memory recognition. Swimming stress altered the frontal cortical and hippocampal BDNF expression and the activity of hippocampal astrocytes by reducing hippocampal glutamate uptake and enhancing glutathione content in a time-dependent manner. In conclusion, these data support the assumption that astrocytes may regulate the activity of brain structures related to cognition in a manner that alters complex behaviours. Moreover, they provide new insight regarding the dynamics immediately after an aversive experience, such as after behavioural despair induction, and suggest that forced swimming can be employed to study altered glutamatergic activity and PPI disruption in rodents.

  16. Analytic first derivatives of floating occupation molecular orbital-complete active space configuration interaction on graphical processing units.

    PubMed

    Hohenstein, Edward G; Bouduban, Marine E F; Song, Chenchen; Luehr, Nathan; Ufimtsev, Ivan S; Martínez, Todd J

    2015-07-01

    The floating occupation molecular orbital-complete active space configuration interaction (FOMO-CASCI) method is a promising alternative to the state-averaged complete active space self-consistent field (SA-CASSCF) method. We have formulated the analytic first derivative of FOMO-CASCI in a manner that is well-suited for a highly efficient implementation using graphical processing units (GPUs). Using this implementation, we demonstrate that FOMO-CASCI gradients are of similar computational expense to configuration interaction singles (CIS) or time-dependent density functional theory (TDDFT). In contrast to CIS and TDDFT, FOMO-CASCI can describe multireference character of the electronic wavefunction. We show that FOMO-CASCI compares very favorably to SA-CASSCF in its ability to describe molecular geometries and potential energy surfaces around minimum energy conical intersections. Finally, we apply FOMO-CASCI to the excited state hydrogen transfer reaction in methyl salicylate. PMID:26156469

  17. Analytic first derivatives of floating occupation molecular orbital-complete active space configuration interaction on graphical processing units.

    PubMed

    Hohenstein, Edward G; Bouduban, Marine E F; Song, Chenchen; Luehr, Nathan; Ufimtsev, Ivan S; Martínez, Todd J

    2015-07-01

    The floating occupation molecular orbital-complete active space configuration interaction (FOMO-CASCI) method is a promising alternative to the state-averaged complete active space self-consistent field (SA-CASSCF) method. We have formulated the analytic first derivative of FOMO-CASCI in a manner that is well-suited for a highly efficient implementation using graphical processing units (GPUs). Using this implementation, we demonstrate that FOMO-CASCI gradients are of similar computational expense to configuration interaction singles (CIS) or time-dependent density functional theory (TDDFT). In contrast to CIS and TDDFT, FOMO-CASCI can describe multireference character of the electronic wavefunction. We show that FOMO-CASCI compares very favorably to SA-CASSCF in its ability to describe molecular geometries and potential energy surfaces around minimum energy conical intersections. Finally, we apply FOMO-CASCI to the excited state hydrogen transfer reaction in methyl salicylate.

  18. Interaction of a new bis-indol derivative, KAR-2 with tubulin and its antimitotic activity

    PubMed Central

    Orosz, Ferenc; Kovács, János; Löw, Péter; Vértessy, Beáta G; Urbányi, Zoltán; Ács, Tibor; Keve, Tibor; Ovádi, Judit

    1997-01-01

    KAR-2 (3′'-(β-chloroethyl)-2′',4′'-dioxo-3,5′'-spiro-oxazolidino-4-deacetoxy-vinblastine), is a bis-indol derivative; catharantine is coupled with the vindoline moiety which contains a substituted oxazolidino group. Our binding studies showed that KAR-2 exhibited high affinity for bovine purified brain tubulin (Kd=3 μM) and it inhibited microtubule assembly at a concentration of 10 nM. Anti-microtubular activity of KAR-2 was highly dependent on the ultrastructure of microtubules: while the single tubules were sensitive, the tubules cross-linked by phosphofructokinase (ATP: D-fructose-6-phosphate-1-phosphotransferase, EC 2.7.1.11) exhibited significant resistance against KAR-2. The cytoplasmic microtubules of Chinese hamster ovary mammalian and Sf9 insect cells were damaged by 1 μg ml−1 KAR-2, as observed by indirect immunofluorescence and transmission electron microscopy. Scanning electron microscopy revealed intensive surface blebbing on both types of cells in the presence of KAR-2. KAR-2 was effective in the mouse leukaemia P338 test in vivo without significant toxicity. Studies on a primary cerebro-cortical culture of rat brain and differentiated PC12 cells indicated that the toxicity of KAR-2 was significantly lower than that of vinblastine. The additional property of KAR-2 that distinguishes it from bis-indol derivatives is the lack of anti-calmodulin activity. PMID:9222552

  19. Twenty-Two Years of Combined GPS Daily Coordinate Time Series and Derived Parameters: Implications for ITRF

    NASA Astrophysics Data System (ADS)

    Bock, Y.; Kedar, S.; Moore, A. W.; Fang, P.; Liu, Z.; Owen, S. E.; Squibb, M. B.

    2014-12-01

    The NASA-funded "Solid Earth Science ESDR System (SESES)" MEaSUREs project publishes long-term Earth Science Data Records (ESDRs), the result of a combined solution of independent daily JPL (GIPSY-OASIS software) and SIO (GAMIT software) GPS analyses, using a common source of metadata from the SOPAC database. The project has now produced up to twenty-two years of consistent, calibrated and validated ESDR products for over 3200 GPS stations from Western North America, other plate boundaries, and global networks made available through the GPS Explorer data portal and NASA's CDDIS archive. The combined solution of daily coordinate time series uses SOPAC h-files and JPL STACOV files as input to the st_filter software. The combined time series are then fit with the analyze_tseri software for daily positions/displacements, secular velocities, coseismic and postseismic displacements, as well as annual and semi-annual signatures and non-coseismic offsets due primarily to equipment (antenna) changes. Published uncertainties for the estimated parameters take into account temporal noise in the daily coordinate time series. The resulting residual coordinate time series with typical daily RMS values of 1.5-4.0 mm in the horizontal and 4.0-8.0 mm in the vertical can then can be mined for other signals such as transient deformation associated with earthquake tremor and slip (ETS) and hydrological effects. As part of this process we have catalogued and characterized coseismic displacements due to more than 80 earthquakes affecting over hundreds of regional and global stations, as well as significant postseismic deformation for the larger events. The larger events can affect stations 1000's of km from the earthquake epicenters and thus significantly affect the positions of stations used in defining the reference frame. We discuss the implications and contributions of our ongoing analysis to the long-term maintenance of the international terrestrial reference frame.

  20. Self-Assembly and Lipid Interactions of Diacylglycerol Lactone Derivatives Studied at the Air/Water Interface

    PubMed Central

    Philosof-Mazor, Liron; Volinsky, Roman; Comin, Maria J.; Lewin, Nancy E.; Kedei, Noemi; Blumberg, Peter M.; Marquez, Victor E.; Jelinek, Raz

    2009-01-01

    Synthetic diacylglycerol lactones (DAG-lactones) have been shown to be effective modulators of critical cellular signaling pathways. The biological activity of these amphiphilic molecules depends in part upon their lipid interactions within the cellular plasma membrane. This study explores the thermodynamic and structural features of DAG-lactone derivatives and their lipid interactions at the air/water interface. Surface-pressure/area isotherms and Brewster angle microscopy revealed the significance of specific side-groups attached to the terminus of a very rigid 4-(2-phenylethynyl) benzoyl chain of the DAG-lactones, which affected both the self-assembly of the molecules and their interactions with phospholipids. The experimental data highlight the formation of different phases within mixed DAG-lactone/phospholipid monolayers and underscore the relationship between the two components in binary mixtures of different mole ratios. Importantly, the results suggest that DAG-lactones are predominantly incorporated within fluid phospholipid phases rather than in the condensed phases that form, for example, by cholesterol. Moreover, the size and charge of the phospholipid headgroups do not seem to affect DAG-lactone interactions with lipids. PMID:18788772

  1. Potential-derived point-charge model study of electrostatic interaction energies in some hydrogen-bonded systems.

    PubMed

    Ray, N K; Shibata, M; Bolis, G; Rein, R

    1985-01-01

    Mulliken's atomic changes (MC) and potential derived (PD) point charges obtained from STO-3G wave functions are used to study the electrostatic interaction energies for a series of representative hydrogen-bonded complexes. The results of the above-mentioned models are compared with the more accurate results of segmental multipole moment (SMM) expansion, and it is shown that the PD model is superior to the MC model. The results of PD model are shown to be well correlated with the results of SMM expansion technique. Results of our calculations using 6-31G and 6-31G** PD charges are also reported here. Electrostatic interaction energies obtained using 6-31G** PD charges are compared with the 6-31G** SCF interaction energies available for the nine hydrogen-bonded dimers of ammonia, water, and hydrogen fluoride and a good correlation between the two is shown. The interrelationship between the results of different basis sets are also examined for the PD point-charge model. The electrostatic interaction energies obtained using STO-3G PD model are shown to be well correlated to the results of 6-31G and 6-31G** PD models.

  2. Inhibition of human aldehyde oxidase activity by diet-derived constituents: structural influence, enzyme-ligand interactions, and clinical relevance.

    PubMed

    Barr, John T; Jones, Jeffrey P; Oberlies, Nicholas H; Paine, Mary F

    2015-01-01

    The mechanistic understanding of interactions between diet-derived substances and conventional medications in humans is nascent. Most investigations have examined cytochrome P450-mediated interactions. Interactions mediated by other phase I enzymes are understudied. Aldehyde oxidase (AO) is a phase I hydroxylase that is gaining recognition in drug design and development programs. Taken together, a panel of structurally diverse phytoconstituents (n = 24) was screened for inhibitors of the AO-mediated oxidation of the probe substrate O(6)-benzylguanine. Based on the estimated IC50 (<100 μM), 17 constituents were advanced for Ki determination. Three constituents were described best by a competitive inhibition model, whereas 14 constituents were described best by a mixed-mode model. The latter model consists of two Ki terms, Kis and Kii, which ranged from 0.26-73 and 0.80-120 μM, respectively. Molecular modeling was used to glean mechanistic insight into AO inhibition. Docking studies indicated that the tested constituents bound within the AO active site and elucidated key enzyme-inhibitor interactions. Quantitative structure-activity relationship modeling identified three structural descriptors that correlated with inhibition potency (r(2) = 0.85), providing a framework for developing in silico models to predict the AO inhibitory activity of a xenobiotic based solely on chemical structure. Finally, a simple static model was used to assess potential clinically relevant AO-mediated dietary substance-drug interactions. Epicatechin gallate and epigallocatechin gallate, prominent constituents in green tea, were predicted to have moderate to high risk. Further characterization of this uncharted type of interaction is warranted, including dynamic modeling and, potentially, clinical evaluation. PMID:25326286

  3. Steric parameters, molecular modeling and hydropathic interaction analysis of the pharmacology of para-substituted methcathinone analogues

    PubMed Central

    Sakloth, F; Kolanos, R; Mosier, P D; Bonano, J S; Banks, M L; Partilla, J S; Baumann, M H; Negus, S S; Glennon, R A

    2015-01-01

    Background and Purpose There is growing concern over the abuse of certain psychostimulant methcathinone (MCAT) analogues. This study extends an initial quantitative structure–activity relationship (QSAR) investigation that demonstrated important steric considerations of seven 4- (or para-)substituted analogues of MCAT. Specifically, the steric character (Taft's steric ES) of the 4-position substituent affected in vitro potency to induce monoamine release via dopamine and 5-HT transporters (DAT and SERT) and in vivo modulation of intracranial self-stimulation (ICSS). Here, we have assessed the effects of other steric properties of the 4-position substituents. Experimental Approach Definitive steric parameters that more explicitly focus on the volume, width and length of the MCAT 4-position substituents were assessed. In addition, homology models of human DAT and human SERT based upon the crystallized Drosophila DAT were constructed and docking studies were performed, followed by hydropathic interaction (HINT) analysis of the docking results. Key Results The potency of seven MCAT analogues at DAT was negatively correlated with the volume and maximal width of their 4-position substituents, whereas potency at SERT increased as substituent volume and length increased. SERT/DAT selectivity, as well as abuse-related drug effects in the ICSS procedure, also correlated with the same parameters. Docking solutions offered a means of visualizing these findings. Conclusions and Implications These results suggest that steric aspects of the 4-position substituents of MCAT analogues are key determinants of their action and selectivity, and that the hydrophobic nature of these substituents is involved in their potency at SERT. PMID:25522019

  4. Kinetic model framework for aerosol and cloud surface chemistry and gas-particle interactions - Part 1: General equations, parameters, and terminology

    NASA Astrophysics Data System (ADS)

    Pöschl, U.; Rudich, Y.; Ammann, M.

    2007-12-01

    of intermediate species, sequential processes, and surface layers; and full compatibility with traditional resistor model formulations. The outlined double-layer surface concept and formalisms represent a minimum of model complexity required for a consistent description of the non-linear concentration and time dependences observed in experimental studies of atmospheric multiphase processes (competitive co-adsorption and surface saturation effects, etc.). Exemplary practical applications and model calculations illustrating the relevance of the above aspects are presented in a companion paper (Ammann and Pöschl, 2007). We expect that the presented model framework will serve as a useful tool and basis for experimental and theoretical studies investigating and describing atmospheric aerosol and cloud surface chemistry and gas-particle interactions. It shall help to end the "Babylonian confusion" that seems to inhibit scientific progress in the understanding of heterogeneous chemical reactions and other multiphase processes in aerosols and clouds. In particular, it shall support the planning and design of laboratory experiments for the elucidation and determination of fundamental kinetic parameters; the establishment, evaluation, and quality assurance of comprehensive and self-consistent collections of rate parameters; and the development of detailed master mechanisms for process models and derivation of simplified but yet realistic parameterizations for atmospheric and climate models.

  5. User's manual for interactive LINEAR: A FORTRAN program to derive linear aircraft models

    NASA Technical Reports Server (NTRS)

    Antoniewicz, Robert F.; Duke, Eugene L.; Patterson, Brian P.

    1988-01-01

    An interactive FORTRAN program that provides the user with a powerful and flexible tool for the linearization of aircraft aerodynamic models is documented in this report. The program LINEAR numerically determines a linear system model using nonlinear equations of motion and a user-supplied linear or nonlinear aerodynamic model. The nonlinear equations of motion used are six-degree-of-freedom equations with stationary atmosphere and flat, nonrotating earth assumptions. The system model determined by LINEAR consists of matrices for both the state and observation equations. The program has been designed to allow easy selection and definition of the state, control, and observation variables to be used in a particular model.

  6. In vitro interaction of Stenotrophomonas maltophilia with human monocyte-derived dendritic cells.

    PubMed

    Roscetto, Emanuela; Vitiello, Laura; Muoio, Rosa; Soriano, Amata A; Iula, Vita D; Vollaro, Antonio; De Gregorio, Eliana; Catania, Maria R

    2015-01-01

    Stenotrophomonas maltophilia is increasingly identified as an opportunistic pathogen in immunocompromised, cancer and cystic fibrosis (CF) patients. Knowledge on innate immune responses to S. maltophilia and its potential modulation is poor. The present work investigated the ability of 12 clinical S. maltophilia strains (five from CF patients, seven from non-CF patients) and one environmental strain to survive inside human monocyte-derived dendritic cells (DCs). The effects of the bacteria on maturation of and cytokine secretion by DCs were also measured. S. maltophilia strains presented a high degree of heterogeneity in internalization and intracellular replication efficiencies as well as in the ability of S. maltophilia to interfere with normal DCs maturation. By contrast, all S. maltophilia strains were able to activate DCs, as measured by increase in the expression of surface maturation markers and proinflammatory cytokines secretion.

  7. A soft, mean-field potential derived from crystal contacts for predicting protein-protein interactions.

    PubMed

    Robert, C H; Janin, J

    1998-11-13

    We derive a series of novel mean-field potentials from statistical analyses of protein-protein contact regions in crystal structures. These potentials are parameterized in terms of the number of contacts made by an atom in an interface region. Such an explicit number dependence avoids the pairwise assumption and is intrinsically softer than distance-based approaches. It appears well suited to protein-protein docking applications, for which detailed interface geometry is generally lacking. In tests including protein complex reconstitution and docking of independently determined protein structures, we show that a hydrophobic potential of this type performs remarkably well, identifying native-like complexes by their favourable potential energies and in several cases demonstrating a recognition energy gap of 4-8 kcal/mol according to the system.

  8. Towards successful user interaction with systems: focusing on user-derived gestures for smart home systems.

    PubMed

    Choi, Eunjung; Kwon, Sunghyuk; Lee, Donghun; Lee, Hogin; Chung, Min K

    2014-07-01

    Various studies that derived gesture commands from users have used the frequency ratio to select popular gestures among the users. However, the users select only one gesture from a limited number of gestures that they could imagine during an experiment, and thus, the selected gesture may not always be the best gesture. Therefore, two experiments including the same participants were conducted to identify whether the participants maintain their own gestures after observing other gestures. As a result, 66% of the top gestures were different between the two experiments. Thus, to verify the changed gestures between the two experiments, a third experiment including another set of participants was conducted, which showed that the selected gestures were similar to those from the second experiment. This finding implies that the method of using the frequency in the first step does not necessarily guarantee the popularity of the gestures.

  9. Hedgehog-mediated paracrine interaction between hepatic stellate cells and marrow-derived mesenchymal stem cells

    SciTech Connect

    Lin Nan Tang Zhaofeng; Deng Meihai; Zhong Yuesi; Lin Jizong; Yang Xuhui; Xiang Peng; Xu Ruiyun

    2008-07-18

    During liver injury, bone marrow-derived mesenchymal stem cells (MSCs) can migrate and differentiate into hepatocytes. Hepatic stellate cell (SC) activation is a pivotal event in the development of liver fibrosis. Therefore, we hypothesized that SCs may play an important role in regulating MSC proliferation and differentiation through the paracrine signaling pathway. We demonstrate that MSCs and SCs both express hedgehog (Hh) pathway components, including its ligands, receptors, and target genes. Transwell co-cultures of SCs and MSCs showed that the SCs produced sonic hedgehog (Shh), which enhanced the proliferation and differentiation of MSCs. These findings demonstrate that SCs indirectly modulate the activity of MSCs in vitro via the Hh pathway, and provide a plausible explanation for the mechanisms of transplanted MSCs in the treatment of liver fibrosis.

  10. Towards successful user interaction with systems: focusing on user-derived gestures for smart home systems.

    PubMed

    Choi, Eunjung; Kwon, Sunghyuk; Lee, Donghun; Lee, Hogin; Chung, Min K

    2014-07-01

    Various studies that derived gesture commands from users have used the frequency ratio to select popular gestures among the users. However, the users select only one gesture from a limited number of gestures that they could imagine during an experiment, and thus, the selected gesture may not always be the best gesture. Therefore, two experiments including the same participants were conducted to identify whether the participants maintain their own gestures after observing other gestures. As a result, 66% of the top gestures were different between the two experiments. Thus, to verify the changed gestures between the two experiments, a third experiment including another set of participants was conducted, which showed that the selected gestures were similar to those from the second experiment. This finding implies that the method of using the frequency in the first step does not necessarily guarantee the popularity of the gestures. PMID:24685287

  11. Virus-host interactions in persistently FMDV-infected cells derived from bovine pharynx.

    PubMed

    O'Donnell, V; Pacheco, J M; Larocco, Michael; Gladue, D P; Pauszek, S J; Smoliga, G; Krug, P W; Baxt, B; Borca, M V; Rodriguez, L

    2014-11-01

    Foot-and-mouth disease virus (FMDV) produces a disease in cattle characterized by vesicular lesions and a persistent infection with asymptomatic low-level production of virus in pharyngeal tissues. Here we describe the establishment of a persistently infected primary cell culture derived from bovine pharynx tissue (PBPT) infected with FMDV serotype O1 Manisa, where surviving cells were serially passed until a persistently infected culture was generated. Characterization of the persistent virus demonstrated changes in its plaque size, ability to grow in different cell lines, and change in the use of integrins as receptors, when compared with the parental virus. These results demonstrate the establishment of persistently infected PBPT cell cultures where co-adaptation has taken place between the virus and host cells. This in vitro model for FMDV persistence may help further understanding of the molecular mechanisms of the cattle carrier state.

  12. Direct intercellular communications dominate the interaction between adipose-derived MSCs and myofibroblasts against cardiac fibrosis.

    PubMed

    Li, Xiaokang; Zhao, Hui; Qi, Chunxiao; Zeng, Yang; Xu, Feng; Du, Yanan

    2015-10-01

    The onset of cardiac fibrosis post myocardial infarction greatly impairs the function of heart. Recent advances of cell transplantation showed great benefits to restore myocardial function, among which the mesenchymal stem cells (MSCs) has gained much attention. However, the underlying cellular mechanisms of MSC therapy are still not fully understood. Although paracrine effects of MSCs on residual cardiomyocytes have been discussed, the amelioration of fibrosis was rarely studied as the hostile environment cannot support the survival of most cell populations and impairs the diffusion of soluble factors. Here in order to decipher the potential mechanism of MSC therapy for cardiac fibrosis, we investigated the interplay between MSCs and cardiac myofibroblasts (mFBs) using interactive co-culture method, with comparison to paracrine approaches, namely treatment by MSC conditioned medium and gap co-culture method. Various fibrotic features of mFBs were analyzed and the most prominent anti-fibrosis effects were always obtained using direct co-culture that allowed cell-to-cell contacts. Hepatocyte growth factor (HGF), a well-known anti-fibrosis factor, was demonstrated to be a major contributor for MSCs' anti-fibrosis function. Moreover, physical contacts and tube-like structures between MSCs and mFBs were observed by live cell imaging and TEM which demonstrate the direct cellular interactions.

  13. Model membrane interaction and DNA-binding of antimicrobial peptide Lasioglossin II derived from bee venom.

    PubMed

    Bandyopadhyay, Susmita; Lee, Meryl; Sivaraman, J; Chatterjee, Chiradip

    2013-01-01

    Lasioglossins, a new family of antimicrobial peptide, have been shown to have strong antimicrobial activity with low haemo-lytic and mast cell degranulation activity, and exhibit cytotoxic activity against various cancer cells in vitro. In order to understand the active conformation of these pentadecapeptides in membranes, we have studied the interaction of Lasioglossin II (LL-II), one of the members of Lasioglossins family with membrane mimetic micelle Dodecylphosphocholine (DPC) by fluorescence, Circular Dichroism (CD) and two dimensional (2D) (1)H NMR spectroscopy. Fluorescence experiments provide evidence of interaction of the N-terminal tryptophan residue of LL-II with the hydrophobic core of DPC micelle. CD results show an extended chain conformation of LL-II in water which is converted to a partial helical conformation in the presence of DPC micelle. Moreover we have determined the first three-dimensional NMR structure of LL-II bound to DPC micelle with rmsd of 0.36Å. The solution structure of LL-II shows hydrophobic and hydrophilic core formation in peptide pointing towards different direction in the presence of DPC. This amphipathic structure may allow this peptide to penetrate deeply into the interfacial region of negatively charged membranes and leading to local membrane destabilization. Further we have elucidated the DNA binding ability of LL-II by agarose gel retardation and fluorescence quenching experiments.

  14. Direct intercellular communications dominate the interaction between adipose-derived MSCs and myofibroblasts against cardiac fibrosis.

    PubMed

    Li, Xiaokang; Zhao, Hui; Qi, Chunxiao; Zeng, Yang; Xu, Feng; Du, Yanan

    2015-10-01

    The onset of cardiac fibrosis post myocardial infarction greatly impairs the function of heart. Recent advances of cell transplantation showed great benefits to restore myocardial function, among which the mesenchymal stem cells (MSCs) has gained much attention. However, the underlying cellular mechanisms of MSC therapy are still not fully understood. Although paracrine effects of MSCs on residual cardiomyocytes have been discussed, the amelioration of fibrosis was rarely studied as the hostile environment cannot support the survival of most cell populations and impairs the diffusion of soluble factors. Here in order to decipher the potential mechanism of MSC therapy for cardiac fibrosis, we investigated the interplay between MSCs and cardiac myofibroblasts (mFBs) using interactive co-culture method, with comparison to paracrine approaches, namely treatment by MSC conditioned medium and gap co-culture method. Various fibrotic features of mFBs were analyzed and the most prominent anti-fibrosis effects were always obtained using direct co-culture that allowed cell-to-cell contacts. Hepatocyte growth factor (HGF), a well-known anti-fibrosis factor, was demonstrated to be a major contributor for MSCs' anti-fibrosis function. Moreover, physical contacts and tube-like structures between MSCs and mFBs were observed by live cell imaging and TEM which demonstrate the direct cellular interactions. PMID:26271509

  15. The fluorescent interactions between amphiphilic chitosan derivatives and water-soluble quantum dots

    NASA Astrophysics Data System (ADS)

    Fei, Xuening; Yu, Miaozhuo; Zhang, Baolian; Cao, Lingyun; Yu, Lu; Jia, Guozhi; Zhou, Jianguo

    2016-01-01

    The LCC-CdTe quantum dots (QDs) hybrid was fabricated by mixing the N-lauryl-N, O-carboxymethyl chitosan (LCC) micelle with water-soluble CdTe QDs in an aqueous solution via hydrophobic forces and the electronic attraction. The structures of LCC and LCC-CdTe QDs hybrid were determined by differential scanning calorimetry (DSC), Fourier transform infrared (FT-IR) spectroscopy and transmission electron microscopy (TEM). The results showed that the lauryl and carboxymethyl were successfully grafted to chitosan oligosaccharide (CSO), and a number of CdTe QDs were encapsulated by LCC micelle to form a core/shell structure. The tested results of the fluorescent characteristics of LCC, CdTe QDs and LCC-CdTe QDs hybrid showed that there were some obvious fluorescent interactions between LCC and CdTe QDs. Meanwhile, with the change in LCC space structure, the fluorescent interactions between LCC and QDs showed different fluorescent characteristics. The QDs fluorescent (FL) intensity increased first and then decreased to almost quenching, while LCC FL intensity decreased continually.

  16. A theoretical investigation of the interaction between substituted carbonyl derivatives and water: open or cyclic complexes?

    PubMed

    Chandra, Asit K; Zeegers-Huyskens, Thérèse

    2012-04-30

    The structures and binding energies of complexes between substituted carbonyl bases and water are the B3LYP/6-311++G(d,p) computational level. The calculations also include the proton affinity (PA) of the O of the C=O group, the deprotonation enthalpies (DPE) of the CH bonds along a natural bond orbital analysis. The calculations reveal that stable open C=O···H(w) O(w) as well as cyclic CH···O(w)H(w) ···O=C complexes are formed. The binding energies for the open complexes are linearly related to the PAs, whereas the binding energies for the cyclic complexes depend on both the PA and DPE. Different indicators of hydrogen bonds strength such as electron charge density, intramolecular and intermolecular hyperconjugation energy, occupation of orbitals, and charge transfer show significant differences between open and cyclic complexes. The contraction of the CH bond of the formyl group and the corresponding blue shift of the ν(CH) vibration are explained by the classical trans lone pair effect. In contrast, the elongation or contraction of the CH(3) group involved in the interaction with water results from the variation of the orbital interaction energies from the σ(CH) bonding orbital to the σ* and π* antibonding orbitals of the C=O group. The resulting blue or red shifts of the ν(CH(3)) vibrations are calculated in the partially deuterated isotopomers. PMID:22344933

  17. TRADES: A new software to derive orbital parameters from observed transit times and radial velocities. Revisiting Kepler-11 and Kepler-9

    NASA Astrophysics Data System (ADS)

    Borsato, L.; Marzari, F.; Nascimbeni, V.; Piotto, G.; Granata, V.; Bedin, L. R.; Malavolta, L.

    2014-11-01

    Aims: With the purpose of determining the orbital parameters of exoplanetary systems from observational data, we have developed a software, named TRADES (TRAnsits and Dynamics of Exoplanetary Systems), to simultaneously fit observed radial velocities and transit times data. Methods: We implemented a dynamical simulator for N-body systems, which also fits the available data during the orbital integration and determines the best combination of the orbital parameters using grid search, χ2 minimization, genetic algorithms, particle swarm optimization, and bootstrap analysis. Results: To validate TRADES, we tested the code on a synthetic three-body system and on two real systems discovered by the Kepler mission: Kepler-9 and Kepler-11. These systems are good benchmarks to test multiple exoplanet systems showing transit time variations (TTVs) due to the gravitational interaction among planets. We have found that orbital parameters of Kepler-11 planets agree well with the values proposed in the discovery paper and with a a recent work from the same authors. We analyzed the first three quarters of Kepler-9 system and found parameters in partial agreement with discovery paper. Analyzing transit times (T0s), covering 12 quarters of Kepler data, that we have found a new best-fit solution. This solution outputs masses that are about 55% of the values proposed in the discovery paper; this leads to a reduced semi-amplitude of the radial velocities of about 12.80 ms-1.

  18. Accuracy of Quantum Mechanically Derived Force-Fields Parameterized from Dispersion-Corrected DFT Data: The Benzene Dimer as a Prototype for Aromatic Interactions.

    PubMed

    Prampolini, Giacomo; Livotto, Paolo Roberto; Cacelli, Ivo

    2015-11-10

    A multilevel approach is presented to assess the ability of several popular dispersion corrected density functionals (M06-2X, CAM-B3LYP-D3, BLYP-D3, and B3LYP-D3) to reliably describe two-body interaction potential energy surfaces (IPESs). To this end, the automated Picky procedure ( Cacelli et al. J. Comput. Chem. 2012 , 33 , 1055 ) was exploited, which consists in parametrizing specific intermolecular force fields through an iterative approach, based on the comparison with quantum mechanical data. For each of the tested functionals, the resulting force field was employed in classical Monte Carlo and Molecular Dynamics simulations, performed on systems of up to 1000 molecules in ambient conditions, to calculate a number of condensed phase properties. The comparison of the resulting structural and dynamic properties with experimental data allows us to assess the quality of each IPES and, consequently, even the quality of the DFT functionals. The methodology is tested on the benzene dimer, commonly used as a benchmark molecule, a prototype of aromatic interactions. The best results were obtained with the CAM-B3LYP-D3 functional. Besides assessing the reliability of DFT functionals in describing aromatic IPESs, this work provides a further step toward a robust protocol for the derivation of sound force field parameters from quantum mechanical data. This method can be relevant in all those cases where standard force fields fail in giving accurate predictions.

  19. Multidirectional interactions are bridging human NK cells with plasmacytoid and monocyte-derived dendritic cells during innate immune responses.

    PubMed

    Della Chiesa, Mariella; Romagnani, Chiara; Thiel, Andreas; Moretta, Lorenzo; Moretta, Alessandro

    2006-12-01

    During innate immune responses, natural killer (NK) cells may interact with both plasmacytoid dendritic cells (pDCs) and monocyte-derived dendritic cells (MDDCs). We show that freshly isolated NK cells promote the release by pDCs of IFN-alpha, in a CpG-dependent manner, whereas they induce IL-6 production in a CpG-independent manner. In turn pDC-derived IFN-alpha up-regulates NK-mediated killing, whereas IL-6 could promote B-cell differentiation. We also show that exposure to exogenous IL-12 or coculture with maturing MDDCs up-regulates the NK-cell-dependent IFN-alpha production by pDCs. On the other hand, NK cells cocultured with pDCs acquire the ability to kill immature MDDCs, thus favoring their editing process. Finally, we show that activated NK cells are unable to lyse pDCs because these cells display an intrinsic resistance to lysis. The exposure of pDCs to IL-3 increased their susceptibility to NK-cell cytotoxicity resulting from a de novo expression of ligands for activating NK-cell receptors, such as the DNAM-1 ligand nectin-2. Thus, different cell-to-cell interactions and various cytokines appear to control a multidirectional network between NK cells, MDDCs, and pDCs that is likely to play an important role during the early phase of innate immune responses to viral infections and to tumors. PMID:16873676

  20. Modeling Dengue Virus-Hepatic Cell Interactions Using Human Pluripotent Stem Cell-Derived Hepatocyte-like Cells.

    PubMed

    Lang, Jianshe; Vera, Daniel; Cheng, Yichen; Tang, Hengli

    2016-09-13

    The development of dengue antivirals and vaccine has been hampered by the incomplete understanding of molecular mechanisms of dengue virus (DENV) infection and pathology, partly due to the limited suitable cell culture or animal models that can capture the comprehensive cellular changes induced by DENV. In this study, we differentiated human pluripotent stem cells (hPSCs) into hepatocytes, one of the target cells of DENV, to investigate various aspects of DENV-hepatocyte interaction. hPSC-derived hepatocyte-like cells (HLCs) supported persistent and productive DENV infection. The activation of interferon pathways by DENV protected bystander cells from infection and protected the infected cells from massive apoptosis. Furthermore, DENV infection activated the NF-κB pathway, which led to production of proinflammatory cytokines and downregulated many liver-specific genes such as albumin and coagulation factor V. Our study demonstrates the utility of hPSC-derived hepatocytes as an in vitro model for DENV infection and reveals important aspects of DENV-host interactions. PMID:27546535

  1. Theoretical relationships of receptor and delivery sensitivities and measurable parameters in in vivo neuroreceptor-radioligand interactions

    SciTech Connect

    Zeeberg, B.R.

    1995-09-01

    In vivo quantification of neuroreceptors in human brains by PET or SPECT is complicated by the fact that a number of variables other than receptor concentration may influence the observed radioactivity in a brain region. This consideration has led us to formulate rigorous mathematical definitions of the concepts of receptor and delivery sensitivities. It has been speculated that a neuroreceptor-radioligand system having a high (low) receptor sensitivity would have a low (high) delivery sensitivity, and that the receptor sensitivity of a neuroreceptor-radioligand system can be determined by observing the time-course of the brain radioligand concentration following injection of no carrier added (nca) radioligand. Computer simulation studies of the characteristics of a simple model for in vivo neuroreceptor-radioligand interaction show that, under a set of realistic restrictions, there is a unique and intuitively satisfying relationship between receptor and delivery sensitivities: receptor sensitivity + delivery sensitivity {approx} 1. In addition, the receptor sensitivity can be computed as a function of the observable parameters of the nca radioligand time course. These straightforward relationships are surprising in light of the complexity of the analytical solutions.

  2. Correlation among electronic polarizability, optical basicity and interaction parameter of Bi 2O 3-B 2O 3 glasses

    NASA Astrophysics Data System (ADS)

    Zhao, Xinyu; Wang, Xiaoli; Lin, Hai; Wang, Zhiqiang

    2007-03-01

    For optical basicity and electronic polarizability, the previous studies basically concentrate on the wavelength range of the visible light region. However, heavy metal oxides glasses have a reputation of being good materials for infrared region. In this study, new data of the average electronic polarizability of the oxide ion α, optical basicity Λ and Yamashita-Kurosawa's interaction parameter A of Bi 2O 3-B 2O 3 glasses have been calculated in a wavelength range from 404.66 to 1083.03 nm. The present investigation suggests that both α and Λ increase gradually with increasing wave number, and A decreases with increasing wave number. Furthermore, close correlations are studied among α, Λ, A and refractive index n in this paper. Particularly, it has been found that a quantitative relationship between electronic polarizability and optical basicity is observed in a wavelength range from 404.66 to 1083.03 nm. Our present study extends over a wide range of α, Λ and A values.

  3. Estimation of a common effect parameter from follow-up data when there is no mechanistic interaction.

    PubMed

    Lee, Wen-Chung

    2014-01-01

    In a stratified analysis, the results from different strata if homogeneity assumption is met are pooled together to obtain a single summary estimate for the common effect parameter. However, the effect can appear homogeneous across strata using one measure but heterogeneous using another. Consequently, two researchers analyzing the same data can arrive at conflicting conclusions if they use different effect measures. In this paper, the author draws on the sufficient component cause model to develop a stratified-analysis method regarding a particular effect measure, the 'peril ratio'. When there is no mechanistic interaction between the exposure under study and the stratifying variable (i.e., when they do not work together to complete any sufficient cause), the peril ratio is constant across strata. The author presents formulas for the estimation of such a common peril ratio. Three real data are re-analyzed for illustration. When the data is consistent with peril-ratio homogeneity in a stratified analysis, researchers can use the formulas in this paper to pool the strata. PMID:24466062

  4. Proinflammatory interleukins' production by adipose tissue-derived mesenchymal stromal cells: the impact of cell culture conditions and cell-to-cell interaction.

    PubMed

    Andreeva, Elena; Andrianova, Irina; Rylova, Julia; Gornostaeva, Aleksandra; Bobyleva, Polina; Buravkova, Ludmila

    2015-08-01

    The impact of culture conditions and interaction with activated peripheral blood mononuclear cells on the interleukin (IL) gene expression profile and proinflammatory IL-6 and IL-8 production by adipose-derived stromal cells (ASCs) was investigated. A microarray analysis revealed a wide range of IL genes either under standard (20%) or hypoxic (5%) O2 concentrations, some highly up-regulated at hypoxia. IL-6 and IL-8 production was inversely dependent on cell culture density. In early (first-third) passages, IL-6 and IL-8 concentration was higher at 20% O2 and in late (8th-12th) passages under 5% O2. Interaction between ASCs and mononuclear cells in indirect setting was accompanied with a significant decrease of IL-6 and did not result in the elevation of IL-8 concentration. Thereby, the production of proinflammatory interleukins (IL-6 and IL-8) may be affected by the ASC intrinsic features (density in culture, and duration of expansion), as well as by microenvironmental factors, such as hypoxia and the presence of blood-borne cells. These data are important for elucidating ASC paracrine activity regulation in vitro. They would also be on demand for optimisation of the cell therapy protocols, based on the application of ASC biologically active substances. SIGNIFICANCE PARAGRAPH: Ex vivo expansion is widely used for increasing the number of adipose-derived stromal cells (ASCs) and improving of their quality. The present study was designed to elucidate the particular factors influencing the interleukin production in ASCs. The presented data specified the parameters (i.e. cell density, duration of cultivation, hypoxia, etc.) that should be taken in mind when ASCs are intended to be used in protocols implying their paracrine activity. These data would be of considerable interest for researchers and clinicians working in the biomedical science.

  5. Photophysical characterization of perylene derivatives and their interaction with human serum albumin

    NASA Astrophysics Data System (ADS)

    Farooqi, Mohammed Junaid

    The study of the binding and effects of polyaromatic hydro-carbons (PAH) to proteins remains one of the fundamental aspects of research in biophysics. Among other processes, ligand binding can regulate the function of proteins including inhibiting their action. Binding to small ligands remains a very important aspect in the study of the function of many proteins. We have investigated a number of novel perylene analogues. The investigation includes the photophysical characterization of perylene diimides and their interaction with HSA. In this study we have shown that 3,9-disubstitutes perylenes show weak affinity to binding with HSA and their irradiation produces no observable structural effects on the bound protein. Perylene Diimides were photophysically characterized in organic solvents. PDI phenylalanine and leucine are the only PDIs spectroscopically observable in aqueous solution and bind with HSA with great affinity. Resonance energy transfer was observed in PDIF bound to HSA with an energy efficiency of 0.268.

  6. Citrus-derived oil inhibits Staphylococcus aureus growth and alters its interactions with bovine mammary cells.

    PubMed

    Federman, C; Joo, J; Almario, J A; Salaheen, S; Biswas, D

    2016-05-01

    This experiment examined the effects of cold-pressed, terpeneless citrus-derived oil (CDO) on growth of Staphylococcus aureus, which a major cause of contagious bovine mastitis, and invasion of bovine mammary cells (MAC-T). To determine minimum inhibitory concentration, we used the broth dilution method, using CDO concentrations range from 0.0125 to 0.4% with 2-fold dilutions. Growth inhibition was examined by adding 0.00, 0.05, 0.025, 0.0125, and 0.00625% CDO to 10(5) cfu/mL S. aureus in nutrient broth and enumerating colonies after serial dilution. In a 96-well plate, S. aureus (10(7) cfu/mL) was allowed to form a biofilm, treated with 0, 0.025, 0.5, or 1% CDO, and then was measured using a spectrophotometer. Cytotoxic effect on immortalized MAC-T cells was also examined at various concentrations of CDO using a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay. We observed that the minimum inhibitory concentration of CDO to inhibit the growth of S. aureus in vitro was 0.025% CDO. A time kill curve for CDO action on S. aureus over 4h was generated. The CDO completely eliminated S. aureus after 3h of incubation at a concentration of 0.25%, or after 2h of incubation at concentrations of 0.05%. It was also observed that CDO had no effect on preformed biofilms except at a concentration of 0.05%, in which a significant reduction in the measured absorbance was noted. In addition, the association and invasion of S. aureus to MAC-T cells were significantly inhibited after 1h of treatment with CDO. Citrus-derived oil was also able to increase cellular proliferation of MAC-T cells at concentrations up 0.05% and had no effect at a concentration of 0.1% after 1 h. Our data suggests that CDO should be considered for further research as a preventive and therapeutic against bovine mastitis. PMID:26947297

  7. Secretion Modification Region-Derived Peptide Disrupts HIV-1 Nef's Interaction with Mortalin and Blocks Virus and Nef Exosome Release

    PubMed Central

    Shelton, Martin N.; Huang, Ming-Bo; Ali, Syed A.; Powell, Michael D.

    2012-01-01

    Nef is secreted from infected cells in exosomes and is found in abundance in the sera of HIV-infected individuals. Secreted exosomal Nef (exNef) induces apoptosis in uninfected CD4+ T cells and may be a key component of HIV pathogenesis. The exosomal pathway has been implicated in HIV-1 virus release, suggesting a possible link between these two viral processes. However, the underlying mechanisms and cellular components of exNef secretion have not been elucidated. We have previously described a Nef motif, the secretion modification region (SMR; amino acids 66 to 70), that is required for exNef secretion. In silico modeling data suggest that this motif can form a putative binding pocket. We hypothesized that the Nef SMR binds a cellular protein involved in protein trafficking and that inhibition of this interaction would abrogate exNef secretion. By using tandem mass spectrometry and coimmunoprecipitation with a novel SMR-based peptide (SMRwt) that blocks exNef secretion and HIV-1 virus release, we identified mortalin as an SMR-specific cellular protein. A second set of coimmunoprecipitation experiments with full-length Nef confirmed that mortalin interacts with Nef via Nef's SMR motif and that this interaction is disrupted by the SMRwt peptide. Overexpression and microRNA knockdown of mortalin revealed a positive correlation between exNef secretion levels and mortalin protein expression. Using antibody inhibition we demonstrated that the Nef/mortalin interaction is necessary for exNef secretion. Taken together, this work constitutes a significant step in understanding the underlying mechanism of exNef secretion, identifies a novel host-pathogen interaction, and introduces an HIV-derived peptide with antiviral properties. PMID:22013042

  8. Brain-derived neurotrophic factor interacts with astrocytes and neurons to control respiration.

    PubMed

    Caravagna, Céline; Soliz, Jorge; Seaborn, Tommy

    2013-11-01

    Respiratory rhythm is generated and modulated in the brainstem. Neuronal involvement in respiratory control and rhythmogenesis is now clearly established. However, glial cells have also been shown to modulate the activity of brainstem respiratory groups. Although the potential involvement of other glial cell type(s) cannot be excluded, astrocytes are clearly involved in this modulation. In parallel, brain-derived neurotrophic factor (BDNF) also modulates respiratory rhythm. The currently available data on the respective roles of astrocytes and BDNF in respiratory control and rhythmogenesis lead us to hypothesize that there is BDNF-mediated control of the communication between neurons and astrocytes in the maintenance of a proper neuronal network capable of generating a stable respiratory rhythm. According to this hypothesis, progression of Rett syndrome, an autism spectrum disease with disordered breathing, can be stabilized in mouse models by re-expressing the normal gene pattern in astrocytes or microglia, as well as by stimulating the BDNF signaling pathway. These results illustrate how the signaling mechanisms by which glia exerts its effects in brainstem respiratory groups is of great interest for pathologies associated with neurological respiratory disorders.

  9. Interaction study between wheat-derived peptides and procyanidin B3 by mass spectrometry.

    PubMed

    Dias, Ricardo; Perez-Gregorio, Maria Rosa; Mateus, Nuno; De Freitas, Victor

    2016-03-01

    Tannins have the ability to complex and precipitate proteins, being particularly reactive towards the proline-rich ones. The main structural feature of the wheat peptides responsible for the onset of Celiac Disease (CD) is their high content in proline residues. The aim of this work was to characterize the binding between a common food tannin (procyanidin B3) and different wheat-derived peptidic fractions. For this, seven peptide mixtures were obtained after in vitro digestion of a wheat gliadins crude extract and further characterized by LC-ESI-MS/MS. Several soluble B3-peptide complexes were identified by ESI-MS. The peptides involved in complex formation varied in terms of their size and diversity in CD epitopes. Although binding selectivity of procyanidin B3 towards peptides containing CD epitopes was not found, the major complexes contained or could contain immunoreactive peptides. This study highlights the potential beneficial effects of food polyphenols as a nutritional approach in the modulation of CD. PMID:26471686

  10. Influence of gold(I) complexes involving adenine derivatives on major drug-drug interaction pathway.

    PubMed

    Dvořák, Zdeněk; Novotná, Aneta; Vančo, Ján; Trávníček, Zdeněk

    2013-12-01

    A series of considerably anti-inflammatory active gold(I) mixed-ligand complexes, involving the benzyl-substituted derivatives of N6-benzyladenine (HLn) and triphenylphosphine (PPh3) as ligands and having the general formula [Au(Ln)(PPh3)]·xH2O (1-4; n=1-4 and x=0-1), was evaluated for the ability to influence the expression of CYP1A1/2 and CYP3A4 and transcriptional activity of glucocorticoid (GR) and aryl hydrocarbon (AhR) receptors in primary human hepatocytes and HepG2 cells. In both tests, evaluating the ability of the complexes to modulate the expression of CYP1A1, CYP1A2 and CYP3A4 in primary human hepatocytes and influence the transcriptional activity of AhR and GR in the reporter cell lines, no negative influence on the major drug-metabolizing cytochrome P450 isoenzymes and their signaling pathway (through GR and AhR receptors) was observed. These positive findings revealed another substantial evidence that could lead to utilization of the complexes as effective and relatively safe drugs for the treatment of hard-to-treat inflammation-related diseases, such as rheumatoid arthritis, comparable or even better than clinically used gold-containing drug Auranofin. PMID:24157406

  11. Interactions between heme and tau-derived R1 peptides: binding and oxidative reactivity.

    PubMed

    Pirota, V; Monzani, E; Dell'Acqua, S; Casella, L

    2016-09-28

    The interaction of hemin with the first 18-amino acid repeat in tau protein has been investigated at both the N-terminal free-amine (R1τ) and N-acetylated (AcR1τ) forms for its potential relevance in traumatic brain injury and possibly other neurodegenerative diseases. The binding properties of hemin-R1τ and hemin-AcR1τ were compared with those of the hemin complex with amyloid-β peptide fragment 1-16 (Aβ16) and synthetic hemins. AcR1τ and R1τ bind with moderate affinity to both monomeric and dimeric hemin to form 1 : 1 complexes, but for the acetylated peptide, the affinity is one order of magnitude larger (K1 = 3.3 × 10(6) M(-1)). The binding constants were similar to that of Aβ16 for hemin, but unlike the latter, neither of the two R1τ peptides forms a 2 : 1 complex with hemin. This is mostly due to electrostatic repulsion between R1τ chains, and in particular the C-terminal proline-15 kink, while structural features of the hemin-R1τ complexes do not seem to play a role. In fact, the same features are observed for the interaction between ferric heme and peptide R1τ*, where the P15 residue is replaced by an alanine. Imidazole neither binds to [hemin(R1τ)] nor [hemin(AcR1τ)], whereas small ligands such as CN and CO easily bind to the ferric and ferrous forms of the complexes, respectively. A detailed comparative study of the peroxidase activity of [hemin(R1τ)] and [hemin(AcR1τ)] shows that such activity is very low. Thus, the association between heme and unfolded neuronal peptides does not, per se, involve a significant gain of toxic pseudo-enzymatic activity. However, under conditions of heavy heme release occurring on traumatic brain injury or when this activity is prolonged for long time, it can contribute to neuronal oxidative stress. In addition, the presence of hemin increases the aggregation propensity of R1τ. PMID:27539650

  12. HIV-1 Interacts with Human Endogenous Retrovirus K (HML-2) Envelopes Derived from Human Primary Lymphocytes

    PubMed Central

    Brinzevich, Daria; Young, George R.; Sebra, Robert; Ayllon, Juan; Maio, Susan M.; Deikus, Gintaras; Chen, Benjamin K.; Fernandez-Sesma, Ana; Simon, Viviana

    2014-01-01

    ABSTRACT Human endogenous retroviruses (HERVs) are viruses that have colonized the germ line and spread through vertical passage. Only the more recently acquired HERVs, such as the HERV-K (HML-2) group, maintain coding open reading frames. Expression of HERV-Ks has been linked to different pathological conditions, including HIV infection, but our knowledge on which specific HERV-Ks are expressed in primary lymphocytes currently is very limited. To identify the most expressed HERV-Ks in an unbiased manner, we analyzed their expression patterns in peripheral blood lymphocytes using Pacific Biosciences (PacBio) single-molecule real-time (SMRT) sequencing. We observe that three HERV-Ks (KII, K102, and K18) constitute over 90% of the total HERV-K expression in primary human lymphocytes of five different donors. We also show experimentally that two of these HERV-K env sequences (K18 and K102) retain their ability to produce full-length and posttranslationally processed envelope proteins in cell culture. We show that HERV-K18 Env can be incorporated into HIV-1 but not simian immunodeficiency virus (SIV) particles. Moreover, HERV-K18 Env incorporation into HIV-1 virions is dependent on HIV-1 matrix. Taken together, we generated high-resolution HERV-K expression profiles specific for activated human lymphocytes. We found that one of the most abundantly expressed HERV-K envelopes not only makes a full-length protein but also specifically interacts with HIV-1. Our findings raise the possibility that these endogenous retroviral Env proteins could directly influence HIV-1 replication. IMPORTANCE Here, we report the HERV-K expression profile of primary lymphocytes from 5 different healthy donors. We used a novel deep-sequencing technology (PacBio SMRT) that produces the long reads necessary to discriminate the complexity of HERV-K expression. We find that primary lymphocytes express up to 32 different HERV-K envelopes, and that at least two of the most expressed Env proteins

  13. Spectral Analysis of Interaction between Human Telomeric G-Quadruplex and Liliflorin A, the First Lignan Derivative Interacted with G-Quadruplex DNA.

    PubMed

    Liu, Ting-ting; Zhou, Shuang; Jia, Qian-lan; Wang, Wen-shu; Yan, Xiao-qian; Zhang, Wen-hao; Wang, Shuai-qi; Jiao, Yu-guo

    2016-03-01

    Human telomeric G-quadruplex is a four-stranded structure folded by guanines (G) via Hoogsteen hydrogen bonding. The ligands which stabilize the G-quadruplex are often telomerase inhibitors and may become antitumor agents. Here, the interaction between a lignan derivative liliflorin A and human telomeric sequence dGGG (TTAGGG)3G-quadruplex HTG21 were examined by CD, FRET, and NMR spectroscopic methods. In addition, Molecular Docking was used to study the binding of liliflorin A to dTAGGG (TTAGGG)3 G-quadruplex HTG23. The CD data showed that liliflorin A enhanced HTG21 T(m). The T(m) value of G-quadruplex was enhanced 3.2 degrees C by 4.0 μmol x L(-1) liliflorin A in FRET. The NMR spectra of HTG21 showed vivid alteration after reacting with liliflorin A in 3 hours. Molecular Docking suggested liliflorin A bound to the wide groove of HTG23 at G9, G10, G16 and G17. Liliflorin A was the first lignan derivative that could stabilize HTG21 selectively and provided a new candidate for antitumor drug design targeting on human telomeric G-quadruplex.

  14. Spectral Analysis of Interaction between Human Telomeric G-Quadruplex and Liliflorin A, the First Lignan Derivative Interacted with G-Quadruplex DNA.

    PubMed

    Liu, Ting-ting; Zhou, Shuang; Jia, Qian-lan; Wang, Wen-shu; Yan, Xiao-qian; Zhang, Wen-hao; Wang, Shuai-qi; Jiao, Yu-guo

    2016-03-01

    Human telomeric G-quadruplex is a four-stranded structure folded by guanines (G) via Hoogsteen hydrogen bonding. The ligands which stabilize the G-quadruplex are often telomerase inhibitors and may become antitumor agents. Here, the interaction between a lignan derivative liliflorin A and human telomeric sequence dGGG (TTAGGG)3G-quadruplex HTG21 were examined by CD, FRET, and NMR spectroscopic methods. In addition, Molecular Docking was used to study the binding of liliflorin A to dTAGGG (TTAGGG)3 G-quadruplex HTG23. The CD data showed that liliflorin A enhanced HTG21 T(m). The T(m) value of G-quadruplex was enhanced 3.2 degrees C by 4.0 μmol x L(-1) liliflorin A in FRET. The NMR spectra of HTG21 showed vivid alteration after reacting with liliflorin A in 3 hours. Molecular Docking suggested liliflorin A bound to the wide groove of HTG23 at G9, G10, G16 and G17. Liliflorin A was the first lignan derivative that could stabilize HTG21 selectively and provided a new candidate for antitumor drug design targeting on human telomeric G-quadruplex. PMID:27400545

  15. Experimental and theoretical electron-density study of three isoindole derivatives: topological and Hirshfeld surface analysis of weak intermolecular interactions.

    PubMed

    Chęcińska, Lilianna; Grabowsky, Simon; Małecka, Magdalena; Rybarczyk-Pirek, Agnieszka J; Jóźwiak, Andrzej; Paulmann, Carsten; Luger, Peter

    2011-12-01

    A combined experimental and theoretical study of three isoindole derivatives was made on the basis of a topological analysis of their electron-density distributions. Experimental electron densities were determined from high-resolution X-ray diffraction data sets measured with synchrotron radiation at 100 K, whereas theoretical calculations were performed using DFT methods at the B3LYP\\6-311++G(3df,3pd) level of approximation. Both experimental and theoretical models are in good agreement with each other. Since the analysed structures possess a variety of hydrogen-bonding interactions, weak intermolecular contacts of C-H···C(π), C,N(π)···C,N(π) and H···H types were subject to our special interest and are discussed in detail. They were characterized quantitatively and qualitatively by topological properties using Bader's Atoms in Molecules theory and by mapping the electron-density distribution, electrostatic potential and a geometric function on the Hirshfeld surface. This way the forces and directions of intermolecular interactions as present on the molecular surfaces were depicted and described. These interactions not only guide crystal packing, but are likewise important for recognition processes involving (aza)isoindole fragments in a biological environment.

  16. Host-Parasite Interaction: Parasite-Derived and -Induced Proteases That Degrade Human Extracellular Matrix

    PubMed Central

    Piña-Vázquez, Carolina; Reyes-López, Magda; Ortíz-Estrada, Guillermo; de la Garza, Mireya; Serrano-Luna, Jesús

    2012-01-01

    Parasitic protozoa are among the most important pathogens worldwide. Diseases such as malaria, leishmaniasis, amoebiasis, giardiasis, trichomoniasis, and trypanosomiasis affect millions of people. Humans are constantly threatened by infections caused by these pathogens. Parasites engage a plethora of surface and secreted molecules to attach to and enter mammalian cells. The secretion of lytic enzymes by parasites into host organs mediates critical interactions because of the invasion and destruction of interstitial tissues, enabling parasite migration to other sites within the hosts. Extracellular matrix is a complex, cross-linked structure that holds cells together in an organized assembly and that forms the basement membrane lining (basal lamina). The extracellular matrix represents a major barrier to parasites. Therefore, the evolution of mechanisms for connective-tissue degradation may be of great importance for parasite survival. Recent advances have been achieved in our understanding of the biochemistry and molecular biology of proteases from parasitic protozoa. The focus of this paper is to discuss the role of protozoan parasitic proteases in the degradation of host ECM proteins and the participation of these molecules as virulence factors. We divide the paper into two sections, extracellular and intracellular protozoa. PMID:22792442

  17. Interactions between chensinin-1, a natural antimicrobial peptide derived from Rana chensinensis, and lipopolysaccharide.

    PubMed

    Dong, Weibing; Sun, Yue; Shang, Dejing

    2015-12-01

    Lipopolysaccharide (LPS) plays a critical role in the pathogenesis of sepsis caused by gram-negative bacterial infections. Therefore, LPS-neutralizing molecules would have important clinical applications. Chensinin-1, a novel antimicrobial peptide with atypical structural features, was found in the skin secretions of the Chinese brown frog Rana chensinensis. To understand the role of LPS in the bacterial susceptibility to chensinin-1 and to investigate its anti-endotoxin effects, the interactions of chensinin-1 with LPS were investigated in this study using circular dichroism, in situ IR, isothermal titration calorimetry, and zeta potential. This study is the first to use in situ IR spectroscopy to evaluate the secondary structural changes of this peptide. The capacity of chensinin-1 to block the LPS-dependent cytokine secretion of macrophages was also investigated. Our results show that chensinin-1 can form α-helical structures in LPS suspensions. LPS can affect the antimicrobial activity of chensinin-1, and chensinin-1 was able to mitigate the effects of LPS. These data may facilitate the development of antimicrobial peptides with potent antimicrobial and anti-endotoxin activities. PMID:26340228

  18. Food plant derived disease tolerance and resistance in a natural butterfly-plant-parasite interactions.

    PubMed

    Sternberg, Eleanore D; Lefèvre, Thierry; Li, James; de Castillejo, Carlos Lopez Fernandez; Li, Hui; Hunter, Mark D; de Roode, Jacobus C

    2012-11-01

    Organisms can protect themselves against parasite-induced fitness costs through resistance or tolerance. Resistance includes mechanisms that prevent infection or limit parasite growth while tolerance alleviates the fitness costs from parasitism without limiting infection. Although tolerance and resistance affect host-parasite coevolution in fundamentally different ways, tolerance has often been ignored in animal-parasite systems. Where it has been studied, tolerance has been assumed to be a genetic mechanism, unaffected by the host environment. Here we studied the effects of host ecology on tolerance and resistance to infection by rearing monarch butterflies on 12 different species of milkweed food plants and infecting them with a naturally occurring protozoan parasite. Our results show that monarch butterflies experience different levels of tolerance to parasitism depending on the species of milkweed that they feed on, with some species providing over twofold greater tolerance than other milkweed species. Resistance was also affected by milkweed species, but there was no relationship between milkweed-conferred resistance and tolerance. Chemical analysis suggests that infected monarchs obtain highest fitness when reared on milkweeds with an intermediate concentration, diversity, and polarity of toxic secondary plant chemicals known as cardenolides. Our results demonstrate that environmental factors-such as interacting species in ecological food webs-are important drivers of disease tolerance. PMID:23106703

  19. Interaction of the protein transduction domain of HIV-1 TAT with heparan sulfate: binding mechanism and thermodynamic parameters.

    PubMed

    Ziegler, André; Seelig, Joachim

    2004-01-01

    titration calorimetry. The thermodynamic parameters are K0 = (6.0 +/- 0.8) x 10(5) M(-1) and kcal/mol for heparin and K0 = (2.5 +/- 0.5) x 10(5) M(-1) and kcal/mol for chondroitin sulfate B at 28 degrees C. The close thermodynamic similarity of the three binding molecules also implies a close structural relationship. The ubiquitous occurrence of glycosaminoglycans on the cell surface together with their tight and rapid interaction with the TAT protein transduction domain makes complex formation a strong candidate as the primary step of protein translocation.

  20. Relationship between diffusion parameters derived from intravoxel incoherent motion MRI and perfusion measured by dynamic contrast-enhanced MRI of soft tissue tumors.

    PubMed

    Marzi, Simona; Stefanetti, Linda; Sperati, Francesca; Anelli, Vincenzo

    2016-01-01

    Our aim was to evaluate the link between diffusion parameters measured by intravoxel incoherent motion (IVIM) diffusion-weighted imaging (DWI) and the perfusion metrics obtained with dynamic contrast-enhanced (DCE) MRI in soft tissue tumors (STTs). Twenty-eight patients affected by histopathologically confirmed STT were included in a prospective study. All patients underwent both DCE MRI and IVIM DWI. The perfusion fraction f, diffusion coefficient D and perfusion-related diffusion coefficient D* were estimated using a bi-exponential function to fit the DWI data. DCE MRI was acquired with a temporal resolution of 3-5 s. Maps of the initial area under the gadolinium concentration curve (IAUGC), time to peak (TTP) and maximum slope of increase (MSI) were derived using commercial software. The relationships between the DCE MRI and IVIM DWI measurements were assessed by Spearman's test. To exclude false positive results under multiple testing, the false discovery rate (FDR) procedure was applied. The Mann-Whitney test was used to evaluate the differences between all variables in patients with non-myxoid and myxoid STT. No significant relationship was found between IVIM parameters and any DCE MRI parameters. Higher f and D*f values were found in non-myxoid tumors compared with myxoid tumors (p = 0.004 and p = 0.003, respectively). MSI was significantly higher in non-myxoid tumors than in myxoid tumors (p = 0.029). From the visual assessments of single clinical cases, both f and D*f maps were in satisfactory agreement with DCE maps in the extreme cases of an avascular mass and a highly vascularized mass, whereas, for tumors with slight vascularity or with a highly heterogeneous perfusion pattern, this association was not straightforward. Although IVIM DWI was demonstrated to be feasible in STT, our data did not support evident relationships between perfusion-related IVIM parameters and perfusion measured by DCE MRI.

  1. Sequential identification of model parameters by derivative double two-dimensional correlation spectroscopy and calibration-free approach for chemical reaction systems.

    PubMed

    Spegazzini, Nicolas; Siesler, Heinz W; Ozaki, Yukihiro

    2012-10-01

    A sequential identification approach by two-dimensional (2D) correlation analysis for the identification of a chemical reaction model, activation, and thermodynamic parameters is presented in this paper. The identification task is decomposed into a sequence of subproblems. The first step is the construction of a reaction model with the suggested information by model-free 2D correlation analysis using a novel technique called derivative double 2D correlation spectroscopy (DD2DCOS), which enables one to analyze intensities with nonlinear behavior and overlapped bands. The second step is a model-based 2D correlation analysis where the activation and thermodynamic parameters are estimated by an indirect implicit calibration or a calibration-free approach. In this way, a minimization process for the spectral information by sample-sample 2D correlation spectroscopy and kinetic hard modeling (using ordinary differential equations) of the chemical reaction model is carried out. The sequential identification by 2D correlation analysis is illustrated with reference to the isomeric structure of diphenylurethane synthesized from phenylisocyanate and phenol. The reaction was investigated by FT-IR spectroscopy. The activation and thermodynamic parameters of the isomeric structures of diphenylurethane linked through a hydrogen bonding equilibrium were studied by means of an integration of model-free and model-based 2D correlation analysis called a sequential identification approach. The study determined the enthalpy (ΔH = 15.25 kJ/mol) and entropy (TΔS = 13.20 kJ/mol) of C═O···H hydrogen bonding of diphenylurethane through direct calculation from the differences in the kinetic parameters (δΔ(‡)H, -TδΔ(‡)S) at equilibrium in the chemical reaction system.

  2. Interactive effects of elevated CO2 concentration and irrigation on photosynthetic parameters and yield of maize in Northeast China.

    PubMed

    Meng, Fanchao; Zhang, Jiahua; Yao, Fengmei; Hao, Cui

    2014-01-01

    Maize is one of the major cultivated crops of China, having a central role in ensuring the food security of the country. There has been a significant increase in studies of maize under interactive effects of elevated CO2 concentration ([CO2]) and other factors, yet the interactive effects of elevated [CO2] and increasing precipitation on maize has remained unclear. In this study, a manipulative experiment in Jinzhou, Liaoning province, Northeast China was performed so as to obtain reliable results concerning the later effects. The Open Top Chambers (OTCs) experiment was designed to control contrasting [CO2] i.e., 390, 450 and 550 µmol·mol(-1), and the experiment with 15% increasing precipitation levels was also set based on the average monthly precipitation of 5-9 month from 1981 to 2010 and controlled by irrigation. Thus, six treatments, i.e. C550W+15%, C550W0, C450W+15%, C450W0, C390W+15% and C390W0 were included in this study. The results showed that the irrigation under elevated [CO2] levels increased the leaf net photosynthetic rate (Pn) and intercellular CO2 concentration (Ci) of maize. Similarly, the stomatal conductance (Gs) and transpiration rate (Tr) decreased with elevated [CO2], but irrigation have a positive effect on increased of them at each [CO2] level, resulting in the water use efficiency (WUE) higher in natural precipitation treatment than irrigation treatment at elevated [CO2] levels. Irradiance-response parameters, e.g., maximum net photosynthetic rate (Pnmax) and light saturation points (LSP) were increased under elevated [CO2] and irrigation, and dark respiration (Rd) was increased as well. The growth characteristics, e.g., plant height, leaf area and aboveground biomass were enhanced, resulting in an improved of yield and ear characteristics except axle diameter. The study concluded by reporting that, future elevated [CO2] may favor to maize when coupled with increasing amount of precipitation in Northeast China. PMID:24848097

  3. Interactive Effects of Elevated CO2 Concentration and Irrigation on Photosynthetic Parameters and Yield of Maize in Northeast China

    PubMed Central

    Meng, Fanchao; Zhang, Jiahua; Yao, Fengmei; Hao, Cui

    2014-01-01

    Maize is one of the major cultivated crops of China, having a central role in ensuring the food security of the country. There has been a significant increase in studies of maize under interactive effects of elevated CO2 concentration ([CO2]) and other factors, yet the interactive effects of elevated [CO2] and increasing precipitation on maize has remained unclear. In this study, a manipulative experiment in Jinzhou, Liaoning province, Northeast China was performed so as to obtain reliable results concerning the later effects. The Open Top Chambers (OTCs) experiment was designed to control contrasting [CO2] i.e., 390, 450 and 550 µmol·mol−1, and the experiment with 15% increasing precipitation levels was also set based on the average monthly precipitation of 5–9 month from 1981 to 2010 and controlled by irrigation. Thus, six treatments, i.e. C550W+15%, C550W0, C450W+15%, C450W0, C390W+15% and C390W0 were included in this study. The results showed that the irrigation under elevated [CO2] levels increased the leaf net photosynthetic rate (Pn) and intercellular CO2 concentration (Ci) of maize. Similarly, the stomatal conductance (Gs) and transpiration rate (Tr) decreased with elevated [CO2], but irrigation have a positive effect on increased of them at each [CO2] level, resulting in the water use efficiency (WUE) higher in natural precipitation treatment than irrigation treatment at elevated [CO2] levels. Irradiance-response parameters, e.g., maximum net photosynthetic rate (Pnmax) and light saturation points (LSP) were increased under elevated [CO2] and irrigation, and dark respiration (Rd) was increased as well. The growth characteristics, e.g., plant height, leaf area and aboveground biomass were enhanced, resulting in an improved of yield and ear characteristics except axle diameter. The study concluded by reporting that, future elevated [CO2] may favor to maize when coupled with increasing amount of precipitation in Northeast China. PMID:24848097

  4. Interactive effects of elevated CO2 concentration and irrigation on photosynthetic parameters and yield of maize in Northeast China.

    PubMed

    Meng, Fanchao; Zhang, Jiahua; Yao, Fengmei; Hao, Cui

    2014-01-01

    Maize is one of the major cultivated crops of China, having a central role in ensuring the food security of the country. There has been a significant increase in studies of maize under interactive effects of elevated CO2 concentration ([CO2]) and other factors, yet the interactive effects of elevated [CO2] and increasing precipitation on maize has remained unclear. In this study, a manipulative experiment in Jinzhou, Liaoning province, Northeast China was performed so as to obtain reliable results concerning the later effects. The Open Top Chambers (OTCs) experiment was designed to control contrasting [CO2] i.e., 390, 450 and 550 µmol·mol(-1), and the experiment with 15% increasing precipitation levels was also set based on the average monthly precipitation of 5-9 month from 1981 to 2010 and controlled by irrigation. Thus, six treatments, i.e. C550W+15%, C550W0, C450W+15%, C450W0, C390W+15% and C390W0 were included in this study. The results showed that the irrigation under elevated [CO2] levels increased the leaf net photosynthetic rate (Pn) and intercellular CO2 concentration (Ci) of maize. Similarly, the stomatal conductance (Gs) and transpiration rate (Tr) decreased with elevated [CO2], but irrigation have a positive effect on increased of them at each [CO2] level, resulting in the water use efficiency (WUE) higher in natural precipitation treatment than irrigation treatment at elevated [CO2] levels. Irradiance-response parameters, e.g., maximum net photosynthetic rate (Pnmax) and light saturation points (LSP) were increased under elevated [CO2] and irrigation, and dark respiration (Rd) was increased as well. The growth characteristics, e.g., plant height, leaf area and aboveground biomass were enhanced, resulting in an improved of yield and ear characteristics except axle diameter. The study concluded by reporting that, future elevated [CO2] may favor to maize when coupled with increasing amount of precipitation in Northeast China.

  5. Lattice cluster theory of associating polymers. II. Enthalpy and entropy of self-assembly and Flory-Huggins interaction parameter χ for solutions of telechelic molecules.

    PubMed

    Dudowicz, Jacek; Freed, Karl F; Douglas, Jack F

    2012-02-14

    The lattice cluster theory for solutions of telechelic polymer chains, developed in paper I, is applied to determine the enthalpy Δh(p) and entropy Δs(p) of self-assembly of linear telechelics and to evaluate the Flory-Huggins (FH) interaction parameter χ governing the phase behavior of these systems. Particular focus is placed on examining how these interaction variables depend on the composition of the solution, temperature, van der Waals and local "sticky" interaction energies, and the length of the individual telechelic chains. The FH interaction parameter χ is found to exhibit an entropy-enthalpy compensation effect between the "entropic" and "enthalpic" portions as either the composition or mass of the telechelic species is varied, providing unique theoretical insights into this commonly reported, yet, enigmatic phenomenon.

  6. Chromogranin A-derived peptides: interaction with the rat posterior cerebral artery.

    PubMed

    Mandalà, Maurizio; Brekke, Johan Fredrik; Serck-Hanssen, Guldborg; Metz-Boutigue, Marie-Hélène; Helle, Karen B

    2005-01-15

    Chromogranin A (CgA), an acidic granule protein of the regulated secretory pathway in the diffuse neuroendocrine system, is postulated to serve as a prohormone for regulatory peptides. Betagranin (rCgA(1-128)), the first N-terminal cleavage product of rat CgA, is 87% homologous to the bovine vasostatin I (bCgA(1-76)), previously shown to be vasoinhibitory in bovine resistance arteries. In this study the vasoactivity of homologous rat and bovine peptides was investigated in the rat posterior cerebral artery. Firstly, we examined the interaction of rhodamine (Rh)-labelled bCgA(7-40) and bCgA(47-70) with elements of the arterial wall by fluorescence microscopy. Secondly, rCgA(7-57), bCgA(1-40), bCgA(7-40) and bCgA(47-66) (chromofungin) were studied for effects on arterial tone and intracellular calcium as function of pressure in an arteriograph. Although without dilator or constrictor responses at 60-150 mm Hg, the rat peptide (rCgA(7-57)) evoked a significant delay in the onset of forced dilatation at 170 mm Hg, in contrast to the bovine peptides bCgA(1-40), bCgA(7-40) and bCgA(47-66) (chromofungin). Neither Rh-bCgA(7-40) nor Rh-bCgA(47-70) stained the endothelial layer, while Rh-bCgA(47-70) but not Rh-bCgA(7-40) stained the smooth muscle compartment. Analogously, bCgA(47-66) but not bCgA(7-40) reduced intracellular calcium, however without modifying the myogenic response. Thus, the betagranin peptide rCgA(7-57) and the two bovine chromofungin-containing peptides, highly homologous to the corresponding sequence (rCgA(47-66)), affected the rat cerebral artery without vasodilator effects, indicating significant species differences in vasoactivity of the N-terminal domain of CgA.

  7. Characterising the interaction of individual-wheel drives with traction by linear parameter-varying model: a method for analysing the role of traction in torsional vibrations in wheel drives and active damping

    NASA Astrophysics Data System (ADS)

    Zhun Yeap, Khang; Müller, Steffen

    2016-02-01

    A model-based approach for characterising the interaction of individual-wheel drives with traction is contributed in this article. The primary aim is to investigate the influence of traction on torsional vibration behaviour in the drive train. The essence of this approach lies in reformulating the nonlinear traction behaviour into its differential form, which enables an analytical description of this interaction in its linear parameter-varying model equivalence. Analytical statements on the vibration behaviour for different driving scenarios are inferred from this model and validated with measurement samples from a high-performance electric road vehicle. Subsequent influences of traction on the performance of active damping of torsional vibrations are derived from this model.

  8. Study of chemical reactivity in relation to experimental parameters of efficiency in coumarin derivatives for dye sensitized solar cells using DFT.

    PubMed

    Soto-Rojo, Rody; Baldenebro-López, Jesús; Glossman-Mitnik, Daniel

    2015-06-01

    A group of dyes derived from coumarin was studied, which consisted of nine molecules using a very similar manufacturing process of dye sensitized solar cells (DSSCs). Optimized geometries, energy levels of the highest occupied molecular orbital and the lowest unoccupied molecular orbital, and ultraviolet-visible spectra were obtained using theoretical calculations, and they were also compared with experimental conversion efficiencies of the DSSC. The representation of an excited state in terms of natural transition orbitals (NTOs) was studied. Chemical reactivity parameters were calculated and correlated with the experimental data linked to the efficiency of the DSSC. A new proposal was obtained to design new molecular systems and to predict their potential use as a dye in DSSCs. PMID:25959071

  9. Study of chemical reactivity in relation to experimental parameters of efficiency in coumarin derivatives for dye sensitized solar cells using DFT.

    PubMed

    Soto-Rojo, Rody; Baldenebro-López, Jesús; Glossman-Mitnik, Daniel

    2015-06-01

    A group of dyes derived from coumarin was studied, which consisted of nine molecules using a very similar manufacturing process of dye sensitized solar cells (DSSCs). Optimized geometries, energy levels of the highest occupied molecular orbital and the lowest unoccupied molecular orbital, and ultraviolet-visible spectra were obtained using theoretical calculations, and they were also compared with experimental conversion efficiencies of the DSSC. The representation of an excited state in terms of natural transition orbitals (NTOs) was studied. Chemical reactivity parameters were calculated and correlated with the experimental data linked to the efficiency of the DSSC. A new proposal was obtained to design new molecular systems and to predict their potential use as a dye in DSSCs.

  10. Modeling techniques and fluorescence imaging investigation of the interactions of an anthraquinone derivative with HSA and ctDNA.

    PubMed

    Fu, Zheng; Cui, Yanrui; Cui, Fengling; Zhang, Guisheng

    2016-01-15

    A new anthraquinone derivative (AORha) was synthesized. Its interactions with human serum albumin (HSA) and calf thymus DNA (ctDNA) were investigated by fluorescence spectroscopy, UV-visible absorption spectroscopy and molecular modeling. Cell viability assay and cell imaging experiment were performed using cervical cancer cells (HepG2 cells). The fluorescence results revealed that the quenching mechanism was static quenching. At different temperatures (290, 300, 310 K), the binding constants (K) and the number of binding sites (n) were determined, respectively. The positive ΔH and ΔS values showed that the binding of AORha with HSA was hydrophobic force, which was identical with the molecular docking result. Studying the fluorescence spectra, UV spectra and molecular modeling also verified that the binding mode of AORha and ctDNA might be intercalative. When HepG2 cells were treated with AORha, the fluorescence became brighter and turned green, which could be used for bioimaging.

  11. Two thiosemicarbazones derived from salicylaldehyde: very specific hydrogen-bonding interactions of the N-H...S=C type.

    PubMed

    Rubcić, Mirta; Dilović, Ivica; Cindrić, Marina; Matković-Calogović, Dubravka

    2008-10-01

    The molecular structures of two salicylaldehyde thiosemicarbazone derivatives, namely salicylaldehyde 4-phenylthiosemicarbazone, C(14)H(13)N(3)OS, (I), and 4-methoxysalicylaldehyde 4-phenylthiosemicarbazone, C(15)H(15)N(3)O(2)S, (II), both of potential pharmacological interest, are found in the keto (thione) tautomeric form. The first compound represents a second triclinic polymorph of composition beta-C(14)H(13)N(3)OS. Although both polymorphs crystallize in the same space group (P1), the alpha-polymorph [Seena, Kurup & Suresh (2008). J. Chem. Crystallogr. 38, 93-96] differs from the beta form in its unit-cell volume at 293 K. The molecules in the crystal structures of (I) and (II) are linked into centrosymmetric R(2)(2)(8) dimers by hydrogen bonds of the N-H...S=C type. These dimers are connected through pi-pi stacking and T-shaped C-H...pi interactions into three-dimensional networks.

  12. Modeling techniques and fluorescence imaging investigation of the interactions of an anthraquinone derivative with HSA and ctDNA

    NASA Astrophysics Data System (ADS)

    Fu, Zheng; Cui, Yanrui; Cui, Fengling; Zhang, Guisheng

    2016-01-01

    A new anthraquinone derivative (AORha) was synthesized. Its interactions with human serum albumin (HSA) and calf thymus DNA (ctDNA) were investigated by fluorescence spectroscopy, UV-visible absorption spectroscopy and molecular modeling. Cell viability assay and cell imaging experiment were performed using cervical cancer cells (HepG2 cells). The fluorescence results revealed that the quenching mechanism was static quenching. At different temperatures (290, 300, 310 K), the binding constants (K) and the number of binding sites (n) were determined, respectively. The positive ΔH and ΔS values showed that the binding of AORha with HSA was hydrophobic force, which was identical with the molecular docking result. Studying the fluorescence spectra, UV spectra and molecular modeling also verified that the binding mode of AORha and ctDNA might be intercalative. When HepG2 cells were treated with AORha, the fluorescence became brighter and turned green, which could be used for bioimaging.

  13. Improved Quantification of Cerebral Hemodynamics Using Individualized Time Thresholds for Assessment of Peak Enhancement Parameters Derived from Dynamic Susceptibility Contrast Enhanced Magnetic Resonance Imaging

    PubMed Central

    Nasel, Christian; Kalcher, Klaudius; Boubela, Roland; Moser, Ewald

    2014-01-01

    Purpose Assessment of cerebral ischemia often employs dynamic susceptibility contrast enhanced magnetic resonance imaging (DSC-MRI) with evaluation of various peak enhancement time parameters. All of these parameters use a single time threshold to judge the maximum tolerable peak enhancement delay that is supposed to reliably differentiate sufficient from critical perfusion. As the validity of this single threshold approach still remains unclear, in this study, (1) the definition of a threshold on an individual patient-basis, nevertheless (2) preserving the comparability of the data, was investigated. Methods The histogram of time-to-peak (TTP) values derived from DSC-MRI, the so-called TTP-distribution curve (TDC), was modeled using a double-Gaussian model in 61 patients without severe cerebrovascular disease. Particular model-based zf-scores were used to describe the arterial, parenchymal and venous bolus-transit phase as time intervals Ia,p,v. Their durations (delta Ia,p,v), were then considered as maximum TTP-delays of each phase. Results Mean-R2 for the model-fit was 0.967. Based on the generic zf-scores the proposed bolus transit phases could be differentiated. The Ip-interval reliably depicted the parenchymal bolus-transit phase with durations of 3.4 s–10.1 s (median = 4.3s), where an increase with age was noted (∼30 ms/year). Conclusion Individual threshold-adjustment seems rational since regular bolus-transit durations in brain parenchyma obtained from the TDC overlap considerably with recommended critical TTP-thresholds of 4 s–8 s. The parenchymal transit time derived from the proposed model may be utilized to individually correct TTP-thresholds, thereby potentially improving the detection of critical perfusion. PMID:25521121

  14. A SNAP-Tagged Derivative of HIV-1—A Versatile Tool to Study Virus-Cell Interactions

    PubMed Central

    Eckhardt, Manon; Anders, Maria; Muranyi, Walter; Heilemann, Mike; Krijnse-Locker, Jacomine; Müller, Barbara

    2011-01-01

    Fluorescently labeled human immunodeficiency virus (HIV) derivatives, combined with the use of advanced fluorescence microscopy techniques, allow the direct visualization of dynamic events and individual steps in the viral life cycle. HIV proteins tagged with fluorescent proteins (FPs) have been successfully used for live-cell imaging analyses of HIV-cell interactions. However, FPs display limitations with respect to their physicochemical properties, and their maturation kinetics. Furthermore, several independent FP-tagged constructs have to be cloned and characterized in order to obtain spectral variations suitable for multi-color imaging setups. In contrast, the so-called SNAP-tag represents a genetically encoded non-fluorescent tag which mediates specific covalent coupling to fluorescent substrate molecules in a self-labeling reaction. Fusion of the SNAP-tag to the protein of interest allows specific labeling of the fusion protein with a variety of synthetic dyes, thereby offering enhanced flexibility for fluorescence imaging approaches. Here we describe the construction and characterization of the HIV derivative HIVSNAP, which carries the SNAP-tag as an additional domain within the viral structural polyprotein Gag. Introduction of the tag close to the C-terminus of the matrix domain of Gag did not interfere with particle assembly, release or proteolytic virus maturation. The modified virions were infectious and could be propagated in tissue culture, albeit with reduced replication capacity. Insertion of the SNAP domain within Gag allowed specific staining of the viral polyprotein in the context of virus producing cells using a SNAP reactive dye as well as the visualization of individual virions and viral budding sites by stochastic optical reconstruction microscopy. Thus, HIVSNAP represents a versatile tool which expands the possibilities for the analysis of HIV-cell interactions using live cell imaging and sub-diffraction fluorescence microscopy. PMID:21799764

  15. Deriving Macropore and Preferential Flow Parameters from Tracer and Time-lapse 3D GPR Experiments at the Plot-Scale

    NASA Astrophysics Data System (ADS)

    Jackisch, Conrad; Allroggen, Niklas; Tronicke, Jens; Zehe, Erwin

    2014-05-01

    "Hydrology - a science in which all processes are preferential" (Uhlenbrook, 2006) - as such preferential flow is known and discussed in hydrology since almost three decades. At the same time, preferential flow remains problematic as explicit descriptions are hard to define and upscale and implicit descriptions remain rather case sensitive. Moreover, our techniques to monitor preferential flow and especially flow structures are very limited. We conducted three multi-tracer plot-scale (1m x 1m) sprinkler experiments at a forested hillslope in the Attert Basin in Luxembourg with prevailing geogenic and biogenic preferential flow structures. It was accompanied by a 3D time-lapse GPR (Ground Penetrating Radar) survey covering an area of 3m x 3m. We present the results with special emphasis on the derivation of macropore parameters for further modelling. To do so, we developed an automated analysis of images from excavated Brilliant Blue stained profiles. Additionally, we analyse our time-lapse GPR data with respect to temporal changes and derive 3D strutural information of the preferential flow patterns. Superior to tracers, this high resolution subsurface imaging technique is non-invasive, repeatable and therefore helps to disentangle the dye stained patterns towards process observation. The results of the image analyses and the GPR surveys are compared and referenced to soil moisture monitoring, sampled Bromide profiles and stable isotope signatures. We further discuss implications for joint development of model concepts and observation methods.

  16. Human umbilical cord blood-derived mesenchymal stromal cells display a novel interaction between P-selectin and galectin-1.

    PubMed

    Suila, H; Hirvonen, T; Kotovuori, A; Ritamo, I; Kerkelä, E; Anderson, H; Natunen, S; Tuimala, J; Laitinen, S; Nystedt, J; Räbinä, J; Valmu, L

    2014-07-01

    Human multipotent mesenchymal stromal/stem cells (MSCs) have been shown to exert immunomodulatory properties that have great potential in therapies for various inflammatory and autoimmune disorders. However, intravenous delivery of these cells is followed by massive cell entrapment in the lungs and insufficient homing to target tissues or organs. In targeting to tissues, MSCs and other therapeutic cells employ similar mechanisms as leucocytes, including a cascade of rolling and adhesion steps mediated by selectins, integrins and their ligands. However, the mechanisms of MSCs homing are not well understood. We discovered that P-selectin (CD62P) binds to umbilical cord blood (UCB)-derived MSCs independently of the previously known sialyl Lewis x (sLex)-containing ligands such as P-selectin glycoprotein ligand-1 (PSGL-1, CD162). By biochemical assays, we identified galectin-1 as a novel ligand for P-selectin. Galectin-1 has previously been shown to be a key mediator of the immunosuppressive effects of human MSCs. We conclude that this novel interaction is likely to play a major role in the immunomodulatory targeting of human UCB-derived MSCs.

  17. Specific interaction between Mycobacterium tuberculosis lipoprotein-derived peptides and target cells inhibits mycobacterial entry in vitro

    PubMed Central

    Ocampo, Marisol; Curtidor, Hernando; Vanegas, Magnolia; Patarroyo, Manuel Alfonso; Patarroyo, Manuel Elkin

    2014-01-01

    Summary Tuberculosis (TB) continues being one of the diseases having the greatest mortality rates around the world, 8.7 million cases having been reported in 2011. An efficient vaccine against TB having a great impact on public health is an urgent need. Usually, selecting antigens for vaccines has been based on proteins having immunogenic properties for patients suffering TB and having had promising results in mice and non-human primates. Our approach has been based on a functional approach involving the pathogen–host interaction in the search for antigens to be included in designing an efficient, minimal, subunit-based anti-tuberculosis vaccine. This means that Mycobacterium tuberculosis has mainly been involved in studies and that lipoproteins represent an important kind of protein on the cell envelope which can also contribute towards this pathogen's virulence. This study has assessed the expression of four lipoproteins from M. tuberculosis H37Rv, i.e. Rv1411c (LprG), Rv1911c (LppC), Rv2270 (LppN) and Rv3763 (LpqH), and the possible biological activity of peptides derived from these. Five peptides were found for these proteins which had high specific binding to both alveolar A549 epithelial cells and U937 monocyte-derived macrophages which were able to significantly inhibit mycobacterial entry to these cells in vitro. PMID:25041568

  18. Formation of 1:2 host-guest complexes based on triptycene-derived macrotricycle and paraquat derivatives: anion-π interactions between PF6(-) and bipyridinium rings in the solid state.

    PubMed

    Guo, Jia-Bin; Han, Ying; Cao, Jing; Chen, Chuan-Feng

    2011-10-21

    A triptycene-derived macrotricyclic host containing two dibenzo-[30]-crown-10 moieties forms stable 1:2 host-guest complexes with paraquat derivatives in both solution and the solid state, in which anion-π interactions between PF(6)(-) and the bipyridinium rings play an important role. Moreover, it was found that binding and release of the guest molecules in the complexes could be easily controlled by the addition and removal of potassium ions. PMID:21962056

  19. Interactions and hybrid complex formation of anionic algal polysaccharides with a cationic glycine betaine-derived surfactant.

    PubMed

    Covis, Rudy; Vives, Thomas; Gaillard, Cédric; Benoit, Maud; Benvegnu, Thierry

    2015-05-01

    The interaction between anionic algal polysaccharides ((κ)-, (ι)-, (λ)-carrageenans, alginate and ulvan) and a cationic glycine betaine (GB) amide surfactant possessing a C18:1 alkyl chain has been studied using isothermal titration calorimetry (ITC), zeta-potential measurements, dynamic light scattering (DLS), transmission electron microscopy (TEM), atomic force microscopy (AFM), and surface tension measurements. It was observed that this cationic surfactant derived from renewable raw materials induced cooperative binding with the anionic polymers at critical aggregation concentration (CAC) and the CAC values are significantly lower than the corresponding critical micelle concentration (CMC) for the surfactant. The CMC of cationic GB surfactant was obtained at higher surfactant concentration in polysaccharide solution than in pure water. More interestingly, the presence of original polysaccharide/surfactant hybrid complexes formed above the CMC value was evidenced from (κ)-carrageenan by microscopy (TEM and AFM). Preliminary investigations of the structure of these complexes revealed the existence of surfactant nanoparticles surrounded with polysaccharide matrix, probably resulting from electrostatic attraction. In addition, ITC measurements clearly showed that the interactions of the κ-carrageenan was stronger than for other polysaccharides ((ι)-, (λ)-carrageenans, alginate and ulvan). These results may have important impact on the use of the GB amide surfactant in formulations based on algal polysaccharides for several applications such as in food, cosmetics, and detergency fields.

  20. Determination of pharmacological interactions of uliginosin B, a natural phloroglucinol derivative, with amitriptyline, clonidine and morphine by isobolographic analysis.

    PubMed

    Stolz, Eveline D; Müller, Liz G; Antonio, Camila B; da Costa, Paola F; von Poser, Gilsane L; Noël, François; Rates, Stela M K

    2014-10-15

    Uliginosin B is a natural phloroglucinol derivative, obtained from Hypericum species native to South America. Previous studies have shown that uliginosin B presents antidepressant-like and antinociceptive effects. Although its mechanism of action is still not completely elucidated, it is known that it involves the activation of monoaminergic neurotransmission. The aim of the current study was to further investigate the antinociceptive mechanism of action of uliginosin B by combining it with different drugs used for treating pain in clinical practice. The intraperitoneal administration of uliginosin B, morphine, amitriptyline and clonidine, alone or in mixture, produced a dose-dependent antinociceptive effect in the hot-plate assay in mice. The effect of the mixtures of drugs was studied using an adapted isobologram analysis at the effect level of 50% of the maximal effect observed. The analysis showed that the interactions between uliginosin B and morphine was synergistic, while the interactions between uliginosin B and amitriptyline or clonidine were additive. These findings point to uliginosin B as a potential adjuvant for pain pharmacotherapy, especially for opioid analgesia.

  1. Brain-derived neurotrophic factor as a model system for examining gene by environment interactions across development.

    PubMed

    Casey, B J; Glatt, C E; Tottenham, N; Soliman, F; Bath, K; Amso, D; Altemus, M; Pattwell, S; Jones, R; Levita, L; McEwen, B; Magariños, A M; Gunnar, M; Thomas, K M; Mezey, J; Clark, A G; Hempstead, B L; Lee, F S

    2009-11-24

    There has been a dramatic rise in gene x environment studies of human behavior over the past decade that have moved the field beyond simple nature versus nurture debates. These studies offer promise in accounting for more variability in behavioral and biological phenotypes than studies that focus on genetic or experiential factors alone. They also provide clues into mechanisms of modifying genetic risk or resilience in neurodevelopmental disorders. Yet, it is rare that these studies consider how these interactions change over the course of development. In this paper, we describe research that focuses on the impact of a polymorphism in a brain-derived neurotrophic factor (BDNF) gene, known to be involved in learning and development. Specifically we present findings that assess the effects of genotypic and environmental loadings on neuroanatomic and behavioral phenotypes across development. The findings illustrate the use of a genetic mouse model that mimics the human polymorphism, to constrain the interpretation of gene-environment interactions across development in humans. PMID:19358879

  2. Computational Study Exploring the Interaction Mechanism of Benzimidazole Derivatives as Potent Cattle Bovine Viral Diarrhea Virus Inhibitors.

    PubMed

    Wang, Jinghui; Yang, Yinfeng; Li, Yan; Wang, Yonghua

    2016-07-27

    Bovine viral diarrhea virus (BVDV) infections are prevailing in cattle populations on a worldwide scale. The BVDV RNA-dependent RNA polymerase (RdRp), as a promising target for new anti-BVDV drug development, has attracted increasing attention. To explore the interaction mechanism of 65 benzimidazole scaffold-based derivatives as BVDV inhibitors, presently, a computational study was performed based on a combination of 3D-QSAR, molecular docking, and molecular dynamics (MD) simulations. The resultant optimum CoMFA and CoMSIA models present proper reliabilities and strong predictive abilities (with Q(2) = 0. 64, R(2)ncv = 0.93, R(2)pred = 0.80 and Q(2) = 0. 65, R(2)ncv = 0.98, R(2)pred = 0.86, respectively). In addition, there was good concordance between these models, molecular docking, and MD results. Moreover, the MM-PBSA energy analysis reveals that the major driving force for ligand binding is the polar solvation contribution term. Hopefully, these models and the obtained findings could offer better understanding of the interaction mechanism of BVDV inhibitors as well as benefit the new discovery of more potent BVDV inhibitors. PMID:27355875

  3. Improving homology modeling of G-protein coupled receptors through multiple-template derived conserved inter-residue interactions.

    PubMed

    Chaudhari, Rajan; Heim, Andrew J; Li, Zhijun

    2015-05-01

    Evidenced by the three-rounds of G-protein coupled receptors (GPCR) Dock competitions, improving homology modeling methods of helical transmembrane proteins including the GPCRs, based on templates of low sequence identity, remains an eminent challenge. Current approaches addressing this challenge adopt the philosophy of "modeling first, refinement next". In the present work, we developed an alternative modeling approach through the novel application of available multiple templates. First, conserved inter-residue interactions are derived from each additional template through conservation analysis of each template-target pairwise alignment. Then, these interactions are converted into distance restraints and incorporated in the homology modeling process. This approach was applied to modeling of the human β2 adrenergic receptor using the bovin rhodopsin and the human protease-activated receptor 1 as templates and improved model quality was demonstrated compared to the homology model generated by standard single-template and multiple-template methods. This method of "refined restraints first, modeling next", provides a fast and complementary way to the current modeling approaches. It allows rational identification and implementation of additional conserved distance restraints extracted from multiple templates and/or experimental data, and has the potential to be applicable to modeling of all helical transmembrane proteins.

  4. Interactions of histatin 5 and histatin 5-derived peptides with liposome membranes: surface effects, translocation and permeabilization.

    PubMed Central

    Den Hertog, Alice L; Wong Fong Sang, Harro W; Kraayenhof, Ruud; Bolscher, Jan G M; Van't Hof, Wim; Veerman, Enno C I; Nieuw Amerongen, Arie V

    2004-01-01

    A number of cationic antimicrobial peptides, among which are histatin 5 and the derived peptides dhvar4 and dhvar5, enter their target cells and interact with internal organelles. There still are questions about the mechanisms by which antimicrobial peptides translocate across the membrane. We used a liposome model to study membrane binding, translocation and membrane-perturbing capacities of histatin 5, dhvar4 and dhvar5. Despite the differences in amphipathic characters of these peptides, they bound equally well to liposomes, whereas their membrane activities differed remarkably: dhvar4 translocated at the fastest rate, followed by dhvar5, whereas the histatin 5 translocation rate was much lower. The same pattern was seen for the extent of calcein release: highest with dhvar4, less with dhvar5 and almost none with histatin 5. The translocation and disruptive actions of dhvar5 did not seem to be coupled, because translocation occurred on a much longer timescale than calcein release, which ended within a few minutes. We conclude that peptide translocation can occur through peptide-phospholipid interactions, and that this is a possible mechanism by which antimicrobial peptides enter cells. However, the translocation rate was much lower in this model membrane system than that seen in yeast cells. Thus it is likely that, at least for some peptides, additional features promoting the translocation across biological membranes are involved as well. PMID:14733612

  5. PfCRT and PfMDR1 modulate interactions of artemisinin derivatives and ion channel blockers

    PubMed Central

    Eastman, Richard T.; Khine, Pwint; Huang, Ruili; Thomas, Craig J.; Su, Xin-zhuan

    2016-01-01

    Treatment of the symptomatic asexual stage of Plasmodium falciparum relies almost exclusively on artemisinin (ART) combination therapies (ACTs) in endemic regions. ACTs combine ART or its derivative with a long-acting partner drug to maximize efficacy during the typical three-day regimen. Both laboratory and clinical studies have previously demonstrated that the common drug resistance determinants P. falciparum chloroquine resistance transporter (PfCRT) and multidrug resistance transporter (PfMDR1) can modulate the susceptibility to many current antimalarial drugs and chemical compounds. Here we investigated the parasite responses to dihydroartemisinin (DHA) and various Ca2+ and Na+ channel blockers and showed positively correlated responses between DHA and several channel blockers, suggesting potential shared transport pathways or mode of action. Additionally, we demonstrated that PfCRT and PfMDR1 could also significantly modulate the pharmacodynamic interactions of the compounds and that the interactions were influenced by the parasite genetic backgrounds. These results provide important information for better understanding of drug resistance and for assessing the overall impact of drug resistance markers on parasite response to ACTs. PMID:27147113

  6. Feasibility and correlation of standard 2D speckle tracking echocardiography and automated function imaging derived parameters of left ventricular function during dobutamine stress test.

    PubMed

    Wierzbowska-Drabik, Karina; Hamala, Piotr; Roszczyk, Nikolina; Lipiec, Piotr; Plewka, Michał; Kręcki, Radosław; Kasprzak, Jarosław Damian

    2014-04-01

    Speckle tracking echocardiography (STE) is a method of quantitative assessment of myocardial function complementary to ejection fraction and visual evaluation. Standard STE analysis, demands manual tracing of the myocardium whereas automated function imaging (AFI) offers more convenient (based on selection of three points) assessment of longitudinal strain. Nevertheless, feasibility and correlation between both methods were not thoroughly examined, especially during tachycardia at peak stage of dobutamine stress echocardiography (DSE). We performed DSE in 238 patients (pts) with recording of apical views during baseline (0) and peak (1) DSE and analyzed them by STE and AFI. According to angiography, 127/238 pts had significant (≥70%) lesions in coronary arteries. We assessed correlations between STE and AFI derived peak systolic longitudinal strain values for global and regional parameters, feasibility, time of analysis and interobserver agreement. Global systolic longitudinal strain measured during baseline and peak stage of DSE by AFI showed very good correlation with standard STE parameters, with correlation coefficients r = 0.90 and r = 0.86 respectively (p < 0.0001). For regional parameters correlation coefficients ranged from 0.83 to 0.85 for baseline and from 0.70 to 0.79 for peak DSE. Both methods provided good and similar feasibility with only 1% segments excluded from analysis at peak stage of DSE with shorter time and lower coefficient of variance offered by AFI. Global and regional longitudinal strain achieved by faster and less operator-dependent AFI method correlate well with standard more time-consuming STE analysis during baseline and peak stage of DSE.

  7. Dependence of the average spatial and energy characteristics of the hadron-lepton cascade on the strong interaction parameters at superhigh energies

    NASA Technical Reports Server (NTRS)

    Boyadjian, N. G.; Dallakyan, P. Y.; Garyaka, A. P.; Mamidjanian, E. A.

    1985-01-01

    A method for calculating the average spatial and energy characteristics of hadron-lepton cascades in the atmosphere is described. The results of calculations for various strong interaction models of primary protons and nuclei are presented. The sensitivity of the experimentally observed extensive air showers (EAS) characteristics to variations of the elementary act parameters is analyzed.

  8. Source Parameters and Crustal Attenuation in Interior Alaska: Estimates Using Broadband Lg-Wave Spectra Derived from the BEAAR Experiment Data.

    NASA Astrophysics Data System (ADS)

    Marriott, D. A.; Hansen, R. A.

    2002-12-01

    Source parameters, site effects, and regional crustal attenuation in interior Alaska were estimated using displacement amplitude spectra of Lg phase arrivals derived from the Broadband Experiment Across the Alaska Range (BEAAR) seismic data. The BEAAR project consisted of 36 three component broadband seismometers temporarily installed across the Alaska Range. This array stretched across a large portion of interior Alaska, providing excellent recordings of regional events. The model parameters were estimated using a simultaneous nonlinear least squares inversion including all the spectral data. The source parameters estimated were the seismic moment, Mo, and the corner frequency, fo, for each event. The values of Mo were well constrained and yielded an empirical relationship between ML and Mo for interior Alaska. Estimates of the corner frequency for each event, along with the Mo values, yielded an estimate of stress drop for each event. For events larger then ML = 3 in Alaska, stress drop showed no significant dependence on magnitude. A frequency dependent local site amplification term was estimated for each station in the inversion as an average of the residuals for each station over many events. The inclusion of this site term reduced the total residuals of the regional attenuation model calculations. A preliminary model for regional attenuation of the Lg seismic phase averaged over all tectonic regions across continental Alaska from BEAAR data was derived to be: QLg(f) = 166f0.58. This model was estimated from 123 shallow earthquakes larger than M =3 located in continental Alaska, and more than 1,000 spectra. Because the Lg phase was trapped in the crustal wave-guide, QLg gave a good representation of attenuation in the crust, and appears to correlate with crustal structure. Estimates of attenuation for each ray path show local variation in QLg. This variation may be caused by changes in crustal structure such as faulting, deformation, or differences in

  9. Interaction Analysis of T7 RNA Polymerase with Heparin and Its Low Molecular Weight Derivatives – An In Silico Approach

    PubMed Central

    Borkotoky, Subhomoi; Meena, Chetan Kumar; Murali, Ayaluru

    2016-01-01

    The single subunit T7 RNA polymerase (T7RNAP) is a model enzyme for studying the transcription process and for various biochemical and biophysical studies. Heparin is a commonly used inhibitor against T7RNAP and other RNA polymerases. However, exact interaction between heparin and T7RNAP is still not completely understood. In this work, we analyzed the binding pattern of heparin by docking heparin and few of its low molecular weight derivatives to T7RNAP, which helps in better understanding of T7RNAP inhibition mechanism. The efficiency of the compounds was calculated by docking the selected compounds and post-docking molecular mechanics/generalized Born surface area analysis. Evaluation of the simulation trajectories and binding free energies of the complexes after simulation showed enoxaparin to be the best among low molecular weight heparins. Binding free energy analysis revealed that van der Waals interactions and polar solvation energy provided the substantial driving force for the binding process. Furthermore, per-residue free energy decomposition analysis revealed that the residues Asp 471, Asp 506, Asp 537, Tyr 571, Met 635, Asp 653, Pro 780, and Asp 812 are important for heparin interaction. Apart from these residues, most favorable contribution in all the three complexes came from Asp 506, Tyr 571, Met 635, Glu 652, and Asp 653, which can be essential for binding of heparin-like structures with T7RNAP. The results obtained from this study will be valuable for the future rational design of novel and potent inhibitors against T7RNAP and related proteins.

  10. Interaction Analysis of T7 RNA Polymerase with Heparin and Its Low Molecular Weight Derivatives – An In Silico Approach

    PubMed Central

    Borkotoky, Subhomoi; Meena, Chetan Kumar; Murali, Ayaluru

    2016-01-01

    The single subunit T7 RNA polymerase (T7RNAP) is a model enzyme for studying the transcription process and for various biochemical and biophysical studies. Heparin is a commonly used inhibitor against T7RNAP and other RNA polymerases. However, exact interaction between heparin and T7RNAP is still not completely understood. In this work, we analyzed the binding pattern of heparin by docking heparin and few of its low molecular weight derivatives to T7RNAP, which helps in better understanding of T7RNAP inhibition mechanism. The efficiency of the compounds was calculated by docking the selected compounds and post-docking molecular mechanics/generalized Born surface area analysis. Evaluation of the simulation trajectories and binding free energies of the complexes after simulation showed enoxaparin to be the best among low molecular weight heparins. Binding free energy analysis revealed that van der Waals interactions and polar solvation energy provided the substantial driving force for the binding process. Furthermore, per-residue free energy decomposition analysis revealed that the residues Asp 471, Asp 506, Asp 537, Tyr 571, Met 635, Asp 653, Pro 780, and Asp 812 are important for heparin interaction. Apart from these residues, most favorable contribution in all the three complexes came from Asp 506, Tyr 571, Met 635, Glu 652, and Asp 653, which can be essential for binding of heparin-like structures with T7RNAP. The results obtained from this study will be valuable for the future rational design of novel and potent inhibitors against T7RNAP and related proteins. PMID:27594785

  11. Interaction Analysis of T7 RNA Polymerase with Heparin and Its Low Molecular Weight Derivatives - An In Silico Approach.

    PubMed

    Borkotoky, Subhomoi; Meena, Chetan Kumar; Murali, Ayaluru

    2016-01-01

    The single subunit T7 RNA polymerase (T7RNAP) is a model enzyme for studying the transcription process and for various biochemical and biophysical studies. Heparin is a commonly used inhibitor against T7RNAP and other RNA polymerases. However, exact interaction between heparin and T7RNAP is still not completely understood. In this work, we analyzed the binding pattern of heparin by docking heparin and few of its low molecular weight derivatives to T7RNAP, which helps in better understanding of T7RNAP inhibition mechanism. The efficiency of the compounds was calculated by docking the selected compounds and post-docking molecular mechanics/generalized Born surface area analysis. Evaluation of the simulation trajectories and binding free energies of the complexes after simulation showed enoxaparin to be the best among low molecular weight heparins. Binding free energy analysis revealed that van der Waals interactions and polar solvation energy provided the substantial driving force for the binding process. Furthermore, per-residue free energy decomposition analysis revealed that the residues Asp 471, Asp 506, Asp 537, Tyr 571, Met 635, Asp 653, Pro 780, and Asp 812 are important for heparin interaction. Apart from these residues, most favorable contribution in all the three complexes came from Asp 506, Tyr 571, Met 635, Glu 652, and Asp 653, which can be essential for binding of heparin-like structures with T7RNAP. The results obtained from this study will be valuable for the future rational design of novel and potent inhibitors against T7RNAP and related proteins. PMID:27594785

  12. Genotype × Environment Interactions of Yield Traits in Backcross Introgression Lines Derived from Oryza sativa cv. Swarna/Oryza nivara

    PubMed Central

    Balakrishnan, Divya; Subrahmanyam, Desiraju; Badri, Jyothi; Raju, Addanki Krishnam; Rao, Yadavalli Venkateswara; Beerelli, Kavitha; Mesapogu, Sukumar; Surapaneni, Malathi; Ponnuswamy, Revathi; Padmavathi, G.; Babu, V. Ravindra; Neelamraju, Sarla

    2016-01-01

    Advanced backcross introgression lines (BILs) developed from crosses of Oryza sativa var. Swarna/O. nivara accessions were grown and evaluated for yield and related traits. Trials were conducted for consecutive three seasons in field conditions in a randomized complete block design with three replications. Data on yield traits under irrigated conditions were analyzed using the Additive Main Effect and Multiplicative Interaction (AMMI), Genotype and Genotype × Environment Interaction (GGE) and modified rank-sum statistic (YSi) for yield stability. BILs viz., G3 (14S) and G6 (166S) showed yield stability across the seasons along with high mean yield performance. G3 is early in flowering with high yield and has good grain quality and medium height, hence could be recommended for most of the irrigated locations. G6 is a late duration genotype, with strong culm strength, high grain number and panicle weight. G6 has higher yield and stability than Swarna but has Swarna grain type. Among the varieties tested DRRDhan 40 and recurrent parent Swarna showed stability for yield traits across the seasons. The component traits thousand grain weight, panicle weight, panicle length, grain number and plant height explained highest genotypic percentage over environment and interaction factors and can be prioritized to dissect stable QTLs/ genes. These lines were genotyped using microsatellite markers covering the entire rice genome and also using a set of markers linked to previously reported yield QTLs. It was observed that wild derived lines with more than 70% of recurrent parent genome were stable and showed enhanced yield levels compared to genotypes with higher donor genome introgressions. PMID:27807437

  13. Tables and graphs of electron-interaction cross sections from 10 eV to 100 GeV derived from the LLNL Evaluated Electron Data Library (EEDL), Z = 1--100

    SciTech Connect

    Perkins, S.T.; Cullen, D.E. ); Seltzer, S.M. , Gaithersburg, MD . Center for Radiation Research)

    1991-11-12

    Energy-dependent evaluated electron interaction cross sections and related parameters are presented for elements H through Fm (Z = 1 to 100). Data are given over the energy range from 10 eV to 100 GeV. Cross sections and average energy deposits are presented in tabulated and graphic form. In addition, ionization cross sections and average energy deposits for each shell are presented in graphic form. This information is derived from the Livermore Evaluated Electron Data Library (EEDL) as of July, 1991.

  14. Colorimetric detection of platelet-derived growth factors through competitive interactions between proteins and functional gold nanoparticles.

    PubMed

    Lin, Tzu-En; Chen, Wei-His; Shiang, Yen-Chun; Huang, Chih-Ching; Chang, Huan-Tsung

    2011-11-15

    We have developed a colorimetric assay-using aptamer modified 13-nm gold nanoparticles (Apt-Au NPs) and fibrinogen adsorbed Au NPs (Fib-Au NPs, 56nm)-for the highly selective and sensitive detection of platelet-derived growth factors (PDGF). Apt-Au NPs and Fib-Au NPs act as recognition and reporting units, respectively. PDGF-binding-aptamer (Apt(PDGF)) and 29-base-long thrombin-binding-aptamer (Apt(thr29)) are conjugated with Au NPs to prepare functional Apt-Au NPs (Apt(PDGF)/Apt(thr29)-Au NPs) for specific interaction with PDGF and thrombin, respectively. Thrombin interacts with Fib-Au NPs in solutions to catalyze the formation of insoluble fibrillar fibrin-Au NPs agglutinates through the polymerization of the unconjugated and conjugated fibrinogen. The activity of thrombin is suppressed once it interacts with the Apt(PDGF)/Apt(thr29)-Au NPs. The suppression decreases due to steric effects through the specific interaction of PDGF with Apt(PDGF), occurring on the surfaces of Apt(PDGF)/Apt(thr29)-Au NPs. Under optimal conditions [Apt(PDGF)/Apt(thr29)-Au NPs (25pM), thrombin (400pM) and Fib-Au NPs (30pM)], the Apt(PDGF)/Apt(thr29)-Au NPs/Fib-Au NPs probe responds linearly to PDGF over the concentration range of 0.5-20nM with a correlation coefficient of 0.96. The limit of detection (LOD, signal-to-noise ratio=3) for each of the three PDGF isoforms is 0.3nM in the presence of bovine serum albumin at 100μM. When using the Apt(PDGF)/Apt(thr29)-Au NPs as selectors for the enrichment of PDGF and for the removal of interferences from cell media, the LOD for PDGF provided by this probe is 35pM. The present probe reveals that the concentration of PDGF in the three cell media is 230 (±20)pM, showing its advantages of simplicity, sensitivity, and specificity.

  15. The modified extended Hansen method to determine partial solubility parameters of drugs containing a single hydrogen bonding group and their sodium derivatives: benzoic acid/Na and ibuprofen/Na.

    PubMed

    Bustamante, P; Pena, M A; Barra, J

    2000-01-20

    Sodium salts are often used in drug formulation but their partial solubility parameters are not available. Sodium alters the physical properties of the drug and the knowledge of these parameters would help to predict adhesion properties that cannot be estimated using the solubility parameters of the parent acid. This work tests the applicability of the modified extended Hansen method to determine partial solubility parameters of sodium salts of acidic drugs containing a single hydrogen bonding group (ibuprofen, sodium ibuprofen, benzoic acid and sodium benzoate). The method uses a regression analysis of the logarithm of the experimental mole fraction solubility of the drug against the partial solubility parameters of the solvents, using models with three and four parameters. The solubility of the drugs was determined in a set of solvents representative of several chemical classes, ranging from low to high solubility parameter values. The best results were obtained with the four parameter model for the acidic drugs and with the three parameter model for the sodium derivatives. The four parameter model includes both a Lewis-acid and a Lewis-base term. Since the Lewis acid properties of the sodium derivatives are blocked by sodium, the three parameter model is recommended for these kind of compounds. Comparison of the parameters obtained shows that sodium greatly changes the polar parameters whereas the dispersion parameter is not much affected. Consequently the total solubility parameters of the salts are larger than for the parent acids in good agreement with the larger hydrophilicity expected from the introduction of sodium. The results indicate that the modified extended Hansen method can be applied to determine the partial solubility parameters of acidic drugs and their sodium salts.

  16. Interaction of cinnamic acid derivatives with commercial hypoglycemic drugs on 2-deoxyglucose uptake in 3T3-L1 adipocytes.

    PubMed

    Prabhakar, Pranav Kumar; Doble, Mukesh

    2011-09-28

    Hydroxycinnamic acid derivatives are naturally occurring substances found in fruits, vegetables, and flowers and are consumed as dietary phenolic compounds. The effect of cinnamic acid, ferulic acid, p-coumaric acid, eugenol, chlorogenic acid, and caffeic acid, alone and in combination with two commercial oral hypoglycemic drugs (OHD), namely, thiazolidinedione (THZ) and metformin, on the uptake of 2-deoxyglucose (2DG) by 3T3-L1 adipocytes is studied. All of the phytochemicals other than cinnamic acid show synergistic interaction in 2DG uptake with both of the OHDs. THZ (20 μM) in combination with ferulic acid (25 μM) or p-coumaric acid (25 μM) increases 2DG uptake by 7- or 6.34-fold, respectively, with respect to control, whereas metformin (20 μM), along with ferulic acid (25 μM) or cinnamic acid (25 μM), increases 2DG uptake by 6.45- or 5.87-fold, respectively, when compared to control. Chlorogenic and cinnamic acids increased the expression of PPARγ, whereas other hydroxycinnamic acids enhanced the expression of PI3K, indicating different mechanisms of action between these compounds. These phytochemicals were able to reduce the expressions of the fatty acid synthase and HMG CoA reductase genes, indicating that they may be able to reduce the secondary complications caused by the accumulation of lipids. These studies suggest that hydroxycinnamic acid derivatives may be beneficial for the treatment of diabetes mellitus. They may act as a supplement with commercial drugs and may reduce the secondary complications caused by OHDs.

  17. Establishing Porcine Monocyte-Derived Macrophage and Dendritic Cell Systems for Studying the Interaction with PRRSV-1

    PubMed Central

    Singleton, Helen; Graham, Simon P.; Bodman-Smith, Katherine B.; Frossard, Jean-Pierre; Steinbach, Falko

    2016-01-01

    Monocyte-derived macrophages (MoMØ) and monocyte-derived dendritic cells (MoDC) are two model systems well established in human and rodent systems that can be used to study the interaction of pathogens with host cells. Porcine reproductive and respiratory syndrome virus (PRRSV) is known to infect myeloid cells, such as macrophages (MØ) and dendritic cells (DC). Therefore, this study aimed to establish systems for the differentiation and characterization of MoMØ and MoDC for subsequent infection with PRRSV-1. M-CSF differentiated MoMØ were stimulated with activators for classical (M1) or alternative (M2) activation. GM-CSF and IL-4 generated MoDC were activated with the well established maturation cocktail containing PAMPs and cytokines. In addition, MoMØ and MoDC were treated with dexamethasone and IL-10, which are known immuno-suppressive reagents. Cells were characterized by morphology, phenotype, and function and porcine MØ subsets highlighted some divergence from described human counterparts, while MoDC, appeared more similar to mouse and human DCs. The infection with PRRSV-1 strain Lena demonstrated different replication kinetics between MoMØ and MoDC and within subsets of each cell type. While MoMØ susceptibility was significantly increased by dexamethasone and IL-10 with an accompanying increase in CD163/CD169 expression, MoDC supported only a minimal replication of PRRSV These findings underline the high variability in the susceptibility of porcine myeloid cells toward PRRSV-1 infection. PMID:27313573

  18. Establishing Porcine Monocyte-Derived Macrophage and Dendritic Cell Systems for Studying the Interaction with PRRSV-1.

    PubMed

    Singleton, Helen; Graham, Simon P; Bodman-Smith, Katherine B; Frossard, Jean-Pierre; Steinbach, Falko

    2016-01-01

    Monocyte-derived macrophages (MoMØ) and monocyte-derived dendritic cells (MoDC) are two model systems well established in human and rodent systems that can be used to study the interaction of pathogens with host cells. Porcine reproductive and respiratory syndrome virus (PRRSV) is known to infect myeloid cells, such as macrophages (MØ) and dendritic cells (DC). Therefore, this study aimed to establish systems for the differentiation and characterization of MoMØ and MoDC for subsequent infection with PRRSV-1. M-CSF differentiated MoMØ were stimulated with activators for classical (M1) or alternative (M2) activation. GM-CSF and IL-4 generated MoDC were activated with the well established maturation cocktail containing PAMPs and cytokines. In addition, MoMØ and MoDC were treated with dexamethasone and IL-10, which are known immuno-suppressive reagents. Cells were characterized by morphology, phenotype, and function and porcine MØ subsets highlighted some divergence from described human counterparts, while MoDC, appeared more similar to mouse and human DCs. The infection with PRRSV-1 strain Lena demonstrated different replication kinetics between MoMØ and MoDC and within subsets of each cell type. While MoMØ susceptibility was significantly increased by dexamethasone and IL-10 with an accompanying increase in CD163/CD169 expression, MoDC supported only a minimal replication of PRRSV These findings underline the high variability in the susceptibility of porcine myeloid cells toward PRRSV-1 infection.

  19. A systematic study on hydrogen bond interactions in sulfabenzamide: DFT calculations of the N-14, O-17, and H-2 NQR parameters.

    PubMed

    Nozad, Ahmad G; Najafi, Hamidreza; Meftah, Sakineh; Aghazadeh, Mustafa

    2009-02-01

    A systematic computational study was carried out to characterize the hydrogen bond, HB, interactions of sulfabenzamide crystal structure by DFT calculations of electric field gradient, EFG, tensors at the sites of 14N, 17O, and 2H nuclei. The computations were performed with the B3LYP and B3PW91 DFT methods and 6-311+G and 6-311++G* standard basis sets using the Gaussian 98 package. To perform the calculations, a hydrogen-bonded heptameric cluster of sulfabenzamide was created by X-ray coordinates where the hydrogen atom positions were optimized and the EFG tensors were calculat